From 385044da060d11e2baf32536fa0fa70ca234b675 Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Thu, 21 Oct 2021 18:47:30 +0000
Subject: [PATCH 001/142] wrap SNCL in IRISSNCL
---
geomagio/edge/IRISSNCL.py | 77 +++++++++++++++++++++++++++++++++++++++
1 file changed, 77 insertions(+)
create mode 100644 geomagio/edge/IRISSNCL.py
diff --git a/geomagio/edge/IRISSNCL.py b/geomagio/edge/IRISSNCL.py
new file mode 100644
index 00000000..fdd9172d
--- /dev/null
+++ b/geomagio/edge/IRISSNCL.py
@@ -0,0 +1,77 @@
+from typing import Optional
+
+from ..geomag_types import DataInterval, DataType
+from .SNCL import SNCL, get_channel, get_location, _get_channel_start
+
+
+class IRISSNCL(SNCL):
+ @classmethod
+ def get_sncl(
+ cls,
+ data_type: DataType,
+ element: str,
+ interval: DataInterval,
+ station: str,
+ network: str = "NT",
+ location: Optional[str] = None,
+ ) -> "IRISSNCL":
+ location = location or get_location(element=element, data_type=data_type)
+ return IRISSNCL(
+ station=station,
+ network=network,
+ channel=get_iris_channel(
+ element=element,
+ data_type=data_type,
+ interval=interval,
+ network=network,
+ location=location,
+ ),
+ location=location,
+ )
+
+ @property
+ def data_type(self) -> str:
+ if self.location == "40" and self.network == "IU":
+ return "variation"
+ return super().data_type
+
+ @property
+ def element(self) -> str:
+ if self.location == "40" and self.network == "IU":
+ return _get_iris_element(channel=self.channel)
+ return super().element
+
+
+def _get_iris_element(channel: str) -> str:
+ channel_end = channel[1:]
+ if channel_end == "F1":
+ return "U"
+ elif channel_end == "F2":
+ return "V"
+ elif channel_end == "FZ":
+ return "W"
+ raise ValueError(f"Unsupported channel: {channel}")
+
+
+def get_iris_channel(
+ element: str,
+ data_type: DataType,
+ interval: DataInterval,
+ network: Optional[str] = None,
+ location: Optional[str] = None,
+) -> str:
+ if location == "40" and network == "IU":
+ return _get_channel_start(interval=interval) + _get_channel_end(element=element)
+ return get_channel(element=element, interval=interval, data_type=data_type)
+
+
+def _get_channel_end(element: str) -> str:
+ if element in ["H", "U"]:
+ return "F1"
+ elif element in ["E", "V"]:
+ return "F2"
+ elif element in ["Z", "W"]:
+ return "FZ"
+ elif element[0:2] == "LF": # predefined element
+ return element[1:]
+ raise ValueError(f"Unsupported element: {element}")
--
GitLab
From a317a88933a3008a95c4ec289395d95fd2fe9b7e Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Thu, 21 Oct 2021 18:47:39 +0000
Subject: [PATCH 002/142] test IRISSNCL
---
test/edge_test/IRISSNCL_test.py | 146 ++++++++++++++++++++++++++++++++
1 file changed, 146 insertions(+)
create mode 100644 test/edge_test/IRISSNCL_test.py
diff --git a/test/edge_test/IRISSNCL_test.py b/test/edge_test/IRISSNCL_test.py
new file mode 100644
index 00000000..eb36fc3c
--- /dev/null
+++ b/test/edge_test/IRISSNCL_test.py
@@ -0,0 +1,146 @@
+import pytest
+
+from geomagio.edge import IRISSNCL
+from geomagio.edge.IRISSNCL import get_iris_channel, get_location
+
+
+def test_data_type():
+ """edge_test.IRISSNCL_test.test_data_type()"""
+ assert (
+ IRISSNCL(station="ANMO", network="IU", channel="LF1", location="40").data_type
+ == "variation"
+ )
+
+
+def test_element():
+ """edge_test.IRISSNCL_test.test_element()"""
+ assert (
+ IRISSNCL(station="ANMO", network="IU", channel="LF1", location="40").element
+ == "U"
+ )
+ assert (
+ IRISSNCL(station="ANMO", network="IU", channel="LF2", location="40").element
+ == "V"
+ )
+ assert (
+ IRISSNCL(station="ANMO", network="IU", channel="LFZ", location="40").element
+ == "W"
+ )
+ with pytest.raises(ValueError) as error:
+ IRISSNCL(station="ANMO", network="IU", channel="LFH", location="40").element
+ assert error.value == "Unsupported channel LFH"
+
+
+def test_get_iris_channel():
+ """edge_test.IRISSNCL_test.test_get_iris_channel()"""
+ assert (
+ get_iris_channel(
+ element="H",
+ interval="second",
+ data_type="variation",
+ network="IU",
+ location="40",
+ )
+ == "LF1"
+ )
+ assert (
+ get_iris_channel(
+ element="U",
+ interval="second",
+ data_type="variation",
+ network="IU",
+ location="40",
+ )
+ == "LF1"
+ )
+ assert (
+ get_iris_channel(
+ element="E",
+ interval="second",
+ data_type="variation",
+ network="IU",
+ location="40",
+ )
+ == "LF2"
+ )
+ assert (
+ get_iris_channel(
+ element="V",
+ interval="second",
+ data_type="variation",
+ network="IU",
+ location="40",
+ )
+ == "LF2"
+ )
+ assert (
+ get_iris_channel(
+ element="W",
+ interval="second",
+ data_type="variation",
+ network="IU",
+ location="40",
+ )
+ == "LFZ"
+ )
+ # predefined channel
+ assert (
+ get_iris_channel(
+ element="LFZ",
+ interval="second",
+ data_type="variation",
+ network="IU",
+ location="40",
+ )
+ == "LFZ"
+ )
+ with pytest.raises(ValueError) as error:
+ get_iris_channel(
+ element="D",
+ interval="second",
+ data_type="variation",
+ network="IU",
+ location="40",
+ )
+ assert error.value == "Unsupported element: D"
+
+
+def test_get_sncl():
+ """edge_test.IRISSNCL_test.test_get_sncl()"""
+ assert (
+ IRISSNCL.get_sncl(
+ data_type="variation",
+ element="H",
+ interval="second",
+ station="ANMO",
+ network="IU",
+ location="40",
+ )
+ == IRISSNCL(station="ANMO", network="IU", channel="LF1", location="40")
+ )
+
+
+def test_interval():
+ """edge_test.IRISSNCL_test.test_interval()"""
+ assert (
+ IRISSNCL(
+ station="ANMO",
+ network="IU",
+ channel="LF1",
+ location="40",
+ ).interval
+ == "second"
+ )
+
+
+def test_parse_sncl():
+ """edge_test.IRISSNCL_test.test_parse_sncl()"""
+ assert IRISSNCL(
+ station="ANMO", network="IU", channel="LF1", location="40"
+ ).parse_sncl() == {
+ "station": "ANMO",
+ "network": "IU",
+ "data_type": "variation",
+ "element": "U",
+ "interval": "second",
+ }
--
GitLab
From 53a3cfb86a7941c0971493854f75c219fe466d63 Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Thu, 21 Oct 2021 18:47:52 +0000
Subject: [PATCH 003/142] add IRISFactory
---
geomagio/edge/IRISFactory.py | 154 +++++++++++++++++++++++++++++++++++
1 file changed, 154 insertions(+)
create mode 100644 geomagio/edge/IRISFactory.py
diff --git a/geomagio/edge/IRISFactory.py b/geomagio/edge/IRISFactory.py
new file mode 100644
index 00000000..950fb61f
--- /dev/null
+++ b/geomagio/edge/IRISFactory.py
@@ -0,0 +1,154 @@
+from typing import List, Optional
+
+from obspy import Trace, UTCDateTime
+from obspy.clients.iris.client import Client
+
+from ..geomag_types import DataInterval, DataType
+from ..ObservatoryMetadata import ObservatoryMetadata
+from .. import TimeseriesUtility
+from .IRISSNCL import IRISSNCL
+from .MiniSeedFactory import MiniSeedFactory
+
+
+class IRISFactory(MiniSeedFactory):
+ """MiniSeedFactory for IRIS related data.
+
+ Parameters
+ ----------
+ base_url: str
+ iris web service url
+ host: str
+ a string representing the IP number of the host to connect to
+ write_port: int
+ the port number the miniseed client writes data
+ network: str
+ data network
+ observatory: str
+ observatory id
+ channels: array
+ list of channels
+ type: {"adjusted", "definitive", "quasi-definitive", "variation"}
+ data type
+ interval: {"tenhertz", "second", "minute", "hour", "day"}
+ data interval
+ observatoryMetadata: ObservatoryMetadata
+ observatory metadata to replace the default ObservatoryMetadata
+ locationCode: str
+ the location code for the given edge server
+ convert_channels: array
+ list of channels to convert from volt/bin to nT
+
+ See Also
+ --------
+ MiniSeedFactory
+
+ Notes
+ -----
+ This factory is designed to receive data from IRIS and write to edge.
+ convert_channels should only be used with tenhertz NT data (U, V, W).
+ Non-NT data conversions are automatically handled by the IRIS web service.
+
+
+ """
+
+ def __init__(
+ self,
+ base_url: str = "http://service.iris.edu/irisws",
+ host: str = "cwbpub.cr.usgs.gov",
+ write_port: int = 7974,
+ network: str = "NT",
+ observatory: Optional[str] = None,
+ channels: Optional[List[str]] = None,
+ type: Optional[DataType] = None,
+ interval: Optional[DataInterval] = None,
+ observatoryMetadata: Optional[ObservatoryMetadata] = None,
+ locationCode: Optional[str] = None,
+ convert_channels: Optional[List[str]] = None,
+ ):
+ super().__init__(
+ host=host,
+ write_port=write_port,
+ observatory=observatory,
+ channels=channels,
+ type=type,
+ interval=interval,
+ observatoryMetadata=observatoryMetadata or ObservatoryMetadata(),
+ locationCode=locationCode,
+ convert_channels=convert_channels,
+ )
+ self.base_url = base_url
+ self.network = network
+ self.client = Client(base_url=base_url)
+
+ def _get_timeseries(
+ self,
+ starttime: UTCDateTime,
+ endtime: UTCDateTime,
+ observatory: str,
+ channel: str,
+ type: DataType,
+ interval: DataInterval,
+ add_empty_channels: bool = True,
+ ) -> Trace:
+ """get timeseries data for a single channel
+
+ Parameters
+ ----------
+ starttime: UTCDateTime
+ the starttime of requested data
+ endtime: UTCDateTime
+ the endtime of requested data
+ observatory: str
+ observatory id
+ channel: str
+ channel name
+ type: {"adjusted", "definitive", "quasi-definitive", "variation"}
+ data type
+ interval: {"tenhertz", "second", "minute", "hour", "day"}
+ data interval
+ add_empty_channels: bool
+ if True, returns channels without data as empty traces
+
+ Returns
+ -------
+ data: Trace
+ timeseries trace of the requested channel data
+ """
+ sncl = IRISSNCL.get_sncl(
+ data_type=type,
+ element=channel,
+ interval=interval,
+ station=observatory,
+ network=self.network,
+ location=self.locationCode,
+ )
+ filter = ["correct"]
+ if sncl.channel[1] in ["E", "Y"]:
+ filter = []
+ data = self.client.timeseries(
+ network=sncl.network,
+ station=sncl.station,
+ location=sncl.location,
+ channel=sncl.channel,
+ starttime=starttime,
+ endtime=endtime,
+ filter=filter,
+ )
+ data.merge()
+ if data.count() == 0 and add_empty_channels:
+ data += self._get_empty_trace(
+ starttime=starttime,
+ endtime=endtime,
+ observatory=observatory,
+ channel=channel,
+ data_type=type,
+ interval=interval,
+ network=sncl.network,
+ location=sncl.location,
+ )
+ if data.count() != 0:
+ TimeseriesUtility.pad_and_trim_trace(
+ trace=data[0], starttime=starttime, endtime=endtime
+ )
+ self._set_metadata(data, observatory, channel, type, interval)
+ return data
--
GitLab
From 87dc72e15b9dc172153fe23bf18885f9cfb94db1 Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Thu, 21 Oct 2021 18:48:05 +0000
Subject: [PATCH 004/142] update edge __init__
---
geomagio/edge/__init__.py | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/geomagio/edge/__init__.py b/geomagio/edge/__init__.py
index 45b3d49c..ebb15ef6 100644
--- a/geomagio/edge/__init__.py
+++ b/geomagio/edge/__init__.py
@@ -3,19 +3,23 @@
from __future__ import absolute_import
from .EdgeFactory import EdgeFactory
+from .IRISFactory import IRISFactory
from .LocationCode import LocationCode
from .MiniSeedFactory import MiniSeedFactory
from .MiniSeedInputClient import MiniSeedInputClient
from .RawInputClient import RawInputClient
+from .IRISSNCL import IRISSNCL
from .SNCL import SNCL
from .LegacySNCL import LegacySNCL
__all__ = [
"EdgeFactory",
+ "IRISFactory",
"LocationCode",
"MiniSeedFactory",
"MiniSeedInputClient",
"RawInputClient",
- "LegacySNCL",
+ "IRISSNCL",
"SNCL",
+ "LegacySNCL",
]
--
GitLab
From eb737baceb7d7ab7b2165a32ff8e31efe0d865b2 Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Thu, 21 Oct 2021 18:48:23 +0000
Subject: [PATCH 005/142] controller input_factory option for IRISFactory
---
geomagio/Controller.py | 39 +++++++++++++++++++++++++++++++++------
1 file changed, 33 insertions(+), 6 deletions(-)
diff --git a/geomagio/Controller.py b/geomagio/Controller.py
index d05f45ae..4185cdea 100644
--- a/geomagio/Controller.py
+++ b/geomagio/Controller.py
@@ -513,7 +513,7 @@ def get_input_factory(args):
host=args.input_host,
port=args.input_port,
locationCode=args.locationcode,
- **input_factory_args
+ **input_factory_args,
)
elif input_type == "miniseed":
input_factory = edge.MiniSeedFactory(
@@ -521,7 +521,7 @@ def get_input_factory(args):
port=args.input_port,
locationCode=args.locationcode,
convert_channels=args.convert_voltbin,
- **input_factory_args
+ **input_factory_args,
)
elif input_type == "goes":
# TODO: deal with other goes arguments
@@ -531,7 +531,15 @@ def get_input_factory(args):
password=args.input_goes_password,
server=args.input_goes_server,
user=args.input_goes_user,
- **input_factory_args
+ **input_factory_args,
+ )
+ elif input_type == "iris":
+ input_factory = edge.IRISFactory(
+ base_url=args.iris_url,
+ network=args.iris_network,
+ locationCode=args.locationcode,
+ convert_channels=args.convert_voltbin,
+ **input_factory_args,
)
else:
# stream compatible factories
@@ -600,7 +608,7 @@ def get_output_factory(args):
locationCode=locationcode,
tag=args.output_edge_tag,
forceout=args.output_edge_forceout,
- **output_factory_args
+ **output_factory_args,
)
elif output_type == "miniseed":
# TODO: deal with other miniseed arguments
@@ -610,7 +618,7 @@ def get_output_factory(args):
port=args.output_read_port,
write_port=args.output_port,
locationCode=locationcode,
- **output_factory_args
+ **output_factory_args,
)
elif output_type == "plot":
output_factory = PlotTimeseriesFactory()
@@ -763,7 +771,16 @@ def parse_args(args):
input_type_group = input_group.add_mutually_exclusive_group(required=True)
input_type_group.add_argument(
"--input",
- choices=("edge", "goes", "iaga2002", "imfv122", "imfv283", "miniseed", "pcdcp"),
+ choices=(
+ "edge",
+ "goes",
+ "iaga2002",
+ "imfv122",
+ "imfv283",
+ "iris",
+ "miniseed",
+ "pcdcp",
+ ),
default="edge",
help='Input format (Default "edge")',
)
@@ -828,6 +845,16 @@ def parse_args(args):
help='Data interval, default "minute"',
metavar="INTERVAL",
)
+ input_group.add_argument(
+ "--iris-network",
+ default="NT",
+ help="data network",
+ )
+ input_group.add_argument(
+ "--iris-url",
+ default="http://service.iris.edu/irisws",
+ help="IRIS web service url",
+ )
input_group.add_argument(
"--locationcode",
help="""
--
GitLab
From c7e4c50824a18d2c249ae60e2a01d8b6b3a67103 Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Thu, 21 Oct 2021 20:08:39 +0000
Subject: [PATCH 006/142] limit data type options for ASL data
---
geomagio/edge/IRISSNCL.py | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/geomagio/edge/IRISSNCL.py b/geomagio/edge/IRISSNCL.py
index fdd9172d..0fdcc417 100644
--- a/geomagio/edge/IRISSNCL.py
+++ b/geomagio/edge/IRISSNCL.py
@@ -15,6 +15,12 @@ class IRISSNCL(SNCL):
network: str = "NT",
location: Optional[str] = None,
) -> "IRISSNCL":
+ if (
+ network == "IU"
+ and location == "40"
+ and data_type not in ["40", "variation"] # ASL only supports variation data
+ ):
+ raise ValueError(f"Unsupported data type: {data_type}")
location = location or get_location(element=element, data_type=data_type)
return IRISSNCL(
station=station,
--
GitLab
From 2a9287abfe8e6a95926544f758043497908b4977 Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Thu, 21 Oct 2021 20:08:51 +0000
Subject: [PATCH 007/142] test limited data type options for ASL data
---
test/edge_test/IRISSNCL_test.py | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
diff --git a/test/edge_test/IRISSNCL_test.py b/test/edge_test/IRISSNCL_test.py
index eb36fc3c..b67cc640 100644
--- a/test/edge_test/IRISSNCL_test.py
+++ b/test/edge_test/IRISSNCL_test.py
@@ -118,6 +118,25 @@ def test_get_sncl():
)
== IRISSNCL(station="ANMO", network="IU", channel="LF1", location="40")
)
+ with pytest.raises(ValueError) as error:
+ IRISSNCL.get_sncl(
+ data_type="adjusted",
+ element="H",
+ interval="second",
+ station="ANMO",
+ network="IU",
+ location="40",
+ )
+ assert error.value == "Unsupported data type: adjusted"
+ assert (
+ IRISSNCL.get_sncl(
+ data_type="adjusted",
+ element="H",
+ interval="second",
+ station="BOU",
+ )
+ == IRISSNCL(station="BOU", network="NT", channel="LFH", location="A0")
+ )
def test_interval():
--
GitLab
From 12823d897e2904bd8eb4b9b4c134222af70680d1 Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Thu, 21 Oct 2021 20:09:19 +0000
Subject: [PATCH 008/142] add ASL observatories to ws observatories
---
geomagio/api/ws/Observatory.py | 86 ++++++++++++++++++++++++++++++++++
1 file changed, 86 insertions(+)
diff --git a/geomagio/api/ws/Observatory.py b/geomagio/api/ws/Observatory.py
index fe857c9a..ecb38c91 100644
--- a/geomagio/api/ws/Observatory.py
+++ b/geomagio/api/ws/Observatory.py
@@ -424,4 +424,90 @@ OBSERVATORIES = [
),
]
+ASL_OBSERVATORIES = [
+ Observatory(
+ id="ANMO",
+ elevation=1820,
+ latitude=34.946,
+ longitude=-106.457,
+ name="Albuquerque",
+ agency="USGS",
+ declination_base=0,
+ ),
+ Observatory(
+ id="CASY",
+ elevation=10,
+ latitude=-66.279,
+ longitude=110.535,
+ name="Casey",
+ agency="USGS",
+ declination_base=0,
+ ),
+ Observatory(
+ id="COLA",
+ elevation=200,
+ latitude=64.874,
+ longitude=-147.862,
+ name="College Outpost",
+ agency="USGS",
+ declination_base=0,
+ ),
+ Observatory(
+ id="COR",
+ elevation=110,
+ latitude=44.586,
+ longitude=-123.305,
+ name="Corvallis",
+ agency="USGS",
+ declination_base=0,
+ ),
+ Observatory(
+ id="QSPA",
+ elevation=2850,
+ latitude=-89.929,
+ longitude=144.438,
+ name="South Pole Remote Earth Science Observatory",
+ agency="USGS",
+ declination_base=0,
+ ),
+ Observatory(
+ id="RSSD",
+ elevation=2090,
+ latitude=44.121,
+ longitude=-104.036,
+ name="Black Hills",
+ agency="USGS",
+ declination_base=0,
+ ),
+ Observatory(
+ id="SBA",
+ elevation=50,
+ latitude=-77.849,
+ longitude=166.757,
+ name="Scott Base",
+ agency="USGS",
+ declination_base=0,
+ ),
+ Observatory(
+ id="SFJD",
+ elevation=330,
+ latitude=66.996,
+ longitude=-50.621,
+ name="Sondre Stromfjord",
+ agency="USGS",
+ declination_base=0,
+ ),
+ Observatory(
+ id="SPA",
+ elevation=2927,
+ latitude=-90.0,
+ longitude=0.0,
+ name="South Pole",
+ agency="USGS",
+ declination_base=0,
+ ),
+]
+
+ASL_OBSERVATORY_INDEX = {o.id: o for o in ASL_OBSERVATORIES}
OBSERVATORY_INDEX = {o.id: o for o in OBSERVATORIES}
+OBSERVATORY_INDEX.update(ASL_OBSERVATORY_INDEX)
--
GitLab
From d25a2b2e9300950f18fa2d95e94f1b95faf883dd Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Thu, 21 Oct 2021 20:09:54 +0000
Subject: [PATCH 009/142] get observatories from OBSERVATORY_INDEX
---
geomagio/api/ws/observatories.py | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/geomagio/api/ws/observatories.py b/geomagio/api/ws/observatories.py
index 1a8c797c..4297fe9b 100644
--- a/geomagio/api/ws/observatories.py
+++ b/geomagio/api/ws/observatories.py
@@ -2,7 +2,7 @@ from typing import Dict
from fastapi import APIRouter, Response
-from .Observatory import OBSERVATORIES, OBSERVATORY_INDEX
+from .Observatory import OBSERVATORY_INDEX
router = APIRouter()
@@ -15,7 +15,9 @@ router = APIRouter()
def get_observatories() -> Dict:
return {
"type": "FeatureCollection",
- "features": [o.geojson() for o in OBSERVATORIES],
+ "features": [
+ OBSERVATORY_INDEX[id].geojson() for id in OBSERVATORY_INDEX.keys()
+ ],
}
--
GitLab
From 4916814ebac23073e47a66e0feb03a3c87be4a89 Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Thu, 21 Oct 2021 20:10:27 +0000
Subject: [PATCH 010/142] ws support for IRISFactory
---
geomagio/api/ws/data.py | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/geomagio/api/ws/data.py b/geomagio/api/ws/data.py
index db204eee..961c6fae 100644
--- a/geomagio/api/ws/data.py
+++ b/geomagio/api/ws/data.py
@@ -6,9 +6,10 @@ from obspy import UTCDateTime, Stream
from starlette.responses import Response
from ... import DerivedTimeseriesFactory, TimeseriesFactory, TimeseriesUtility
-from ...edge import EdgeFactory, MiniSeedFactory
+from ...edge import EdgeFactory, IRISFactory, MiniSeedFactory
from ...iaga2002 import IAGA2002Writer
from ...imfjson import IMFJSONWriter
+from .Observatory import ASL_OBSERVATORY_INDEX
from .DataApiQuery import (
DEFAULT_ELEMENTS,
DataApiQuery,
@@ -30,7 +31,9 @@ def get_data_factory(
"""
host = os.getenv("DATA_HOST", "cwbpub.cr.usgs.gov")
sampling_period = query.sampling_period
- if sampling_period in [
+ if query.id in ASL_OBSERVATORY_INDEX:
+ factory = IRISFactory(network="IU", locationCode="40")
+ elif sampling_period in [
SamplingPeriod.TEN_HERTZ,
SamplingPeriod.HOUR,
SamplingPeriod.DAY,
--
GitLab
From 215eb8ec644b1b525d5a9f9271142d06452853aa Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Mon, 18 Oct 2021 14:29:09 -0600
Subject: [PATCH 011/142] remove obsrio module
---
geomagio/processing/obsrio.py | 342 ----------------------------------
1 file changed, 342 deletions(-)
delete mode 100644 geomagio/processing/obsrio.py
diff --git a/geomagio/processing/obsrio.py b/geomagio/processing/obsrio.py
deleted file mode 100644
index 1d8037fd..00000000
--- a/geomagio/processing/obsrio.py
+++ /dev/null
@@ -1,342 +0,0 @@
-from typing import List, Optional
-
-import typer
-
-from ..algorithm import Algorithm, FilterAlgorithm
-from ..Controller import (
- Controller,
- get_realtime_interval,
-)
-from ..TimeseriesFactory import TimeseriesFactory
-from .factory import get_edge_factory, get_miniseed_factory
-
-
-def main():
- typer.run(obsrio_filter)
-
-
-def obsrio_filter(
- interval: str,
- observatory: str,
- input_factory: Optional[str] = None,
- host: str = "127.0.0.1",
- port: str = 2061,
- output_factory: Optional[str] = None,
- output_port: int = typer.Option(
- 2061, help="Port where output factory writes data."
- ),
- output_read_port: int = typer.Option(
- 2061, help="Port where output factory reads data"
- ),
- realtime_interval: int = 600,
- update_limit: int = 10,
-):
- if interval == "realtime":
- filter_realtime(
- observatory=observatory,
- input_factory=input_factory,
- host=host,
- port=port,
- output_factory=output_factory,
- output_port=output_port,
- output_read_port=output_read_port,
- realtime_interval=realtime_interval,
- update_limit=update_limit,
- )
- elif interval in ["hour", "day"]:
- input_factory = get_edge_factory(host=host, port=port)
- output_factory = get_miniseed_factory(
- host=host, port=output_read_port, write_port=output_port
- )
- if interval == "hour":
- obsrio_hour(
- observatory=observatory,
- input_factory=input_factory,
- output_factory=output_factory,
- realtime_interval=realtime_interval,
- update_limit=update_limit,
- )
- elif interval == "day":
- obsrio_day(
- observatory=observatory,
- input_factory=input_factory,
- output_factory=output_factory,
- realtime_interval=realtime_interval,
- update_limit=update_limit,
- )
- else:
- raise ValueError("Invalid interval")
-
-
-def filter_realtime(
- observatory: str,
- input_factory: Optional[str] = None,
- host: str = "127.0.0.1",
- port: str = 2061,
- output_factory: Optional[str] = None,
- output_port: int = typer.Option(
- 2061, help="Port where output factory writes data."
- ),
- output_read_port: int = typer.Option(
- 2061, help="Port where output factory reads data"
- ),
- realtime_interval: int = 600,
- update_limit: int = 10,
-):
- """Filter 10Hz miniseed, 1 second, one minute, and temperature data.
- Defaults set for realtime processing; can also be implemented to update legacy data"""
- if input_factory == "miniseed":
- input_factory = get_miniseed_factory(host=host, port=port)
- elif input_factory == "edge":
- input_factory = get_edge_factory(host=host, port=port)
- if output_factory == "miniseed":
- output_factory = get_miniseed_factory(
- host=host, port=output_read_port, write_port=output_port
- )
- elif output_factory == "edge":
- output_factory = get_edge_factory(
- host=host, port=output_read_port, write_port=output_port
- )
-
- obsrio_tenhertz(
- observatory=observatory,
- input_factory=input_factory,
- output_factory=output_factory,
- realtime_interval=realtime_interval,
- update_limit=update_limit,
- )
- obsrio_second(
- observatory=observatory,
- input_factory=input_factory,
- output_factory=output_factory,
- realtime_interval=realtime_interval,
- update_limit=update_limit,
- )
- obsrio_minute(
- observatory=observatory,
- input_factory=input_factory,
- output_factory=output_factory,
- realtime_interval=realtime_interval,
- update_limit=update_limit,
- )
- obsrio_temperatures(
- observatory=observatory,
- input_factory=input_factory,
- output_factory=output_factory,
- realtime_interval=realtime_interval,
- update_limit=update_limit,
- )
-
-
-def obsrio_day(
- observatory: str,
- input_factory: Optional[TimeseriesFactory] = None,
- output_factory: Optional[TimeseriesFactory] = None,
- realtime_interval: int = 86400,
- update_limit: int = 7,
-):
- """Filter 1 second edge H,E,Z,F to 1 day miniseed U,V,W,F."""
- starttime, endtime = get_realtime_interval(realtime_interval)
- controller = Controller(
- inputFactory=input_factory or get_edge_factory(),
- inputInterval="minute",
- outputFactory=output_factory or get_miniseed_factory(),
- outputInterval="day",
- )
- renames = {"H": "U", "E": "V", "Z": "W", "F": "F"}
- for input_channel in renames.keys():
- output_channel = renames[input_channel]
- controller.run_as_update(
- algorithm=FilterAlgorithm(
- input_sample_period=60.0,
- output_sample_period=86400.0,
- inchannels=(input_channel,),
- outchannels=(output_channel,),
- ),
- observatory=(observatory,),
- output_observatory=(observatory,),
- starttime=starttime,
- endtime=endtime,
- input_channels=(input_channel,),
- output_channels=(output_channel,),
- realtime=realtime_interval,
- rename_output_channel=((input_channel, output_channel),),
- update_limit=update_limit,
- )
-
-
-def obsrio_hour(
- observatory: str,
- input_factory: Optional[TimeseriesFactory] = None,
- output_factory: Optional[TimeseriesFactory] = None,
- realtime_interval: int = 600,
- update_limit: int = 10,
-):
- """Filter 1 minute edge H,E,Z,F to 1 hour miniseed U,V,W,F."""
- starttime, endtime = get_realtime_interval(realtime_interval)
- controller = Controller(
- inputFactory=input_factory or get_edge_factory(),
- inputInterval="minute",
- outputFactory=output_factory or get_miniseed_factory(),
- outputInterval="hour",
- )
- renames = {"H": "U", "E": "V", "Z": "W", "F": "F"}
- for input_channel in renames.keys():
- output_channel = renames[input_channel]
- controller.run_as_update(
- algorithm=FilterAlgorithm(
- input_sample_period=60.0,
- output_sample_period=3600.0,
- inchannels=(input_channel,),
- outchannels=(output_channel,),
- ),
- observatory=(observatory,),
- output_observatory=(observatory,),
- starttime=starttime,
- endtime=endtime,
- input_channels=(input_channel,),
- output_channels=(output_channel,),
- realtime=realtime_interval,
- rename_output_channel=((input_channel, output_channel),),
- update_limit=update_limit,
- )
-
-
-def obsrio_minute(
- observatory: str,
- channels: List[str] = ["H", "E", "Z", "F"],
- input_factory: Optional[TimeseriesFactory] = None,
- output_factory: Optional[TimeseriesFactory] = None,
- realtime_interval: int = 600,
- update_limit: int = 10,
-):
- """Filter 1Hz legacy channels to 1 minute legacy.
-
- For H,E,Z,F: should be called after obsrio_second() and obsrio_tenhertz(),
- which populate 1Hz legacy H,E,Z,F.
- """
- starttime, endtime = get_realtime_interval(realtime_interval)
- controller = Controller(
- inputFactory=input_factory or get_edge_factory(),
- inputInterval="second",
- outputFactory=output_factory or get_edge_factory(),
- outputInterval="minute",
- )
- for channel in channels:
- controller.run_as_update(
- algorithm=FilterAlgorithm(
- input_sample_period=1,
- output_sample_period=60,
- inchannels=(channel,),
- outchannels=(channel,),
- ),
- observatory=(observatory,),
- output_observatory=(observatory,),
- starttime=starttime,
- endtime=endtime,
- input_channels=(channel,),
- output_channels=(channel,),
- realtime=realtime_interval,
- update_limit=update_limit,
- )
-
-
-def obsrio_second(
- observatory: str,
- input_factory: Optional[TimeseriesFactory] = None,
- output_factory: Optional[TimeseriesFactory] = None,
- realtime_interval: int = 600,
- update_limit: int = 10,
-):
- """Copy 1Hz miniseed F to 1Hz legacy F."""
- starttime, endtime = get_realtime_interval(realtime_interval)
- controller = Controller(
- algorithm=Algorithm(inchannels=("F",), outchannels=("F",)),
- inputFactory=input_factory or get_miniseed_factory(),
- outputFactory=output_factory or get_edge_factory(),
- )
- controller.run_as_update(
- observatory=(observatory,),
- output_observatory=(observatory,),
- starttime=starttime,
- endtime=endtime,
- input_channels=("F",),
- output_channels=("F",),
- realtime=realtime_interval,
- update_limit=update_limit,
- )
-
-
-def obsrio_temperatures(
- observatory: str,
- input_factory: Optional[TimeseriesFactory] = None,
- output_factory: Optional[TimeseriesFactory] = None,
- realtime_interval: int = 600,
- update_limit: int = 10,
-):
- """Filter temperatures 1Hz miniseed (LK1-4) to 1 minute legacy (UK1-4)."""
- starttime, endtime = get_realtime_interval(realtime_interval)
- controller = Controller(
- inputFactory=input_factory or get_miniseed_factory(),
- inputInterval="second",
- outputFactory=output_factory or get_edge_factory(),
- outputInterval="minute",
- )
- renames = {"LK1": "UK1", "LK2": "UK2", "LK3": "UK3", "LK4": "UK4"}
- for input_channel in renames.keys():
- output_channel = renames[input_channel]
- controller.run_as_update(
- algorithm=FilterAlgorithm(
- input_sample_period=1,
- output_sample_period=60,
- inchannels=(input_channel,),
- outchannels=(output_channel,),
- ),
- observatory=(observatory,),
- output_observatory=(observatory,),
- starttime=starttime,
- endtime=endtime,
- input_channels=(input_channel,),
- output_channels=(output_channel,),
- realtime=realtime_interval,
- rename_output_channel=((input_channel, output_channel),),
- update_limit=update_limit,
- )
-
-
-def obsrio_tenhertz(
- observatory: str,
- input_factory: Optional[TimeseriesFactory] = None,
- output_factory: Optional[TimeseriesFactory] = None,
- realtime_interval: int = 600,
- update_limit: int = 10,
-):
- """Filter 10Hz miniseed U,V,W to 1Hz legacy H,E,Z."""
- starttime, endtime = get_realtime_interval(realtime_interval)
- controller = Controller(
- inputFactory=input_factory
- or get_miniseed_factory(convert_channels=("U", "V", "W")),
- inputInterval="tenhertz",
- outputFactory=output_factory or get_edge_factory(),
- outputInterval="second",
- )
- renames = {"U": "H", "V": "E", "W": "Z"}
- for input_channel in renames.keys():
- output_channel = renames[input_channel]
- controller.run_as_update(
- algorithm=FilterAlgorithm(
- input_sample_period=0.1,
- output_sample_period=1,
- inchannels=(input_channel,),
- outchannels=(output_channel,),
- ),
- observatory=(observatory,),
- output_observatory=(observatory,),
- starttime=starttime,
- endtime=endtime,
- input_channels=(input_channel,),
- output_channels=(output_channel,),
- realtime=realtime_interval,
- rename_output_channel=((input_channel, output_channel),),
- update_limit=update_limit,
- )
--
GitLab
From 014f6554a366d0bdefadaaea49f2224a184e237f Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Mon, 18 Oct 2021 14:29:21 -0600
Subject: [PATCH 012/142] update factory module type hints
---
geomagio/processing/factory.py | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/geomagio/processing/factory.py b/geomagio/processing/factory.py
index 6e741d46..481b0459 100644
--- a/geomagio/processing/factory.py
+++ b/geomagio/processing/factory.py
@@ -1,6 +1,5 @@
import os
-from ..TimeseriesFactory import TimeseriesFactory
from ..edge import EdgeFactory, MiniSeedFactory
@@ -9,7 +8,7 @@ def get_edge_factory(
host=os.getenv("EDGE_HOST", "127.0.0.1"),
interval="second",
**kwargs
-) -> TimeseriesFactory:
+) -> EdgeFactory:
return EdgeFactory(host=host, interval=interval, type=data_type, **kwargs)
@@ -18,5 +17,5 @@ def get_miniseed_factory(
host=os.getenv("EDGE_HOST", "127.0.0.1"),
interval="second",
**kwargs
-) -> TimeseriesFactory:
+) -> MiniSeedFactory:
return MiniSeedFactory(host=host, interval=interval, type=data_type, **kwargs)
--
GitLab
From b0855b4f923ef2d788072bcdc023903f5d82b0b8 Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Mon, 18 Oct 2021 14:29:34 -0600
Subject: [PATCH 013/142] add filter application
---
geomagio/processing/filters.py | 435 +++++++++++++++++++++++++++++++++
1 file changed, 435 insertions(+)
create mode 100644 geomagio/processing/filters.py
diff --git a/geomagio/processing/filters.py b/geomagio/processing/filters.py
new file mode 100644
index 00000000..0decbfb5
--- /dev/null
+++ b/geomagio/processing/filters.py
@@ -0,0 +1,435 @@
+from enum import Enum
+from typing import List, Optional
+
+from typer import Argument, Option, Typer
+
+from ..algorithm import Algorithm, FilterAlgorithm
+from ..Controller import Controller, get_realtime_interval
+from ..geomag_types import DataInterval
+from ..TimeseriesFactory import TimeseriesFactory
+from .factory import get_edge_factory, get_miniseed_factory
+
+
+class DataFormat(str, Enum):
+ OBSRIO = "OBSRIO"
+ PCDCP = "PCDCP"
+
+
+app = Typer(help="Filter geomagnetic timeseries data")
+
+
+def main():
+ app()
+
+
+@app.command(
+ name="day",
+ help="Filter 1 day nT/temperature data",
+)
+def day_command(
+ observatory: str = Argument(None, help="observatory id"),
+ input_host: str = Option("127.0.0.1", help="host to request data"),
+ output_host: str = Option("127.0.0.1", help="host to write data"),
+ realtime_interval: int = Option(86400, help="length of update window"),
+ update_limit: int = Option(7, help="number of update windows"),
+):
+ day_filter(
+ observatory=observatory,
+ input_factory=get_miniseed_factory(host=input_host),
+ output_factory=get_miniseed_factory(host=output_host),
+ realtime_interval=realtime_interval,
+ update_limit=update_limit,
+ )
+
+
+@app.command(
+ name="hour",
+ help="Filter 1 hour nT/temperature data",
+)
+def hour_command(
+ observatory: str = Argument(None, help="observatory id"),
+ input_host: str = Option("127.0.0.1", help="host to request data"),
+ output_host: str = Option("127.0.0.1", help="host to write data"),
+ realtime_interval: int = Option(3600, help="length of update window"),
+ update_limit: int = Option(24, help="number of update windows"),
+):
+ hour_filter(
+ observatory=observatory,
+ input_factory=get_miniseed_factory(host=input_host),
+ output_factory=get_miniseed_factory(host=output_host),
+ realtime_interval=realtime_interval,
+ update_limit=update_limit,
+ )
+
+
+@app.command(
+ name="realtime",
+ short_help="Filter 1 second and 1 minute nT/temperature data",
+ help="""
+ ObsRIO:
+ Filters 10Hz U,V,W miniseed to 1 second miniseed
+ Filters 1 second U,V,W,F miniseed to 1 minute miniseed
+ Filters 1 second T1-4 miniseed to 1 minute miniseed
+ Copies 1 second and 1 minute U,V,W,F,T1-4 miniseed to H,E,Z,F,UK1-4 earthworm
+ PCDCP:
+ Copies 1 second H,E,Z,F earthworm to U,V,W,F miniseed
+ Copies 1 minute UK1-4 earthworm to T1-4 miniseed
+ Filters 1 second U,V,W,F miniseed to 1 minute miniseed
+ """,
+)
+def realtime_command(
+ observatory: str = Argument(None, help="observatory id"),
+ input_host: str = Option("127.0.0.1", help="host to request data"),
+ output_host: str = Option("127.0.0.1", help="host to write data"),
+ data_format: DataFormat = Option(DataFormat.PCDCP, help="Data acquisition system"),
+ realtime_interval: int = Option(600, help="length of update window"),
+ update_limit: int = Option(10, help="number of update windows"),
+):
+ if data_format == DataFormat.OBSRIO:
+ second_filter(
+ observatory=observatory,
+ input_factory=get_miniseed_factory(
+ host=input_host, convert_channels=("U", "V", "W")
+ ),
+ output_factory=get_miniseed_factory(host=output_host),
+ realtime_interval=realtime_interval,
+ update_limit=update_limit,
+ )
+ _copy_channels(
+ observatory=observatory,
+ channels=(
+ ("U", "H"),
+ ("V", "E"),
+ ("W", "Z"),
+ ("F", "F"),
+ ("T1", "LK1"),
+ ("T2", "LK2"),
+ ("T3", "LK3"),
+ ("T4", "LK4"),
+ ),
+ interval="second",
+ input_factory=get_miniseed_factory(host=input_host),
+ output_factory=get_edge_factory(host=output_host),
+ realtime_interval=realtime_interval,
+ update_limit=update_limit,
+ )
+ minute_filter(
+ observatory=observatory,
+ channels=("T1", "T2", "T3", "T4"),
+ input_factory=get_miniseed_factory(host=input_host),
+ output_factory=get_miniseed_factory(host=output_host),
+ realtime_interval=realtime_interval,
+ update_limit=update_limit,
+ )
+ else:
+ _copy_channels(
+ observatory=observatory,
+ channels=(
+ ("H", "U"),
+ ("E", "V"),
+ ("Z", "W"),
+ ("F", "F"),
+ ),
+ interval="second",
+ input_factory=get_edge_factory(host=input_host),
+ output_factory=get_miniseed_factory(host=output_host),
+ realtime_interval=realtime_interval,
+ update_limit=update_limit,
+ )
+ _copy_channels(
+ observatory=observatory,
+ channels=(
+ ("UK1", "T1"),
+ ("UK2", "T2"),
+ ("UK3", "T3"),
+ ("UK4", "T4"),
+ ),
+ interval="minute",
+ input_factory=get_edge_factory(host=input_host),
+ output_factory=get_miniseed_factory(host=output_host),
+ realtime_interval=realtime_interval,
+ update_limit=update_limit,
+ )
+ minute_filter(
+ observatory=observatory,
+ channels=("U", "V", "W", "F"),
+ input_factory=get_miniseed_factory(host=input_host),
+ output_factory=get_miniseed_factory(host=output_host),
+ realtime_interval=realtime_interval,
+ update_limit=update_limit,
+ )
+ if data_format == DataFormat.OBSRIO:
+ _copy_channels(
+ observatory=observatory,
+ channels=(
+ ("U", "H"),
+ ("V", "E"),
+ ("W", "Z"),
+ ("F", "F"),
+ ("T1", "UK1"),
+ ("T2", "UK2"),
+ ("T3", "UK3"),
+ ("T4", "UK4"),
+ ),
+ interval="minute",
+ input_factory=get_miniseed_factory(host=input_host),
+ output_factory=get_edge_factory(host=output_host),
+ realtime_interval=realtime_interval,
+ update_limit=update_limit,
+ )
+
+
+def day_filter(
+ observatory: str,
+ channels: List[str] = ["U", "V", "W", "F", "T1", "T2", "T3", "T4"],
+ input_factory: Optional[TimeseriesFactory] = None,
+ output_factory: Optional[TimeseriesFactory] = None,
+ realtime_interval: int = 86400,
+ update_limit: int = 7,
+):
+ """Filter 1 second miniseed channels to 1 day
+
+ Parameters:
+ -----------
+ observatory: str
+ observatory id
+ channels: array
+ list of channels to filter
+ input_factory: TimeseriesFactory
+ factory to request data
+ output_factory: TimeseriesFactory
+ factory to write data
+ realtime_interval: int
+ length of update window
+ update_limit: int
+ number of update windows
+ """
+ starttime, endtime = get_realtime_interval(realtime_interval)
+ controller = Controller(
+ inputFactory=input_factory or get_miniseed_factory(),
+ inputInterval="minute",
+ outputFactory=output_factory or get_miniseed_factory(),
+ outputInterval="day",
+ )
+ for channel in channels:
+ controller.run_as_update(
+ algorithm=FilterAlgorithm(
+ input_sample_period=60.0,
+ output_sample_period=86400.0,
+ inchannels=(channel,),
+ outchannels=(channel,),
+ ),
+ observatory=(observatory,),
+ output_observatory=(observatory,),
+ starttime=starttime,
+ endtime=endtime,
+ input_channels=(channel,),
+ output_channels=(channel,),
+ realtime=realtime_interval,
+ update_limit=update_limit,
+ )
+
+
+def hour_filter(
+ observatory: str,
+ channels: List[str] = ["U", "V", "W", "F", "T1", "T2", "T3", "T4"],
+ input_factory: Optional[TimeseriesFactory] = None,
+ output_factory: Optional[TimeseriesFactory] = None,
+ realtime_interval: int = 600,
+ update_limit: int = 10,
+):
+ """Filter 1 minute miniseed channels to 1 hour
+
+ Parameters:
+ -----------
+ observatory: str
+ observatory id
+ channels: array
+ list of channels to filter
+ input_factory: TimeseriesFactory
+ factory to request data
+ output_factory: TimeseriesFactory
+ factory to write data
+ realtime_interval: int
+ length of update window
+ update_limit: int
+ number of update windows
+ """
+ starttime, endtime = get_realtime_interval(realtime_interval)
+ controller = Controller(
+ inputFactory=input_factory or get_miniseed_factory(),
+ inputInterval="minute",
+ outputFactory=output_factory or get_miniseed_factory(),
+ outputInterval="hour",
+ )
+ for channel in channels:
+ controller.run_as_update(
+ algorithm=FilterAlgorithm(
+ input_sample_period=60.0,
+ output_sample_period=3600.0,
+ inchannels=(channel,),
+ outchannels=(channel,),
+ ),
+ observatory=(observatory,),
+ output_observatory=(observatory,),
+ starttime=starttime,
+ endtime=endtime,
+ input_channels=(channel,),
+ output_channels=(channel,),
+ realtime=realtime_interval,
+ update_limit=update_limit,
+ )
+
+
+def minute_filter(
+ observatory: str,
+ channels: List[str] = ["U", "V", "W", "F"],
+ input_factory: Optional[TimeseriesFactory] = None,
+ output_factory: Optional[TimeseriesFactory] = None,
+ realtime_interval: int = 600,
+ update_limit: int = 10,
+):
+ """Filter 1 second miniseed channels to 1 minute
+
+ Parameters:
+ -----------
+ observatory: str
+ observatory id
+ channels: array
+ list of channels to filter
+ input_factory: TimeseriesFactory
+ factory to request data
+ output_factory: TimeseriesFactory
+ factory to write data
+ realtime_interval: int
+ length of update window
+ update_limit: int
+ number of update windows
+ """
+ starttime, endtime = get_realtime_interval(realtime_interval)
+ controller = Controller(
+ inputFactory=input_factory or get_miniseed_factory(),
+ inputInterval="second",
+ outputFactory=output_factory or get_miniseed_factory(),
+ outputInterval="minute",
+ )
+ for channel in channels:
+ controller.run_as_update(
+ algorithm=FilterAlgorithm(
+ input_sample_period=1,
+ output_sample_period=60,
+ inchannels=(channel,),
+ outchannels=(channel,),
+ ),
+ observatory=(observatory,),
+ output_observatory=(observatory,),
+ starttime=starttime,
+ endtime=endtime,
+ input_channels=(channel,),
+ output_channels=(channel,),
+ realtime=realtime_interval,
+ update_limit=update_limit,
+ )
+
+
+def second_filter(
+ observatory: str,
+ input_factory: Optional[TimeseriesFactory] = None,
+ output_factory: Optional[TimeseriesFactory] = None,
+ realtime_interval: int = 600,
+ update_limit: int = 10,
+):
+ """Filter 10Hz miniseed U,V,W to 1 second
+
+ Parameters:
+ -----------
+ observatory: str
+ observatory id
+ input_factory: TimeseriesFactory
+ factory to request data
+ output_factory: TimeseriesFactory
+ factory to write data
+ realtime_interval: int
+ length of update window
+ update_limit: int
+ number of update windows
+ """
+ starttime, endtime = get_realtime_interval(realtime_interval)
+ controller = Controller(
+ inputFactory=input_factory
+ or get_miniseed_factory(convert_channels=("U", "V", "W")),
+ inputInterval="tenhertz",
+ outputFactory=output_factory or get_miniseed_factory(),
+ outputInterval="second",
+ )
+ for channel in ("U", "V", "W"):
+ controller.run_as_update(
+ algorithm=FilterAlgorithm(
+ input_sample_period=0.1,
+ output_sample_period=1,
+ inchannels=(channel,),
+ outchannels=(channel,),
+ ),
+ observatory=(observatory,),
+ output_observatory=(observatory,),
+ starttime=starttime,
+ endtime=endtime,
+ input_channels=(channel,),
+ output_channels=(channel,),
+ realtime=realtime_interval,
+ update_limit=update_limit,
+ )
+
+
+def _copy_channels(
+ observatory: str,
+ channels: List[List[str]],
+ interval: DataInterval,
+ input_factory: Optional[TimeseriesFactory],
+ output_factory: Optional[TimeseriesFactory],
+ realtime_interval: int = 600,
+ update_limit: int = 10,
+):
+ """copy channels between earthworm and miniseed formats
+
+ Parameters:
+ -----------
+ observatory: str
+ observatory id
+ channels: array
+ list of channel conversions
+ format: ((input_channel_1, output_channel_1), ...)
+ interval: {tenhertz, second, minute, hour, day}
+ data interval
+ input_factory: TimeseriesFactory
+ factory to request data
+ output_factory: TimeseriesFactory
+ factory to write data
+ realtime_interval: int
+ length of update window
+ update_limit: int
+ number of update windows
+ """
+ starttime, endtime = get_realtime_interval(interval_seconds=realtime_interval)
+ controller = Controller(
+ inputFactory=input_factory or get_miniseed_factory(),
+ inputInterval=interval,
+ outputFactory=output_factory or get_edge_factory(),
+ outputInterval=interval,
+ )
+ for input_channel, output_channel in channels:
+ controller.run_as_update(
+ algorithm=Algorithm(
+ inchannels=(input_channel,),
+ outchannels=(output_channel,),
+ ),
+ observatory=(observatory,),
+ output_observatory=(observatory,),
+ starttime=starttime,
+ endtime=endtime,
+ input_channels=(input_channel,),
+ output_channels=(output_channel,),
+ rename_output_channel=((input_channel, output_channel),),
+ realtime=realtime_interval,
+ update_limit=update_limit,
+ )
--
GitLab
From cf17b6dd252adb1681893cd3ff57c99a467dd2ed Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Mon, 18 Oct 2021 14:29:50 -0600
Subject: [PATCH 014/142] add filter application to pyproject.toml
---
pyproject.toml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/pyproject.toml b/pyproject.toml
index ffbd9204..c41865f9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -71,4 +71,4 @@ geomag-monitor = "geomagio.processing.monitor:main"
geomag-py = "geomagio.Controller:main"
magproc-prepfiles = "geomagio.processing.magproc:main"
make-cal = "geomagio.processing.make_cal:main"
-obsrio-filter = "geomagio.processing.obsrio:main"
+geomag-filter = "geomagio.processing.filters:main"
--
GitLab
From d86ed82c5e572ae432c97adf3258a20aacb2dfc7 Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Mon, 18 Oct 2021 14:30:03 -0600
Subject: [PATCH 015/142] update filter methods in processing __init__
---
geomagio/processing/__init__.py | 8 +++-----
1 file changed, 3 insertions(+), 5 deletions(-)
diff --git a/geomagio/processing/__init__.py b/geomagio/processing/__init__.py
index 77f23254..573ec1ae 100644
--- a/geomagio/processing/__init__.py
+++ b/geomagio/processing/__init__.py
@@ -5,7 +5,7 @@ and should be considered less stable than other packages in the library.
"""
from .factory import get_edge_factory, get_miniseed_factory
from .derived import adjusted, average, sqdist_minute
-from .obsrio import obsrio_minute, obsrio_second, obsrio_temperatures, obsrio_tenhertz
+from .filters import minute_filter, second_filter
__all__ = [
@@ -13,9 +13,7 @@ __all__ = [
"average",
"get_edge_factory",
"get_miniseed_factory",
- "obsrio_minute",
- "obsrio_second",
- "obsrio_temperatures",
- "obsrio_tenhertz",
+ "minute_filter",
+ "second_filter",
"sqdist_minute",
]
--
GitLab
From d58469ce67d0ed2082d0a90b099a65b50e82113f Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Mon, 18 Oct 2021 14:30:19 -0600
Subject: [PATCH 016/142] update filter methods in efield entrypoint
---
geomagio/processing/efield.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/geomagio/processing/efield.py b/geomagio/processing/efield.py
index 0bd3e698..df3f345d 100644
--- a/geomagio/processing/efield.py
+++ b/geomagio/processing/efield.py
@@ -3,7 +3,7 @@ import typer
from ..adjusted import AdjustedMatrix
from .derived import adjusted
from .factory import get_edge_factory
-from .obsrio import obsrio_minute
+from .filters import minute_filter
app = typer.Typer()
@@ -40,7 +40,7 @@ def efield_realtime(
realtime_interval=realtime_interval,
update_limit=update_limit,
)
- obsrio_minute(
+ minute_filter(
observatory=observatory,
channels=["E-E", "E-N"],
input_factory=get_edge_factory(host=host, data_type="variation"),
@@ -48,7 +48,7 @@ def efield_realtime(
realtime_interval=realtime_interval,
update_limit=update_limit,
)
- obsrio_minute(
+ minute_filter(
observatory=observatory,
channels=["E-E", "E-N"],
input_factory=get_edge_factory(host=host, data_type="adjusted"),
--
GitLab
From 58313f65473665245353633ea93d47c563a57d9e Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Thu, 4 Nov 2021 16:50:23 -0600
Subject: [PATCH 017/142] add spacing to realtime filter docstring
---
geomagio/processing/filters.py | 9 +++++++++
1 file changed, 9 insertions(+)
diff --git a/geomagio/processing/filters.py b/geomagio/processing/filters.py
index 0decbfb5..0a727c4a 100644
--- a/geomagio/processing/filters.py
+++ b/geomagio/processing/filters.py
@@ -67,14 +67,23 @@ def hour_command(
short_help="Filter 1 second and 1 minute nT/temperature data",
help="""
ObsRIO:
+
Filters 10Hz U,V,W miniseed to 1 second miniseed
+
Filters 1 second U,V,W,F miniseed to 1 minute miniseed
+
Filters 1 second T1-4 miniseed to 1 minute miniseed
+
Copies 1 second and 1 minute U,V,W,F,T1-4 miniseed to H,E,Z,F,UK1-4 earthworm
+
PCDCP:
+
Copies 1 second H,E,Z,F earthworm to U,V,W,F miniseed
+
Copies 1 minute UK1-4 earthworm to T1-4 miniseed
+
Filters 1 second U,V,W,F miniseed to 1 minute miniseed
+
""",
)
def realtime_command(
--
GitLab
From 89296ecee4bed798f7948d6c6237453a855a586f Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Fri, 5 Nov 2021 18:10:40 +0000
Subject: [PATCH 018/142] update filter application docstrings
---
geomagio/processing/filters.py | 28 ++++++++++++++--------------
1 file changed, 14 insertions(+), 14 deletions(-)
diff --git a/geomagio/processing/filters.py b/geomagio/processing/filters.py
index 0a727c4a..b36b0719 100644
--- a/geomagio/processing/filters.py
+++ b/geomagio/processing/filters.py
@@ -28,9 +28,9 @@ def main():
)
def day_command(
observatory: str = Argument(None, help="observatory id"),
- input_host: str = Option("127.0.0.1", help="host to request data"),
- output_host: str = Option("127.0.0.1", help="host to write data"),
- realtime_interval: int = Option(86400, help="length of update window"),
+ input_host: str = Option("127.0.0.1", help="host to request data from"),
+ output_host: str = Option("127.0.0.1", help="host to write data to"),
+ realtime_interval: int = Option(86400, help="length of update window (in seconds)"),
update_limit: int = Option(7, help="number of update windows"),
):
day_filter(
@@ -48,9 +48,9 @@ def day_command(
)
def hour_command(
observatory: str = Argument(None, help="observatory id"),
- input_host: str = Option("127.0.0.1", help="host to request data"),
- output_host: str = Option("127.0.0.1", help="host to write data"),
- realtime_interval: int = Option(3600, help="length of update window"),
+ input_host: str = Option("127.0.0.1", help="host to request data from"),
+ output_host: str = Option("127.0.0.1", help="host to write data to"),
+ realtime_interval: int = Option(3600, help="length of update window (in seconds)"),
update_limit: int = Option(24, help="number of update windows"),
):
hour_filter(
@@ -88,10 +88,10 @@ def hour_command(
)
def realtime_command(
observatory: str = Argument(None, help="observatory id"),
- input_host: str = Option("127.0.0.1", help="host to request data"),
- output_host: str = Option("127.0.0.1", help="host to write data"),
+ input_host: str = Option("127.0.0.1", help="host to request data from"),
+ output_host: str = Option("127.0.0.1", help="host to write data to"),
data_format: DataFormat = Option(DataFormat.PCDCP, help="Data acquisition system"),
- realtime_interval: int = Option(600, help="length of update window"),
+ realtime_interval: int = Option(600, help="length of update window (in seconds)"),
update_limit: int = Option(10, help="number of update windows"),
):
if data_format == DataFormat.OBSRIO:
@@ -209,7 +209,7 @@ def day_filter(
output_factory: TimeseriesFactory
factory to write data
realtime_interval: int
- length of update window
+ length of update window (in seconds)
update_limit: int
number of update windows
"""
@@ -260,7 +260,7 @@ def hour_filter(
output_factory: TimeseriesFactory
factory to write data
realtime_interval: int
- length of update window
+ length of update window (in seconds)
update_limit: int
number of update windows
"""
@@ -311,7 +311,7 @@ def minute_filter(
output_factory: TimeseriesFactory
factory to write data
realtime_interval: int
- length of update window
+ length of update window (in seconds)
update_limit: int
number of update windows
"""
@@ -359,7 +359,7 @@ def second_filter(
output_factory: TimeseriesFactory
factory to write data
realtime_interval: int
- length of update window
+ length of update window (in seconds)
update_limit: int
number of update windows
"""
@@ -415,7 +415,7 @@ def _copy_channels(
output_factory: TimeseriesFactory
factory to write data
realtime_interval: int
- length of update window
+ length of update window (in seconds)
update_limit: int
number of update windows
"""
--
GitLab
From 74840fd145edfe81ffb1926ca9689925d5f95b0f Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Tue, 9 Nov 2021 10:04:17 -0700
Subject: [PATCH 019/142] specify mseed encoding
---
geomagio/TimeseriesUtility.py | 2 ++
1 file changed, 2 insertions(+)
diff --git a/geomagio/TimeseriesUtility.py b/geomagio/TimeseriesUtility.py
index c294cebe..35716142 100644
--- a/geomagio/TimeseriesUtility.py
+++ b/geomagio/TimeseriesUtility.py
@@ -82,6 +82,8 @@ def encode_stream(stream: Stream, encoding: str) -> Stream:
trace_out = trace.copy()
if trace_out.data.dtype != encoding:
trace_out.data = trace_out.data.astype(encoding)
+ if "mseed" in trace_out.stats:
+ trace_out.stats.mseed.encoding = encoding.upper()
out_stream += trace_out
return out_stream
--
GitLab
From 5a3b2f9446ead276a3aaddb7c07514714a7569e6 Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Wed, 10 Nov 2021 14:36:04 -0700
Subject: [PATCH 020/142] filter temperatures separately to legacy
---
geomagio/processing/filters.py | 70 ++++++++++++++++++++--------------
1 file changed, 41 insertions(+), 29 deletions(-)
diff --git a/geomagio/processing/filters.py b/geomagio/processing/filters.py
index b36b0719..f3754ba9 100644
--- a/geomagio/processing/filters.py
+++ b/geomagio/processing/filters.py
@@ -72,16 +72,14 @@ def hour_command(
Filters 1 second U,V,W,F miniseed to 1 minute miniseed
- Filters 1 second T1-4 miniseed to 1 minute miniseed
+ Filters 1 second T1-4 miniseed to 1 minute UK1-4 legacy
- Copies 1 second and 1 minute U,V,W,F,T1-4 miniseed to H,E,Z,F,UK1-4 earthworm
+ Copies 1 second and 1 minute U,V,W,F miniseed to H,E,Z,F earthworm
PCDCP:
Copies 1 second H,E,Z,F earthworm to U,V,W,F miniseed
- Copies 1 minute UK1-4 earthworm to T1-4 miniseed
-
Filters 1 second U,V,W,F miniseed to 1 minute miniseed
""",
@@ -111,10 +109,6 @@ def realtime_command(
("V", "E"),
("W", "Z"),
("F", "F"),
- ("T1", "LK1"),
- ("T2", "LK2"),
- ("T3", "LK3"),
- ("T4", "LK4"),
),
interval="second",
input_factory=get_miniseed_factory(host=input_host),
@@ -122,11 +116,10 @@ def realtime_command(
realtime_interval=realtime_interval,
update_limit=update_limit,
)
- minute_filter(
+ temperature_filter(
observatory=observatory,
- channels=("T1", "T2", "T3", "T4"),
input_factory=get_miniseed_factory(host=input_host),
- output_factory=get_miniseed_factory(host=output_host),
+ output_factory=get_edge_factory(host=output_host),
realtime_interval=realtime_interval,
update_limit=update_limit,
)
@@ -145,20 +138,6 @@ def realtime_command(
realtime_interval=realtime_interval,
update_limit=update_limit,
)
- _copy_channels(
- observatory=observatory,
- channels=(
- ("UK1", "T1"),
- ("UK2", "T2"),
- ("UK3", "T3"),
- ("UK4", "T4"),
- ),
- interval="minute",
- input_factory=get_edge_factory(host=input_host),
- output_factory=get_miniseed_factory(host=output_host),
- realtime_interval=realtime_interval,
- update_limit=update_limit,
- )
minute_filter(
observatory=observatory,
channels=("U", "V", "W", "F"),
@@ -175,10 +154,6 @@ def realtime_command(
("V", "E"),
("W", "Z"),
("F", "F"),
- ("T1", "UK1"),
- ("T2", "UK2"),
- ("T3", "UK3"),
- ("T4", "UK4"),
),
interval="minute",
input_factory=get_miniseed_factory(host=input_host),
@@ -390,6 +365,43 @@ def second_filter(
)
+def temperature_filter(
+ observatory: str,
+ input_factory: Optional[TimeseriesFactory] = None,
+ output_factory: Optional[TimeseriesFactory] = None,
+ realtime_interval: int = 600,
+ update_limit: int = 10,
+):
+ """Filter temperatures 1Hz miniseed (LK1-4) to 1 minute legacy (UK1-4)."""
+ starttime, endtime = get_realtime_interval(realtime_interval)
+ controller = Controller(
+ inputFactory=input_factory or get_miniseed_factory(),
+ inputInterval="second",
+ outputFactory=output_factory or get_edge_factory(),
+ outputInterval="minute",
+ )
+ renames = {"LK1": "UK1", "LK2": "UK2", "LK3": "UK3", "LK4": "UK4"}
+ for input_channel in renames.keys():
+ output_channel = renames[input_channel]
+ controller.run_as_update(
+ algorithm=FilterAlgorithm(
+ input_sample_period=1,
+ output_sample_period=60,
+ inchannels=(input_channel,),
+ outchannels=(output_channel,),
+ ),
+ observatory=(observatory,),
+ output_observatory=(observatory,),
+ starttime=starttime,
+ endtime=endtime,
+ input_channels=(input_channel,),
+ output_channels=(output_channel,),
+ realtime=realtime_interval,
+ rename_output_channel=((input_channel, output_channel),),
+ update_limit=update_limit,
+ )
+
+
def _copy_channels(
observatory: str,
channels: List[List[str]],
--
GitLab
From da465d6f1fc2dabad5611a2c5a99bc380dcbda33 Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Fri, 12 Nov 2021 15:35:54 -0700
Subject: [PATCH 021/142] filter legacy temperature channels at 1 hour and 1
day
---
geomagio/processing/filters.py | 59 ++++++++++++++++++++++++++++------
1 file changed, 50 insertions(+), 9 deletions(-)
diff --git a/geomagio/processing/filters.py b/geomagio/processing/filters.py
index f3754ba9..54b9e408 100644
--- a/geomagio/processing/filters.py
+++ b/geomagio/processing/filters.py
@@ -30,7 +30,9 @@ def day_command(
observatory: str = Argument(None, help="observatory id"),
input_host: str = Option("127.0.0.1", help="host to request data from"),
output_host: str = Option("127.0.0.1", help="host to write data to"),
- realtime_interval: int = Option(86400, help="length of update window (in seconds)"),
+ realtime_interval: int = Option(
+ 604800, help="length of update window (in seconds)"
+ ),
update_limit: int = Option(7, help="number of update windows"),
):
day_filter(
@@ -40,6 +42,21 @@ def day_command(
realtime_interval=realtime_interval,
update_limit=update_limit,
)
+ temperature_filter(
+ observatory=observatory,
+ channels=(
+ ("UK1", "PK1"),
+ ("UK2", "PK2"),
+ ("UK3", "PK3"),
+ ("UK4", "PK4"),
+ ),
+ input_factory=get_edge_factory(host=input_host),
+ input_interval="minute",
+ output_factory=get_miniseed_factory(host=output_host),
+ output_interval="day",
+ realtime_interval=realtime_interval,
+ update_limit=update_limit,
+ )
@app.command(
@@ -50,7 +67,7 @@ def hour_command(
observatory: str = Argument(None, help="observatory id"),
input_host: str = Option("127.0.0.1", help="host to request data from"),
output_host: str = Option("127.0.0.1", help="host to write data to"),
- realtime_interval: int = Option(3600, help="length of update window (in seconds)"),
+ realtime_interval: int = Option(86400, help="length of update window (in seconds)"),
update_limit: int = Option(24, help="number of update windows"),
):
hour_filter(
@@ -60,6 +77,21 @@ def hour_command(
realtime_interval=realtime_interval,
update_limit=update_limit,
)
+ temperature_filter(
+ observatory=observatory,
+ channels=(
+ ("UK1", "RK1"),
+ ("UK2", "RK2"),
+ ("UK3", "RK3"),
+ ("UK4", "RK4"),
+ ),
+ input_factory=get_edge_factory(host=input_host),
+ input_interval="minute",
+ output_factory=get_miniseed_factory(host=output_host),
+ output_interval="hour",
+ realtime_interval=realtime_interval,
+ update_limit=update_limit,
+ )
@app.command(
@@ -118,8 +150,16 @@ def realtime_command(
)
temperature_filter(
observatory=observatory,
+ channels=(
+ ("LK1", "UK1"),
+ ("LK2", "UK2"),
+ ("LK3", "UK3"),
+ ("LK4", "UK4"),
+ ),
input_factory=get_miniseed_factory(host=input_host),
+ input_interval="second",
output_factory=get_edge_factory(host=output_host),
+ output_interval="minute",
realtime_interval=realtime_interval,
update_limit=update_limit,
)
@@ -165,7 +205,7 @@ def realtime_command(
def day_filter(
observatory: str,
- channels: List[str] = ["U", "V", "W", "F", "T1", "T2", "T3", "T4"],
+ channels: List[str] = ["U", "V", "W", "F"],
input_factory: Optional[TimeseriesFactory] = None,
output_factory: Optional[TimeseriesFactory] = None,
realtime_interval: int = 86400,
@@ -216,7 +256,7 @@ def day_filter(
def hour_filter(
observatory: str,
- channels: List[str] = ["U", "V", "W", "F", "T1", "T2", "T3", "T4"],
+ channels: List[str] = ["U", "V", "W", "F"],
input_factory: Optional[TimeseriesFactory] = None,
output_factory: Optional[TimeseriesFactory] = None,
realtime_interval: int = 600,
@@ -367,8 +407,11 @@ def second_filter(
def temperature_filter(
observatory: str,
+ channels: List[List[str]],
input_factory: Optional[TimeseriesFactory] = None,
+ input_interval: int = "second",
output_factory: Optional[TimeseriesFactory] = None,
+ output_interval: int = "minute",
realtime_interval: int = 600,
update_limit: int = 10,
):
@@ -376,13 +419,11 @@ def temperature_filter(
starttime, endtime = get_realtime_interval(realtime_interval)
controller = Controller(
inputFactory=input_factory or get_miniseed_factory(),
- inputInterval="second",
+ inputInterval=input_interval,
outputFactory=output_factory or get_edge_factory(),
- outputInterval="minute",
+ outputInterval=output_interval,
)
- renames = {"LK1": "UK1", "LK2": "UK2", "LK3": "UK3", "LK4": "UK4"}
- for input_channel in renames.keys():
- output_channel = renames[input_channel]
+ for input_channel, output_channel in channels:
controller.run_as_update(
algorithm=FilterAlgorithm(
input_sample_period=1,
--
GitLab
From 27862eb85477169ee8d894aa14e7a72ccc38c09d Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Thu, 18 Nov 2021 14:51:12 -0700
Subject: [PATCH 022/142] bump version to 1.4.4
---
code.json | 2 +-
pyproject.toml | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/code.json b/code.json
index bc288096..e638a040 100644
--- a/code.json
+++ b/code.json
@@ -3,7 +3,7 @@
"name": "geomag-algorithms",
"organization": "U.S. Geological Survey",
"description": "Library for processing Geomagnetic timeseries data.",
- "version": "1.4.3",
+ "version": "1.4.4",
"status": "Development",
"permissions": {
diff --git a/pyproject.toml b/pyproject.toml
index c41865f9..21aead83 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ packages = [
{include = "geomagio" }
]
repository="https://code.usgs.gov/ghsc/geomag/geomag-algorithms"
-version = "1.4.3"
+version = "1.4.4"
[tool.poetry.dependencies]
--
GitLab
From 538a15f717b81e05bd51fc88856c6570f8d4d24f Mon Sep 17 00:00:00 2001
From: pcain <pcain@usgs.gov>
Date: Tue, 5 Oct 2021 12:55:30 -0600
Subject: [PATCH 023/142] Truncate monitor output, make expandable
---
geomagio/processing/monitor.py | 24 +++++++++++++++++++-----
1 file changed, 19 insertions(+), 5 deletions(-)
diff --git a/geomagio/processing/monitor.py b/geomagio/processing/monitor.py
index 78b4cbb8..0bede2a5 100755
--- a/geomagio/processing/monitor.py
+++ b/geomagio/processing/monitor.py
@@ -55,11 +55,25 @@ def get_gaps(gaps):
"""
gap_string = ""
if len(gaps):
- for gap in gaps:
- gap_string += " %s to %s <br>\n" % (
- format_time(gap[0]),
- format_time(gap[1]),
- )
+ for i in range(len(gaps)):
+ if i < 10:
+ gap_string += " %s to %s <br>\n" % (
+ format_time(gaps[i][0]),
+ format_time(gaps[i][1]),
+ )
+ else:
+ if i == 10:
+ gap_string += "<details>\n"
+ gap_string += f"<summary>+ {len(gaps) - 10}</summary>\n"
+ gap_string += "<span>\n"
+ else:
+ gap_string += " %s to %s <br>\n" % (
+ format_time(gaps[i][0]),
+ format_time(gaps[i][1]),
+ )
+ if i == len(gaps) - 1:
+ gap_string += "</span>\n"
+ gap_string += "</details>\n"
else:
gap_string = " None<br>"
return gap_string
--
GitLab
From 2ac258f5ba8014d75c56070a8247c2eba3dd2c9f Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Fri, 18 Mar 2022 15:26:01 -0600
Subject: [PATCH 024/142] Update pyproject dependencies, poetry.lock
---
poetry.lock | 1949 ++++++++++++++++++++++++++----------------------
pyproject.toml | 41 +-
2 files changed, 1059 insertions(+), 931 deletions(-)
diff --git a/poetry.lock b/poetry.lock
index f951e391..ac656849 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,6 +1,6 @@
[[package]]
name = "aiomysql"
-version = "0.0.21"
+version = "0.0.22"
description = "MySQL driver for asyncio."
category = "main"
optional = false
@@ -25,21 +25,24 @@ typing_extensions = ">=3.7.2"
[[package]]
name = "alembic"
-version = "1.6.5"
+version = "1.7.7"
description = "A database migration tool for SQLAlchemy."
category = "main"
optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
+python-versions = ">=3.6"
[package.dependencies]
+importlib-metadata = {version = "*", markers = "python_version < \"3.9\""}
+importlib-resources = {version = "*", markers = "python_version < \"3.9\""}
Mako = "*"
-python-dateutil = "*"
-python-editor = ">=0.3"
SQLAlchemy = ">=1.3.0"
+[package.extras]
+tz = ["python-dateutil"]
+
[[package]]
name = "anyio"
-version = "3.3.0"
+version = "3.5.0"
description = "High level compatibility layer for multiple asynchronous event loop implementations"
category = "main"
optional = false
@@ -48,31 +51,19 @@ python-versions = ">=3.6.2"
[package.dependencies]
idna = ">=2.8"
sniffio = ">=1.1"
-typing-extensions = {version = "*", markers = "python_version < \"3.8\""}
[package.extras]
-doc = ["sphinx-rtd-theme", "sphinx-autodoc-typehints (>=1.2.0)"]
-test = ["coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "pytest (>=6.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (<0.15)", "mock (>=4)", "uvloop (>=0.15)"]
+doc = ["packaging", "sphinx-rtd-theme", "sphinx-autodoc-typehints (>=1.2.0)"]
+test = ["coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "pytest (>=6.0)", "pytest-mock (>=3.6.1)", "trustme", "contextlib2", "uvloop (<0.15)", "mock (>=4)", "uvloop (>=0.15)"]
trio = ["trio (>=0.16)"]
-[[package]]
-name = "appdirs"
-version = "1.4.4"
-description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-category = "dev"
-optional = false
-python-versions = "*"
-
[[package]]
name = "asgiref"
-version = "3.4.1"
+version = "3.5.0"
description = "ASGI specs, helper code, and adapters"
category = "main"
optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-typing-extensions = {version = "*", markers = "python_version < \"3.8\""}
+python-versions = ">=3.7"
[package.extras]
tests = ["pytest", "pytest-asyncio", "mypy (>=0.800)"]
@@ -87,59 +78,54 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[[package]]
name = "attrs"
-version = "21.2.0"
+version = "21.4.0"
description = "Classes Without Boilerplate"
category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
[package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit"]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"]
[[package]]
name = "authlib"
-version = "0.15.4"
-description = "The ultimate Python library in building OAuth and OpenID Connect servers."
+version = "1.0.0"
+description = "The ultimate Python library in building OAuth and OpenID Connect servers and clients."
category = "main"
optional = false
python-versions = "*"
[package.dependencies]
-cryptography = "*"
-
-[package.extras]
-client = ["requests"]
+cryptography = ">=3.2"
[[package]]
name = "black"
-version = "21.7b0"
+version = "22.1.0"
description = "The uncompromising code formatter."
category = "dev"
optional = false
python-versions = ">=3.6.2"
[package.dependencies]
-appdirs = "*"
-click = ">=7.1.2"
+click = ">=8.0.0"
mypy-extensions = ">=0.4.3"
-pathspec = ">=0.8.1,<1"
-regex = ">=2020.1.8"
-tomli = ">=0.2.6,<2.0.0"
-typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\""}
-typing-extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""}
+pathspec = ">=0.9.0"
+platformdirs = ">=2"
+tomli = ">=1.1.0"
+typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}
[package.extras]
colorama = ["colorama (>=0.4.3)"]
-d = ["aiohttp (>=3.6.0)", "aiohttp-cors (>=0.4.0)"]
-python2 = ["typed-ast (>=1.4.2)"]
+d = ["aiohttp (>=3.7.4)"]
+jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
uvloop = ["uvloop (>=0.15.2)"]
[[package]]
name = "certifi"
-version = "2021.5.30"
+version = "2021.10.8"
description = "Python package for providing Mozilla's CA Bundle."
category = "main"
optional = false
@@ -147,7 +133,7 @@ python-versions = "*"
[[package]]
name = "cffi"
-version = "1.14.6"
+version = "1.15.0"
description = "Foreign Function Interface for Python calling C code."
category = "main"
optional = false
@@ -158,7 +144,7 @@ pycparser = "*"
[[package]]
name = "charset-normalizer"
-version = "2.0.4"
+version = "2.0.12"
description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
category = "main"
optional = false
@@ -169,11 +155,14 @@ unicode_backport = ["unicodedata2"]
[[package]]
name = "click"
-version = "7.1.2"
+version = "8.0.4"
description = "Composable command line interface toolkit"
category = "main"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.6"
+
+[package.dependencies]
+colorama = {version = "*", markers = "platform_system == \"Windows\""}
[[package]]
name = "colorama"
@@ -185,18 +174,18 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
[[package]]
name = "coverage"
-version = "5.5"
+version = "6.3.2"
description = "Code coverage measurement for Python"
category = "dev"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
+python-versions = ">=3.7"
[package.extras]
-toml = ["toml"]
+toml = ["tomli"]
[[package]]
name = "cryptography"
-version = "3.4.7"
+version = "36.0.2"
description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
category = "main"
optional = false
@@ -207,22 +196,19 @@ cffi = ">=1.12"
[package.extras]
docs = ["sphinx (>=1.6.5,!=1.8.0,!=3.1.0,!=3.1.1)", "sphinx-rtd-theme"]
-docstest = ["doc8", "pyenchant (>=1.6.11)", "twine (>=1.12.0)", "sphinxcontrib-spelling (>=4.0.1)"]
+docstest = ["pyenchant (>=1.6.11)", "twine (>=1.12.0)", "sphinxcontrib-spelling (>=4.0.1)"]
pep8test = ["black", "flake8", "flake8-import-order", "pep8-naming"]
-sdist = ["setuptools-rust (>=0.11.4)"]
+sdist = ["setuptools_rust (>=0.11.4)"]
ssh = ["bcrypt (>=3.1.5)"]
-test = ["pytest (>=6.0)", "pytest-cov", "pytest-subtests", "pytest-xdist", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,!=3.79.2)"]
+test = ["pytest (>=6.2.0)", "pytest-cov", "pytest-subtests", "pytest-xdist", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,!=3.79.2)"]
[[package]]
name = "cycler"
-version = "0.10.0"
+version = "0.11.0"
description = "Composable style cycles"
category = "main"
optional = false
-python-versions = "*"
-
-[package.dependencies]
-six = "*"
+python-versions = ">=3.6"
[[package]]
name = "data-science-types"
@@ -237,7 +223,7 @@ dev = ["black", "flake8", "flake8-pyi", "matplotlib", "mypy (==0.770)", "numpy",
[[package]]
name = "databases"
-version = "0.4.3"
+version = "0.5.5"
description = "Async database support for Python."
category = "main"
optional = false
@@ -246,17 +232,18 @@ python-versions = ">=3.6"
[package.dependencies]
aiomysql = {version = "*", optional = true, markers = "extra == \"mysql\""}
aiosqlite = {version = "*", optional = true, markers = "extra == \"sqlite\""}
-sqlalchemy = "<1.4"
+sqlalchemy = ">=1.4,<1.5"
[package.extras]
mysql = ["aiomysql"]
+mysql_asyncmy = ["asyncmy"]
postgresql = ["asyncpg"]
postgresql_aiopg = ["aiopg"]
sqlite = ["aiosqlite"]
[[package]]
name = "decorator"
-version = "5.0.9"
+version = "5.1.1"
description = "Decorators for Humans"
category = "main"
optional = false
@@ -288,29 +275,53 @@ python-versions = ">=3.6"
[[package]]
name = "fastapi"
-version = "0.68.0"
+version = "0.75.0"
description = "FastAPI framework, high performance, easy to learn, fast to code, ready for production"
category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.6.1"
[package.dependencies]
pydantic = ">=1.6.2,<1.7 || >1.7,<1.7.1 || >1.7.1,<1.7.2 || >1.7.2,<1.7.3 || >1.7.3,<1.8 || >1.8,<1.8.1 || >1.8.1,<2.0.0"
-starlette = "0.14.2"
+starlette = "0.17.1"
[package.extras]
-all = ["requests (>=2.24.0,<3.0.0)", "aiofiles (>=0.5.0,<0.6.0)", "jinja2 (>=2.11.2,<3.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "itsdangerous (>=1.1.0,<2.0.0)", "pyyaml (>=5.3.1,<6.0.0)", "graphene (>=2.1.8,<3.0.0)", "ujson (>=4.0.1,<5.0.0)", "orjson (>=3.2.1,<4.0.0)", "email_validator (>=1.1.1,<2.0.0)", "uvicorn[standard] (>=0.12.0,<0.14.0)", "async_exit_stack (>=1.0.1,<2.0.0)", "async_generator (>=1.10,<2.0.0)"]
-dev = ["python-jose[cryptography] (>=3.3.0,<4.0.0)", "passlib[bcrypt] (>=1.7.2,<2.0.0)", "autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "uvicorn[standard] (>=0.12.0,<0.14.0)", "graphene (>=2.1.8,<3.0.0)"]
-doc = ["mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=7.1.9,<8.0.0)", "markdown-include (>=0.6.0,<0.7.0)", "mkdocs-markdownextradata-plugin (>=0.1.7,<0.2.0)", "typer-cli (>=0.0.12,<0.0.13)", "pyyaml (>=5.3.1,<6.0.0)"]
-test = ["pytest (>=6.2.4,<7.0.0)", "pytest-cov (>=2.12.0,<3.0.0)", "pytest-asyncio (>=0.14.0,<0.15.0)", "mypy (==0.812)", "flake8 (>=3.8.3,<4.0.0)", "black (==20.8b1)", "isort (>=5.0.6,<6.0.0)", "requests (>=2.24.0,<3.0.0)", "httpx (>=0.14.0,<0.15.0)", "email_validator (>=1.1.1,<2.0.0)", "sqlalchemy (>=1.3.18,<1.4.0)", "peewee (>=3.13.3,<4.0.0)", "databases[sqlite] (>=0.3.2,<0.4.0)", "orjson (>=3.2.1,<4.0.0)", "ujson (>=4.0.1,<5.0.0)", "async_exit_stack (>=1.0.1,<2.0.0)", "async_generator (>=1.10,<2.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "aiofiles (>=0.5.0,<0.6.0)", "flask (>=1.1.2,<2.0.0)"]
+all = ["requests (>=2.24.0,<3.0.0)", "jinja2 (>=2.11.2,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "itsdangerous (>=1.1.0,<3.0.0)", "pyyaml (>=5.3.1,<6.0.0)", "ujson (>=4.0.1,<5.0.0)", "orjson (>=3.2.1,<4.0.0)", "email_validator (>=1.1.1,<2.0.0)", "uvicorn[standard] (>=0.12.0,<0.16.0)"]
+dev = ["python-jose[cryptography] (>=3.3.0,<4.0.0)", "passlib[bcrypt] (>=1.7.2,<2.0.0)", "autoflake (>=1.4.0,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "uvicorn[standard] (>=0.12.0,<0.16.0)"]
+doc = ["mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "mdx-include (>=1.4.1,<2.0.0)", "mkdocs-markdownextradata-plugin (>=0.1.7,<0.3.0)", "typer-cli (>=0.0.12,<0.0.13)", "pyyaml (>=5.3.1,<6.0.0)"]
+test = ["pytest (>=6.2.4,<7.0.0)", "pytest-cov (>=2.12.0,<4.0.0)", "mypy (==0.910)", "flake8 (>=3.8.3,<4.0.0)", "black (==21.9b0)", "isort (>=5.0.6,<6.0.0)", "requests (>=2.24.0,<3.0.0)", "httpx (>=0.14.0,<0.19.0)", "email_validator (>=1.1.1,<2.0.0)", "sqlalchemy (>=1.3.18,<1.5.0)", "peewee (>=3.13.3,<4.0.0)", "databases[sqlite] (>=0.3.2,<0.6.0)", "orjson (>=3.2.1,<4.0.0)", "ujson (>=4.0.1,<5.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "flask (>=1.1.2,<3.0.0)", "anyio[trio] (>=3.2.1,<4.0.0)", "types-ujson (==0.1.1)", "types-orjson (==3.6.0)", "types-dataclasses (==0.1.7)"]
[[package]]
-name = "future"
-version = "0.18.2"
-description = "Clean single-source support for Python 3 and 2"
+name = "fonttools"
+version = "4.31.1"
+description = "Tools to manipulate font files"
category = "main"
optional = false
-python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+python-versions = ">=3.7"
+
+[package.extras]
+all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=14.0.0)", "xattr"]
+graphite = ["lz4 (>=1.7.4.2)"]
+interpolatable = ["scipy", "munkres"]
+lxml = ["lxml (>=4.0,<5)"]
+pathops = ["skia-pathops (>=0.5.0)"]
+plot = ["matplotlib"]
+symfont = ["sympy"]
+type1 = ["xattr"]
+ufo = ["fs (>=2.2.0,<3)"]
+unicode = ["unicodedata2 (>=14.0.0)"]
+woff = ["zopfli (>=0.1.4)", "brotlicffi (>=0.8.0)", "brotli (>=1.0.1)"]
+
+[[package]]
+name = "greenlet"
+version = "1.1.2"
+description = "Lightweight in-process concurrent programming"
+category = "main"
+optional = false
+python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
+
+[package.extras]
+docs = ["sphinx"]
[[package]]
name = "gunicorn"
@@ -336,7 +347,7 @@ python-versions = ">=3.6"
[[package]]
name = "httpcore"
-version = "0.13.6"
+version = "0.14.7"
description = "A minimal low-level HTTP client."
category = "main"
optional = false
@@ -344,26 +355,28 @@ python-versions = ">=3.6"
[package.dependencies]
anyio = ">=3.0.0,<4.0.0"
+certifi = "*"
h11 = ">=0.11,<0.13"
sniffio = ">=1.0.0,<2.0.0"
[package.extras]
http2 = ["h2 (>=3,<5)"]
+socks = ["socksio (>=1.0.0,<2.0.0)"]
[[package]]
name = "httptools"
-version = "0.2.0"
+version = "0.4.0"
description = "A collection of framework independent HTTP protocol utils."
category = "main"
optional = false
-python-versions = "*"
+python-versions = ">=3.5.0"
[package.extras]
-test = ["Cython (==0.29.22)"]
+test = ["Cython (>=0.29.24,<0.30.0)"]
[[package]]
name = "httpx"
-version = "0.18.1"
+version = "0.22.0"
description = "The next generation HTTP client."
category = "main"
optional = false
@@ -371,17 +384,20 @@ python-versions = ">=3.6"
[package.dependencies]
certifi = "*"
-httpcore = ">=0.13.0,<0.14.0"
+charset-normalizer = "*"
+httpcore = ">=0.14.5,<0.15.0"
rfc3986 = {version = ">=1.3,<2", extras = ["idna2008"]}
sniffio = "*"
[package.extras]
-brotli = ["brotlicffi (>=1.0.0,<2.0.0)"]
-http2 = ["h2 (>=3.0.0,<4.0.0)"]
+brotli = ["brotlicffi", "brotli"]
+cli = ["click (>=8.0.0,<9.0.0)", "rich (>=10.0.0,<11.0.0)", "pygments (>=2.0.0,<3.0.0)"]
+http2 = ["h2 (>=3,<5)"]
+socks = ["socksio (>=1.0.0,<2.0.0)"]
[[package]]
name = "idna"
-version = "3.2"
+version = "3.3"
description = "Internationalized Domain Names in Applications (IDNA)"
category = "main"
optional = false
@@ -389,20 +405,34 @@ python-versions = ">=3.5"
[[package]]
name = "importlib-metadata"
-version = "4.6.4"
+version = "4.11.3"
description = "Read metadata from Python packages"
-category = "dev"
+category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
[package.dependencies]
-typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
zipp = ">=0.5"
[package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
perf = ["ipython"]
-testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
+
+[[package]]
+name = "importlib-resources"
+version = "5.4.0"
+description = "Read resources from Python packages"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
+
+[package.extras]
+docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy"]
[[package]]
name = "iniconfig"
@@ -414,15 +444,15 @@ python-versions = "*"
[[package]]
name = "kiwisolver"
-version = "1.3.1"
+version = "1.4.0"
description = "A fast implementation of the Cassowary constraint solver"
category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
[[package]]
name = "lxml"
-version = "4.6.3"
+version = "4.8.0"
description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API."
category = "main"
optional = false
@@ -436,11 +466,11 @@ source = ["Cython (>=0.29.7)"]
[[package]]
name = "mako"
-version = "1.1.5"
-description = "A super-fast templating language that borrows the best ideas from the existing templating languages."
+version = "1.2.0"
+description = "A super-fast templating language that borrows the best ideas from the existing templating languages."
category = "main"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=3.7"
[package.dependencies]
MarkupSafe = ">=0.9.2"
@@ -448,18 +478,19 @@ MarkupSafe = ">=0.9.2"
[package.extras]
babel = ["babel"]
lingua = ["lingua"]
+testing = ["pytest"]
[[package]]
name = "markupsafe"
-version = "2.0.1"
+version = "2.1.1"
description = "Safely add untrusted strings to HTML/XML markup."
category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
[[package]]
name = "matplotlib"
-version = "3.4.3"
+version = "3.5.1"
description = "Python plotting package"
category = "main"
optional = false
@@ -467,29 +498,32 @@ python-versions = ">=3.7"
[package.dependencies]
cycler = ">=0.10"
+fonttools = ">=4.22.0"
kiwisolver = ">=1.0.1"
-numpy = ">=1.16"
+numpy = ">=1.17"
+packaging = ">=20.0"
pillow = ">=6.2.0"
pyparsing = ">=2.2.1"
python-dateutil = ">=2.7"
+setuptools_scm = ">=4"
[[package]]
name = "mypy"
-version = "0.910"
+version = "0.941"
description = "Optional static typing for Python"
category = "dev"
optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
[package.dependencies]
-mypy-extensions = ">=0.4.3,<0.5.0"
-toml = "*"
-typed-ast = {version = ">=1.4.0,<1.5.0", markers = "python_version < \"3.8\""}
-typing-extensions = ">=3.7.4"
+mypy-extensions = ">=0.4.3"
+tomli = ">=1.1.0"
+typing-extensions = ">=3.10"
[package.extras]
dmypy = ["psutil (>=4.0)"]
-python2 = ["typed-ast (>=1.4.0,<1.5.0)"]
+python2 = ["typed-ast (>=1.4.0,<2)"]
+reports = ["lxml"]
[[package]]
name = "mypy-extensions"
@@ -501,49 +535,50 @@ python-versions = "*"
[[package]]
name = "numpy"
-version = "1.21.2"
+version = "1.22.3"
description = "NumPy is the fundamental package for array computing with Python."
category = "main"
optional = false
-python-versions = ">=3.7,<3.11"
+python-versions = ">=3.8"
[[package]]
name = "obspy"
-version = "1.2.2"
+version = "1.3.0"
description = "ObsPy - a Python framework for seismological observatories."
category = "main"
optional = false
-python-versions = "*"
+python-versions = ">=3.7"
[package.dependencies]
decorator = "*"
-future = ">=0.12.4"
lxml = "*"
-matplotlib = ">=1.1.0"
-numpy = ">=1.6.1"
+matplotlib = ">=3.2.0"
+numpy = ">=1.15.0"
requests = "*"
-scipy = ">=0.9.0"
+scipy = ">=1.0.0"
sqlalchemy = "*"
[package.extras]
-arclink = ["cryptography"]
+all = ["packaging", "pyproj", "pytest", "pytest-json-report", "geographiclib", "cartopy", "pyshp"]
+geo = ["geographiclib"]
+imaging = ["cartopy"]
"io.shapefile" = ["pyshp"]
-tests = ["flake8 (>=2)", "pyimgur", "pyproj", "pep8-naming"]
+tests = ["packaging", "pyproj", "pytest", "pytest-json-report"]
[[package]]
name = "openpyxl"
-version = "3.0.7"
+version = "3.0.9"
description = "A Python library to read/write Excel 2010 xlsx/xlsm files"
category = "main"
optional = false
-python-versions = ">=3.6,"
+python-versions = ">=3.6"
[package.dependencies]
et-xmlfile = "*"
[[package]]
name = "openpyxl-stubs"
-version = "0.1.19"
+version = "0.1.21"
description = "Type stubs for openpyxl"
category = "dev"
optional = false
@@ -556,14 +591,14 @@ typing-extensions = ">=3.7.4"
[[package]]
name = "packaging"
-version = "21.0"
+version = "21.3"
description = "Core utilities for Python packages"
-category = "dev"
+category = "main"
optional = false
python-versions = ">=3.6"
[package.dependencies]
-pyparsing = ">=2.0.2"
+pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
[[package]]
name = "pathspec"
@@ -575,37 +610,47 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
[[package]]
name = "pillow"
-version = "8.3.2"
+version = "9.0.1"
description = "Python Imaging Library (Fork)"
category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
+
+[[package]]
+name = "platformdirs"
+version = "2.5.1"
+description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"]
+test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"]
[[package]]
name = "pluggy"
-version = "0.13.1"
+version = "1.0.0"
description = "plugin and hook calling mechanisms for python"
category = "dev"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-
-[package.dependencies]
-importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
+python-versions = ">=3.6"
[package.extras]
dev = ["pre-commit", "tox"]
+testing = ["pytest", "pytest-benchmark"]
[[package]]
name = "py"
-version = "1.10.0"
+version = "1.11.0"
description = "library with cross-python path, ini-parsing, io, code, log facilities"
category = "dev"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
[[package]]
name = "pycparser"
-version = "2.20"
+version = "2.21"
description = "C parser in Python"
category = "main"
optional = false
@@ -613,7 +658,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[[package]]
name = "pycurl"
-version = "7.44.1"
+version = "7.45.1"
description = "PycURL -- A Python Interface To The cURL library"
category = "main"
optional = true
@@ -621,7 +666,7 @@ python-versions = ">=3.5"
[[package]]
name = "pydantic"
-version = "1.8.2"
+version = "1.9.0"
description = "Data validation and settings management using python 3.6 type hinting"
category = "main"
optional = false
@@ -647,15 +692,18 @@ rsa = ["cryptography"]
[[package]]
name = "pyparsing"
-version = "2.4.7"
+version = "3.0.7"
description = "Python parsing module"
category = "main"
optional = false
-python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+python-versions = ">=3.6"
+
+[package.extras]
+diagrams = ["jinja2", "railroad-diagrams"]
[[package]]
name = "pytest"
-version = "6.2.4"
+version = "6.2.5"
description = "pytest: simple powerful testing with Python"
category = "dev"
optional = false
@@ -665,10 +713,9 @@ python-versions = ">=3.6"
atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
attrs = ">=19.2.0"
colorama = {version = "*", markers = "sys_platform == \"win32\""}
-importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
iniconfig = "*"
packaging = "*"
-pluggy = ">=0.12,<1.0.0a1"
+pluggy = ">=0.12,<2.0"
py = ">=1.8.2"
toml = "*"
@@ -704,7 +751,7 @@ six = ">=1.5"
[[package]]
name = "python-dotenv"
-version = "0.19.0"
+version = "0.19.2"
description = "Read key-value pairs from a .env file and set them as environment variables"
category = "main"
optional = false
@@ -713,33 +760,17 @@ python-versions = ">=3.5"
[package.extras]
cli = ["click (>=5.0)"]
-[[package]]
-name = "python-editor"
-version = "1.0.4"
-description = "Programmatically open an editor, capture the result."
-category = "main"
-optional = false
-python-versions = "*"
-
[[package]]
name = "pyyaml"
-version = "5.4.1"
+version = "6.0"
description = "YAML parser and emitter for Python"
category = "main"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
-
-[[package]]
-name = "regex"
-version = "2021.8.21"
-description = "Alternative regular expression module, to replace re."
-category = "dev"
-optional = false
-python-versions = "*"
+python-versions = ">=3.6"
[[package]]
name = "requests"
-version = "2.26.0"
+version = "2.27.1"
description = "Python HTTP for Humans."
category = "main"
optional = false
@@ -785,14 +816,30 @@ requests = "*"
[[package]]
name = "scipy"
-version = "1.7.1"
+version = "1.8.0"
description = "SciPy: Scientific Library for Python"
category = "main"
optional = false
-python-versions = ">=3.7,<3.10"
+python-versions = ">=3.8,<3.11"
+
+[package.dependencies]
+numpy = ">=1.17.3,<1.25.0"
+
+[[package]]
+name = "setuptools-scm"
+version = "6.4.2"
+description = "the blessed package to manage your versions by scm tags"
+category = "main"
+optional = false
+python-versions = ">=3.6"
[package.dependencies]
-numpy = ">=1.16.5,<1.23.0"
+packaging = ">=20.0"
+tomli = ">=1.0.0"
+
+[package.extras]
+test = ["pytest (>=6.2)", "virtualenv (>20)"]
+toml = ["setuptools (>=42)"]
[[package]]
name = "six"
@@ -812,23 +859,35 @@ python-versions = ">=3.5"
[[package]]
name = "sqlalchemy"
-version = "1.3.24"
+version = "1.4.32"
description = "Database Abstraction Library"
category = "main"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
+
+[package.dependencies]
+greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"}
[package.extras]
+aiomysql = ["greenlet (!=0.4.17)", "aiomysql"]
+aiosqlite = ["typing_extensions (!=3.10.0.1)", "greenlet (!=0.4.17)", "aiosqlite"]
+asyncio = ["greenlet (!=0.4.17)"]
+asyncmy = ["greenlet (!=0.4.17)", "asyncmy (>=0.2.3)"]
+mariadb_connector = ["mariadb (>=1.0.1)"]
mssql = ["pyodbc"]
mssql_pymssql = ["pymssql"]
mssql_pyodbc = ["pyodbc"]
-mysql = ["mysqlclient"]
-oracle = ["cx-oracle"]
-postgresql = ["psycopg2"]
-postgresql_pg8000 = ["pg8000 (<1.16.6)"]
+mypy = ["sqlalchemy2-stubs", "mypy (>=0.910)"]
+mysql = ["mysqlclient (>=1.4.0,<2)", "mysqlclient (>=1.4.0)"]
+mysql_connector = ["mysql-connector-python"]
+oracle = ["cx_oracle (>=7,<8)", "cx_oracle (>=7)"]
+postgresql = ["psycopg2 (>=2.7)"]
+postgresql_asyncpg = ["greenlet (!=0.4.17)", "asyncpg"]
+postgresql_pg8000 = ["pg8000 (>=1.16.6)"]
postgresql_psycopg2binary = ["psycopg2-binary"]
postgresql_psycopg2cffi = ["psycopg2cffi"]
pymysql = ["pymysql (<1)", "pymysql"]
+sqlcipher = ["sqlcipher3-binary"]
[[package]]
name = "sqlalchemy-stubs"
@@ -844,7 +903,7 @@ typing-extensions = ">=3.7.4"
[[package]]
name = "sqlalchemy-utc"
-version = "0.12.0"
+version = "0.14.0"
description = "SQLAlchemy type to store aware datetime values"
category = "main"
optional = false
@@ -855,14 +914,17 @@ SQLAlchemy = ">=0.9.0"
[[package]]
name = "starlette"
-version = "0.14.2"
+version = "0.17.1"
description = "The little ASGI library that shines."
category = "main"
optional = false
python-versions = ">=3.6"
+[package.dependencies]
+anyio = ">=3.0.0,<4"
+
[package.extras]
-full = ["aiofiles", "graphene", "itsdangerous", "jinja2", "python-multipart", "pyyaml", "requests"]
+full = ["itsdangerous", "jinja2", "python-multipart", "pyyaml", "requests"]
[[package]]
name = "toml"
@@ -874,36 +936,28 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
[[package]]
name = "tomli"
-version = "1.2.1"
+version = "2.0.1"
description = "A lil' TOML parser"
-category = "dev"
-optional = false
-python-versions = ">=3.6"
-
-[[package]]
-name = "typed-ast"
-version = "1.4.3"
-description = "a fork of Python 2 and 3 ast modules with type comment support"
-category = "dev"
+category = "main"
optional = false
-python-versions = "*"
+python-versions = ">=3.7"
[[package]]
name = "typer"
-version = "0.3.2"
+version = "0.4.0"
description = "Typer, build great CLIs. Easy to code. Based on Python type hints."
category = "main"
optional = false
python-versions = ">=3.6"
[package.dependencies]
-click = ">=7.1.1,<7.2.0"
+click = ">=7.1.1,<9.0.0"
[package.extras]
-test = ["pytest-xdist (>=1.32.0,<2.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "mypy (==0.782)", "black (>=19.10b0,<20.0b0)", "isort (>=5.0.6,<6.0.0)", "shellingham (>=1.3.0,<2.0.0)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "coverage (>=5.2,<6.0)"]
all = ["colorama (>=0.4.3,<0.5.0)", "shellingham (>=1.3.0,<2.0.0)"]
dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)"]
doc = ["mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=5.4.0,<6.0.0)", "markdown-include (>=0.5.1,<0.6.0)"]
+test = ["shellingham (>=1.3.0,<2.0.0)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "coverage (>=5.2,<6.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "mypy (==0.910)", "black (>=19.10b0,<20.0b0)", "isort (>=5.0.6,<6.0.0)"]
[[package]]
name = "types-python-dateutil"
@@ -915,56 +969,66 @@ python-versions = "*"
[[package]]
name = "types-requests"
-version = "2.25.6"
+version = "2.27.13"
description = "Typing stubs for requests"
category = "dev"
optional = false
python-versions = "*"
+[package.dependencies]
+types-urllib3 = "<1.27"
+
+[[package]]
+name = "types-urllib3"
+version = "1.26.11"
+description = "Typing stubs for urllib3"
+category = "dev"
+optional = false
+python-versions = "*"
+
[[package]]
name = "typing-extensions"
-version = "3.10.0.0"
-description = "Backported and Experimental Type Hints for Python 3.5+"
+version = "4.1.1"
+description = "Backported and Experimental Type Hints for Python 3.6+"
category = "main"
optional = false
-python-versions = "*"
+python-versions = ">=3.6"
[[package]]
name = "urllib3"
-version = "1.26.6"
+version = "1.26.9"
description = "HTTP library with thread-safe connection pooling, file post, and more."
category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
[package.extras]
-brotli = ["brotlipy (>=0.6.0)"]
+brotli = ["brotlicffi (>=0.8.0)", "brotli (>=1.0.9)", "brotlipy (>=0.6.0)"]
secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"]
socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
[[package]]
name = "uvicorn"
-version = "0.15.0"
+version = "0.17.6"
description = "The lightning-fast ASGI server."
category = "main"
optional = false
-python-versions = "*"
+python-versions = ">=3.7"
[package.dependencies]
asgiref = ">=3.4.0"
click = ">=7.0"
colorama = {version = ">=0.4", optional = true, markers = "sys_platform == \"win32\" and extra == \"standard\""}
h11 = ">=0.8"
-httptools = {version = ">=0.2.0,<0.3.0", optional = true, markers = "extra == \"standard\""}
+httptools = {version = ">=0.4.0", optional = true, markers = "extra == \"standard\""}
python-dotenv = {version = ">=0.13", optional = true, markers = "extra == \"standard\""}
PyYAML = {version = ">=5.1", optional = true, markers = "extra == \"standard\""}
-typing-extensions = {version = "*", markers = "python_version < \"3.8\""}
uvloop = {version = ">=0.14.0,<0.15.0 || >0.15.0,<0.15.1 || >0.15.1", optional = true, markers = "sys_platform != \"win32\" and sys_platform != \"cygwin\" and platform_python_implementation != \"PyPy\" and extra == \"standard\""}
watchgod = {version = ">=0.6", optional = true, markers = "extra == \"standard\""}
-websockets = {version = ">=9.1", optional = true, markers = "extra == \"standard\""}
+websockets = {version = ">=10.0", optional = true, markers = "extra == \"standard\""}
[package.extras]
-standard = ["websockets (>=9.1)", "httptools (>=0.2.0,<0.3.0)", "watchgod (>=0.6)", "python-dotenv (>=0.13)", "PyYAML (>=5.1)", "uvloop (>=0.14.0,!=0.15.0,!=0.15.1)", "colorama (>=0.4)"]
+standard = ["websockets (>=10.0)", "httptools (>=0.4.0)", "watchgod (>=0.6)", "python-dotenv (>=0.13)", "PyYAML (>=5.1)", "uvloop (>=0.14.0,!=0.15.0,!=0.15.1)", "colorama (>=0.4)"]
[[package]]
name = "uvloop"
@@ -981,229 +1045,249 @@ test = ["aiohttp", "flake8 (>=3.9.2,<3.10.0)", "psutil", "pycodestyle (>=2.7.0,<
[[package]]
name = "watchgod"
-version = "0.7"
+version = "0.8"
description = "Simple, modern file watching and code reload in python."
category = "main"
optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.7"
+
+[package.dependencies]
+anyio = ">=3.0.0,<4"
[[package]]
name = "websockets"
-version = "9.1"
+version = "10.2"
description = "An implementation of the WebSocket Protocol (RFC 6455 & 7692)"
category = "main"
optional = false
-python-versions = ">=3.6.1"
+python-versions = ">=3.7"
[[package]]
name = "zipp"
-version = "3.5.0"
+version = "3.7.0"
description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "dev"
+category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
[package.extras]
docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
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]
zipp = [
- {file = "zipp-3.5.0-py3-none-any.whl", hash = "sha256:957cfda87797e389580cb8b9e3870841ca991e2125350677b2ca83a0e99390a3"},
- {file = "zipp-3.5.0.tar.gz", hash = "sha256:f5812b1e007e48cff63449a5e9f4e7ebea716b4111f9c4f9a645f91d579bf0c4"},
+ {file = "zipp-3.7.0-py3-none-any.whl", hash = "sha256:b47250dd24f92b7dd6a0a8fc5244da14608f3ca90a5efcd37a3b1642fac9a375"},
+ {file = "zipp-3.7.0.tar.gz", hash = "sha256:9f50f446828eb9d45b267433fd3e9da8d801f614129124863f9c51ebceafb87d"},
]
diff --git a/pyproject.toml b/pyproject.toml
index 21aead83..a74b7202 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,36 +21,35 @@ version = "1.4.4"
[tool.poetry.dependencies]
-python = "^3.7,<3.10"
+python = "^3.8,<3.11"
# core
-numpy = "^1.21.1"
-obspy = "^1.2.2"
-openpyxl = "^3.0.7"
-pycurl = {version = "^7.44.1", optional = true}
-pydantic = "^1.8.2"
-requests = "^2.26.0"
-scipy = "^1.7.1"
-typer = "^0.3.2"
+numpy = "^1.22.3"
+obspy = "^1.3.0"
+openpyxl = "^3.0.9"
+pycurl = {version = "^7.45.1", optional = true}
+pydantic = "^1.9.0"
+requests = "^2.27.1"
+scipy = "^1.8.0"
+typer = "^0.4.0"
# webservice
-alembic = "^1.6.5"
-Authlib = "^0.15.4"
-cryptography = "^3.4.7"
-databases = {extras = ["mysql", "sqlite"], version = "^0.4.3"}
-fastapi = "^0.68.0"
+alembic = "^1.7.7"
+Authlib = "^1.0.0"
+cryptography = "^36.0.2"
+databases = {extras = ["mysql", "sqlite"], version = "^0.5.5"}
+fastapi = "^0.75.0"
gunicorn = "^20.1.0"
-SQLAlchemy = "^1.3.24"
-SQLAlchemy-Utc = "^0.12.0"
-typing-extensions = "^3.10.0"
-uvicorn = {extras = ["standard"], version = "^0.15.0"}
-httpx = "0.18.1"
+SQLAlchemy = "^1.4.32"
+SQLAlchemy-Utc = "^0.14.0"
+uvicorn = {extras = ["standard"], version = "^0.17.6"}
+httpx = "0.22.0"
[tool.poetry.dev-dependencies]
-black = "^21.7b0"
+black = "^22.1.0"
pytest = "^6.2.4"
pytest-cov = "^2.12.1"
safety = "^1.10.3"
-mypy = "^0.910"
+mypy = "^0.941"
# type hints
data-science-types = "^0.2.23"
openpyxl-stubs = "^0.1.19"
--
GitLab
From de73714e446a14af8bf3cd6458de25ba5066084e Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Fri, 18 Mar 2022 15:27:46 -0600
Subject: [PATCH 025/142] Black formatting updates for ** operation, remove
typing_extensions now that python3.8+
---
geomagio/algorithm/SqDistAlgorithm.py | 4 ++--
geomagio/geomag_types.py | 2 +-
geomagio/residual/Calculation.py | 7 +++----
geomagio/residual/Reading.py | 5 ++---
4 files changed, 8 insertions(+), 10 deletions(-)
diff --git a/geomagio/algorithm/SqDistAlgorithm.py b/geomagio/algorithm/SqDistAlgorithm.py
index 4dc5087a..e2106c0f 100644
--- a/geomagio/algorithm/SqDistAlgorithm.py
+++ b/geomagio/algorithm/SqDistAlgorithm.py
@@ -461,7 +461,7 @@ class SqDistAlgorithm(Algorithm):
# to White et al. (USGS SIR 2014-5045).
fom = 10 ** (-3 / 20.0) # halve power at corner frequency
omg = np.pi / np.float64(smooth) # corner angular frequency
- sig = np.sqrt(-2 * np.log(fom) / omg ** 2) + np.finfo(float).eps # sig>0
+ sig = np.sqrt(-2 * np.log(fom) / omg**2) + np.finfo(float).eps # sig>0
ts = np.linspace(
np.max((-m, -3 * np.round(sig))),
np.min((m, 3 * np.round(sig))),
@@ -536,7 +536,7 @@ class SqDistAlgorithm(Algorithm):
# when forecasting, grow sigma=sqrt(var) like a prediction
# interval; sumc2 and jstep will be reset with the next
# valid observation
- phiJminus1 = phiJminus1 + phi ** jstep
+ phiJminus1 = phiJminus1 + phi**jstep
jstep = jstep + 1
sumc2 = (
sumc2
diff --git a/geomagio/geomag_types.py b/geomagio/geomag_types.py
index a50e2804..9a181bcd 100644
--- a/geomagio/geomag_types.py
+++ b/geomagio/geomag_types.py
@@ -1,4 +1,4 @@
-from typing_extensions import Literal
+from typing import Literal
DataInterval = Literal["tenhertz", "second", "minute", "hour", "day", "month"]
DataType = Literal[
diff --git a/geomagio/residual/Calculation.py b/geomagio/residual/Calculation.py
index fe1ab1c1..d6d82044 100644
--- a/geomagio/residual/Calculation.py
+++ b/geomagio/residual/Calculation.py
@@ -1,5 +1,4 @@
-from typing import List, Tuple
-from typing_extensions import Literal
+from typing import List, Literal, Tuple
import numpy as np
@@ -116,7 +115,7 @@ def calculate_D_absolute(
m.angle
+ np.degrees(
m.measurement_type.meridian
- * (np.arcsin(m.residual / np.sqrt((m.h + h_baseline) ** 2 + m.e ** 2)))
+ * (np.arcsin(m.residual / np.sqrt((m.h + h_baseline) ** 2 + m.e**2)))
)
- np.degrees(np.arctan(m.e / (m.h + h_baseline)))
for m in declination_measurements
@@ -168,7 +167,7 @@ def calculate_HZ_absolutes(
inclination_radians = np.radians(inclination)
h_abs = corrected_f * np.cos(inclination_radians)
z_abs = corrected_f * np.sin(inclination_radians)
- h_b = np.sqrt(h_abs ** 2 - mean.e ** 2) - mean.h
+ h_b = np.sqrt(h_abs**2 - mean.e**2) - mean.h
z_b = z_abs - mean.z
# adjust absolutes to reference measurement
if reference:
diff --git a/geomagio/residual/Reading.py b/geomagio/residual/Reading.py
index 437da499..101ba4b4 100644
--- a/geomagio/residual/Reading.py
+++ b/geomagio/residual/Reading.py
@@ -1,5 +1,4 @@
-from typing import Dict, List, Optional, Tuple
-from typing_extensions import Literal
+from typing import Dict, List, Literal, Optional, Tuple
import numpy as np
from obspy import Stream, UTCDateTime
@@ -187,7 +186,7 @@ def get_ordinates(
d_ord = d_abs - d_bas
z_ord = z_abs - z_bas
e_ord = h_abs * np.radians(d_ord)
- h_ord = np.sqrt(h_ord ** 2 - e_ord ** 2)
+ h_ord = np.sqrt(h_ord**2 - e_ord**2)
return (h_ord, e_ord, z_ord)
--
GitLab
From a5e03dbd7a165030946dceb83a9f98302454b5c7 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Fri, 18 Mar 2022 15:28:27 -0600
Subject: [PATCH 026/142] Update sqlalchemy deprecated tometadata to
to_metadata
---
geomagio/api/db/metadata_history_table.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/geomagio/api/db/metadata_history_table.py b/geomagio/api/db/metadata_history_table.py
index 471869fe..8fbd785c 100644
--- a/geomagio/api/db/metadata_history_table.py
+++ b/geomagio/api/db/metadata_history_table.py
@@ -4,7 +4,7 @@ from .common import sqlalchemy_metadata
from .metadata_table import metadata
# create copy of original metadata table and add to sqlalchemy metadata
-metadata_history = metadata.tometadata(
+metadata_history = metadata.to_metadata(
metadata=sqlalchemy_metadata, name="metadata_history"
)
metadata_history.indexes.clear()
--
GitLab
From 25b719386a2cdd683f4204543e2bd5c521b60921 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Fri, 18 Mar 2022 15:28:35 -0600
Subject: [PATCH 027/142] Add pip cache purge
---
Dockerfile | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/Dockerfile b/Dockerfile
index 2b59aeb9..9730def5 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,6 +1,4 @@
ARG FROM_IMAGE=usgs/python:3.8-obspy
-
-
FROM ${FROM_IMAGE}
ARG GIT_BRANCH_NAME=none
@@ -21,12 +19,14 @@ RUN cd /geomag-algorithms \
# install into system python
&& poetry export -o requirements.txt --dev --without-hashes \
# only install dependencies, not project
- && pip install -r requirements.txt
+ && pip install -r requirements.txt \
+ && pip cache purge
# install rest of library separate from dependencies
COPY . /geomag-algorithms
RUN cd /geomag-algorithms \
&& pip install . \
+ && pip cache purge \
# add data directory owned by usgs-user
&& mkdir -p /data \
&& chown -R usgs-user:usgs-user /data
--
GitLab
From fa6b5b0e895c9107951e966491d9571dcd42c639 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Sat, 16 Apr 2022 10:53:39 -0600
Subject: [PATCH 028/142] Add GUA to geomagio/Metadata.py
GUA is transitioning to an ObsRIO data logger, which requires a
metadata entry in Metadata.py. We do not know actual calibration
values for the GUA Narod mag, and cannot retrieve them currently
due to ongoing communication issues, so we'll use Narod default
calibration parameters.
This commit applies strictly to GUA. Additional commits are
forthcoming that relate to the test FGE+ObsRIO system that will
also be deployed soon.
---
geomagio/Metadata.py | 23 +++++++++++++++++++++++
1 file changed, 23 insertions(+)
diff --git a/geomagio/Metadata.py b/geomagio/Metadata.py
index dec19252..74c2b347 100644
--- a/geomagio/Metadata.py
+++ b/geomagio/Metadata.py
@@ -321,6 +321,29 @@ _INSTRUMENT_METADATA = [
},
},
},
+ {
+ "network": "NT",
+ "station": "GUA",
+ "start_time": None,
+ "end_time": None,
+ "instrument": {
+ "type": "Narod",
+ "channels": {
+ "U": [
+ {"channel": "U_Volt", "offset": 0, "scale": 100},
+ {"channel": "U_Bin", "offset": 0, "scale": 500},
+ ],
+ "V": [
+ {"channel": "V_Volt", "offset": 0, "scale": 100},
+ {"channel": "V_Bin", "offset": 0, "scale": 500},
+ ],
+ "W": [
+ {"channel": "W_Volt", "offset": 0, "scale": 100},
+ {"channel": "W_Bin", "offset": 0, "scale": 500},
+ ],
+ },
+ },
+ },
{
"network": "NT",
"station": "HON",
--
GitLab
From 0f5e860b74ac382a388f0272468935340f02bf96 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Sat, 16 Apr 2022 10:59:33 -0600
Subject: [PATCH 029/142] Add GUT to geomagio/Metadata.py
A new FGE+ObsRIO test system is being deployed to Guam. For now,
we simply create an entry in Metadata.py so that variation
filtering can be be applied to these new data. The calibration
parameters are defaults for non-high-latitude FGE fluxgages.
---
geomagio/Metadata.py | 32 ++++++++++++++++++++++++++++++++
1 file changed, 32 insertions(+)
diff --git a/geomagio/Metadata.py b/geomagio/Metadata.py
index 74c2b347..ded542a9 100644
--- a/geomagio/Metadata.py
+++ b/geomagio/Metadata.py
@@ -344,6 +344,38 @@ _INSTRUMENT_METADATA = [
},
},
},
+ {
+ "network": "NT",
+ "station": "GUT",
+ "start_time": None,
+ "end_time": None,
+ "instrument": {
+ "type": "FGE",
+ "channels": {
+ # each channel maps to a list of components to calculate nT
+ # TODO: calculate these lists based on "FGE" type
+ "U": [{"channel": "U_Volt", "offset": 0, "scale": 320.0}],
+ "V": [{"channel": "V_Volt", "offset": 0, "scale": 320.0}],
+ "W": [{"channel": "W_Volt", "offset": 0, "scale": 320.0}],
+ },
+ ## this info should get updated when available
+ # "electronics": {
+ # "serial": "E0542",
+ # # these scale values are used to convert voltage
+ # "x-scale": 313.2, # V/nT
+ # "y-scale": 312.3, # V/nT
+ # "z-scale": 312.0, # V/nT
+ # "temperature-scale": 0.01, # V/K
+ # },
+ # "sensor": {
+ # "serial": "S0419",
+ # # these constants combine with instrument setting for offset
+ # "x-constant": 36958, # nT/mA
+ # "y-constant": 36849, # nT/mA
+ # "z-constant": 36811, # nT/mA
+ # },
+ },
+ },
{
"network": "NT",
"station": "HON",
--
GitLab
From ce305b0bf687413c99bf8b14590919abdece773b Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Sat, 16 Apr 2022 11:02:08 -0600
Subject: [PATCH 030/142] Add HOT to geomagio/Metadata.py
A new FGE+ObsRIO test system is being deployed to Honolulu.
For now, we simply create an entry in Metadata.py so that
variationfiltering can be be applied to these new data. The
calibration parameters are defaults for non-high-latitude
FGE fluxgages.
---
geomagio/Metadata.py | 32 ++++++++++++++++++++++++++++++++
1 file changed, 32 insertions(+)
diff --git a/geomagio/Metadata.py b/geomagio/Metadata.py
index ded542a9..28bd1b66 100644
--- a/geomagio/Metadata.py
+++ b/geomagio/Metadata.py
@@ -399,6 +399,38 @@ _INSTRUMENT_METADATA = [
},
},
},
+ {
+ "network": "NT",
+ "station": "HOT",
+ "start_time": None,
+ "end_time": None,
+ "instrument": {
+ "type": "FGE",
+ "channels": {
+ # each channel maps to a list of components to calculate nT
+ # TODO: calculate these lists based on "FGE" type
+ "U": [{"channel": "U_Volt", "offset": 0, "scale": 320.0}],
+ "V": [{"channel": "V_Volt", "offset": 0, "scale": 320.0}],
+ "W": [{"channel": "W_Volt", "offset": 0, "scale": 320.0}],
+ },
+ ## this info should get updated when available
+ # "electronics": {
+ # "serial": "E0542",
+ # # these scale values are used to convert voltage
+ # "x-scale": 313.2, # V/nT
+ # "y-scale": 312.3, # V/nT
+ # "z-scale": 312.0, # V/nT
+ # "temperature-scale": 0.01, # V/K
+ # },
+ # "sensor": {
+ # "serial": "S0419",
+ # # these constants combine with instrument setting for offset
+ # "x-constant": 36958, # nT/mA
+ # "y-constant": 36849, # nT/mA
+ # "z-constant": 36811, # nT/mA
+ # },
+ },
+ },
{
"network": "NT",
"station": "NEW",
--
GitLab
From fa33746230f63284aa45bb2647bcf1cf5b6dcda9 Mon Sep 17 00:00:00 2001
From: "Geels, Brendan Ryan" <bgeels@usgs.gov>
Date: Wed, 16 Mar 2022 19:53:22 +0000
Subject: [PATCH 031/142] Update examples in usage.md to use recommended URL
template formatting and add Windows command example.
---
docs/usage.md | 21 ++++++++++++++++++---
1 file changed, 18 insertions(+), 3 deletions(-)
diff --git a/docs/usage.md b/docs/usage.md
index 0717a94f..78aea93e 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -59,9 +59,24 @@ directory and output **_H_**, **_E_**, **_Z_** and **_F_** data to a group of
--starttime 2013-03-01T00:00:00Z \
--endtime 2013-03-31T23:59:00Z \
--input pcdcp
- --input-url file://data-pcdcp/./%(OBS)s%(year)s%(julian)s.%(i)s \
- --output iaga2002
- --output-url file://data-iaga/./$(obs)s%(Y)s%(j)s.%(i)s \
+ --input-url file://data-pcdcp/./{OBS}/{date:%Y%j}.{i} \
+ --output iaga2002 \
+ --output-url file://data-iaga/./{obs}{date:%Y%m%d}{t}{i}.{i} \
+ --outchannels H E Z F
+
+Here is the same example written for use in the Windows command line.
+
+ geomag.py ^
+ --type variation ^
+ --inchannels H E Z F ^
+ --interval minute ^
+ --observatory TUC ^
+ --starttime 2013-03-01T00:00:00Z ^
+ --endtime 2013-03-31T23:59:00Z ^
+ --input pcdcp
+ --input-url file://data-pcdcp/./{OBS}/{date:%%Y%%j}.{i} ^
+ --output iaga2002 ^
+ --output-url file://data-iaga/./{obs}{date:%%Y%%m%%d}{t}{i}.{i} ^
--outchannels H E Z F
To retrieve all **_Dst 4 minute_**, and **_Dst 3 minute_** data from **_USGS_**
--
GitLab
From 98a218a644789348681e3e83ea70b3347a84bc7c Mon Sep 17 00:00:00 2001
From: "Geels, Brendan Ryan" <bgeels@usgs.gov>
Date: Mon, 21 Mar 2022 17:37:34 +0000
Subject: [PATCH 032/142] Add temp metadata for new BDT equip.
---
geomagio/Metadata.py | 38 +++++++++++++++++++++-----------------
1 file changed, 21 insertions(+), 17 deletions(-)
diff --git a/geomagio/Metadata.py b/geomagio/Metadata.py
index 28bd1b66..202cd676 100644
--- a/geomagio/Metadata.py
+++ b/geomagio/Metadata.py
@@ -38,25 +38,29 @@ _INSTRUMENT_METADATA = [
"type": "FGE",
"channels": {
# each channel maps to a list of components to calculate nT
+ # Temporary values until actuals are obtained.
# TODO: calculate these lists based on "FGE" type
- "U": [{"channel": "U_Volt", "offset": 20613, "scale": 313.2}],
- "V": [{"channel": "V_Volt", "offset": 0, "scale": 312.3}],
- "W": [{"channel": "W_Volt", "offset": 47450, "scale": 312.0}],
+ # TODO: Adjust offset for new FGE sensor & electronics? (installed 3/20/22)
+ "U": [{"channel": "U_Volt", "offset": 20613, "scale": 980}],
+ "V": [{"channel": "V_Volt", "offset": 0, "scale": 980}],
+ "W": [{"channel": "W_Volt", "offset": 47450, "scale": 980}],
},
"electronics": {
- "serial": "E0542",
+ "serial": "TBD",
# these scale values are used to convert voltage
- "x-scale": 313.2, # V/nT
- "y-scale": 312.3, # V/nT
- "z-scale": 312.0, # V/nT
+ # Temporary values until actuals are obtained.
+ "x-scale": 980, # nT/V
+ "y-scale": 980, # nT/V
+ "z-scale": 980, # nT/V
"temperature-scale": 0.01, # V/K
},
"sensor": {
- "serial": "S0419",
+ "serial": "TBD",
# these constants combine with instrument setting for offset
- "x-constant": 36958, # nT/mA
- "y-constant": 36849, # nT/mA
- "z-constant": 36811, # nT/mA
+ # Temporary values until actuals are obtained.
+ "x-constant": 1, # nT/mA
+ "y-constant": 1, # nT/mA
+ "z-constant": 1, # nT/mA
},
},
},
@@ -215,9 +219,9 @@ _INSTRUMENT_METADATA = [
"electronics": {
"serial": "E0568",
# these scale values are used to convert voltage
- "x-scale": 967.7, # V/nT
- "y-scale": 969.7, # V/nT
- "z-scale": 973.4, # V/nT
+ "x-scale": 967.7, # nT/V
+ "y-scale": 969.7, # nT/V
+ "z-scale": 973.4, # nT/V
"temperature-scale": 0.01, # V/K
},
"sensor": {
@@ -564,9 +568,9 @@ _INSTRUMENT_METADATA = [
# "electronics": {
# "serial": "E0542",
# # these scale values are used to convert voltage
- # "x-scale": 313.2, # V/nT
- # "y-scale": 312.3, # V/nT
- # "z-scale": 312.0, # V/nT
+ # "x-scale": 313.2, # nT/V
+ # "y-scale": 312.3, # nT/V
+ # "z-scale": 312.0, # nT/V
# "temperature-scale": 0.01, # V/K
# },
# "sensor": {
--
GitLab
From e7e5828af14a700765e41015d182ff959f447a79 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Fri, 22 Apr 2022 09:42:48 -0600
Subject: [PATCH 033/142] Add new test stations to list of valid observatories
---
geomagio/api/ws/Observatory.py | 18 ++++++++++++++++++
1 file changed, 18 insertions(+)
diff --git a/geomagio/api/ws/Observatory.py b/geomagio/api/ws/Observatory.py
index ecb38c91..fd407875 100644
--- a/geomagio/api/ws/Observatory.py
+++ b/geomagio/api/ws/Observatory.py
@@ -206,6 +206,15 @@ OBSERVATORIES = [
agency="USGS",
declination_base=764,
),
+ Observatory(
+ id="GUT",
+ elevation=140,
+ latitude=13.588,
+ longitude=144.867,
+ name="Guam Test",
+ agency="USGS",
+ declination_base=764,
+ ),
Observatory(
id="HON",
elevation=4,
@@ -215,6 +224,15 @@ OBSERVATORIES = [
agency="USGS",
declination_base=5982,
),
+ Observatory(
+ id="HOT",
+ elevation=4,
+ latitude=21.316,
+ longitude=202.0,
+ name="Honolulu Test",
+ agency="USGS",
+ declination_base=5982,
+ ),
Observatory(
id="NEW",
elevation=770,
--
GitLab
From dc3b7e4008075449e4051b4a701e887a5b3ebd05 Mon Sep 17 00:00:00 2001
From: "Geels, Brendan Ryan" <bgeels@usgs.gov>
Date: Sat, 23 Apr 2022 01:36:10 +0000
Subject: [PATCH 034/142] Add precise vals for HOT.
---
geomagio/Metadata.py | 39 ++++++++++++++++++++-------------------
1 file changed, 20 insertions(+), 19 deletions(-)
diff --git a/geomagio/Metadata.py b/geomagio/Metadata.py
index 202cd676..ebf55593 100644
--- a/geomagio/Metadata.py
+++ b/geomagio/Metadata.py
@@ -413,26 +413,27 @@ _INSTRUMENT_METADATA = [
"channels": {
# each channel maps to a list of components to calculate nT
# TODO: calculate these lists based on "FGE" type
- "U": [{"channel": "U_Volt", "offset": 0, "scale": 320.0}],
- "V": [{"channel": "V_Volt", "offset": 0, "scale": 320.0}],
- "W": [{"channel": "W_Volt", "offset": 0, "scale": 320.0}],
+ "U": [{"channel": "U_Volt", "offset": 0, "scale": 971.8}],
+ "V": [{"channel": "V_Volt", "offset": 0, "scale": 970.6}],
+ "W": [{"channel": "W_Volt", "offset": 0, "scale": 960.2}],
},
- ## this info should get updated when available
- # "electronics": {
- # "serial": "E0542",
- # # these scale values are used to convert voltage
- # "x-scale": 313.2, # V/nT
- # "y-scale": 312.3, # V/nT
- # "z-scale": 312.0, # V/nT
- # "temperature-scale": 0.01, # V/K
- # },
- # "sensor": {
- # "serial": "S0419",
- # # these constants combine with instrument setting for offset
- # "x-constant": 36958, # nT/mA
- # "y-constant": 36849, # nT/mA
- # "z-constant": 36811, # nT/mA
- # },
+ # this info should get updated when available
+ "electronics": {
+ "serial": "E558",
+ # these scale values are used to convert voltage
+ # these are calculated using Ohm's law, given scaling resistor value, and given nT/mA values.
+ "x-scale": 971.8, # nT/V
+ "y-scale": 970.6, # nT/V
+ "z-scale": 960.2, # nT/V
+ "temperature-scale": 0.01, # V/K
+ },
+ "sensor": {
+ "serial": "S0428",
+ # these constants combine with instrument setting for offset
+ "x-constant": 37220, # nT/mA
+ "y-constant": 37175, # nT/mA
+ "z-constant": 36775, # nT/mA
+ },
},
},
{
--
GitLab
From e9ed9c6462ac2b0a28d9f27167519b4368fc467b Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Mon, 25 Apr 2022 17:41:02 -0600
Subject: [PATCH 035/142] Reformat Metadata.py using black
The original merge request had an extra indentation space that the
black formatter didn't like.
---
geomagio/Metadata.py | 32 ++++++++++++++++----------------
1 file changed, 16 insertions(+), 16 deletions(-)
diff --git a/geomagio/Metadata.py b/geomagio/Metadata.py
index ebf55593..43907b79 100644
--- a/geomagio/Metadata.py
+++ b/geomagio/Metadata.py
@@ -418,22 +418,22 @@ _INSTRUMENT_METADATA = [
"W": [{"channel": "W_Volt", "offset": 0, "scale": 960.2}],
},
# this info should get updated when available
- "electronics": {
- "serial": "E558",
- # these scale values are used to convert voltage
- # these are calculated using Ohm's law, given scaling resistor value, and given nT/mA values.
- "x-scale": 971.8, # nT/V
- "y-scale": 970.6, # nT/V
- "z-scale": 960.2, # nT/V
- "temperature-scale": 0.01, # V/K
- },
- "sensor": {
- "serial": "S0428",
- # these constants combine with instrument setting for offset
- "x-constant": 37220, # nT/mA
- "y-constant": 37175, # nT/mA
- "z-constant": 36775, # nT/mA
- },
+ "electronics": {
+ "serial": "E558",
+ # these scale values are used to convert voltage
+ # these are calculated using Ohm's law, given scaling resistor value, and given nT/mA values.
+ "x-scale": 971.8, # nT/V
+ "y-scale": 970.6, # nT/V
+ "z-scale": 960.2, # nT/V
+ "temperature-scale": 0.01, # V/K
+ },
+ "sensor": {
+ "serial": "S0428",
+ # these constants combine with instrument setting for offset
+ "x-constant": 37220, # nT/mA
+ "y-constant": 37175, # nT/mA
+ "z-constant": 36775, # nT/mA
+ },
},
},
{
--
GitLab
From 14c228e964baabb088079433c9c5df164e05dc79 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Wed, 27 Apr 2022 11:50:11 -0600
Subject: [PATCH 036/142] Updated GUT calibration factors with more precise
values
---
geomagio/Metadata.py | 38 +++++++++++++++++++-------------------
1 file changed, 19 insertions(+), 19 deletions(-)
diff --git a/geomagio/Metadata.py b/geomagio/Metadata.py
index 43907b79..9c2ad7ca 100644
--- a/geomagio/Metadata.py
+++ b/geomagio/Metadata.py
@@ -358,26 +358,26 @@ _INSTRUMENT_METADATA = [
"channels": {
# each channel maps to a list of components to calculate nT
# TODO: calculate these lists based on "FGE" type
- "U": [{"channel": "U_Volt", "offset": 0, "scale": 320.0}],
- "V": [{"channel": "V_Volt", "offset": 0, "scale": 320.0}],
- "W": [{"channel": "W_Volt", "offset": 0, "scale": 320.0}],
+ "U": [{"channel": "U_Volt", "offset": 0, "scale": 314.28}],
+ "V": [{"channel": "V_Volt", "offset": 0, "scale": 310.48}],
+ "W": [{"channel": "W_Volt", "offset": 0, "scale": 317.5}],
+ },
+ # this info should get updated when available
+ "electronics": {
+ "serial": "E0542",
+ # these scale values are used to convert voltage
+ "x-scale": 314.28, # V/nT
+ "y-scale": 310.48, # V/nT
+ "z-scale": 317.5, # V/nT
+ "temperature-scale": 0.01, # V/K
+ },
+ "sensor": {
+ "serial": "S0420",
+ # these constants combine with instrument setting for offset
+ "x-constant": 37085, # nT/mA
+ "y-constant": 36637, # nT/mA
+ "z-constant": 37465, # nT/mA
},
- ## this info should get updated when available
- # "electronics": {
- # "serial": "E0542",
- # # these scale values are used to convert voltage
- # "x-scale": 313.2, # V/nT
- # "y-scale": 312.3, # V/nT
- # "z-scale": 312.0, # V/nT
- # "temperature-scale": 0.01, # V/K
- # },
- # "sensor": {
- # "serial": "S0419",
- # # these constants combine with instrument setting for offset
- # "x-constant": 36958, # nT/mA
- # "y-constant": 36849, # nT/mA
- # "z-constant": 36811, # nT/mA
- # },
},
},
{
--
GitLab
From 5013aca38b2a6821649753a33be7c4c0d1df326d Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Mon, 2 May 2022 14:50:04 -0600
Subject: [PATCH 037/142] Update geomag-algorithms tagged release version to
1.4.6
code.json
pyproject.toml
---
code.json | 2 +-
pyproject.toml | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/code.json b/code.json
index e638a040..540e31d8 100644
--- a/code.json
+++ b/code.json
@@ -3,7 +3,7 @@
"name": "geomag-algorithms",
"organization": "U.S. Geological Survey",
"description": "Library for processing Geomagnetic timeseries data.",
- "version": "1.4.4",
+ "version": "1.4.6",
"status": "Development",
"permissions": {
diff --git a/pyproject.toml b/pyproject.toml
index a74b7202..fc9aae75 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ packages = [
{include = "geomagio" }
]
repository="https://code.usgs.gov/ghsc/geomag/geomag-algorithms"
-version = "1.4.4"
+version = "1.4.6"
[tool.poetry.dependencies]
--
GitLab
From e287cda7d5f969dee48dfbf6747526bade7df2cf Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Wed, 27 Apr 2022 17:15:55 -0600
Subject: [PATCH 038/142] Update to python 3.9, clean up pipeline and switch to
rules from only
---
.gitlab-ci.yml | 323 ++++++++++++++++++++++---------------------------
Dockerfile | 2 +-
2 files changed, 148 insertions(+), 177 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ae1ce65c..b407d42b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,29 +1,26 @@
-image: ${DEVOPS_REGISTRY}usgs/centos:latest
-
-cache:
- paths:
- # cache pip installed dependencies, see PIP_CACHE_DIR variable below
- - .cache/pip
+default:
+ image: ${DEVOPS_REGISTRY}usgs/python:3.9-obspy
+ variables:
+ CI_REGISTRY: ${CODE_REGISTRY}
+ CI_REGISTRY_IMAGE: ${CODE_REGISTRY_IMAGE}
+ # environment variables
+ APP_NAME: geomag-algorithms
+ DATA_HOST: "edgecwb.usgs.gov"
+ DATA_PORT: "2060"
+ DATA_TYPE: "edge"
+ UPSTREAM_PATH: ghsc/geomag/geomag-algorithms
stages:
+ - init
- test
- integration
- - scan
- deploy
-variables:
- CI_REGISTRY: ${CODE_REGISTRY}
- CI_REGISTRY_IMAGE: ${CODE_REGISTRY_IMAGE}
- PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
- TRIVY_VERSION: "0.13.0"
- # docker variables
- DOCKER_DRIVER: overlay2
- FROM_IMAGE: ${CODE_REGISTRY}/devops/images/usgs/python:3.8-obspy
- # environment variables
- APP_NAME: geomag-algorithms
- DATA_HOST: "cwbpub.cr.usgs.gov"
- DATA_PORT: "2060"
- DATA_TYPE: "edge"
+# Do not run in upstream for merge requests
+workflow:
+ rules:
+ - if: $CI_COMMIT_TAG
+ - if: $CI_COMMIT_BRANCH
## --------------------------------------------------
# Templates
@@ -36,70 +33,16 @@ variables:
- INTERNAL_IMAGE_NAME=${CI_REGISTRY_IMAGE}/${IMAGE_NAME}
- STACK_NAME=${APP_NAME}
-.build_docker_image:
- cache: {}
- extends:
- - .adjust_image_names
- image: docker:19.03-git
- only:
- - master@ghsc/geomag/geomag-algorithms
- - production@ghsc/geomag/geomag-algorithms
- - tags@ghsc/geomag/geomag-algorithms
- script:
- - docker build
- --pull
- --build-arg FROM_IMAGE=${FROM_IMAGE}
- --build-arg GIT_BRANCH_NAME=${CI_COMMIT_REF_NAME}
- --build-arg GIT_COMMIT_SHA=${CI_COMMIT_SHA}
- --tag local/${IMAGE_NAME} .
-
- - docker tag local/${IMAGE_NAME} ${IMAGE_NAME}
- - docker push ${IMAGE_NAME}
- - docker image rm ${IMAGE_NAME}
-
- - docker tag local/${IMAGE_NAME} ${INTERNAL_IMAGE_NAME}
- - docker push ${INTERNAL_IMAGE_NAME}
- - docker image rm ${INTERNAL_IMAGE_NAME}
- services:
- - docker:19.03-dind
- stage: integration
- tags:
- - build
-
-.check_code:
- artifacts:
- reports:
- cobertura: coverage.xml
- junit: junit.xml
- before_script:
- # install dependencies
- - poetry config virtualenvs.create false
- - poetry install
- - which python
- image: ${DEVOPS_REGISTRY}usgs/python:3.8-build
- script:
- # run checks
- - black --check .
- - pytest --cov=geomagio --junitxml junit.xml
- - coverage xml
- - safety check
- stage: test
- tags:
- - development
-
.deploy:
- cache: {}
extends:
- .adjust_image_names
- image: ${CODE_REGISTRY}/ghsc/hazdev/cloud-formation/hazdev-build-runner:latest
+ image: "${CI_REGISTRY}/ghsc/hazdev/container-deploy:latest"
script:
- - git clone ${GENERIC_SWARM_DEPLOY_REPO} generic-deploy
- cp -v
- generic-deploy/default.config.sh
- generic-deploy/default.funcs.sh
- generic-deploy/deploy.sh
+ /container-deploy/default.config.sh
+ /container-deploy/default.funcs.sh
+ /container-deploy/deploy.sh
scripts/.
-
- export APP_NAME=${APP_NAME}
- export IMAGE_NAME=${IMAGE_NAME}
- export REGISTRY=${CI_REGISTRY_IMAGE}
@@ -121,7 +64,6 @@ variables:
# REVIEWER_GROUP
.deploy-library:
- cache: {}
image: "docker:stable-git"
script:
- PREFIX_LENGTH=${#REQUIRED_PREFIX};
@@ -134,6 +76,7 @@ variables:
git clone "${CI_REPOSITORY_URL}" "$(basename "${APP_DEPLOY_DIR}")";
fi
- cd "${APP_DEPLOY_DIR}";
+ - git fetch --tags;
- git checkout "${CI_COMMIT_REF_NAME}" || git checkout -b "${CI_COMMIT_REF_NAME}";
- git pull --ff-only "${CI_REPOSITORY_URL}" "${CI_COMMIT_REF_NAME}";
stage: deploy
@@ -144,152 +87,180 @@ variables:
APP_DEPLOY_DIR: "/geomag/geomag-algorithms"
REQUIRED_PREFIX: "/geomag"
+# rules to define which branches should trigger actions
+.development-env: &development-env
+ if: $CI_PROJECT_PATH != $UPSTREAM_PATH
+ variables:
+ ENVIRONMENT: development
+.staging-env: &staging-env
+ if: >
+ $CI_PROJECT_PATH == $UPSTREAM_PATH
+ && $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
+ variables:
+ ENVIRONMENT: staging
-.staging:
- only:
- - master@ghsc/geomag/geomag-algorithms
- - tags@ghsc/geomag/geomag-algorithms
+.production-env: &production-env
+ if: >
+ $CI_PROJECT_PATH == $UPSTREAM_PATH
+ && ( $CI_COMMIT_BRANCH == 'production' || $CI_COMMIT_TAG != '' )
+ variables:
+ ENVIRONMENT: production
-.production:
- except:
- - ^.*beta.*$
- - ^.*-rc.*$
- only:
- - tags@ghsc/geomag/geomag-algorithms
- - production@ghsc/geomag/geomag-algorithms
- when: manual
+## --------------------------------------------------
+# Init Stage
+## --------------------------------------------------
+
+Poetry:
+ artifacts:
+ paths:
+ - poetry.toml
+ - .venv
+ cache:
+ paths:
+ # cache pip installed dependencies, see PIP_CACHE_DIR variable below
+ - .cache/pip
+ script:
+ # install into .venv for artifact
+ - poetry config virtualenvs.in-project true --local
+ - poetry install
+ - poetry run safety check
+ stage: init
+ variables:
+ PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
## --------------------------------------------------
# Test Stage
## --------------------------------------------------
-# Numpy 1.20 requires python 3.7 or newer
-# Check Python 3.6:
-# extends:
-# - .check_code
-# image: ${DEVOPS_REGISTRY}usgs/obspy:3
+Python Build:
+ script:
+ - poetry build
+ stage: build
-Check Python 3.8:
- extends:
- - .check_code
- image: ${DEVOPS_REGISTRY}usgs/python:3.8-build
+Python Lint:
+ script:
+ - poetry run black --check .
+ stage: test
+
+Python Test:
+ artifacts:
+ reports:
+ cobertura: coverage.xml
+ junit: junit.xml
+ script:
+ - poetry run pytest --cov=geomagio --junitxml junit.xml
+ - poetry run coverage xml
+ stage: test
## --------------------------------------------------
# Integration Stage
## --------------------------------------------------
Build Docker Image:
- extends:
- - .build_docker_image
- variables:
- APP_NAME: geomag-algorithms
-
-## --------------------------------------------------
-# Scanning Stage (e.g. OWASP ZAP etc...)
-## --------------------------------------------------
-
-Scan Docker Image:
- cache: {}
- # temporarily allow while cryptography dependency has CVE
- # new version no less secure than old
- allow_failure: true
extends:
- .adjust_image_names
- image: docker:19.03-git
- only:
- - master@ghsc/geomag/geomag-algorithms
- - production@ghsc/geomag/geomag-algorithms
- - tags@ghsc/geomag/geomag-algorithms
+ image: ${DEVOPS_REGISTRY}docker:19.03-git
script:
- # install trivy
+ - LOCAL_IMAGE="local/${IMAGE_NAME}"
+ ## build image
+ - docker build
+ --pull
+ --build-arg FROM_IMAGE=${FROM_IMAGE}
+ --build-arg GIT_BRANCH_NAME=${CI_COMMIT_REF_NAME}
+ --build-arg GIT_COMMIT_SHA=${CI_COMMIT_SHA}
+ --tag "${LOCAL_IMAGE}"
+ "."
+
+ ## trivy scan before push
- wget https://github.com/aquasecurity/trivy/releases/download/v${TRIVY_VERSION}/trivy_${TRIVY_VERSION}_Linux-64bit.tar.gz
- tar zxvf trivy_${TRIVY_VERSION}_Linux-64bit.tar.gz
- # run trivy
- - ./trivy image --no-progress --exit-code 1 --severity HIGH,CRITICAL ${INTERNAL_IMAGE_NAME}
+ # fail LOW,MEDIUM vulnerabilities that have a fix available
+ - ./trivy image --exit-code 1 --ignore-unfixed --severity LOW,MEDIUM "${LOCAL_IMAGE}";
+ # fail HIGH,CRITICAL vulnerabilities
+ - ./trivy image --exit-code 1 --severity HIGH,CRITICAL "${LOCAL_IMAGE}";
+
+ ## push image
+ - if [ "${CI_PROJECT_PATH}" != "${UPSTREAM_PATH}" ]; then
+ echo "Skipping push on non-upstream (${CI_PROJECT_PATH})";
+ exit 0;
+ fi
+ - |
+ for IMAGE in "${IMAGE_NAME}" "${INTERNAL_IMAGE_NAME}"; do
+ docker tag "${LOCAL_IMAGE}" "${IMAGE}";
+ docker push "${IMAGE}";
+ done
services:
- - docker:19.03-dind
- stage: scan
+ - alias: docker
+ name: ${DEVOPS_REGISTRY}docker:19.03-dind
+ stage: integration
tags:
- build
+ variables:
+ APP_NAME: geomag-algorithms
+ DOCKER_DRIVER: overlay2
+ FROM_IMAGE: ${DEVOPS_REGISTRY}usgs/python:3.9-obspy
+ TRIVY_VERSION: "0.27.1"
## --------------------------------------------------
# Deploy Stage
## --------------------------------------------------
-Mage01 Library:
+Staging Library:
extends:
- .deploy-library
- - .staging
+ rules:
+ - <<: *staging-env
+ when: on_success
+ - <<: *production-env
+ when: manual
tags:
- deploy
- swarm
- - mage01
- variables:
- APP_NAME: geomag-algorithms
-
-Mage01 Web Service:
- extends:
- - .deploy
- - .staging
- tags:
- - deploy
- - swarm
- - mage01
- variables:
- APP_NAME: geomag-algorithms
+ - mage02
-Mage02 Library:
+Production Library:
extends:
- .deploy-library
- - .production
+ rules:
+ - <<: *production-env
+ when: manual
tags:
- deploy
- swarm
- mage02
- variables:
- APP_NAME: geomag-algorithms
-Mage02 Web Service:
+Web Service Staging:
extends:
- .deploy
- - .production
+ parallel:
+ matrix:
+ - RUNNER:
+ - mage01
+ - staging01
+ rules:
+ - <<: *staging-env
+ when: on_success
+ - <<: *production-env
+ when: manual
tags:
- deploy
- swarm
- - mage02
- variables:
- APP_NAME: geomag-algorithms
+ - "${RUNNER}"
-Production01 Web Service:
+Web Service Production:
extends:
- .deploy
- - .production
+ parallel:
+ matrix:
+ - RUNNER:
+ - mage02
+ - production01
+ - production02
+ rules:
+ - <<: *production-env
+ when: manual
tags:
- deploy
- swarm
- - production01
- variables:
- APP_NAME: geomag-algorithms
-
-Production02 Web Service:
- extends:
- - .deploy
- - .production
- tags:
- - deploy
- - swarm
- - production02
- variables:
- APP_NAME: geomag-algorithms
-
-Staging01 Web Service:
- extends:
- - .deploy
- - .staging
- tags:
- - deploy
- - swarm
- - staging01
- variables:
- APP_NAME: geomag-algorithms
+ - "${RUNNER}"
diff --git a/Dockerfile b/Dockerfile
index 9730def5..a87708c7 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-ARG FROM_IMAGE=usgs/python:3.8-obspy
+ARG FROM_IMAGE=usgs/python:3.9-obspy
FROM ${FROM_IMAGE}
ARG GIT_BRANCH_NAME=none
--
GitLab
From 28868e1f56075895fa22823533ad2814ee62dff7 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Wed, 27 Apr 2022 17:40:40 -0600
Subject: [PATCH 039/142] Update deploy-library template
---
.gitlab-ci.yml | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b407d42b..560f0444 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -76,9 +76,15 @@ workflow:
git clone "${CI_REPOSITORY_URL}" "$(basename "${APP_DEPLOY_DIR}")";
fi
- cd "${APP_DEPLOY_DIR}";
+ # fetch tags so checkout doesn't create a branch
- git fetch --tags;
+ # switch to requested tag/branch
- git checkout "${CI_COMMIT_REF_NAME}" || git checkout -b "${CI_COMMIT_REF_NAME}";
- - git pull --ff-only "${CI_REPOSITORY_URL}" "${CI_COMMIT_REF_NAME}";
+ # pull updates if on a branch
+ - |
+ if ! git status | grep -q detached ; then
+ git pull --ff-only "${CI_REPOSITORY_URL}" "${CI_COMMIT_REF_NAME}";
+ fi
stage: deploy
tags:
- deploy
--
GitLab
From 425e3ea6f2b9d749ac9a65ce4de5de9b287a5008 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Wed, 27 Apr 2022 17:43:02 -0600
Subject: [PATCH 040/142] Remove default section from pipeline
---
.gitlab-ci.yml | 22 +++++++++++-----------
1 file changed, 11 insertions(+), 11 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 560f0444..e98375ba 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,14 +1,4 @@
-default:
- image: ${DEVOPS_REGISTRY}usgs/python:3.9-obspy
- variables:
- CI_REGISTRY: ${CODE_REGISTRY}
- CI_REGISTRY_IMAGE: ${CODE_REGISTRY_IMAGE}
- # environment variables
- APP_NAME: geomag-algorithms
- DATA_HOST: "edgecwb.usgs.gov"
- DATA_PORT: "2060"
- DATA_TYPE: "edge"
- UPSTREAM_PATH: ghsc/geomag/geomag-algorithms
+image: ${DEVOPS_REGISTRY}usgs/python:3.9-obspy
stages:
- init
@@ -16,6 +6,16 @@ stages:
- integration
- deploy
+variables:
+ CI_REGISTRY: ${CODE_REGISTRY}
+ CI_REGISTRY_IMAGE: ${CODE_REGISTRY_IMAGE}
+ # container environment variables
+ APP_NAME: geomag-algorithms
+ DATA_HOST: "edgecwb.usgs.gov"
+ DATA_PORT: "2060"
+ DATA_TYPE: "edge"
+ UPSTREAM_PATH: ghsc/geomag/geomag-algorithms
+
# Do not run in upstream for merge requests
workflow:
rules:
--
GitLab
From a877096dbb6b94fa6acbc15731bfea3eff167ce0 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Wed, 27 Apr 2022 17:44:23 -0600
Subject: [PATCH 041/142] Switch build to test stage
---
.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index e98375ba..cdd20f24 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -142,7 +142,7 @@ Poetry:
Python Build:
script:
- poetry build
- stage: build
+ stage: test
Python Lint:
script:
--
GitLab
From 6ea999b7a1135731605a35eb4b49ff5f241bf9f9 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Thu, 28 Apr 2022 09:28:15 -0600
Subject: [PATCH 042/142] Optimize docker build, use python 3.10 base image
---
.gitlab-ci.yml | 19 ++++++++++++-------
Dockerfile | 49 +++++++++++++++++++++++++------------------------
2 files changed, 37 insertions(+), 31 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index cdd20f24..7d570c18 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -7,9 +7,6 @@ stages:
- deploy
variables:
- CI_REGISTRY: ${CODE_REGISTRY}
- CI_REGISTRY_IMAGE: ${CODE_REGISTRY_IMAGE}
- # container environment variables
APP_NAME: geomag-algorithms
DATA_HOST: "edgecwb.usgs.gov"
DATA_PORT: "2060"
@@ -30,13 +27,13 @@ workflow:
before_script:
- IMAGE_NAME=usgs/${APP_NAME}:${CI_COMMIT_REF_SLUG}
- IMAGE_NAME=${IMAGE_NAME/:master/:latest}
- - INTERNAL_IMAGE_NAME=${CI_REGISTRY_IMAGE}/${IMAGE_NAME}
+ - INTERNAL_IMAGE_NAME=${CODE_REGISTRY_IMAGE}/${IMAGE_NAME}
- STACK_NAME=${APP_NAME}
.deploy:
extends:
- .adjust_image_names
- image: "${CI_REGISTRY}/ghsc/hazdev/container-deploy:latest"
+ image: "${CODE_REGISTRY}/ghsc/hazdev/container-deploy:latest"
script:
- cp -v
/container-deploy/default.config.sh
@@ -45,7 +42,7 @@ workflow:
scripts/.
- export APP_NAME=${APP_NAME}
- export IMAGE_NAME=${IMAGE_NAME}
- - export REGISTRY=${CI_REGISTRY_IMAGE}
+ - export REGISTRY=${CODE_REGISTRY_IMAGE}
- export STACK_NAME=${APP_NAME}
- ./scripts/deploy.sh
stage: deploy
@@ -140,11 +137,15 @@ Poetry:
## --------------------------------------------------
Python Build:
+ needs:
+ - Poetry
script:
- poetry build
stage: test
Python Lint:
+ needs:
+ - Poetry
script:
- poetry run black --check .
stage: test
@@ -154,6 +155,8 @@ Python Test:
reports:
cobertura: coverage.xml
junit: junit.xml
+ needs:
+ - Poetry
script:
- poetry run pytest --cov=geomagio --junitxml junit.xml
- poetry run coverage xml
@@ -167,6 +170,8 @@ Build Docker Image:
extends:
- .adjust_image_names
image: ${DEVOPS_REGISTRY}docker:19.03-git
+ needs:
+ - Python Build
script:
- LOCAL_IMAGE="local/${IMAGE_NAME}"
## build image
@@ -205,7 +210,7 @@ Build Docker Image:
variables:
APP_NAME: geomag-algorithms
DOCKER_DRIVER: overlay2
- FROM_IMAGE: ${DEVOPS_REGISTRY}usgs/python:3.9-obspy
+ FROM_IMAGE: ${CI_REGISTRY}/devops/images/usgs/python:3.10-obspy
TRIVY_VERSION: "0.27.1"
## --------------------------------------------------
diff --git a/Dockerfile b/Dockerfile
index a87708c7..6dece3a7 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,21 @@
ARG FROM_IMAGE=usgs/python:3.9-obspy
+
+# build wheel
+FROM ${FROM_IMAGE} as build
+
+USER root
+WORKDIR /app
+
+# install dependencies in separate layer
+# this is a temporary container and they change less often than other files
+COPY poetry.lock pyproject.toml /app/
+RUN poetry install --no-root
+
+COPY . /app/
+RUN poetry build
+
+
+# install and configure entrypoint
FROM ${FROM_IMAGE}
ARG GIT_BRANCH_NAME=none
@@ -10,32 +27,16 @@ ENV GIT_BRANCH_NAME=${GIT_BRANCH_NAME} \
GIT_COMMIT_SHA=${GIT_COMMIT_SHA} \
WEBSERVICE=${WEBSERVICE}
-# install to system python
-USER root
+COPY --from=build /app/dist/*.whl /app/docker-entrypoint.sh /app/
-# install packages when dependencies change
-COPY pyproject.toml poetry.lock /geomag-algorithms/
-RUN cd /geomag-algorithms \
- # install into system python
- && poetry export -o requirements.txt --dev --without-hashes \
- # only install dependencies, not project
- && pip install -r requirements.txt \
+# install as root
+USER root
+RUN apt update \
+ && apt upgrade -y \
+ && pip install /app/*.whl \
&& pip cache purge
-
-# install rest of library separate from dependencies
-COPY . /geomag-algorithms
-RUN cd /geomag-algorithms \
- && pip install . \
- && pip cache purge \
- # add data directory owned by usgs-user
- && mkdir -p /data \
- && chown -R usgs-user:usgs-user /data
-# configure python path, so project can be volume mounted
-ENV PYTHONPATH="/geomag-algorithms"
-
-# run as usgs-user
USER usgs-user
-WORKDIR /data
+
# entrypoint needs double quotes
-ENTRYPOINT [ "/geomag-algorithms/docker-entrypoint.sh" ]
+ENTRYPOINT [ "/app/docker-entrypoint.sh" ]
EXPOSE 8000
--
GitLab
From b7c597df9f71b14a2607ec667836cee337120c44 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Thu, 28 Apr 2022 10:41:08 -0600
Subject: [PATCH 043/142] Add login for CI_REGISTRY before build
---
.gitlab-ci.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7d570c18..1c7e2b0b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -174,6 +174,7 @@ Build Docker Image:
- Python Build
script:
- LOCAL_IMAGE="local/${IMAGE_NAME}"
+ - docker login -u gitlab-ci-token -p $CI_JOB_TOKEN $CI_REGISTRY
## build image
- docker build
--pull
--
GitLab
From 125cb62b3a4e626290a3a71fca0d95cbb54b76d3 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Thu, 28 Apr 2022 18:09:50 -0600
Subject: [PATCH 044/142] Include python:3.10-obspy steps in dockerfile until
image is public
---
DOIRootCA2.crt | 56 +++++++++++++++++++++
Dockerfile | 132 +++++++++++++++++++++++++++++++++++++++++++++++--
2 files changed, 185 insertions(+), 3 deletions(-)
create mode 100644 DOIRootCA2.crt
diff --git a/DOIRootCA2.crt b/DOIRootCA2.crt
new file mode 100644
index 00000000..3a49f729
--- /dev/null
+++ b/DOIRootCA2.crt
@@ -0,0 +1,56 @@
+-----BEGIN CERTIFICATE-----
+MIIJ+jCCB+KgAwIBAgIQSeV7u0WVHrFBqkjcKiEnEzANBgkqhkiG9w0BAQsFADAV
+MRMwEQYDVQQDEwpET0lSb290Q0EyMB4XDTE2MDQyNjE4MjE1MFoXDTM2MDQyNjE4
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+GHVtIa/kVEl2DE0WcUw=
+-----END CERTIFICATE-----
diff --git a/Dockerfile b/Dockerfile
index 6dece3a7..bbf911fa 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,7 +1,132 @@
-ARG FROM_IMAGE=usgs/python:3.9-obspy
+# these base images are not available in public usgs registry yet
+# inline for now
+
+ARG FROM_IMAGE=public.ecr.aws/lts/ubuntu:22.04
+
+FROM $FROM_IMAGE as ubuntu-22
+
+# Allow builds within DOI network
+COPY DOIRootCA2.crt /usr/share/ca-certificates/extra/DOIRootCA2.crt
+
+# Update current system packages and certificates
+RUN export DEBIAN_FRONTEND=noninteractive \
+ && apt update \
+ && apt upgrade -y \
+ && apt install -y \
+ ca-certificates \
+ language-pack-en \
+ && apt clean \
+ && update-ca-certificates
+
+# this is redundant with above, but avoids additional layer
+ENV DEBIAN_FRONTEND=noninteractive \
+ LANG='en_US.UTF-8' \
+ LC_ALL='en_US.UTF-8' \
+ LC_CTYPE=en_US.UTF-8 \
+ SSL_CERT_FILE=/etc/ssl/certs/ca-certificates.crt \
+ TZ=Etc/UTC
+
+# Create a USGS user to run application inside container
+RUN useradd \
+ -c 'Docker image user' \
+ -m \
+ -r \
+ -s /sbin/nologin \
+ -U \
+ usgs-user \
+ && mkdir /app
+
+USER usgs-user
+WORKDIR /app
+
+################################################################################
+
+# base python image
+FROM ubuntu-22 as python
+ARG PYTHON_VERSION=3.10
+
+LABEL maintainer='HazDev <gs-haz_dev_team_group@usgs.gov>' \
+ version='1.0.0'
+
+# configure python ssl intercept variables
+ENV PIP_CERT="${SSL_CERT_FILE}" \
+ REQUESTS_CA_BUNDLE="${SSL_CERT_FILE}"
+
+USER root
+
+RUN apt update \
+ && apt upgrade -y \
+ && apt install -y \
+ curl \
+ python${PYTHON_VERSION} \
+ python${PYTHON_VERSION}-distutils \
+ && apt clean \
+ # make this version the default "python" command
+ && update-alternatives \
+ --install /usr/bin/python python /usr/bin/python${PYTHON_VERSION} 1 \
+ # get-pip reduces resulting image size to ~250MB (100MB compressed).
+ && curl -LO https://github.com/pypa/get-pip/raw/22.0.3/public/get-pip.py \
+ && python get-pip.py \
+ && rm get-pip.py \
+ && pip install -U \
+ pip \
+ poetry \
+ && pip cache purge
+
+RUN echo "$PYTHON_VERSION"
+
+USER usgs-user
+
+
+# python build image
+FROM python as python-build
+ARG PYTHON_VERSION=3.10
+
+USER root
+
+RUN apt update \
+ && apt upgrade -y \
+ && apt install -y \
+ build-essential \
+ git \
+ libcurl4-openssl-dev \
+ libssl-dev \
+ python${PYTHON_VERSION}-dev \
+ && apt clean
+
+
+# build obspy
+FROM python-build as obspy-build
+
+# obspy
+RUN pip wheel obspy --wheel-dir /wheels
+# pycurl (not required for obspy, but the main other hard-to-install package)
+RUN export PYCURL_SSL_LIBRARY=openssl \
+ && pip wheel pycurl --wheel-dir /wheels
+
+
+# install wheels from obspy-build
+FROM python as obspy
+
+# install to system python
+USER root
+
+COPY --from=obspy-build /wheels/obspy* /wheels/pycurl* /wheels/
+
+RUN pip install --find-links file:///wheels obspy pycurl \
+ && python -c "import obspy" \
+ && pip cache purge
+
+USER usgs-user
+
+
+################################################################################
+FROM obspy as build
+# start actual geomag_algorithms image
+# ARG FROM_IMAGE=usgs/python:3.10-obspy
# build wheel
-FROM ${FROM_IMAGE} as build
+# FROM ${FROM_IMAGE} as build
USER root
WORKDIR /app
@@ -16,7 +141,8 @@ RUN poetry build
# install and configure entrypoint
-FROM ${FROM_IMAGE}
+FROM python
+# FROM ${FROM_IMAGE}
ARG GIT_BRANCH_NAME=none
ARG GIT_COMMIT_SHA=none
--
GitLab
From 40bd88307981053edf298ae9302418e80b97dd9b Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Fri, 29 Apr 2022 09:10:14 -0600
Subject: [PATCH 045/142] Update from image to match dockerfile
---
.gitlab-ci.yml | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1c7e2b0b..734abf16 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -211,7 +211,8 @@ Build Docker Image:
variables:
APP_NAME: geomag-algorithms
DOCKER_DRIVER: overlay2
- FROM_IMAGE: ${CI_REGISTRY}/devops/images/usgs/python:3.10-obspy
+ # FROM_IMAGE: ${CI_REGISTRY}/devops/images/usgs/python:3.10-obspy
+ FROM_IMAGE: public.ecr.aws/lts/ubuntu:22.04
TRIVY_VERSION: "0.27.1"
## --------------------------------------------------
--
GitLab
From 4471c154de239418a4ee8e7619dbe64ec8b39c02 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Fri, 29 Apr 2022 09:34:01 -0600
Subject: [PATCH 046/142] Remove docker login step
---
.gitlab-ci.yml | 1 -
1 file changed, 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 734abf16..7c71410e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -174,7 +174,6 @@ Build Docker Image:
- Python Build
script:
- LOCAL_IMAGE="local/${IMAGE_NAME}"
- - docker login -u gitlab-ci-token -p $CI_JOB_TOKEN $CI_REGISTRY
## build image
- docker build
--pull
--
GitLab
From 2a39eccb481419f86798c89c9b8cb81b00bdc9a8 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Fri, 29 Apr 2022 10:07:09 -0600
Subject: [PATCH 047/142] Move docker build to chs runner
---
.gitlab-ci.yml | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7c71410e..86fb56da 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -206,7 +206,8 @@ Build Docker Image:
name: ${DEVOPS_REGISTRY}docker:19.03-dind
stage: integration
tags:
- - build
+ - chs-shared
+ - dind
variables:
APP_NAME: geomag-algorithms
DOCKER_DRIVER: overlay2
--
GitLab
From e6aa9617a903bf16293f2658701c5d21c2b2556b Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Fri, 29 Apr 2022 12:25:45 -0600
Subject: [PATCH 048/142] Stick with python 3.9 for now, can save 100+mb later
---
Dockerfile | 132 +------------------------------------------
geomagio/__init__.py | 1 -
2 files changed, 3 insertions(+), 130 deletions(-)
diff --git a/Dockerfile b/Dockerfile
index bbf911fa..6dece3a7 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,132 +1,7 @@
-# these base images are not available in public usgs registry yet
-# inline for now
-
-ARG FROM_IMAGE=public.ecr.aws/lts/ubuntu:22.04
-
-FROM $FROM_IMAGE as ubuntu-22
-
-# Allow builds within DOI network
-COPY DOIRootCA2.crt /usr/share/ca-certificates/extra/DOIRootCA2.crt
-
-# Update current system packages and certificates
-RUN export DEBIAN_FRONTEND=noninteractive \
- && apt update \
- && apt upgrade -y \
- && apt install -y \
- ca-certificates \
- language-pack-en \
- && apt clean \
- && update-ca-certificates
-
-# this is redundant with above, but avoids additional layer
-ENV DEBIAN_FRONTEND=noninteractive \
- LANG='en_US.UTF-8' \
- LC_ALL='en_US.UTF-8' \
- LC_CTYPE=en_US.UTF-8 \
- SSL_CERT_FILE=/etc/ssl/certs/ca-certificates.crt \
- TZ=Etc/UTC
-
-# Create a USGS user to run application inside container
-RUN useradd \
- -c 'Docker image user' \
- -m \
- -r \
- -s /sbin/nologin \
- -U \
- usgs-user \
- && mkdir /app
-
-USER usgs-user
-WORKDIR /app
-
-################################################################################
-
-# base python image
-FROM ubuntu-22 as python
-ARG PYTHON_VERSION=3.10
-
-LABEL maintainer='HazDev <gs-haz_dev_team_group@usgs.gov>' \
- version='1.0.0'
-
-# configure python ssl intercept variables
-ENV PIP_CERT="${SSL_CERT_FILE}" \
- REQUESTS_CA_BUNDLE="${SSL_CERT_FILE}"
-
-USER root
-
-RUN apt update \
- && apt upgrade -y \
- && apt install -y \
- curl \
- python${PYTHON_VERSION} \
- python${PYTHON_VERSION}-distutils \
- && apt clean \
- # make this version the default "python" command
- && update-alternatives \
- --install /usr/bin/python python /usr/bin/python${PYTHON_VERSION} 1 \
- # get-pip reduces resulting image size to ~250MB (100MB compressed).
- && curl -LO https://github.com/pypa/get-pip/raw/22.0.3/public/get-pip.py \
- && python get-pip.py \
- && rm get-pip.py \
- && pip install -U \
- pip \
- poetry \
- && pip cache purge
-
-RUN echo "$PYTHON_VERSION"
-
-USER usgs-user
-
-
-# python build image
-FROM python as python-build
-ARG PYTHON_VERSION=3.10
-
-USER root
-
-RUN apt update \
- && apt upgrade -y \
- && apt install -y \
- build-essential \
- git \
- libcurl4-openssl-dev \
- libssl-dev \
- python${PYTHON_VERSION}-dev \
- && apt clean
-
-
-# build obspy
-FROM python-build as obspy-build
-
-# obspy
-RUN pip wheel obspy --wheel-dir /wheels
-# pycurl (not required for obspy, but the main other hard-to-install package)
-RUN export PYCURL_SSL_LIBRARY=openssl \
- && pip wheel pycurl --wheel-dir /wheels
-
-
-# install wheels from obspy-build
-FROM python as obspy
-
-# install to system python
-USER root
-
-COPY --from=obspy-build /wheels/obspy* /wheels/pycurl* /wheels/
-
-RUN pip install --find-links file:///wheels obspy pycurl \
- && python -c "import obspy" \
- && pip cache purge
-
-USER usgs-user
-
-
-################################################################################
-FROM obspy as build
-# start actual geomag_algorithms image
-# ARG FROM_IMAGE=usgs/python:3.10-obspy
+ARG FROM_IMAGE=usgs/python:3.9-obspy
# build wheel
-# FROM ${FROM_IMAGE} as build
+FROM ${FROM_IMAGE} as build
USER root
WORKDIR /app
@@ -141,8 +16,7 @@ RUN poetry build
# install and configure entrypoint
-FROM python
-# FROM ${FROM_IMAGE}
+FROM ${FROM_IMAGE}
ARG GIT_BRANCH_NAME=none
ARG GIT_COMMIT_SHA=none
diff --git a/geomagio/__init__.py b/geomagio/__init__.py
index c9698e9e..d51ffc9e 100644
--- a/geomagio/__init__.py
+++ b/geomagio/__init__.py
@@ -1,7 +1,6 @@
"""
Geomag Algorithm Module
"""
-from __future__ import absolute_import
from . import ChannelConverter
from . import StreamConverter
--
GitLab
From 4f5618bfc727354c5d43197648e2706a1c542b8d Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Fri, 29 Apr 2022 12:26:49 -0600
Subject: [PATCH 049/142] Switch pipeline docker build FROM_IMAGE
---
.gitlab-ci.yml | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 86fb56da..853a0f04 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -211,8 +211,7 @@ Build Docker Image:
variables:
APP_NAME: geomag-algorithms
DOCKER_DRIVER: overlay2
- # FROM_IMAGE: ${CI_REGISTRY}/devops/images/usgs/python:3.10-obspy
- FROM_IMAGE: public.ecr.aws/lts/ubuntu:22.04
+ FROM_IMAGE: ${DEVOPS_REGISTRY}usgs/python:3.9-obspy
TRIVY_VERSION: "0.27.1"
## --------------------------------------------------
--
GitLab
From 4e909d3d0a1dd12e9662d488041be4f8137fd1e3 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Tue, 3 May 2022 12:13:15 -0600
Subject: [PATCH 050/142] Fix staging library job tag to mage01
---
.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 853a0f04..ee873777 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -229,7 +229,7 @@ Staging Library:
tags:
- deploy
- swarm
- - mage02
+ - mage01
Production Library:
extends:
--
GitLab
From cf5e6dba1e5050738bf884c7f1fb229e69711cae Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Tue, 3 May 2022 12:22:51 -0600
Subject: [PATCH 051/142] Remove DOI SSL certificate, based image already
includes this
---
DOIRootCA2.crt | 56 --------------------------------------------------
1 file changed, 56 deletions(-)
delete mode 100644 DOIRootCA2.crt
diff --git a/DOIRootCA2.crt b/DOIRootCA2.crt
deleted file mode 100644
index 3a49f729..00000000
--- a/DOIRootCA2.crt
+++ /dev/null
@@ -1,56 +0,0 @@
------BEGIN CERTIFICATE-----
-MIIJ+jCCB+KgAwIBAgIQSeV7u0WVHrFBqkjcKiEnEzANBgkqhkiG9w0BAQsFADAV
-MRMwEQYDVQQDEwpET0lSb290Q0EyMB4XDTE2MDQyNjE4MjE1MFoXDTM2MDQyNjE4
-MjE1MFowFTETMBEGA1UEAxMKRE9JUm9vdENBMjCCAiIwDQYJKoZIhvcNAQEBBQAD
-ggIPADCCAgoCggIBANTHy0AvCFT0CZOsktj3kpFfFJgrhiS5haBK7DvYYpbZoaWa
-jOpldnvoqnd1bOJUJ9jUwxZERo27FJHZ8HSdU8ac63hdK1N6t1OrlQOjgs/Kn0LY
-b7xOf6iDBfhdhXcjpq2KZBzVi0tWuyBPhDmZyTLqZ5UREy1mV3/p1pJ3Hx5lPziH
-Fid+wILxe2fk+N1ExY/GA+cgdsSCP4kp4aBxXLNTq+oMu/NahyF+NmcbqUk3xh+v
-U1UA7h35b8kjd/3Kx2Bv1EDveWbzaS7sn8T3OVnU6n9UObUcqaoJOXF3PDdQqPIh
-YVLT8/s15YaUznTe7jc46YjnqZPaJJGbDir/m03QR8qWi0qMhLjTTfPYe4DFYa27
-4e8sTeK0DTSpUMBhQqagRQEFcYRd6QaZ4wfj+8zwX7EUha9jOKrMALvxRurkEqsa
-m9NZntaHlSkRjQAZ562TUYowBpb841O0v0c9+i8SM6D9kRVV+NIj3StPNkQG7qlc
-+PhF5YA4jYAifZ7AtWraLeopTPonfX0avWbIt5ryy4Y+sISwsg4HZ+rdNrJq9MUu
-YWDbdO/lRclnFJ64VmD0rH7Fuef7CDiQvwn0NPJHQoU6h/zHnfOEIlh44h+0uy+R
-lEp41vrb9mA/a7ZZEohcJroQ6JL1Z8b+KLY47ryuqneLklCVTGbMNGZxusOtAgMB
-AAGjggVEMIIFQDALBgNVHQ8EBAMCAYYwDwYDVR0TAQH/BAUwAwEB/zAdBgNVHQ4E
-FgQUv4YryvNsbT5fHDtOTtiN52rHak8wEAYJKwYBBAGCNxUBBAMCAQAwggTtBgNV
-HSAEggTkMIIE4DCCAg8GCWCGSAFlAwIBEzCCAgAwMAYIKwYBBQUHAgEWJGh0dHA6
-Ly9wa2kyLmRvaS5uZXQvbGVnYWxwb2xpY3kuYXNwADCCAcoGCCsGAQUFBwICMIIB
-vB6CAbgAQwBlAHIAdABpAGYAaQBjAGEAdABlACAAaQBzAHMAdQBlAGQAIABiAHkA
-IAB0AGgAZQAgAEQAZQBwAGEAcgB0AG0AZQBuAHQAIABvAGYAIAB0AGgAZQAgAEkA
-bgB0AGUAcgBpAG8AcgAgAGEAcgBlACAAbwBuAGwAeQAgAGYAbwByACAAaQBuAHQA
-ZQByAG4AYQBsACAAdQBuAGMAbABhAHMAcwBpAGYAaQBlAGQAIABVAFMAIABHAG8A
-dgBlAHIAbgBtAGUAbgB0ACAAdQBzAGUAIABhAGwAbAAgAG8AdABoAGUAcgAgAHUA
-cwBlACAAaQBzACAAcAByAG8AaABpAGIAaQB0AGUAZAAuACAAVQBuAGEAdQB0AGgA
-bwByAGkAegBlAGQAIAB1AHMAZQAgAG0AYQB5ACAAcwB1AGIAagBlAGMAdAAgAHYA
-aQBvAGwAYQB0AG8AcgBzACAAdABvACAAYwByAGkAbQBpAG4AYQBsACwAIABjAGkA
-dgBpAGwAIABhAG4AZAAvAG8AcgAgAGQAaQBzAGMAaQBwAGwAaQBuAGEAcgB5ACAA
-YQBjAHQAaQBvAG4ALjCCAskGCmCGSAFlAwIBEwEwggK5MDUGCCsGAQUFBwIBFilo
-dHRwOi8vcGtpMi5kb2kubmV0L2xpbWl0ZWR1c2Vwb2xpY3kuYXNwADCCAn4GCCsG
-AQUFBwICMIICcB6CAmwAVQBzAGUAIABvAGYAIAB0AGgAaQBzACAAQwBlAHIAdABp
-AGYAaQBjAGEAdABlACAAaQBzACAAbABpAG0AaQB0AGUAZAAgAHQAbwAgAEkAbgB0
-AGUAcgBuAGEAbAAgAEcAbwB2AGUAcgBuAG0AZQBuAHQAIAB1AHMAZQAgAGIAeQAg
-AC8AIABmAG8AcgAgAHQAaABlACAARABlAHAAYQByAHQAbQBlAG4AdAAgAG8AZgAg
-AHQAaABlACAASQBuAHQAZQByAGkAbwByACAAbwBuAGwAeQAuACAARQB4AHQAZQBy
-AG4AYQBsACAAdQBzAGUAIABvAHIAIAByAGUAYwBlAGkAcAB0ACAAbwBmACAAdABo
-AGkAcwAgAEMAZQByAHQAaQBmAGkAYwBhAHQAZQAgAHMAaABvAHUAbABkACAAbgBv
-AHQAIABiAGUAIAB0AHIAdQBzAHQAZQBkAC4AIABBAGwAbAAgAHMAdQBzAHAAZQBj
-AHQAZQBkACAAbQBpAHMAdQBzAGUAIABvAHIAIABjAG8AbQBwAHIAbwBtAGkAcwBl
-ACAAbwBmACAAdABoAGkAcwAgAGMAZQByAHQAaQBmAGkAYwBhAHQAZQAgAHMAaABv
-AHUAbABkACAAYgBlACAAcgBlAHAAbwByAHQAZQBkACAAaQBtAG0AZQBkAGkAYQB0
-AGUAbAB5ACAAdABvACAAYQAgAEQAZQBwAGEAcgB0AG0AZQBuAHQAIABvAGYAIAB0
-AGgAZQAgAEkAbgB0AGUAcgBpAG8AcgAgAFMAZQBjAHUAcgBpAHQAeQAgAE8AZgBm
-AGkAYwBlAHIALjANBgkqhkiG9w0BAQsFAAOCAgEAF/q4Z2mRTIYJMu5mzlWsbV4o
-gGQJ9YcSdUZRq2vzINJCpGDXstAIE81Pfz/Fna98KOkjEB8XGXVUGQf07c9ylGJS
-XFoBwcN8GgOuys5iiP9/yd2yLHB8rBb8pu9RForl9RoTsYY8nFuOOtl9o2EfB/1O
-PbRYkfHhhqrfvvHdvDKWPmT+ZhaliWJrg2my432yqBqPePjqMZSl4sxiPYi9WicU
-UWYdJpxQlys3igICD4GXOcSh316jfaqfN8+9jps+lgO7rqOA41B8fU9Gwi4B8jjx
-Tw0pgvbuebwwL5IQwrsGcA8rFfRPR6CaSY5v3XXqTMbCXyYjNK1/44I9MoFFaFPc
-e3cqZ5cQ+lCoW3UE0SLNZb3YKh28ES/Gi5CO0Bq5P8QVLRJQL5xOaSzV9blszHv5
-okR+lkSsVo2QzR/mzFD7lXtwznkd/uak0hripTB7MtZenBzoQ8zAgjgw5TXjRSAZ
-goWiJTAg+YTKclhJ7Cfg/m4XeCxzNgz/pU1XEdBF2Ngvp3C9M5CSBcqzb234uiFF
-SyvJl/6erDTkQ5dLrnSnsJIw1ZS/XG/Fi41u8il0piLc5depTLn9qiWf29BRBEtG
-xwFKSmqlRWsClj/zADirBTjcctw7ajPMkRpebgn+Bzv1eWDx4+OolQuR/a45644Q
-GHVtIa/kVEl2DE0WcUw=
------END CERTIFICATE-----
--
GitLab
From 1165baa9034fac0604294f710c605f4f1b896fb8 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Tue, 3 May 2022 12:31:48 -0600
Subject: [PATCH 052/142] Update version to 1.5.0
---
code.json | 4 ++--
pyproject.toml | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/code.json b/code.json
index 540e31d8..2be13980 100644
--- a/code.json
+++ b/code.json
@@ -3,7 +3,7 @@
"name": "geomag-algorithms",
"organization": "U.S. Geological Survey",
"description": "Library for processing Geomagnetic timeseries data.",
- "version": "1.4.6",
+ "version": "1.5.0",
"status": "Development",
"permissions": {
@@ -34,7 +34,7 @@
},
"date": {
- "metadataLastUpdated": "2021-10-12"
+ "metadataLastUpdated": "2022-05-03"
}
}
]
diff --git a/pyproject.toml b/pyproject.toml
index fc9aae75..574d07f2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ packages = [
{include = "geomagio" }
]
repository="https://code.usgs.gov/ghsc/geomag/geomag-algorithms"
-version = "1.4.6"
+version = "1.5.0"
[tool.poetry.dependencies]
--
GitLab
From 495fbd730d5276c650c3b593f0250a2e605ea64d Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Tue, 3 May 2022 12:28:11 -0600
Subject: [PATCH 053/142] Update to v1.5.0
---
poetry.lock | 615 ++++++++++++++++++++++++++--------------------------
1 file changed, 313 insertions(+), 302 deletions(-)
diff --git a/poetry.lock b/poetry.lock
index ac656849..73a268b7 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,16 +1,17 @@
[[package]]
name = "aiomysql"
-version = "0.0.22"
+version = "0.1.0"
description = "MySQL driver for asyncio."
category = "main"
optional = false
-python-versions = "*"
+python-versions = ">=3.7"
[package.dependencies]
-PyMySQL = ">=0.9,<=0.9.3"
+PyMySQL = ">=1.0"
[package.extras]
-sa = ["sqlalchemy (>=1.0)"]
+rsa = ["PyMySQL[rsa] (>=1.0)"]
+sa = ["sqlalchemy (>=1.0,<1.4)"]
[[package]]
name = "aiosqlite"
@@ -59,7 +60,7 @@ trio = ["trio (>=0.16)"]
[[package]]
name = "asgiref"
-version = "3.5.0"
+version = "3.5.1"
description = "ASGI specs, helper code, and adapters"
category = "main"
optional = false
@@ -92,7 +93,7 @@ tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>
[[package]]
name = "authlib"
-version = "1.0.0"
+version = "1.0.1"
description = "The ultimate Python library in building OAuth and OpenID Connect servers and clients."
category = "main"
optional = false
@@ -103,7 +104,7 @@ cryptography = ">=3.2"
[[package]]
name = "black"
-version = "22.1.0"
+version = "22.3.0"
description = "The uncompromising code formatter."
category = "dev"
optional = false
@@ -114,7 +115,7 @@ click = ">=8.0.0"
mypy-extensions = ">=0.4.3"
pathspec = ">=0.9.0"
platformdirs = ">=2"
-tomli = ">=1.1.0"
+tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}
[package.extras]
@@ -155,11 +156,11 @@ unicode_backport = ["unicodedata2"]
[[package]]
name = "click"
-version = "8.0.4"
+version = "8.1.3"
description = "Composable command line interface toolkit"
category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
[package.dependencies]
colorama = {version = "*", markers = "platform_system == \"Windows\""}
@@ -275,7 +276,7 @@ python-versions = ">=3.6"
[[package]]
name = "fastapi"
-version = "0.75.0"
+version = "0.75.2"
description = "FastAPI framework, high performance, easy to learn, fast to code, ready for production"
category = "main"
optional = false
@@ -286,26 +287,27 @@ pydantic = ">=1.6.2,<1.7 || >1.7,<1.7.1 || >1.7.1,<1.7.2 || >1.7.2,<1.7.3 || >1.
starlette = "0.17.1"
[package.extras]
-all = ["requests (>=2.24.0,<3.0.0)", "jinja2 (>=2.11.2,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "itsdangerous (>=1.1.0,<3.0.0)", "pyyaml (>=5.3.1,<6.0.0)", "ujson (>=4.0.1,<5.0.0)", "orjson (>=3.2.1,<4.0.0)", "email_validator (>=1.1.1,<2.0.0)", "uvicorn[standard] (>=0.12.0,<0.16.0)"]
-dev = ["python-jose[cryptography] (>=3.3.0,<4.0.0)", "passlib[bcrypt] (>=1.7.2,<2.0.0)", "autoflake (>=1.4.0,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "uvicorn[standard] (>=0.12.0,<0.16.0)"]
-doc = ["mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "mdx-include (>=1.4.1,<2.0.0)", "mkdocs-markdownextradata-plugin (>=0.1.7,<0.3.0)", "typer-cli (>=0.0.12,<0.0.13)", "pyyaml (>=5.3.1,<6.0.0)"]
-test = ["pytest (>=6.2.4,<7.0.0)", "pytest-cov (>=2.12.0,<4.0.0)", "mypy (==0.910)", "flake8 (>=3.8.3,<4.0.0)", "black (==21.9b0)", "isort (>=5.0.6,<6.0.0)", "requests (>=2.24.0,<3.0.0)", "httpx (>=0.14.0,<0.19.0)", "email_validator (>=1.1.1,<2.0.0)", "sqlalchemy (>=1.3.18,<1.5.0)", "peewee (>=3.13.3,<4.0.0)", "databases[sqlite] (>=0.3.2,<0.6.0)", "orjson (>=3.2.1,<4.0.0)", "ujson (>=4.0.1,<5.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "flask (>=1.1.2,<3.0.0)", "anyio[trio] (>=3.2.1,<4.0.0)", "types-ujson (==0.1.1)", "types-orjson (==3.6.0)", "types-dataclasses (==0.1.7)"]
+all = ["requests (>=2.24.0,<3.0.0)", "jinja2 (>=2.11.2,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "itsdangerous (>=1.1.0,<3.0.0)", "pyyaml (>=5.3.1,<7.0.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)", "orjson (>=3.2.1,<4.0.0)", "email_validator (>=1.1.1,<2.0.0)", "uvicorn[standard] (>=0.12.0,<0.18.0)"]
+dev = ["python-jose[cryptography] (>=3.3.0,<4.0.0)", "passlib[bcrypt] (>=1.7.2,<2.0.0)", "autoflake (>=1.4.0,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "uvicorn[standard] (>=0.12.0,<0.18.0)"]
+doc = ["mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "mdx-include (>=1.4.1,<2.0.0)", "mkdocs-markdownextradata-plugin (>=0.1.7,<0.3.0)", "typer (>=0.4.1,<0.5.0)", "pyyaml (>=5.3.1,<7.0.0)"]
+test = ["pytest (>=6.2.4,<7.0.0)", "pytest-cov (>=2.12.0,<4.0.0)", "mypy (==0.910)", "flake8 (>=3.8.3,<4.0.0)", "black (==22.3.0)", "isort (>=5.0.6,<6.0.0)", "requests (>=2.24.0,<3.0.0)", "httpx (>=0.14.0,<0.19.0)", "email_validator (>=1.1.1,<2.0.0)", "sqlalchemy (>=1.3.18,<1.5.0)", "peewee (>=3.13.3,<4.0.0)", "databases[sqlite] (>=0.3.2,<0.6.0)", "orjson (>=3.2.1,<4.0.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "flask (>=1.1.2,<3.0.0)", "anyio[trio] (>=3.2.1,<4.0.0)", "types-ujson (==4.2.1)", "types-orjson (==3.6.2)", "types-dataclasses (==0.6.5)"]
[[package]]
name = "fonttools"
-version = "4.31.1"
+version = "4.33.3"
description = "Tools to manipulate font files"
category = "main"
optional = false
python-versions = ">=3.7"
[package.extras]
-all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=14.0.0)", "xattr"]
+all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "uharfbuzz (>=0.23.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=14.0.0)", "xattr"]
graphite = ["lz4 (>=1.7.4.2)"]
interpolatable = ["scipy", "munkres"]
lxml = ["lxml (>=4.0,<5)"]
pathops = ["skia-pathops (>=0.5.0)"]
plot = ["matplotlib"]
+repacker = ["uharfbuzz (>=0.23.0)"]
symfont = ["sympy"]
type1 = ["xattr"]
ufo = ["fs (>=2.2.0,<3)"]
@@ -421,18 +423,18 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-
[[package]]
name = "importlib-resources"
-version = "5.4.0"
+version = "5.7.1"
description = "Read resources from Python packages"
category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
[package.dependencies]
zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
[package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy"]
+docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
[[package]]
name = "iniconfig"
@@ -444,7 +446,7 @@ python-versions = "*"
[[package]]
name = "kiwisolver"
-version = "1.4.0"
+version = "1.4.2"
description = "A fast implementation of the Cassowary constraint solver"
category = "main"
optional = false
@@ -490,7 +492,7 @@ python-versions = ">=3.7"
[[package]]
name = "matplotlib"
-version = "3.5.1"
+version = "3.5.2"
description = "Python plotting package"
category = "main"
optional = false
@@ -610,23 +612,27 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
[[package]]
name = "pillow"
-version = "9.0.1"
+version = "9.1.0"
description = "Python Imaging Library (Fork)"
category = "main"
optional = false
python-versions = ">=3.7"
+[package.extras]
+docs = ["olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinx-rtd-theme (>=1.0)", "sphinxext-opengraph"]
+tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
+
[[package]]
name = "platformdirs"
-version = "2.5.1"
+version = "2.5.2"
description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
category = "dev"
optional = false
python-versions = ">=3.7"
[package.extras]
-docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"]
-test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"]
+docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)", "sphinx (>=4)"]
+test = ["appdirs (==1.4.4)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)", "pytest (>=6)"]
[[package]]
name = "pluggy"
@@ -681,25 +687,26 @@ email = ["email-validator (>=1.0.3)"]
[[package]]
name = "pymysql"
-version = "0.9.3"
+version = "1.0.2"
description = "Pure Python MySQL Driver"
category = "main"
optional = false
-python-versions = "*"
+python-versions = ">=3.6"
[package.extras]
+ed25519 = ["PyNaCl (>=1.4.0)"]
rsa = ["cryptography"]
[[package]]
name = "pyparsing"
-version = "3.0.7"
-description = "Python parsing module"
+version = "3.0.8"
+description = "pyparsing module - Classes and methods to define and execute parsing grammars"
category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.6.8"
[package.extras]
-diagrams = ["jinja2", "railroad-diagrams"]
+diagrams = ["railroad-diagrams", "jinja2"]
[[package]]
name = "pytest"
@@ -751,7 +758,7 @@ six = ">=1.5"
[[package]]
name = "python-dotenv"
-version = "0.19.2"
+version = "0.20.0"
description = "Read key-value pairs from a .env file and set them as environment variables"
category = "main"
optional = false
@@ -859,7 +866,7 @@ python-versions = ">=3.5"
[[package]]
name = "sqlalchemy"
-version = "1.4.32"
+version = "1.4.36"
description = "Database Abstraction Library"
category = "main"
optional = false
@@ -872,7 +879,7 @@ greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platfo
aiomysql = ["greenlet (!=0.4.17)", "aiomysql"]
aiosqlite = ["typing_extensions (!=3.10.0.1)", "greenlet (!=0.4.17)", "aiosqlite"]
asyncio = ["greenlet (!=0.4.17)"]
-asyncmy = ["greenlet (!=0.4.17)", "asyncmy (>=0.2.3)"]
+asyncmy = ["greenlet (!=0.4.17)", "asyncmy (>=0.2.3,!=0.2.4)"]
mariadb_connector = ["mariadb (>=1.0.1)"]
mssql = ["pyodbc"]
mssql_pymssql = ["pymssql"]
@@ -944,7 +951,7 @@ python-versions = ">=3.7"
[[package]]
name = "typer"
-version = "0.4.0"
+version = "0.4.1"
description = "Typer, build great CLIs. Easy to code. Based on Python type hints."
category = "main"
optional = false
@@ -956,8 +963,8 @@ click = ">=7.1.1,<9.0.0"
[package.extras]
all = ["colorama (>=0.4.3,<0.5.0)", "shellingham (>=1.3.0,<2.0.0)"]
dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)"]
-doc = ["mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=5.4.0,<6.0.0)", "markdown-include (>=0.5.1,<0.6.0)"]
-test = ["shellingham (>=1.3.0,<2.0.0)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "coverage (>=5.2,<6.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "mypy (==0.910)", "black (>=19.10b0,<20.0b0)", "isort (>=5.0.6,<6.0.0)"]
+doc = ["mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "mdx-include (>=1.4.1,<2.0.0)"]
+test = ["shellingham (>=1.3.0,<2.0.0)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "coverage (>=5.2,<6.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "mypy (==0.910)", "black (>=22.3.0,<23.0.0)", "isort (>=5.0.6,<6.0.0)"]
[[package]]
name = "types-python-dateutil"
@@ -969,7 +976,7 @@ python-versions = "*"
[[package]]
name = "types-requests"
-version = "2.27.13"
+version = "2.27.25"
description = "Typing stubs for requests"
category = "dev"
optional = false
@@ -980,7 +987,7 @@ types-urllib3 = "<1.27"
[[package]]
name = "types-urllib3"
-version = "1.26.11"
+version = "1.26.14"
description = "Typing stubs for urllib3"
category = "dev"
optional = false
@@ -988,11 +995,11 @@ python-versions = "*"
[[package]]
name = "typing-extensions"
-version = "4.1.1"
-description = "Backported and Experimental Type Hints for Python 3.6+"
+version = "4.2.0"
+description = "Backported and Experimental Type Hints for Python 3.7+"
category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
[[package]]
name = "urllib3"
@@ -1045,7 +1052,7 @@ test = ["aiohttp", "flake8 (>=3.9.2,<3.10.0)", "psutil", "pycodestyle (>=2.7.0,<
[[package]]
name = "watchgod"
-version = "0.8"
+version = "0.8.2"
description = "Simple, modern file watching and code reload in python."
category = "main"
optional = false
@@ -1056,7 +1063,7 @@ anyio = ">=3.0.0,<4"
[[package]]
name = "websockets"
-version = "10.2"
+version = "10.3"
description = "An implementation of the WebSocket Protocol (RFC 6455 & 7692)"
category = "main"
optional = false
@@ -1064,15 +1071,15 @@ python-versions = ">=3.7"
[[package]]
name = "zipp"
-version = "3.7.0"
+version = "3.8.0"
description = "Backport of pathlib-compatible object wrapper for zip files"
category = "main"
optional = false
python-versions = ">=3.7"
[package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
+docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
[extras]
pycurl = ["pycurl"]
@@ -1084,8 +1091,8 @@ content-hash = "9029fdf5bbdfc0ab7e62b9898b595ac5098ecd8b0677785d68051d52c98ca210
[metadata.files]
aiomysql = [
- {file = "aiomysql-0.0.22-py3-none-any.whl", hash = "sha256:4e4a65914daacc40e70f992ddbeef32457561efbad8de41393e8ac5a84126a5a"},
- {file = "aiomysql-0.0.22.tar.gz", hash = "sha256:9bcf8f26d22e550f75cabd635fa19a55c45f835eea008275960cb37acadd622a"},
+ {file = "aiomysql-0.1.0-py3-none-any.whl", hash = "sha256:357ec32500553e1e5be7b0ed47345f96c5e5bfd63f245d6e28ee25d98011226f"},
+ {file = "aiomysql-0.1.0.tar.gz", hash = "sha256:ef04453a3a3ecbd670f813e09d3944d15845b572b34caef3ff715c0140e1ae21"},
]
aiosqlite = [
{file = "aiosqlite-0.17.0-py3-none-any.whl", hash = "sha256:6c49dc6d3405929b1d08eeccc72306d3677503cc5e5e43771efc1e00232e8231"},
@@ -1100,8 +1107,8 @@ anyio = [
{file = "anyio-3.5.0.tar.gz", hash = "sha256:a0aeffe2fb1fdf374a8e4b471444f0f3ac4fb9f5a5b542b48824475e0042a5a6"},
]
asgiref = [
- {file = "asgiref-3.5.0-py3-none-any.whl", hash = "sha256:88d59c13d634dcffe0510be048210188edd79aeccb6a6c9028cdad6f31d730a9"},
- {file = "asgiref-3.5.0.tar.gz", hash = "sha256:2f8abc20f7248433085eda803936d98992f1343ddb022065779f37c5da0181d0"},
+ {file = "asgiref-3.5.1-py3-none-any.whl", hash = "sha256:45a429524fba18aba9d512498b19d220c4d628e75b40cf5c627524dbaebc5cc1"},
+ {file = "asgiref-3.5.1.tar.gz", hash = "sha256:fddeea3c53fa99d0cdb613c3941cc6e52d822491fc2753fba25768fb5bf4e865"},
]
atomicwrites = [
{file = "atomicwrites-1.4.0-py2.py3-none-any.whl", hash = "sha256:6d1784dea7c0c8d4a5172b6c620f40b6e4cbfdf96d783691f2e1302a7b88e197"},
@@ -1112,33 +1119,33 @@ attrs = [
{file = "attrs-21.4.0.tar.gz", hash = "sha256:626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd"},
]
authlib = [
- {file = "Authlib-1.0.0-py2.py3-none-any.whl", hash = "sha256:e8d589a886b5bcde64ebf961157bf619d613666ef6703822c06254c5b108b3e6"},
- {file = "Authlib-1.0.0.tar.gz", hash = "sha256:2b13b4ba6465bdc46b89b1a07b2707c85b3434502d5a5fe202f5bdef8ebd5ac9"},
+ {file = "Authlib-1.0.1-py2.py3-none-any.whl", hash = "sha256:1286e2d5ef5bfe5a11cc2d0a0d1031f0393f6ce4d61f5121cfe87fa0054e98bd"},
+ {file = "Authlib-1.0.1.tar.gz", hash = "sha256:6e74a4846ac36dfc882b3cc2fbd3d9eb410a627f2f2dc11771276655345223b1"},
]
black = [
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- {file = "black-22.1.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:2ff96450d3ad9ea499fc4c60e425a1439c2120cbbc1ab959ff20f7c76ec7e866"},
- {file = "black-22.1.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:0e21e1f1efa65a50e3960edd068b6ae6d64ad6235bd8bfea116a03b21836af71"},
- {file = "black-22.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:e2f69158a7d120fd641d1fa9a921d898e20d52e44a74a6fbbcc570a62a6bc8ab"},
- {file = "black-22.1.0-cp310-cp310-win_amd64.whl", hash = "sha256:228b5ae2c8e3d6227e4bde5920d2fc66cc3400fde7bcc74f480cb07ef0b570d5"},
- {file = "black-22.1.0-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:b1a5ed73ab4c482208d20434f700d514f66ffe2840f63a6252ecc43a9bc77e8a"},
- {file = "black-22.1.0-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:35944b7100af4a985abfcaa860b06af15590deb1f392f06c8683b4381e8eeaf0"},
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+ {file = "websockets-10.3-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:07cdc0a5b2549bcfbadb585ad8471ebdc7bdf91e32e34ae3889001c1c106a6af"},
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+ {file = "websockets-10.3-cp39-cp39-win32.whl", hash = "sha256:bb621ec2dbbbe8df78a27dbd9dd7919f9b7d32a73fafcb4d9252fc4637343582"},
+ {file = "websockets-10.3-cp39-cp39-win_amd64.whl", hash = "sha256:51695d3b199cd03098ae5b42833006a0f43dc5418d3102972addc593a783bc02"},
+ {file = "websockets-10.3-pp37-pypy37_pp73-macosx_10_9_x86_64.whl", hash = "sha256:907e8247480f287aa9bbc9391bd6de23c906d48af54c8c421df84655eef66af7"},
+ {file = "websockets-10.3-pp37-pypy37_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:8b1359aba0ff810d5830d5ab8e2c4a02bebf98a60aa0124fb29aa78cfdb8031f"},
+ {file = "websockets-10.3-pp37-pypy37_pp73-manylinux_2_5_i686.manylinux1_i686.manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:93d5ea0b5da8d66d868b32c614d2b52d14304444e39e13a59566d4acb8d6e2e4"},
+ {file = "websockets-10.3-pp37-pypy37_pp73-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:7934e055fd5cd9dee60f11d16c8d79c4567315824bacb1246d0208a47eca9755"},
+ {file = "websockets-10.3-pp37-pypy37_pp73-win_amd64.whl", hash = "sha256:3eda1cb7e9da1b22588cefff09f0951771d6ee9fa8dbe66f5ae04cc5f26b2b55"},
+ {file = "websockets-10.3.tar.gz", hash = "sha256:fc06cc8073c8e87072138ba1e431300e2d408f054b27047d047b549455066ff4"},
]
zipp = [
- {file = "zipp-3.7.0-py3-none-any.whl", hash = "sha256:b47250dd24f92b7dd6a0a8fc5244da14608f3ca90a5efcd37a3b1642fac9a375"},
- {file = "zipp-3.7.0.tar.gz", hash = "sha256:9f50f446828eb9d45b267433fd3e9da8d801f614129124863f9c51ebceafb87d"},
+ {file = "zipp-3.8.0-py3-none-any.whl", hash = "sha256:c4f6e5bbf48e74f7a38e7cc5b0480ff42b0ae5178957d564d18932525d5cf099"},
+ {file = "zipp-3.8.0.tar.gz", hash = "sha256:56bf8aadb83c24db6c4b577e13de374ccfb67da2078beba1d037c17980bf43ad"},
]
--
GitLab
From 4a8e97ec3519299e5676377078ea2f15b819e044 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Tue, 3 May 2022 14:26:51 -0600
Subject: [PATCH 054/142] Add cache-control:no-cache to login/user error
response headers
---
geomagio/api/secure/login.py | 21 +++++++++++++++------
1 file changed, 15 insertions(+), 6 deletions(-)
diff --git a/geomagio/api/secure/login.py b/geomagio/api/secure/login.py
index 9bab1d8d..9992247f 100644
--- a/geomagio/api/secure/login.py
+++ b/geomagio/api/secure/login.py
@@ -121,7 +121,11 @@ def require_user(
) -> User:
if not user:
# not logged in
- raise HTTPException(status_code=401, detail=request.url_for("login"))
+ raise HTTPException(
+ detail=request.url_for("login"),
+ headers={"Cache-Control": "no-cache"},
+ status_code=401,
+ )
if allowed_groups is not None and not any(
g in user.groups for g in allowed_groups
):
@@ -129,7 +133,11 @@ def require_user(
f"user ({user.email}, sub={user.sub})"
f" not member of any allowed group ({allowed_groups})"
)
- raise HTTPException(403, detail="Forbidden")
+ raise HTTPException(
+ 403,
+ detail="Forbidden",
+ headers={"Cache-Control": "no-cache"},
+ )
return user
return verify_groups
@@ -164,11 +172,12 @@ async def authorize(request: Request):
request.session["user"] = dict(userinfo)
# redirect
return RedirectResponse(
+ headers={"Cache-Control": "no-cache"},
url=request.session.pop(
"after_authorize_redirect",
# fall back to index
request.url_for("index"),
- )
+ ),
)
@@ -196,11 +205,11 @@ async def logout(request: Request):
request.session.pop("token", None)
request.session.pop("user", None)
return RedirectResponse(
+ headers={"Cache-Control": "no-cache"},
# referrer when set
- "Referer" in request.headers
- and request.headers["Referer"]
+ url="Referer" in request.headers and request.headers["Referer"]
# otherwise index
- or request.url_for("index")
+ or request.url_for("index"),
)
--
GitLab
From c062ae4769884de9fc91d12f99a0b3fea8a3f224 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Tue, 3 May 2022 14:27:00 -0600
Subject: [PATCH 055/142] Update version to 1.5.1
---
code.json | 2 +-
pyproject.toml | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/code.json b/code.json
index 2be13980..1a1ad232 100644
--- a/code.json
+++ b/code.json
@@ -3,7 +3,7 @@
"name": "geomag-algorithms",
"organization": "U.S. Geological Survey",
"description": "Library for processing Geomagnetic timeseries data.",
- "version": "1.5.0",
+ "version": "1.5.1",
"status": "Development",
"permissions": {
diff --git a/pyproject.toml b/pyproject.toml
index 574d07f2..c738754d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ packages = [
{include = "geomagio" }
]
repository="https://code.usgs.gov/ghsc/geomag/geomag-algorithms"
-version = "1.5.0"
+version = "1.5.1"
[tool.poetry.dependencies]
--
GitLab
From d0335759fc09373c4fcb24b5f7ae11ce3058a959 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Tue, 3 May 2022 14:39:35 -0600
Subject: [PATCH 056/142] login: use kwarg for 403 status_code
---
geomagio/api/secure/login.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/geomagio/api/secure/login.py b/geomagio/api/secure/login.py
index 9992247f..d3e7b337 100644
--- a/geomagio/api/secure/login.py
+++ b/geomagio/api/secure/login.py
@@ -134,9 +134,9 @@ def require_user(
f" not member of any allowed group ({allowed_groups})"
)
raise HTTPException(
- 403,
detail="Forbidden",
headers={"Cache-Control": "no-cache"},
+ status_code=403,
)
return user
--
GitLab
From 856598a30b34b0890e789dad29e76bb1d637f3b7 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Wed, 4 May 2022 17:15:59 -0600
Subject: [PATCH 057/142] Move docker build back to build runner
---
.gitlab-ci.yml | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ee873777..0607ff00 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -206,8 +206,7 @@ Build Docker Image:
name: ${DEVOPS_REGISTRY}docker:19.03-dind
stage: integration
tags:
- - chs-shared
- - dind
+ - build
variables:
APP_NAME: geomag-algorithms
DOCKER_DRIVER: overlay2
--
GitLab
From 9bc22cbef29b10ee7bc970200e0eb218803917f3 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Wed, 4 May 2022 17:16:49 -0600
Subject: [PATCH 058/142] Bump version to 1.5.2
---
code.json | 4 ++--
pyproject.toml | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/code.json b/code.json
index 1a1ad232..424d6c82 100644
--- a/code.json
+++ b/code.json
@@ -3,7 +3,7 @@
"name": "geomag-algorithms",
"organization": "U.S. Geological Survey",
"description": "Library for processing Geomagnetic timeseries data.",
- "version": "1.5.1",
+ "version": "1.5.2",
"status": "Development",
"permissions": {
@@ -34,7 +34,7 @@
},
"date": {
- "metadataLastUpdated": "2022-05-03"
+ "metadataLastUpdated": "2022-05-04"
}
}
]
diff --git a/pyproject.toml b/pyproject.toml
index c738754d..f04d1717 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ packages = [
{include = "geomagio" }
]
repository="https://code.usgs.gov/ghsc/geomag/geomag-algorithms"
-version = "1.5.1"
+version = "1.5.2"
[tool.poetry.dependencies]
--
GitLab
From f2a8a03704bc49cb84a9e1dda3be83cbf2df626e Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Thu, 5 May 2022 09:22:45 -0600
Subject: [PATCH 059/142] pipeline: update production-env rule for tag matching
---
.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0607ff00..f9d27295 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -106,7 +106,7 @@ workflow:
.production-env: &production-env
if: >
$CI_PROJECT_PATH == $UPSTREAM_PATH
- && ( $CI_COMMIT_BRANCH == 'production' || $CI_COMMIT_TAG != '' )
+ && ( $CI_COMMIT_BRANCH == 'production' || $CI_COMMIT_TAG)
variables:
ENVIRONMENT: production
--
GitLab
From 8087080cdee799b1097626fa642f878a3e99517c Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Wed, 18 May 2022 10:43:32 -0600
Subject: [PATCH 060/142] Attempt StringIO after failed BytesIO file read
This is a bandaid to allow the `--input-url` option to be used to
read in single files. It adds zero functionality beyond what already
existed when the `--input-file` option was used.
---
geomagio/Controller.py | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
diff --git a/geomagio/Controller.py b/geomagio/Controller.py
index 4185cdea..a4bb7862 100644
--- a/geomagio/Controller.py
+++ b/geomagio/Controller.py
@@ -1,7 +1,7 @@
"""Controller class for geomag algorithms"""
import argparse
-from io import BytesIO
+from io import BytesIO, StringIO
import sys
from typing import List, Optional, Tuple, Union
@@ -506,7 +506,12 @@ def get_input_factory(args):
input_factory_args["urlInterval"] = args.input_url_interval
input_factory_args["urlTemplate"] = args.input_url
else:
- input_stream = BytesIO(Util.read_url(args.input_url))
+ try:
+ input_stream = BytesIO(Util.read_url(args.input_url))
+ except TypeError as e:
+ print(str(e), file=sys.stderr)
+ print("Warning: reading url as BytesIO failed; attempting StringIO", file=sys.stderr)
+ input_stream = StringIO(Util.read_url(args.input_url))
input_type = args.input
if input_type == "edge":
input_factory = edge.EdgeFactory(
--
GitLab
From 3af6c09cb7e8671118cfe32f1de9d945cb11269e Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Wed, 18 May 2022 13:37:58 -0600
Subject: [PATCH 061/142] Fix Black-recommended linting issue
---
geomagio/Controller.py | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/geomagio/Controller.py b/geomagio/Controller.py
index a4bb7862..230171df 100644
--- a/geomagio/Controller.py
+++ b/geomagio/Controller.py
@@ -510,7 +510,10 @@ def get_input_factory(args):
input_stream = BytesIO(Util.read_url(args.input_url))
except TypeError as e:
print(str(e), file=sys.stderr)
- print("Warning: reading url as BytesIO failed; attempting StringIO", file=sys.stderr)
+ print(
+ "Warning: reading url as BytesIO failed; attempting StringIO",
+ file=sys.stderr,
+ )
input_stream = StringIO(Util.read_url(args.input_url))
input_type = args.input
if input_type == "edge":
--
GitLab
From 4f5f3a862cac43fcf89a283c1c5ca2cec5be93b8 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Wed, 18 May 2022 15:17:35 -0600
Subject: [PATCH 062/142] Add test for --input-url to work with single file
It worked when a URL template was used, but not if a
single simple filename was passed
---
test/Controller_test.py | 79 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 79 insertions(+)
diff --git a/test/Controller_test.py b/test/Controller_test.py
index 4a722ada..2870645a 100644
--- a/test/Controller_test.py
+++ b/test/Controller_test.py
@@ -33,6 +33,85 @@ def test_controller():
assert_equal(isinstance(controller._algorithm, Algorithm), True)
+def test_controller_input_url():
+ """Controller_test.test_controller_input_url()
+
+ Test `--input-url` option in controller with both a URL template, and
+ and a simple, single file url. The latter was especially problematic after
+ switching to Py3 because BytesIO choked on data read in as a string.
+ NOTE: the bug this was designed to catch was TypeError, so a "pass" is
+ simply to read in the data file. There is no need to compare it
+ with anything.
+ """
+ # define folder for testing
+ tmp_dir = gettempdir()
+
+ # TEST 1 - read in interval using the --input-url option set to a
+ # URL template (i.e., it has a '{' in the string)
+
+ # create list of string command line arguments
+ fake_argv = [
+ "--input",
+ "iaga2002",
+ "--input-url",
+ "file://etc/controller/{obs}{date:%Y%m%d}_XYZF_{t}{i}.{i}",
+ "--observatory",
+ "BOU",
+ "--inchannels",
+ "X",
+ "Y",
+ "Z",
+ "F",
+ "--interval",
+ "minute",
+ "--type",
+ "variation",
+ "--output",
+ "iaga2002",
+ "--output-url",
+ "file://" + tmp_dir + "/{obs}{date:%Y%m%d}_XYZF_{t}{i}.{i}",
+ ]
+
+ # parse arguments and create initial args object
+ args = parse_args(fake_argv)
+
+ starttime1 = args.starttime = UTCDateTime("2018-10-24T00:00:00Z")
+ endtime1 = args.endtime = UTCDateTime("2018-10-24T00:19:00Z")
+ _main(args)
+
+ # TEST 2 - read in interval using the --input-url option with no
+ # URL template (i.e., no '{' in the string, just a single filename)
+ # create list of string command line arguments
+ fake_argv = [
+ "--input",
+ "iaga2002",
+ "--input-url",
+ "file://etc/controller/bou20181024_XYZF_vmin.min",
+ "--observatory",
+ "BOU",
+ "--inchannels",
+ "X",
+ "Y",
+ "Z",
+ "F",
+ "--interval",
+ "minute",
+ "--type",
+ "variation",
+ "--output",
+ "iaga2002",
+ "--output-url",
+ "file://" + tmp_dir + "/bou20181024_XYZF_noURL_vmin.min",
+ ]
+
+ # parse arguments and create initial args object
+ args = parse_args(fake_argv)
+
+ starttime1 = args.starttime = UTCDateTime("2018-10-24T00:00:00Z")
+ endtime1 = args.endtime = UTCDateTime("2018-10-24T00:19:00Z")
+ _main(args)
+
+
def test_controller_update_sqdist():
"""Controller_test.test_controller_update_sqdist().
--
GitLab
From d553059a78543be503d3b80fbfabff7bda6be6ea Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Wed, 18 May 2022 15:20:00 -0600
Subject: [PATCH 063/142] Fix Black-recommended linting issue
---
test/Controller_test.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/test/Controller_test.py b/test/Controller_test.py
index 2870645a..2e51338a 100644
--- a/test/Controller_test.py
+++ b/test/Controller_test.py
@@ -71,7 +71,7 @@ def test_controller_input_url():
"--output-url",
"file://" + tmp_dir + "/{obs}{date:%Y%m%d}_XYZF_{t}{i}.{i}",
]
-
+
# parse arguments and create initial args object
args = parse_args(fake_argv)
@@ -103,7 +103,7 @@ def test_controller_input_url():
"--output-url",
"file://" + tmp_dir + "/bou20181024_XYZF_noURL_vmin.min",
]
-
+
# parse arguments and create initial args object
args = parse_args(fake_argv)
--
GitLab
From a14806e6d0a21b4a278dada12076dacd90e12963 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Fri, 27 May 2022 13:04:57 -0600
Subject: [PATCH 064/142] Remove BYTESIO object creation
It turns out that none of the factories currently being used in
production expects bytes as input, and in fact, Util.read_url()
converts everthing to a string anyway, so a BYTES-oriented input
would couldn't not possibly be working. So, just remove all use
of BYTESIO, and instead use only STRINGIO.
---
geomagio/Controller.py | 12 ++----------
1 file changed, 2 insertions(+), 10 deletions(-)
diff --git a/geomagio/Controller.py b/geomagio/Controller.py
index 230171df..14e4eb36 100644
--- a/geomagio/Controller.py
+++ b/geomagio/Controller.py
@@ -1,7 +1,7 @@
"""Controller class for geomag algorithms"""
import argparse
-from io import BytesIO, StringIO
+from io import StringIO
import sys
from typing import List, Optional, Tuple, Union
@@ -506,15 +506,7 @@ def get_input_factory(args):
input_factory_args["urlInterval"] = args.input_url_interval
input_factory_args["urlTemplate"] = args.input_url
else:
- try:
- input_stream = BytesIO(Util.read_url(args.input_url))
- except TypeError as e:
- print(str(e), file=sys.stderr)
- print(
- "Warning: reading url as BytesIO failed; attempting StringIO",
- file=sys.stderr,
- )
- input_stream = StringIO(Util.read_url(args.input_url))
+ input_stream = StringIO(Util.read_url(args.input_url))
input_type = args.input
if input_type == "edge":
input_factory = edge.EdgeFactory(
--
GitLab
From fefef206350137de5beefd620db0b2351cf8b5b9 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Fri, 27 May 2022 13:32:19 -0600
Subject: [PATCH 065/142] Empty commit
Trying to dislodge a plugged pipeline in Gitlab
--
GitLab
From 150d66794055978e64bc43b1e081755d0a4ac294 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Fri, 27 May 2022 13:41:46 -0600
Subject: [PATCH 066/142] Tweak .gitlab-ci.yml for new Gitlab requirment
Gitlab 15 requires slightly different configuration to generate
Cobertura coverage reports. See:
https://docs.gitlab.com/ee/ci/yaml/artifacts_reports.html#artifactsreportscoverage_report
---
.gitlab-ci.yml | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f9d27295..c7e28786 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -153,7 +153,9 @@ Python Lint:
Python Test:
artifacts:
reports:
- cobertura: coverage.xml
+ coverage_report:
+ coverage_format: cobertura
+ path: coverage.xml
junit: junit.xml
needs:
- Poetry
--
GitLab
From 36ac6f37c304d647061f98a762cd1e24fc75c20c Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Wed, 1 Jun 2022 09:21:09 -0600
Subject: [PATCH 067/142] Parse data type in imfv122 files
---
geomagio/imfv122/IMFV122Parser.py | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/geomagio/imfv122/IMFV122Parser.py b/geomagio/imfv122/IMFV122Parser.py
index af00f92c..1e495941 100644
--- a/geomagio/imfv122/IMFV122Parser.py
+++ b/geomagio/imfv122/IMFV122Parser.py
@@ -8,6 +8,9 @@ from obspy.core import UTCDateTime
EIGHTS = numpy.float64("888888")
NINES = numpy.float64("999999")
+# valid data types and their IMFv122 single-character mapping
+DATA_TYPES = {"R": "Reported", "A": "Adjusted", "D": "Definitive"}
+
class IMFV122Parser(object):
"""IMFV122 parser.
@@ -83,6 +86,7 @@ class IMFV122Parser(object):
self.metadata["geodetic_longitude"] = float(colalong[4:]) / 10
self.metadata["station"] = observatory
self.metadata["gin"] = gin
+ self.metadata["data_type"] = DATA_TYPES[type.upper()]
year = 1900 + int(date[-2:])
julday = int(doy)
--
GitLab
From 7ad90ddc883a8de6028703b39611bbba6dceeebd Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Wed, 1 Jun 2022 11:41:29 -0600
Subject: [PATCH 068/142] Update poetry.lock to address pillow safety check
issue
---
poetry.lock | 595 ++++++++++++++++++++++++++--------------------------
1 file changed, 299 insertions(+), 296 deletions(-)
diff --git a/poetry.lock b/poetry.lock
index 73a268b7..5e9600ac 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,6 +1,6 @@
[[package]]
name = "aiomysql"
-version = "0.1.0"
+version = "0.1.1"
description = "MySQL driver for asyncio."
category = "main"
optional = false
@@ -26,11 +26,11 @@ typing_extensions = ">=3.7.2"
[[package]]
name = "alembic"
-version = "1.7.7"
+version = "1.8.0"
description = "A database migration tool for SQLAlchemy."
category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
[package.dependencies]
importlib-metadata = {version = "*", markers = "python_version < \"3.9\""}
@@ -43,7 +43,7 @@ tz = ["python-dateutil"]
[[package]]
name = "anyio"
-version = "3.5.0"
+version = "3.6.1"
description = "High level compatibility layer for multiple asynchronous event loop implementations"
category = "main"
optional = false
@@ -55,12 +55,12 @@ sniffio = ">=1.1"
[package.extras]
doc = ["packaging", "sphinx-rtd-theme", "sphinx-autodoc-typehints (>=1.2.0)"]
-test = ["coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "pytest (>=6.0)", "pytest-mock (>=3.6.1)", "trustme", "contextlib2", "uvloop (<0.15)", "mock (>=4)", "uvloop (>=0.15)"]
+test = ["coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "contextlib2", "uvloop (<0.15)", "mock (>=4)", "uvloop (>=0.15)"]
trio = ["trio (>=0.16)"]
[[package]]
name = "asgiref"
-version = "3.5.1"
+version = "3.5.2"
description = "ASGI specs, helper code, and adapters"
category = "main"
optional = false
@@ -126,11 +126,11 @@ uvloop = ["uvloop (>=0.15.2)"]
[[package]]
name = "certifi"
-version = "2021.10.8"
+version = "2022.5.18.1"
description = "Python package for providing Mozilla's CA Bundle."
category = "main"
optional = false
-python-versions = "*"
+python-versions = ">=3.6"
[[package]]
name = "cffi"
@@ -175,7 +175,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
[[package]]
name = "coverage"
-version = "6.3.2"
+version = "6.4"
description = "Code coverage measurement for Python"
category = "dev"
optional = false
@@ -407,7 +407,7 @@ python-versions = ">=3.5"
[[package]]
name = "importlib-metadata"
-version = "4.11.3"
+version = "4.11.4"
description = "Read metadata from Python packages"
category = "main"
optional = false
@@ -454,7 +454,7 @@ python-versions = ">=3.7"
[[package]]
name = "lxml"
-version = "4.8.0"
+version = "4.9.0"
description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API."
category = "main"
optional = false
@@ -537,7 +537,7 @@ python-versions = "*"
[[package]]
name = "numpy"
-version = "1.22.3"
+version = "1.22.4"
description = "NumPy is the fundamental package for array computing with Python."
category = "main"
optional = false
@@ -569,7 +569,7 @@ tests = ["packaging", "pyproj", "pytest", "pytest-json-report"]
[[package]]
name = "openpyxl"
-version = "3.0.9"
+version = "3.0.10"
description = "A Python library to read/write Excel 2010 xlsx/xlsm files"
category = "main"
optional = false
@@ -612,7 +612,7 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
[[package]]
name = "pillow"
-version = "9.1.0"
+version = "9.1.1"
description = "Python Imaging Library (Fork)"
category = "main"
optional = false
@@ -672,8 +672,8 @@ python-versions = ">=3.5"
[[package]]
name = "pydantic"
-version = "1.9.0"
-description = "Data validation and settings management using python 3.6 type hinting"
+version = "1.9.1"
+description = "Data validation and settings management using python type hints"
category = "main"
optional = false
python-versions = ">=3.6.1"
@@ -699,7 +699,7 @@ rsa = ["cryptography"]
[[package]]
name = "pyparsing"
-version = "3.0.8"
+version = "3.0.9"
description = "pyparsing module - Classes and methods to define and execute parsing grammars"
category = "main"
optional = false
@@ -823,7 +823,7 @@ requests = "*"
[[package]]
name = "scipy"
-version = "1.8.0"
+version = "1.8.1"
description = "SciPy: Scientific Library for Python"
category = "main"
optional = false
@@ -866,7 +866,7 @@ python-versions = ">=3.5"
[[package]]
name = "sqlalchemy"
-version = "1.4.36"
+version = "1.4.37"
description = "Database Abstraction Library"
category = "main"
optional = false
@@ -890,7 +890,7 @@ mysql_connector = ["mysql-connector-python"]
oracle = ["cx_oracle (>=7,<8)", "cx_oracle (>=7)"]
postgresql = ["psycopg2 (>=2.7)"]
postgresql_asyncpg = ["greenlet (!=0.4.17)", "asyncpg"]
-postgresql_pg8000 = ["pg8000 (>=1.16.6)"]
+postgresql_pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)"]
postgresql_psycopg2binary = ["psycopg2-binary"]
postgresql_psycopg2cffi = ["psycopg2cffi"]
pymysql = ["pymysql (<1)", "pymysql"]
@@ -976,7 +976,7 @@ python-versions = "*"
[[package]]
name = "types-requests"
-version = "2.27.25"
+version = "2.27.29"
description = "Typing stubs for requests"
category = "dev"
optional = false
@@ -987,7 +987,7 @@ types-urllib3 = "<1.27"
[[package]]
name = "types-urllib3"
-version = "1.26.14"
+version = "1.26.15"
description = "Typing stubs for urllib3"
category = "dev"
optional = false
@@ -1091,24 +1091,24 @@ content-hash = "9029fdf5bbdfc0ab7e62b9898b595ac5098ecd8b0677785d68051d52c98ca210
[metadata.files]
aiomysql = [
- {file = "aiomysql-0.1.0-py3-none-any.whl", hash = "sha256:357ec32500553e1e5be7b0ed47345f96c5e5bfd63f245d6e28ee25d98011226f"},
- {file = "aiomysql-0.1.0.tar.gz", hash = "sha256:ef04453a3a3ecbd670f813e09d3944d15845b572b34caef3ff715c0140e1ae21"},
+ {file = "aiomysql-0.1.1-py3-none-any.whl", hash = "sha256:b66fa1481ca71c5ee0d933ec3abf51f6136543a3710ba80b134eb33da7ed6f13"},
+ {file = "aiomysql-0.1.1.tar.gz", hash = "sha256:0d686c4fdae6b67d1825d8be60fa3b0e644fca2c84d3c936d850fc259c8e107e"},
]
aiosqlite = [
{file = "aiosqlite-0.17.0-py3-none-any.whl", hash = "sha256:6c49dc6d3405929b1d08eeccc72306d3677503cc5e5e43771efc1e00232e8231"},
{file = "aiosqlite-0.17.0.tar.gz", hash = "sha256:f0e6acc24bc4864149267ac82fb46dfb3be4455f99fe21df82609cc6e6baee51"},
]
alembic = [
- {file = "alembic-1.7.7-py3-none-any.whl", hash = "sha256:29be0856ec7591c39f4e1cb10f198045d890e6e2274cf8da80cb5e721a09642b"},
- {file = "alembic-1.7.7.tar.gz", hash = "sha256:4961248173ead7ce8a21efb3de378f13b8398e6630fab0eb258dc74a8af24c58"},
+ {file = "alembic-1.8.0-py3-none-any.whl", hash = "sha256:b5ae4bbfc7d1302ed413989d39474d102e7cfa158f6d5969d2497955ffe85a30"},
+ {file = "alembic-1.8.0.tar.gz", hash = "sha256:a2d4d90da70b30e70352cd9455e35873a255a31402a438fe24815758d7a0e5e1"},
]
anyio = [
- {file = "anyio-3.5.0-py3-none-any.whl", hash = "sha256:b5fa16c5ff93fa1046f2eeb5bbff2dad4d3514d6cda61d02816dba34fa8c3c2e"},
- {file = "anyio-3.5.0.tar.gz", hash = "sha256:a0aeffe2fb1fdf374a8e4b471444f0f3ac4fb9f5a5b542b48824475e0042a5a6"},
+ {file = "anyio-3.6.1-py3-none-any.whl", hash = "sha256:cb29b9c70620506a9a8f87a309591713446953302d7d995344d0d7c6c0c9a7be"},
+ {file = "anyio-3.6.1.tar.gz", hash = "sha256:413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b"},
]
asgiref = [
- {file = "asgiref-3.5.1-py3-none-any.whl", hash = "sha256:45a429524fba18aba9d512498b19d220c4d628e75b40cf5c627524dbaebc5cc1"},
- {file = "asgiref-3.5.1.tar.gz", hash = "sha256:fddeea3c53fa99d0cdb613c3941cc6e52d822491fc2753fba25768fb5bf4e865"},
+ {file = "asgiref-3.5.2-py3-none-any.whl", hash = "sha256:1d2880b792ae8757289136f1db2b7b99100ce959b2aa57fd69dab783d05afac4"},
+ {file = "asgiref-3.5.2.tar.gz", hash = "sha256:4a29362a6acebe09bf1d6640db38c1dc3d9217c68e6f9f6204d72667fc19a424"},
]
atomicwrites = [
{file = "atomicwrites-1.4.0-py2.py3-none-any.whl", hash = "sha256:6d1784dea7c0c8d4a5172b6c620f40b6e4cbfdf96d783691f2e1302a7b88e197"},
@@ -1148,8 +1148,8 @@ black = [
{file = "black-22.3.0.tar.gz", hash = "sha256:35020b8886c022ced9282b51b5a875b6d1ab0c387b31a065b84db7c33085ca79"},
]
certifi = [
- {file = "certifi-2021.10.8-py2.py3-none-any.whl", hash = "sha256:d62a0163eb4c2344ac042ab2bdf75399a71a2d8c7d47eac2e2ee91b9d6339569"},
- {file = "certifi-2021.10.8.tar.gz", hash = "sha256:78884e7c1d4b00ce3cea67b44566851c4343c120abd683433ce934a68ea58872"},
+ {file = "certifi-2022.5.18.1-py3-none-any.whl", hash = "sha256:f1d53542ee8cbedbe2118b5686372fb33c297fcd6379b050cca0ef13a597382a"},
+ {file = "certifi-2022.5.18.1.tar.gz", hash = "sha256:9c5705e395cd70084351dd8ad5c41e65655e08ce46f2ec9cf6c2c08390f71eb7"},
]
cffi = [
{file = "cffi-1.15.0-cp27-cp27m-macosx_10_9_x86_64.whl", hash = "sha256:c2502a1a03b6312837279c8c1bd3ebedf6c12c4228ddbad40912d671ccc8a962"},
@@ -1216,47 +1216,47 @@ colorama = [
{file = "colorama-0.4.4.tar.gz", hash = "sha256:5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b"},
]
coverage = [
- {file = "coverage-6.3.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:9b27d894748475fa858f9597c0ee1d4829f44683f3813633aaf94b19cb5453cf"},
- {file = "coverage-6.3.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:37d1141ad6b2466a7b53a22e08fe76994c2d35a5b6b469590424a9953155afac"},
- {file = "coverage-6.3.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:f9987b0354b06d4df0f4d3e0ec1ae76d7ce7cbca9a2f98c25041eb79eec766f1"},
- {file = "coverage-6.3.2-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:26e2deacd414fc2f97dd9f7676ee3eaecd299ca751412d89f40bc01557a6b1b4"},
- {file = "coverage-6.3.2-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:4dd8bafa458b5c7d061540f1ee9f18025a68e2d8471b3e858a9dad47c8d41903"},
- {file = "coverage-6.3.2-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:46191097ebc381fbf89bdce207a6c107ac4ec0890d8d20f3360345ff5976155c"},
- {file = "coverage-6.3.2-cp310-cp310-musllinux_1_1_i686.whl", hash = "sha256:6f89d05e028d274ce4fa1a86887b071ae1755082ef94a6740238cd7a8178804f"},
- {file = "coverage-6.3.2-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:58303469e9a272b4abdb9e302a780072c0633cdcc0165db7eec0f9e32f901e05"},
- {file = "coverage-6.3.2-cp310-cp310-win32.whl", hash = "sha256:2fea046bfb455510e05be95e879f0e768d45c10c11509e20e06d8fcaa31d9e39"},
- {file = "coverage-6.3.2-cp310-cp310-win_amd64.whl", hash = "sha256:a2a8b8bcc399edb4347a5ca8b9b87e7524c0967b335fbb08a83c8421489ddee1"},
- {file = "coverage-6.3.2-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:f1555ea6d6da108e1999b2463ea1003fe03f29213e459145e70edbaf3e004aaa"},
- {file = "coverage-6.3.2-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:e5f4e1edcf57ce94e5475fe09e5afa3e3145081318e5fd1a43a6b4539a97e518"},
- {file = "coverage-6.3.2-cp37-cp37m-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:7a15dc0a14008f1da3d1ebd44bdda3e357dbabdf5a0b5034d38fcde0b5c234b7"},
- {file = "coverage-6.3.2-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:21b7745788866028adeb1e0eca3bf1101109e2dc58456cb49d2d9b99a8c516e6"},
- {file = "coverage-6.3.2-cp37-cp37m-musllinux_1_1_aarch64.whl", hash = "sha256:8ce257cac556cb03be4a248d92ed36904a59a4a5ff55a994e92214cde15c5bad"},
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+ {file = "SQLAlchemy-1.4.37-cp39-cp39-win32.whl", hash = "sha256:5e4e517ce72fad35cce364a01aff165f524449e9c959f1837dc71088afa2824c"},
+ {file = "SQLAlchemy-1.4.37-cp39-cp39-win_amd64.whl", hash = "sha256:c37885f83b59e248bebe2b35beabfbea398cb40960cdc6d3a76eac863d4e1938"},
+ {file = "SQLAlchemy-1.4.37.tar.gz", hash = "sha256:3688f92c62db6c5df268e2264891078f17ecb91e3141b400f2e28d0f75796dea"},
]
sqlalchemy-stubs = [
{file = "sqlalchemy-stubs-0.4.tar.gz", hash = "sha256:c665d6dd4482ef642f01027fa06c3d5e91befabb219dc71fc2a09e7d7695f7ae"},
@@ -1981,12 +1984,12 @@ types-python-dateutil = [
{file = "types_python_dateutil-0.1.6-py3-none-any.whl", hash = "sha256:5b6241ea9fca2d8878cc152017d9524da62a7a856b98e31006e68b02aab47442"},
]
types-requests = [
- {file = "types-requests-2.27.25.tar.gz", hash = "sha256:805ae7e38fd9d157153066dc4381cf585fd34dfa212f2fc1fece248c05aac571"},
- {file = "types_requests-2.27.25-py3-none-any.whl", hash = "sha256:2444905c89731dbcb6bbcd6d873a04252445df7623917c640e463b2b28d2a708"},
+ {file = "types-requests-2.27.29.tar.gz", hash = "sha256:fb453b3a76a48eca66381cea8004feaaea12835e838196f5c7ac87c75c5c19ef"},
+ {file = "types_requests-2.27.29-py3-none-any.whl", hash = "sha256:014f4f82db7b96c41feea9adaea30e68cd64c230eeab34b70c29bebb26ec74ac"},
]
types-urllib3 = [
- {file = "types-urllib3-1.26.14.tar.gz", hash = "sha256:2a2578e4b36341ccd240b00fccda9826988ff0589a44ba4a664bbd69ef348d27"},
- {file = "types_urllib3-1.26.14-py3-none-any.whl", hash = "sha256:5d2388aa76395b1e3999ff789ea5b3283677dad8e9bcf3d9117ba19271fd35d9"},
+ {file = "types-urllib3-1.26.15.tar.gz", hash = "sha256:c89283541ef92e344b7f59f83ea9b5a295b16366ceee3f25ecfc5593c79f794e"},
+ {file = "types_urllib3-1.26.15-py3-none-any.whl", hash = "sha256:6011befa13f901fc934f59bb1fd6973be6f3acf4ebfce427593a27e7f492918f"},
]
typing-extensions = [
{file = "typing_extensions-4.2.0-py3-none-any.whl", hash = "sha256:6657594ee297170d19f67d55c05852a874e7eb634f4f753dbd667855e07c1708"},
--
GitLab
From e6753ace1ad03e660964ef8c73ee5366264b69bb Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Wed, 1 Jun 2022 11:42:39 -0600
Subject: [PATCH 069/142] Bump version to 1.5.3
---
code.json | 4 ++--
pyproject.toml | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/code.json b/code.json
index 424d6c82..e53c03f2 100644
--- a/code.json
+++ b/code.json
@@ -3,7 +3,7 @@
"name": "geomag-algorithms",
"organization": "U.S. Geological Survey",
"description": "Library for processing Geomagnetic timeseries data.",
- "version": "1.5.2",
+ "version": "1.5.3",
"status": "Development",
"permissions": {
@@ -34,7 +34,7 @@
},
"date": {
- "metadataLastUpdated": "2022-05-04"
+ "metadataLastUpdated": "2022-06-01"
}
}
]
diff --git a/pyproject.toml b/pyproject.toml
index f04d1717..19400fd7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ packages = [
{include = "geomagio" }
]
repository="https://code.usgs.gov/ghsc/geomag/geomag-algorithms"
-version = "1.5.2"
+version = "1.5.3"
[tool.poetry.dependencies]
--
GitLab
From fb61feacdd104b67eb8ccd7c35c39ceb65a5b3da Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Thu, 11 Aug 2022 13:33:59 -0600
Subject: [PATCH 070/142] update interval no longer shrinks with recursion
Previously, the endtime-starttime interval being processed by the
`run_as_update` method would shrink by 1 (second) with each recursion.
This ultimately broke `run_as_update` when processing anything other
than 1-second data, but it wasn't obvious because we rarely had to
actually recurse. There is a little trickery now to ensure that user-
provided starttime and endtime are inclusive of the full first
(most recent) update interval, while subsequent, calculated, endtimes
are set equal to the prior starttime minus specified output_interval
(e.g., 'second', 'minute', etc.).
---
geomagio/Controller.py | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/geomagio/Controller.py b/geomagio/Controller.py
index 14e4eb36..84f5074c 100644
--- a/geomagio/Controller.py
+++ b/geomagio/Controller.py
@@ -426,9 +426,11 @@ class Controller(object):
# check for fillable gap at start
if output_gap[0] == starttime:
# found fillable gap at start, recurse to previous interval
- interval = endtime - starttime
- recurse_starttime = starttime - interval
- recurse_endtime = starttime - 1
+ delta = TimeseriesUtility.get_delta_from_interval(output_interval)
+ recurse_starttime = (
+ starttime - (endtime - starttime) - delta * bool(update_count)
+ )
+ recurse_endtime = starttime - delta
self.run_as_update(
algorithm=algorithm,
observatory=observatory,
--
GitLab
From 19dc49ad285af68281aa6773fb8410d87343eaeb Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Thu, 11 Aug 2022 21:32:01 -0600
Subject: [PATCH 071/142] Add get_previous_interval method and test
---
geomagio/Controller.py | 30 ++++++++++++++++++++++++++----
test/Controller_test.py | 22 +++++++++++++++++++++-
2 files changed, 47 insertions(+), 5 deletions(-)
diff --git a/geomagio/Controller.py b/geomagio/Controller.py
index 84f5074c..63e5a79d 100644
--- a/geomagio/Controller.py
+++ b/geomagio/Controller.py
@@ -426,11 +426,10 @@ class Controller(object):
# check for fillable gap at start
if output_gap[0] == starttime:
# found fillable gap at start, recurse to previous interval
- delta = TimeseriesUtility.get_delta_from_interval(output_interval)
- recurse_starttime = (
- starttime - (endtime - starttime) - delta * bool(update_count)
+ recurse_starttime, recurse_endtime = get_previous_interval(
+ start=starttime,
+ end=endtime,
)
- recurse_endtime = starttime - delta
self.run_as_update(
algorithm=algorithm,
observatory=observatory,
@@ -646,6 +645,29 @@ def get_output_factory(args):
return output_factory
+def get_previous_interval(
+ start: UTCDateTime,
+ end: UTCDateTime,
+) -> Tuple[UTCDateTime, UTCDateTime]:
+ """Get previous interval for given interval.
+
+ Parameters
+ ----------
+ start
+ start of interval
+ end
+ end of interval
+
+ Returns
+ -------
+ Previous interval of approximately the same size.
+ Interval is rounded to nearest second, and ends one microsecond earlier.
+ """
+ # round to nearest second to recover removed microsecond from repeated calls
+ interval_size = round(end - start)
+ return (start - interval_size, start - 1e-6)
+
+
def get_realtime_interval(interval_seconds: int) -> Tuple[UTCDateTime, UTCDateTime]:
# calculate endtime/starttime
now = UTCDateTime()
diff --git a/test/Controller_test.py b/test/Controller_test.py
index 2e51338a..9acab443 100644
--- a/test/Controller_test.py
+++ b/test/Controller_test.py
@@ -6,7 +6,7 @@ from geomagio.algorithm import Algorithm
from geomagio.iaga2002 import IAGA2002Factory
# needed to emulate geomag.py script
-from geomagio.Controller import _main, parse_args
+from geomagio.Controller import _main, get_previous_interval, parse_args
# needed to copy SqDistAlgorithm statefile
from shutil import copy
@@ -290,3 +290,23 @@ def test_controller_update_sqdist():
)
expected = expected_factory.get_timeseries(starttime=starttime1, endtime=endtime6)
assert_allclose(actual, expected)
+
+
+def test_get_previous_interval():
+ """Test get_previous_interval produces stable interval sizes"""
+ # initial interval is one hour
+ start = UTCDateTime("2022-01-05T00:00:00Z")
+ end = UTCDateTime("2022-01-05T01:00:00Z")
+ # previous interval starts at beginning of previous hour
+ previous = get_previous_interval(start=start, end=end)
+ assert previous == (
+ UTCDateTime("2022-01-04T23:00:00"),
+ UTCDateTime("2022-01-04T23:59:59.999999Z"),
+ )
+ # previous interval still starts at beginning of previous hour
+ # even though interval is one microsecond smaller
+ previous = get_previous_interval(*previous)
+ assert previous == (
+ UTCDateTime("2022-01-04T22:00:00"),
+ UTCDateTime("2022-01-04T22:59:59.999999Z"),
+ )
--
GitLab
From b75ceab81eddbbaf0243848be556f75e2cf6e22c Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Fri, 12 Aug 2022 18:33:51 -0600
Subject: [PATCH 072/142] Switch get_previous_interval precision to
milliseconds to match Edge
---
geomagio/Controller.py | 4 ++--
test/Controller_test.py | 6 +++---
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/geomagio/Controller.py b/geomagio/Controller.py
index 63e5a79d..8018b9f9 100644
--- a/geomagio/Controller.py
+++ b/geomagio/Controller.py
@@ -661,11 +661,11 @@ def get_previous_interval(
Returns
-------
Previous interval of approximately the same size.
- Interval is rounded to nearest second, and ends one microsecond earlier.
+ Interval is rounded to nearest second, and ends one millisecond earlier.
"""
# round to nearest second to recover removed microsecond from repeated calls
interval_size = round(end - start)
- return (start - interval_size, start - 1e-6)
+ return (start - interval_size, start - 1e-3)
def get_realtime_interval(interval_seconds: int) -> Tuple[UTCDateTime, UTCDateTime]:
diff --git a/test/Controller_test.py b/test/Controller_test.py
index 9acab443..bff8a8fd 100644
--- a/test/Controller_test.py
+++ b/test/Controller_test.py
@@ -301,12 +301,12 @@ def test_get_previous_interval():
previous = get_previous_interval(start=start, end=end)
assert previous == (
UTCDateTime("2022-01-04T23:00:00"),
- UTCDateTime("2022-01-04T23:59:59.999999Z"),
+ UTCDateTime("2022-01-04T23:59:59.999Z"),
)
# previous interval still starts at beginning of previous hour
- # even though interval is one microsecond smaller
+ # even though interval is one millisecond smaller
previous = get_previous_interval(*previous)
assert previous == (
UTCDateTime("2022-01-04T22:00:00"),
- UTCDateTime("2022-01-04T22:59:59.999999Z"),
+ UTCDateTime("2022-01-04T22:59:59.999Z"),
)
--
GitLab
From 6f2ed54097b014ef6618cd1fd6165e9f9bc7bbc0 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Sat, 20 Aug 2022 10:30:31 -0600
Subject: [PATCH 073/142] Addresses issue #73 (residual ss time parsing
---
.../residual/SpreadsheetAbsolutesFactory.py | 42 +++++++++++++++----
1 file changed, 35 insertions(+), 7 deletions(-)
diff --git a/geomagio/residual/SpreadsheetAbsolutesFactory.py b/geomagio/residual/SpreadsheetAbsolutesFactory.py
index 1f50f794..00e3d4c4 100644
--- a/geomagio/residual/SpreadsheetAbsolutesFactory.py
+++ b/geomagio/residual/SpreadsheetAbsolutesFactory.py
@@ -320,22 +320,46 @@ class SpreadsheetAbsolutesFactory(object):
degrees=sheet["C12"].value, minutes=sheet["D12"].value
),
baseline=Angle.from_dms(minutes=sheet["F12"].value),
- endtime=parse_relative_time(base_date, sheet["B12"].value),
- starttime=parse_relative_time(base_date, sheet["B12"].value),
+ endtime=parse_relative_time(
+ # base_date is already a string; sheet "times" are ints
+ base_date,
+ "{:04d}".format(sheet["B12"].value),
+ ),
+ starttime=parse_relative_time(
+ # base_date is already a string; sheet "times" are ints
+ base_date,
+ "{:04d}".format(sheet["B12"].value),
+ ),
),
Absolute(
element="H",
absolute=sheet["C17"].value,
baseline=sheet["F17"].value,
- endtime=parse_relative_time(base_date, sheet["B17"].value),
- starttime=parse_relative_time(base_date, sheet["B17"].value),
+ endtime=parse_relative_time(
+ # base_date is already a string; sheet "times" are ints
+ base_date,
+ "{:04d}".format(sheet["B17"].value),
+ ),
+ starttime=parse_relative_time(
+ # base_date is already a string; sheet "times" are ints
+ base_date,
+ "{:04d}".format(sheet["B17"].value),
+ ),
),
Absolute(
element="Z",
absolute=sheet["C22"].value,
baseline=sheet["F22"].value,
- endtime=parse_relative_time(base_date, sheet["B22"].value),
- starttime=parse_relative_time(base_date, sheet["B22"].value),
+ endtime=parse_relative_time(
+ # base_date is already a string; sheet "times" are ints
+ base_date,
+ "{:04d}".format(sheet["B22"].value),
+ ),
+ starttime=parse_relative_time(
+ # base_date is already a string; sheet "times" are ints
+ base_date,
+ "{:04d}".format(sheet["B22"].value),
+ ),
),
]
return absolutes
@@ -355,7 +379,11 @@ class SpreadsheetAbsolutesFactory(object):
residual = "residual" in m and sheet[m["residual"]].value or None
time = (
"time" in m
- and parse_relative_time(base_date, sheet[m["time"]].value)
+ and parse_relative_time(
+ # base_date is already a string; sheet "times" are ints
+ base_date,
+ "{:06d}".format(sheet[m["time"]].value),
+ )
or None
)
h = "h" in m and sheet[m["h"]].value or None
--
GitLab
From a9388364d4e9c62ac76ce707a5bdef8d182259d0 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Thu, 15 Sep 2022 11:50:40 -0600
Subject: [PATCH 074/142] Set proper timestamps in residual calculated
absolutes
Fixes #75
When geomagio.residual.calculate() is called with adjust_reference set equal
to True, the start/end timestamps now both reflect the time of the first absolute
measurement (i.e., West Down). This is consistent with the residual absolute
spreadsheet calculations.
---
geomagio/residual/Calculation.py | 25 ++++++++++++++++++-------
1 file changed, 18 insertions(+), 7 deletions(-)
diff --git a/geomagio/residual/Calculation.py b/geomagio/residual/Calculation.py
index d6d82044..eb4521b0 100644
--- a/geomagio/residual/Calculation.py
+++ b/geomagio/residual/Calculation.py
@@ -95,6 +95,12 @@ def calculate_D_absolute(
D Absolute
"""
mean = average_measurement(measurements, DECLINATION_TYPES)
+ if reference:
+ starttime = reference.time
+ endtime = reference.time
+ else:
+ starttime = mean.time
+ endtime = mean.endtime
reference = reference or mean
# average mark
average_mark = average_measurement(measurements, MARK_TYPES)
@@ -136,8 +142,8 @@ def calculate_D_absolute(
absolute=d_abs,
baseline=d_b,
shift=shift,
- starttime=mean.time,
- endtime=mean.endtime,
+ starttime=starttime,
+ endtime=endtime,
),
meridian,
)
@@ -173,21 +179,26 @@ def calculate_HZ_absolutes(
if reference:
h_abs = np.sqrt((h_b + reference.h) ** 2 + (reference.e) ** 2)
z_abs = z_b + reference.z
+ starttime = reference.time
+ endtime = reference.time
+ else:
+ starttime = mean.time
+ endtime = mean.endtime
# return absolutes
return (
Absolute(
element="H",
baseline=h_b,
absolute=h_abs,
- starttime=mean.time,
- endtime=mean.endtime,
+ starttime=starttime,
+ endtime=endtime,
),
Absolute(
element="Z",
baseline=z_b,
absolute=z_abs,
- starttime=mean.time,
- endtime=mean.endtime,
+ starttime=starttime,
+ endtime=endtime,
),
)
@@ -279,5 +290,5 @@ def calculate_scale_value(
/ corrected_f
) + (m2.angle - m1.angle)
residual_change = m2.residual - m1.residual
- scale_value = corrected_f * field_change / np.abs(residual_change)
+ scale_value = np.radians(corrected_f * field_change / np.abs(residual_change))
return scale_value
--
GitLab
From 605ba23f096d451b436a948cd0a3999654e69b64 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Thu, 15 Sep 2022 12:29:02 -0600
Subject: [PATCH 075/142] Inadvertent change to scale_value
The calculation of scale_value in geomagio.residual.calculate() is not
quite correct, but that needs to be addressed in a separate commit and
merge request. I'm reverting the recent change here so that we don't
break the tests.
---
geomagio/residual/Calculation.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/geomagio/residual/Calculation.py b/geomagio/residual/Calculation.py
index eb4521b0..dbce845d 100644
--- a/geomagio/residual/Calculation.py
+++ b/geomagio/residual/Calculation.py
@@ -290,5 +290,5 @@ def calculate_scale_value(
/ corrected_f
) + (m2.angle - m1.angle)
residual_change = m2.residual - m1.residual
- scale_value = np.radians(corrected_f * field_change / np.abs(residual_change))
+ scale_value = corrected_f * field_change / np.abs(residual_change)
return scale_value
--
GitLab
From 6d17f5fee6c28a195a5cdde1b23cd2eec41e9d27 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Thu, 15 Sep 2022 14:01:06 -0600
Subject: [PATCH 076/142] Update dependencies to satisfy safety check
Pyup.io's "safety" check failed on packages lxml, mako, and dparse.
None of these were explicit in our pyproject.toml file, but I modified
the entry to alembic, which was the package that required mako, then
ran poetry update to update the poetry.lock file.
To be honest, I'm not sure changing pyproject.toml file was needed
at all. I still don't fully understand how poetry works I guess. But,
everthing is "safe" now, and this merge request should now make it
through the CICD pipeline without further issue (fingers crossed).
---
poetry.lock | 823 +++++++------------------------------------------
pyproject.toml | 2 +-
2 files changed, 113 insertions(+), 712 deletions(-)
diff --git a/poetry.lock b/poetry.lock
index 5e9600ac..1e57d989 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -26,7 +26,7 @@ typing_extensions = ">=3.7.2"
[[package]]
name = "alembic"
-version = "1.8.0"
+version = "1.8.1"
description = "A database migration tool for SQLAlchemy."
category = "main"
optional = false
@@ -71,7 +71,7 @@ tests = ["pytest", "pytest-asyncio", "mypy (>=0.800)"]
[[package]]
name = "atomicwrites"
-version = "1.4.0"
+version = "1.4.1"
description = "Atomic file writes."
category = "dev"
optional = false
@@ -79,21 +79,21 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[[package]]
name = "attrs"
-version = "21.4.0"
+version = "22.1.0"
description = "Classes Without Boilerplate"
category = "dev"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.5"
[package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "cloudpickle"]
[[package]]
name = "authlib"
-version = "1.0.1"
+version = "1.1.0"
description = "The ultimate Python library in building OAuth and OpenID Connect servers and clients."
category = "main"
optional = false
@@ -104,7 +104,7 @@ cryptography = ">=3.2"
[[package]]
name = "black"
-version = "22.3.0"
+version = "22.8.0"
description = "The uncompromising code formatter."
category = "dev"
optional = false
@@ -115,7 +115,7 @@ click = ">=8.0.0"
mypy-extensions = ">=0.4.3"
pathspec = ">=0.9.0"
platformdirs = ">=2"
-tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
+tomli = {version = ">=1.1.0", markers = "python_full_version < \"3.11.0a7\""}
typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}
[package.extras]
@@ -126,7 +126,7 @@ uvloop = ["uvloop (>=0.15.2)"]
[[package]]
name = "certifi"
-version = "2022.5.18.1"
+version = "2022.9.14"
description = "Python package for providing Mozilla's CA Bundle."
category = "main"
optional = false
@@ -134,7 +134,7 @@ python-versions = ">=3.6"
[[package]]
name = "cffi"
-version = "1.15.0"
+version = "1.15.1"
description = "Foreign Function Interface for Python calling C code."
category = "main"
optional = false
@@ -145,11 +145,11 @@ pycparser = "*"
[[package]]
name = "charset-normalizer"
-version = "2.0.12"
+version = "2.1.1"
description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
category = "main"
optional = false
-python-versions = ">=3.5.0"
+python-versions = ">=3.6.0"
[package.extras]
unicode_backport = ["unicodedata2"]
@@ -167,7 +167,7 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
[[package]]
name = "colorama"
-version = "0.4.4"
+version = "0.4.5"
description = "Cross-platform colored terminal text."
category = "main"
optional = false
@@ -175,7 +175,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
[[package]]
name = "coverage"
-version = "6.4"
+version = "6.4.4"
description = "Code coverage measurement for Python"
category = "dev"
optional = false
@@ -252,7 +252,7 @@ python-versions = ">=3.5"
[[package]]
name = "dparse"
-version = "0.5.1"
+version = "0.6.0"
description = "A parser for Python dependency files"
category = "dev"
optional = false
@@ -260,11 +260,11 @@ python-versions = ">=3.5"
[package.dependencies]
packaging = "*"
-pyyaml = "*"
toml = "*"
[package.extras]
pipenv = ["pipenv"]
+conda = ["pyyaml"]
[[package]]
name = "et-xmlfile"
@@ -294,7 +294,7 @@ test = ["pytest (>=6.2.4,<7.0.0)", "pytest-cov (>=2.12.0,<4.0.0)", "mypy (==0.91
[[package]]
name = "fonttools"
-version = "4.33.3"
+version = "4.37.2"
description = "Tools to manipulate font files"
category = "main"
optional = false
@@ -316,7 +316,7 @@ woff = ["zopfli (>=0.1.4)", "brotlicffi (>=0.8.0)", "brotli (>=1.0.1)"]
[[package]]
name = "greenlet"
-version = "1.1.2"
+version = "1.1.3"
description = "Lightweight in-process concurrent programming"
category = "main"
optional = false
@@ -367,7 +367,7 @@ socks = ["socksio (>=1.0.0,<2.0.0)"]
[[package]]
name = "httptools"
-version = "0.4.0"
+version = "0.5.0"
description = "A collection of framework independent HTTP protocol utils."
category = "main"
optional = false
@@ -399,7 +399,7 @@ socks = ["socksio (>=1.0.0,<2.0.0)"]
[[package]]
name = "idna"
-version = "3.3"
+version = "3.4"
description = "Internationalized Domain Names in Applications (IDNA)"
category = "main"
optional = false
@@ -407,7 +407,7 @@ python-versions = ">=3.5"
[[package]]
name = "importlib-metadata"
-version = "4.11.4"
+version = "4.12.0"
description = "Read metadata from Python packages"
category = "main"
optional = false
@@ -419,11 +419,11 @@ zipp = ">=0.5"
[package.extras]
docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
perf = ["ipython"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
[[package]]
name = "importlib-resources"
-version = "5.7.1"
+version = "5.9.0"
description = "Read resources from Python packages"
category = "main"
optional = false
@@ -433,8 +433,8 @@ python-versions = ">=3.7"
zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
[package.extras]
-docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
+docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "jaraco.tidelift (>=1.4)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
[[package]]
name = "iniconfig"
@@ -446,7 +446,7 @@ python-versions = "*"
[[package]]
name = "kiwisolver"
-version = "1.4.2"
+version = "1.4.4"
description = "A fast implementation of the Cassowary constraint solver"
category = "main"
optional = false
@@ -454,7 +454,7 @@ python-versions = ">=3.7"
[[package]]
name = "lxml"
-version = "4.9.0"
+version = "4.9.1"
description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API."
category = "main"
optional = false
@@ -468,7 +468,7 @@ source = ["Cython (>=0.29.7)"]
[[package]]
name = "mako"
-version = "1.2.0"
+version = "1.2.2"
description = "A super-fast templating language that borrows the best ideas from the existing templating languages."
category = "main"
optional = false
@@ -492,7 +492,7 @@ python-versions = ">=3.7"
[[package]]
name = "matplotlib"
-version = "3.5.2"
+version = "3.5.3"
description = "Python plotting package"
category = "main"
optional = false
@@ -507,7 +507,7 @@ packaging = ">=20.0"
pillow = ">=6.2.0"
pyparsing = ">=2.2.1"
python-dateutil = ">=2.7"
-setuptools_scm = ">=4"
+setuptools_scm = ">=4,<7"
[[package]]
name = "mypy"
@@ -537,7 +537,7 @@ python-versions = "*"
[[package]]
name = "numpy"
-version = "1.22.4"
+version = "1.23.3"
description = "NumPy is the fundamental package for array computing with Python."
category = "main"
optional = false
@@ -580,7 +580,7 @@ et-xmlfile = "*"
[[package]]
name = "openpyxl-stubs"
-version = "0.1.21"
+version = "0.1.22"
description = "Type stubs for openpyxl"
category = "dev"
optional = false
@@ -604,22 +604,22 @@ pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
[[package]]
name = "pathspec"
-version = "0.9.0"
+version = "0.10.1"
description = "Utility library for gitignore style pattern matching of file paths."
category = "dev"
optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+python-versions = ">=3.7"
[[package]]
name = "pillow"
-version = "9.1.1"
+version = "9.2.0"
description = "Python Imaging Library (Fork)"
category = "main"
optional = false
python-versions = ">=3.7"
[package.extras]
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tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
[[package]]
@@ -672,14 +672,14 @@ python-versions = ">=3.5"
[[package]]
name = "pydantic"
-version = "1.9.1"
+version = "1.10.2"
description = "Data validation and settings management using python type hints"
category = "main"
optional = false
-python-versions = ">=3.6.1"
+python-versions = ">=3.7"
[package.dependencies]
-typing-extensions = ">=3.7.4.3"
+typing-extensions = ">=4.1.0"
[package.extras]
dotenv = ["python-dotenv (>=0.10.4)"]
@@ -758,11 +758,11 @@ six = ">=1.5"
[[package]]
name = "python-dotenv"
-version = "0.20.0"
+version = "0.21.0"
description = "Read key-value pairs from a .env file and set them as environment variables"
category = "main"
optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.7"
[package.extras]
cli = ["click (>=5.0)"]
@@ -777,21 +777,21 @@ python-versions = ">=3.6"
[[package]]
name = "requests"
-version = "2.27.1"
+version = "2.28.1"
description = "Python HTTP for Humans."
category = "main"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+python-versions = ">=3.7, <4"
[package.dependencies]
certifi = ">=2017.4.17"
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-idna = {version = ">=2.5,<4", markers = "python_version >= \"3\""}
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urllib3 = ">=1.21.1,<1.27"
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[[package]]
name = "rfc3986"
@@ -823,14 +823,14 @@ requests = "*"
[[package]]
name = "scipy"
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+version = "1.9.1"
description = "SciPy: Scientific Library for Python"
category = "main"
optional = false
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+python-versions = ">=3.8,<3.12"
[package.dependencies]
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+numpy = ">=1.18.5,<1.25.0"
[[package]]
name = "setuptools-scm"
@@ -858,15 +858,15 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
[[package]]
name = "sniffio"
-version = "1.2.0"
+version = "1.3.0"
description = "Sniff out which async library your code is running under"
category = "main"
optional = false
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+python-versions = ">=3.7"
[[package]]
name = "sqlalchemy"
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+version = "1.4.41"
description = "Database Abstraction Library"
category = "main"
optional = false
@@ -880,7 +880,7 @@ aiomysql = ["greenlet (!=0.4.17)", "aiomysql"]
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asyncio = ["greenlet (!=0.4.17)"]
asyncmy = ["greenlet (!=0.4.17)", "asyncmy (>=0.2.3,!=0.2.4)"]
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mssql = ["pyodbc"]
mssql_pymssql = ["pymssql"]
mssql_pyodbc = ["pyodbc"]
@@ -951,7 +951,7 @@ python-versions = ">=3.7"
[[package]]
name = "typer"
-version = "0.4.1"
+version = "0.4.2"
description = "Typer, build great CLIs. Easy to code. Based on Python type hints."
category = "main"
optional = false
@@ -961,10 +961,10 @@ python-versions = ">=3.6"
click = ">=7.1.1,<9.0.0"
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name = "types-python-dateutil"
@@ -976,7 +976,7 @@ python-versions = "*"
[[package]]
name = "types-requests"
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+version = "2.28.10"
description = "Typing stubs for requests"
category = "dev"
optional = false
@@ -987,7 +987,7 @@ types-urllib3 = "<1.27"
[[package]]
name = "types-urllib3"
-version = "1.26.15"
+version = "1.26.24"
description = "Typing stubs for urllib3"
category = "dev"
optional = false
@@ -995,7 +995,7 @@ python-versions = "*"
[[package]]
name = "typing-extensions"
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+version = "4.3.0"
description = "Backported and Experimental Type Hints for Python 3.7+"
category = "main"
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@@ -1003,15 +1003,15 @@ python-versions = ">=3.7"
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description = "HTTP library with thread-safe connection pooling, file post, and more."
category = "main"
optional = false
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@@ -1071,15 +1071,15 @@ python-versions = ">=3.7"
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+urllib3 = []
uvicorn = [
{file = "uvicorn-0.17.6-py3-none-any.whl", hash = "sha256:19e2a0e96c9ac5581c01eb1a79a7d2f72bb479691acd2b8921fce48ed5b961a6"},
{file = "uvicorn-0.17.6.tar.gz", hash = "sha256:5180f9d059611747d841a4a4c4ab675edf54c8489e97f96d0583ee90ac3bfc23"},
]
-uvloop = [
- {file = "uvloop-0.16.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:6224f1401025b748ffecb7a6e2652b17768f30b1a6a3f7b44660e5b5b690b12d"},
- {file = "uvloop-0.16.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:30ba9dcbd0965f5c812b7c2112a1ddf60cf904c1c160f398e7eed3a6b82dcd9c"},
- {file = "uvloop-0.16.0-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:bd53f7f5db562f37cd64a3af5012df8cac2c464c97e732ed556800129505bd64"},
- {file = "uvloop-0.16.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:772206116b9b57cd625c8a88f2413df2fcfd0b496eb188b82a43bed7af2c2ec9"},
- {file = "uvloop-0.16.0-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:b572256409f194521a9895aef274cea88731d14732343da3ecdb175228881638"},
- {file = "uvloop-0.16.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:04ff57aa137230d8cc968f03481176041ae789308b4d5079118331ab01112450"},
- {file = "uvloop-0.16.0-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:3a19828c4f15687675ea912cc28bbcb48e9bb907c801873bd1519b96b04fb805"},
- {file = "uvloop-0.16.0-cp38-cp38-macosx_10_9_universal2.whl", hash = "sha256:e814ac2c6f9daf4c36eb8e85266859f42174a4ff0d71b99405ed559257750382"},
- {file = "uvloop-0.16.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:bd8f42ea1ea8f4e84d265769089964ddda95eb2bb38b5cbe26712b0616c3edee"},
- {file = "uvloop-0.16.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:647e481940379eebd314c00440314c81ea547aa636056f554d491e40503c8464"},
- {file = "uvloop-0.16.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:8e0d26fa5875d43ddbb0d9d79a447d2ace4180d9e3239788208527c4784f7cab"},
- {file = "uvloop-0.16.0-cp39-cp39-macosx_10_9_universal2.whl", hash = "sha256:6ccd57ae8db17d677e9e06192e9c9ec4bd2066b77790f9aa7dede2cc4008ee8f"},
- {file = "uvloop-0.16.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:089b4834fd299d82d83a25e3335372f12117a7d38525217c2258e9b9f4578897"},
- {file = "uvloop-0.16.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:98d117332cc9e5ea8dfdc2b28b0a23f60370d02e1395f88f40d1effd2cb86c4f"},
- {file = "uvloop-0.16.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1e5f2e2ff51aefe6c19ee98af12b4ae61f5be456cd24396953244a30880ad861"},
- {file = "uvloop-0.16.0.tar.gz", hash = "sha256:f74bc20c7b67d1c27c72601c78cf95be99d5c2cdd4514502b4f3eb0933ff1228"},
-]
+uvloop = []
watchgod = [
{file = "watchgod-0.8.2-py3-none-any.whl", hash = "sha256:2f3e8137d98f493ff58af54ea00f4d1433a6afe2ed08ab331a657df468c6bfce"},
{file = "watchgod-0.8.2.tar.gz", hash = "sha256:cb11ff66657befba94d828e3b622d5fb76f22fbda1376f355f3e6e51e97d9450"},
@@ -2075,7 +1479,4 @@ websockets = [
{file = "websockets-10.3-pp37-pypy37_pp73-win_amd64.whl", hash = "sha256:3eda1cb7e9da1b22588cefff09f0951771d6ee9fa8dbe66f5ae04cc5f26b2b55"},
{file = "websockets-10.3.tar.gz", hash = "sha256:fc06cc8073c8e87072138ba1e431300e2d408f054b27047d047b549455066ff4"},
]
-zipp = [
- {file = "zipp-3.8.0-py3-none-any.whl", hash = "sha256:c4f6e5bbf48e74f7a38e7cc5b0480ff42b0ae5178957d564d18932525d5cf099"},
- {file = "zipp-3.8.0.tar.gz", hash = "sha256:56bf8aadb83c24db6c4b577e13de374ccfb67da2078beba1d037c17980bf43ad"},
-]
+zipp = []
diff --git a/pyproject.toml b/pyproject.toml
index 19400fd7..2a599944 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -32,7 +32,7 @@ requests = "^2.27.1"
scipy = "^1.8.0"
typer = "^0.4.0"
# webservice
-alembic = "^1.7.7"
+alembic = "^1.8.0"
Authlib = "^1.0.0"
cryptography = "^36.0.2"
databases = {extras = ["mysql", "sqlite"], version = "^0.5.5"}
--
GitLab
From f8ad53117dfea566bd35e2305b50154d4a7b8741 Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Thu, 4 Aug 2022 11:28:22 -0600
Subject: [PATCH 077/142] new app to tranfer readings from web absolutes to new
webservice
---
geomagio/processing/absolutes.py | 82 ++++++++++++++++++++++++++++++++
1 file changed, 82 insertions(+)
create mode 100644 geomagio/processing/absolutes.py
diff --git a/geomagio/processing/absolutes.py b/geomagio/processing/absolutes.py
new file mode 100644
index 00000000..714482ec
--- /dev/null
+++ b/geomagio/processing/absolutes.py
@@ -0,0 +1,82 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Thu Jul 7 11:05:19 2022
+
+@author: awernle
+"""
+import json
+import typer
+import sys
+from obspy import UTCDateTime
+from datetime import datetime, timedelta
+from geomagio.api.db import database, MetadataDatabaseFactory
+from geomagio.metadata import Metadata, MetadataCategory
+from geomagio.residual import WebAbsolutesFactory
+
+test_metadata = []
+
+app = typer.Typer()
+
+
+@app.command(
+ help=f"""
+ Get existing readings from web absolutes.
+
+ observatory (required): Input 3-letter observatory ID
+
+ starttime (option): Input yyyy-mm-dd, default is 24 hours before current time
+
+ endtime (option): Input yyyy-mm-dd,, default is current time
+
+ """
+)
+def get_readings(observatory: str, starttime: str = None, endtime: str = None):
+ if starttime is None:
+ starttime = UTCDateTime((datetime.today() - timedelta(days=1)))
+ else:
+ starttime = UTCDateTime(starttime)
+ if endtime is None:
+ endtime = UTCDateTime((datetime.today()))
+ else:
+ endtime = UTCDateTime(endtime)
+ readings = WebAbsolutesFactory().get_readings(observatory, starttime, endtime)
+
+ if not readings:
+ print("No readings available for this period")
+ sys.exit()
+ else:
+ print("Readings uploaded")
+
+ for reading in readings:
+ json_string = reading.json()
+ reading_dict = json.loads(json_string)
+ try:
+ reviewer = reading.metadata["reviewer"]
+ except KeyError:
+ reviewer = None
+ test_metadata.append(
+ Metadata(
+ category=MetadataCategory.READING,
+ created_by="absolutes_test.py",
+ network="NT",
+ updated_by=reviewer,
+ starttime=reading.time,
+ endtime=reading.time,
+ station=reading.metadata["station"],
+ metadata=reading_dict,
+ )
+ )
+
+
+async def load_test_metadata():
+ await database.connect()
+ for meta in test_metadata:
+ await MetadataDatabaseFactory(database=database).create_metadata(meta)
+ await database.disconnect()
+
+
+if __name__ == "__main__":
+ import asyncio
+
+ app()
+ asyncio.run(load_test_metadata())
--
GitLab
From f0de5b39b322eb9e2d4bd4c088e966968465ff7a Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Thu, 4 Aug 2022 11:29:30 -0600
Subject: [PATCH 078/142] Test absolutes.py file
---
test/absolutes_test.py | 74 ++++++++++++++++++++++++++++++++++++++++++
1 file changed, 74 insertions(+)
create mode 100644 test/absolutes_test.py
diff --git a/test/absolutes_test.py b/test/absolutes_test.py
new file mode 100644
index 00000000..9e4d1050
--- /dev/null
+++ b/test/absolutes_test.py
@@ -0,0 +1,74 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Thu Jul 7 11:05:19 2022
+
+@author: awernle
+"""
+import json
+
+# import typer
+import sys
+from obspy import UTCDateTime
+from datetime import datetime, timedelta
+from geomagio.api.db import database, MetadataDatabaseFactory
+from geomagio.metadata import Metadata, MetadataCategory
+from geomagio.residual import WebAbsolutesFactory
+
+test_metadata = []
+
+
+def test_get_readings(observatory: str, starttime: str = None, endtime: str = None):
+ if starttime is None:
+ starttime = UTCDateTime((datetime.today() - timedelta(days=1)))
+ else:
+ starttime = UTCDateTime(starttime)
+ if endtime is None:
+ endtime = UTCDateTime((datetime.today()))
+ else:
+ endtime = UTCDateTime(endtime)
+ readings = WebAbsolutesFactory().get_readings(observatory, starttime, endtime)
+
+ if not readings:
+ print("No readings available for this period")
+ sys.exit()
+ else:
+ print("Readings uploaded")
+
+ for reading in readings:
+ json_string = reading.json()
+ reading_dict = json.loads(json_string)
+ try:
+ reviewer = reading.metadata["reviewer"]
+ except KeyError:
+ reviewer = None
+ test_metadata.append(
+ Metadata(
+ category=MetadataCategory.READING,
+ created_by="absolutes_test.py",
+ network="NT",
+ updated_by=reviewer,
+ starttime=reading.time,
+ endtime=reading.time,
+ station=reading.metadata["station"],
+ metadata=reading_dict,
+ )
+ )
+
+
+readings = test_get_readings(
+ observatory="BOU", starttime="2020-01-01", endtime="2020-01-09"
+)
+# print(test_metadata)
+"""
+async def Mock_load_test_metadata():
+ await database.connect()
+ for meta in test_metadata:
+ await MetadataDatabaseFactory(database=database).create_metadata(meta)
+ await database.disconnect()
+
+
+if __name__ == "__main__":
+ import asyncio
+
+ asyncio.run(Mock_load_test_metadata())
+"""
--
GitLab
From d5560aba68a3b2c12029479a646b8aed5deabe29 Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Thu, 11 Aug 2022 15:14:19 -0600
Subject: [PATCH 079/142] Broke up code into smaller functions, changed
starttime/endtime to be defined by first absolutes reading starttime and last
absolutes reading endtime
---
geomagio/processing/absolutes.py | 82 -------------
geomagio/processing/copy_absolutes.py | 166 ++++++++++++++++++++++++++
pyproject.toml | 1 +
3 files changed, 167 insertions(+), 82 deletions(-)
delete mode 100644 geomagio/processing/absolutes.py
create mode 100644 geomagio/processing/copy_absolutes.py
diff --git a/geomagio/processing/absolutes.py b/geomagio/processing/absolutes.py
deleted file mode 100644
index 714482ec..00000000
--- a/geomagio/processing/absolutes.py
+++ /dev/null
@@ -1,82 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Thu Jul 7 11:05:19 2022
-
-@author: awernle
-"""
-import json
-import typer
-import sys
-from obspy import UTCDateTime
-from datetime import datetime, timedelta
-from geomagio.api.db import database, MetadataDatabaseFactory
-from geomagio.metadata import Metadata, MetadataCategory
-from geomagio.residual import WebAbsolutesFactory
-
-test_metadata = []
-
-app = typer.Typer()
-
-
-@app.command(
- help=f"""
- Get existing readings from web absolutes.
-
- observatory (required): Input 3-letter observatory ID
-
- starttime (option): Input yyyy-mm-dd, default is 24 hours before current time
-
- endtime (option): Input yyyy-mm-dd,, default is current time
-
- """
-)
-def get_readings(observatory: str, starttime: str = None, endtime: str = None):
- if starttime is None:
- starttime = UTCDateTime((datetime.today() - timedelta(days=1)))
- else:
- starttime = UTCDateTime(starttime)
- if endtime is None:
- endtime = UTCDateTime((datetime.today()))
- else:
- endtime = UTCDateTime(endtime)
- readings = WebAbsolutesFactory().get_readings(observatory, starttime, endtime)
-
- if not readings:
- print("No readings available for this period")
- sys.exit()
- else:
- print("Readings uploaded")
-
- for reading in readings:
- json_string = reading.json()
- reading_dict = json.loads(json_string)
- try:
- reviewer = reading.metadata["reviewer"]
- except KeyError:
- reviewer = None
- test_metadata.append(
- Metadata(
- category=MetadataCategory.READING,
- created_by="absolutes_test.py",
- network="NT",
- updated_by=reviewer,
- starttime=reading.time,
- endtime=reading.time,
- station=reading.metadata["station"],
- metadata=reading_dict,
- )
- )
-
-
-async def load_test_metadata():
- await database.connect()
- for meta in test_metadata:
- await MetadataDatabaseFactory(database=database).create_metadata(meta)
- await database.disconnect()
-
-
-if __name__ == "__main__":
- import asyncio
-
- app()
- asyncio.run(load_test_metadata())
diff --git a/geomagio/processing/copy_absolutes.py b/geomagio/processing/copy_absolutes.py
new file mode 100644
index 00000000..27d81eed
--- /dev/null
+++ b/geomagio/processing/copy_absolutes.py
@@ -0,0 +1,166 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Thu Jul 7 11:05:19 2022
+
+@author: awernle
+"""
+import os
+import json
+from datetime import date, datetime, time, timedelta
+
+# from types import NoneType
+from typing import List
+
+import typer
+from obspy import UTCDateTime
+
+"""
+from ..metadata import Metadata, MetadataFactory, MetadataCategory
+from ..residual import Reading, WebAbsolutesFactory
+"""
+from geomagio.metadata import Metadata, MetadataFactory, MetadataCategory
+from geomagio.residual import Reading, WebAbsolutesFactory
+
+TODAY = datetime.combine(date.today(), time(0, 0, 0))
+NoneType = type(None)
+
+
+def copy_absolutes(
+ observatory: str = typer.Option(..., help="Observatory code"),
+ starttime: datetime = typer.Option(
+ default=TODAY - timedelta(days=1), help="Search start time, default "
+ ),
+ endtime: datetime = typer.Option(default=TODAY),
+ metadata_token: str = typer.Option(
+ default=os.getenv("GITLAB_API_TOKEN"),
+ help="Token for metadata web service.",
+ metavar="TOKEN",
+ show_default="environment variable GITLAB_API_TOKEN",
+ ),
+ metadata_url: str = typer.Option(
+ default="https://geomag.usgs.gov/ws/secure", # insert staging
+ help="URL to metadata web service",
+ metavar="URL",
+ ),
+ web_absolutes_url: str = typer.Option(
+ default="https://geomag.usgs.gov/baselines/observation.json.php",
+ help="URL to web absolutes service",
+ metavar="URL",
+ ),
+) -> List[Metadata]: # make this nonetype?
+ """Copy absolutes from the web absolutes service into the metadata service."""
+ # read readings from web absolutes
+ web_absolutes_factory = WebAbsolutesFactory(url=web_absolutes_url)
+ readings = get_readings(
+ factory=web_absolutes_factory,
+ observatory=observatory,
+ starttime=UTCDateTime(starttime),
+ endtime=UTCDateTime(endtime),
+ )
+ typer.echo(f"Found {len(readings)} absolutes")
+ # write readings to metadata service
+ metadata_factory = MetadataFactory(token=metadata_token, url=metadata_url)
+ with typer.progressbar(
+ iterable=readings, label="Uploading to metadata service"
+ ) as progressbar:
+ for reading in progressbar:
+ upload_reading(factory=metadata_factory, reading=reading)
+
+
+def create_reading_metadata(reading: Reading) -> Metadata:
+ """Create reading metadata object.
+
+ Parameters
+ ----------
+ reading:
+ reading to convert to metadata.
+
+ Returns
+ -------
+ metadata object for reading
+ """
+ json_string = reading.json()
+ reading_dict = json.loads(json_string)
+ metadata = []
+ try:
+ reviewer = reading.metadata["reviewer"]
+ except KeyError:
+ reviewer = None
+ metadata.append(
+ Metadata(
+ category=MetadataCategory.READING,
+ created_by="absolutes_test.py",
+ network="NT",
+ updated_by=reviewer,
+ starttime=reading.time,
+ endtime=reading.time,
+ station=reading.metadata["station"],
+ metadata=reading_dict,
+ )
+ )
+ return metadata
+ # TODO: should reading starttime/endtime be for range of measurement times?
+ pass
+
+
+def get_readings(
+ factory: WebAbsolutesFactory,
+ observatory: str,
+ starttime: UTCDateTime,
+ endtime: UTCDateTime,
+) -> List[Reading]:
+ """Get readings from web absolutes.
+
+ Parameters
+ ----------
+ factory
+ configured WebAbsolutesFactory
+ observatory
+ search observatory
+ starttime
+ search start time
+ endtime
+ search end time
+
+ Returns
+ -------
+ list of found readings
+ """
+ readings = factory.get_readings(
+ observatory=observatory,
+ starttime=UTCDateTime(starttime),
+ endtime=UTCDateTime(endtime),
+ include_measurements=True,
+ )
+ return readings
+
+
+def upload_reading(factory: MetadataFactory, reading: Reading) -> Metadata:
+ """Upload reading to metadata service
+
+ Parameters
+ ----------
+ factory
+ factory configured for metadata service
+ reading
+ reading to upload
+
+ Returns
+ -------
+ created metadata object
+ """
+ metadata = create_reading_metadata(reading=reading)
+ # TODO: should this check if metadata was already uploaded?
+ # TODO: should that check occur before calling this method?
+ for meta in metadata:
+ return factory.create_metadata(metadata=meta)
+
+
+def main() -> None:
+ """Entrypoint for copy absolutes method."""
+ # for one command, can use typer.run
+ typer.run(copy_absolutes)
+
+
+if __name__ == "__main__":
+ main()
diff --git a/pyproject.toml b/pyproject.toml
index 2a599944..cf5d931e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -71,3 +71,4 @@ geomag-py = "geomagio.Controller:main"
magproc-prepfiles = "geomagio.processing.magproc:main"
make-cal = "geomagio.processing.make_cal:main"
geomag-filter = "geomagio.processing.filters:main"
+copy-absolutes = "geomagio.processing.copy_absolutes:main"
\ No newline at end of file
--
GitLab
From 92b1e91187555e326067324bf8d3219cc1002cde Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Thu, 11 Aug 2022 15:31:20 -0600
Subject: [PATCH 080/142] Delete absolutes_test.py
---
test/absolutes_test.py | 74 ------------------------------------------
1 file changed, 74 deletions(-)
delete mode 100644 test/absolutes_test.py
diff --git a/test/absolutes_test.py b/test/absolutes_test.py
deleted file mode 100644
index 9e4d1050..00000000
--- a/test/absolutes_test.py
+++ /dev/null
@@ -1,74 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Thu Jul 7 11:05:19 2022
-
-@author: awernle
-"""
-import json
-
-# import typer
-import sys
-from obspy import UTCDateTime
-from datetime import datetime, timedelta
-from geomagio.api.db import database, MetadataDatabaseFactory
-from geomagio.metadata import Metadata, MetadataCategory
-from geomagio.residual import WebAbsolutesFactory
-
-test_metadata = []
-
-
-def test_get_readings(observatory: str, starttime: str = None, endtime: str = None):
- if starttime is None:
- starttime = UTCDateTime((datetime.today() - timedelta(days=1)))
- else:
- starttime = UTCDateTime(starttime)
- if endtime is None:
- endtime = UTCDateTime((datetime.today()))
- else:
- endtime = UTCDateTime(endtime)
- readings = WebAbsolutesFactory().get_readings(observatory, starttime, endtime)
-
- if not readings:
- print("No readings available for this period")
- sys.exit()
- else:
- print("Readings uploaded")
-
- for reading in readings:
- json_string = reading.json()
- reading_dict = json.loads(json_string)
- try:
- reviewer = reading.metadata["reviewer"]
- except KeyError:
- reviewer = None
- test_metadata.append(
- Metadata(
- category=MetadataCategory.READING,
- created_by="absolutes_test.py",
- network="NT",
- updated_by=reviewer,
- starttime=reading.time,
- endtime=reading.time,
- station=reading.metadata["station"],
- metadata=reading_dict,
- )
- )
-
-
-readings = test_get_readings(
- observatory="BOU", starttime="2020-01-01", endtime="2020-01-09"
-)
-# print(test_metadata)
-"""
-async def Mock_load_test_metadata():
- await database.connect()
- for meta in test_metadata:
- await MetadataDatabaseFactory(database=database).create_metadata(meta)
- await database.disconnect()
-
-
-if __name__ == "__main__":
- import asyncio
-
- asyncio.run(Mock_load_test_metadata())
-"""
--
GitLab
From fdee3f9d372fb17977c147279c311624d26a092d Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Thu, 18 Aug 2022 14:39:36 -0600
Subject: [PATCH 081/142] Changed starttime/endtime to be defined by first
absolutes reading starttime and last absolutes reading(last commit was
supposed to include this but did not)
---
geomagio/processing/copy_absolutes.py | 28 ++++++++++++---------------
1 file changed, 12 insertions(+), 16 deletions(-)
diff --git a/geomagio/processing/copy_absolutes.py b/geomagio/processing/copy_absolutes.py
index 27d81eed..f5f12763 100644
--- a/geomagio/processing/copy_absolutes.py
+++ b/geomagio/processing/copy_absolutes.py
@@ -8,21 +8,15 @@ import os
import json
from datetime import date, datetime, time, timedelta
-# from types import NoneType
from typing import List
import typer
from obspy import UTCDateTime
-"""
from ..metadata import Metadata, MetadataFactory, MetadataCategory
from ..residual import Reading, WebAbsolutesFactory
-"""
-from geomagio.metadata import Metadata, MetadataFactory, MetadataCategory
-from geomagio.residual import Reading, WebAbsolutesFactory
TODAY = datetime.combine(date.today(), time(0, 0, 0))
-NoneType = type(None)
def copy_absolutes(
@@ -38,7 +32,7 @@ def copy_absolutes(
show_default="environment variable GITLAB_API_TOKEN",
),
metadata_url: str = typer.Option(
- default="https://geomag.usgs.gov/ws/secure", # insert staging
+ default="https://geomag.usgs.gov/ws/secure",
help="URL to metadata web service",
metavar="URL",
),
@@ -47,10 +41,11 @@ def copy_absolutes(
help="URL to web absolutes service",
metavar="URL",
),
-) -> List[Metadata]: # make this nonetype?
+):
"""Copy absolutes from the web absolutes service into the metadata service."""
# read readings from web absolutes
web_absolutes_factory = WebAbsolutesFactory(url=web_absolutes_url)
+ observatory = "BOU"
readings = get_readings(
factory=web_absolutes_factory,
observatory=observatory,
@@ -92,13 +87,14 @@ def create_reading_metadata(reading: Reading) -> Metadata:
created_by="absolutes_test.py",
network="NT",
updated_by=reviewer,
- starttime=reading.time,
- endtime=reading.time,
+ starttime=reading.absolutes[0].starttime,
+ endtime=reading.absolutes[2].endtime,
station=reading.metadata["station"],
metadata=reading_dict,
)
)
return metadata
+
# TODO: should reading starttime/endtime be for range of measurement times?
pass
@@ -135,6 +131,12 @@ def get_readings(
return readings
+def main() -> None:
+ """Entrypoint for copy absolutes method."""
+ # for one command, can use typer.run
+ typer.run(copy_absolutes)
+
+
def upload_reading(factory: MetadataFactory, reading: Reading) -> Metadata:
"""Upload reading to metadata service
@@ -156,11 +158,5 @@ def upload_reading(factory: MetadataFactory, reading: Reading) -> Metadata:
return factory.create_metadata(metadata=meta)
-def main() -> None:
- """Entrypoint for copy absolutes method."""
- # for one command, can use typer.run
- typer.run(copy_absolutes)
-
-
if __name__ == "__main__":
main()
--
GitLab
From 1e2e4ce354150a6fd8eebeb710c62f31c194e33e Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Thu, 22 Sep 2022 10:17:12 -0600
Subject: [PATCH 082/142] Changed starttime and endtime to use list
comprehension
---
geomagio/processing/copy_absolutes.py | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/geomagio/processing/copy_absolutes.py b/geomagio/processing/copy_absolutes.py
index f5f12763..aa786e05 100644
--- a/geomagio/processing/copy_absolutes.py
+++ b/geomagio/processing/copy_absolutes.py
@@ -87,15 +87,14 @@ def create_reading_metadata(reading: Reading) -> Metadata:
created_by="absolutes_test.py",
network="NT",
updated_by=reviewer,
- starttime=reading.absolutes[0].starttime,
- endtime=reading.absolutes[2].endtime,
+ starttime=min([m.time for m in reading.measurements if m.time]),
+ endtime=max([m.time for m in reading.measurements if m.time]),
station=reading.metadata["station"],
metadata=reading_dict,
)
)
return metadata
- # TODO: should reading starttime/endtime be for range of measurement times?
pass
--
GitLab
From 84b649d5da55eb82c0c396ef52297d00ef189b3a Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Fri, 30 Sep 2022 08:45:00 -0600
Subject: [PATCH 083/142] Added status and reviewer to create_reading_metadata
and removed the list of metadata
---
geomagio/processing/copy_absolutes.py | 32 +++++++++++----------------
1 file changed, 13 insertions(+), 19 deletions(-)
diff --git a/geomagio/processing/copy_absolutes.py b/geomagio/processing/copy_absolutes.py
index aa786e05..bd3efb5b 100644
--- a/geomagio/processing/copy_absolutes.py
+++ b/geomagio/processing/copy_absolutes.py
@@ -45,7 +45,6 @@ def copy_absolutes(
"""Copy absolutes from the web absolutes service into the metadata service."""
# read readings from web absolutes
web_absolutes_factory = WebAbsolutesFactory(url=web_absolutes_url)
- observatory = "BOU"
readings = get_readings(
factory=web_absolutes_factory,
observatory=observatory,
@@ -76,23 +75,19 @@ def create_reading_metadata(reading: Reading) -> Metadata:
"""
json_string = reading.json()
reading_dict = json.loads(json_string)
- metadata = []
- try:
- reviewer = reading.metadata["reviewer"]
- except KeyError:
- reviewer = None
- metadata.append(
- Metadata(
- category=MetadataCategory.READING,
- created_by="absolutes_test.py",
- network="NT",
- updated_by=reviewer,
- starttime=min([m.time for m in reading.measurements if m.time]),
- endtime=max([m.time for m in reading.measurements if m.time]),
- station=reading.metadata["station"],
- metadata=reading_dict,
- )
+ reviewer = reading.metadata.get["reviewer"]
+ metadata = Metadata(
+ category=MetadataCategory.READING,
+ created_by=reading.metadata.get("observer", "copy_absolutes"),
+ network="NT",
+ updated_by=reviewer,
+ status="reviewed" if reading.metadata.get("reviewed") else "new",
+ starttime=min([m.time for m in reading.measurements if m.time]),
+ endtime=max([m.time for m in reading.measurements if m.time]),
+ station=reading.metadata["station"],
+ metadata=reading_dict,
)
+
return metadata
pass
@@ -153,8 +148,7 @@ def upload_reading(factory: MetadataFactory, reading: Reading) -> Metadata:
metadata = create_reading_metadata(reading=reading)
# TODO: should this check if metadata was already uploaded?
# TODO: should that check occur before calling this method?
- for meta in metadata:
- return factory.create_metadata(metadata=meta)
+ return factory.create_metadata(metadata=metadata)
if __name__ == "__main__":
--
GitLab
From 6e6ea0f2f5e9cc69cd262d4625996d0c7e2892ae Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Fri, 30 Sep 2022 12:16:26 -0600
Subject: [PATCH 084/142] Clean up copy_absolutes
---
geomagio/processing/copy_absolutes.py | 24 +++++++++---------------
1 file changed, 9 insertions(+), 15 deletions(-)
diff --git a/geomagio/processing/copy_absolutes.py b/geomagio/processing/copy_absolutes.py
index bd3efb5b..f60c214f 100644
--- a/geomagio/processing/copy_absolutes.py
+++ b/geomagio/processing/copy_absolutes.py
@@ -4,16 +4,15 @@ Created on Thu Jul 7 11:05:19 2022
@author: awernle
"""
-import os
import json
+import os
from datetime import date, datetime, time, timedelta
-
from typing import List
import typer
from obspy import UTCDateTime
-from ..metadata import Metadata, MetadataFactory, MetadataCategory
+from ..metadata import Metadata, MetadataCategory, MetadataFactory
from ..residual import Reading, WebAbsolutesFactory
TODAY = datetime.combine(date.today(), time(0, 0, 0))
@@ -51,7 +50,7 @@ def copy_absolutes(
starttime=UTCDateTime(starttime),
endtime=UTCDateTime(endtime),
)
- typer.echo(f"Found {len(readings)} absolutes")
+ print(f"Found {len(readings)} absolutes")
# write readings to metadata service
metadata_factory = MetadataFactory(token=metadata_token, url=metadata_url)
with typer.progressbar(
@@ -73,25 +72,20 @@ def create_reading_metadata(reading: Reading) -> Metadata:
-------
metadata object for reading
"""
- json_string = reading.json()
- reading_dict = json.loads(json_string)
- reviewer = reading.metadata.get["reviewer"]
+ measurement_times = [m.time for m in reading.measurements if m.time]
metadata = Metadata(
category=MetadataCategory.READING,
created_by=reading.metadata.get("observer", "copy_absolutes"),
+ endtime=max(measurement_times),
+ metadata=json.loads(reading.json()),
network="NT",
- updated_by=reviewer,
- status="reviewed" if reading.metadata.get("reviewed") else "new",
- starttime=min([m.time for m in reading.measurements if m.time]),
- endtime=max([m.time for m in reading.measurements if m.time]),
+ starttime=min(measurement_times),
station=reading.metadata["station"],
- metadata=reading_dict,
+ status="reviewed" if reading.metadata.get("reviewed") else "new",
+ updated_by=reading.metadata.get("reviewer"),
)
-
return metadata
- pass
-
def get_readings(
factory: WebAbsolutesFactory,
--
GitLab
From 7373ada00e256ec9ddd89e2d3d2590ea9aeb9ab3 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Thu, 11 Aug 2022 22:32:31 -0600
Subject: [PATCH 085/142] pyproject: add isort, poethepoet, poe tasks for lint,
test
---
poetry.lock | 851 +++++++++++++++++++++++++++++++++++++++++++++----
pyproject.toml | 24 +-
2 files changed, 802 insertions(+), 73 deletions(-)
diff --git a/poetry.lock b/poetry.lock
index 1e57d989..f353b962 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -104,11 +104,11 @@ cryptography = ">=3.2"
[[package]]
name = "black"
-version = "22.8.0"
+version = "22.10.0"
description = "The uncompromising code formatter."
category = "dev"
optional = false
-python-versions = ">=3.6.2"
+python-versions = ">=3.7"
[package.dependencies]
click = ">=8.0.0"
@@ -126,7 +126,7 @@ uvloop = ["uvloop (>=0.15.2)"]
[[package]]
name = "certifi"
-version = "2022.9.14"
+version = "2022.9.24"
description = "Python package for providing Mozilla's CA Bundle."
category = "main"
optional = false
@@ -173,9 +173,27 @@ category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+[[package]]
+name = "contourpy"
+version = "1.0.5"
+description = "Python library for calculating contours of 2D quadrilateral grids"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+numpy = ">=1.16"
+
+[package.extras]
+test-no-codebase = ["pillow", "matplotlib", "pytest"]
+test-minimal = ["pytest"]
+test = ["isort", "flake8", "pillow", "matplotlib", "pytest"]
+docs = ["sphinx-rtd-theme", "sphinx", "docutils (<0.18)"]
+bokeh = ["selenium", "bokeh"]
+
[[package]]
name = "coverage"
-version = "6.4.4"
+version = "6.5.0"
description = "Code coverage measurement for Python"
category = "dev"
optional = false
@@ -252,7 +270,7 @@ python-versions = ">=3.5"
[[package]]
name = "dparse"
-version = "0.6.0"
+version = "0.6.2"
description = "A parser for Python dependency files"
category = "dev"
optional = false
@@ -294,7 +312,7 @@ test = ["pytest (>=6.2.4,<7.0.0)", "pytest-cov (>=2.12.0,<4.0.0)", "mypy (==0.91
[[package]]
name = "fonttools"
-version = "4.37.2"
+version = "4.37.4"
description = "Tools to manipulate font files"
category = "main"
optional = false
@@ -316,7 +334,7 @@ woff = ["zopfli (>=0.1.4)", "brotlicffi (>=0.8.0)", "brotli (>=1.0.1)"]
[[package]]
name = "greenlet"
-version = "1.1.3"
+version = "1.1.3.post0"
description = "Lightweight in-process concurrent programming"
category = "main"
optional = false
@@ -407,7 +425,7 @@ python-versions = ">=3.5"
[[package]]
name = "importlib-metadata"
-version = "4.12.0"
+version = "5.0.0"
description = "Read metadata from Python packages"
category = "main"
optional = false
@@ -417,13 +435,13 @@ python-versions = ">=3.7"
zipp = ">=0.5"
[package.extras]
-docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
+docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
perf = ["ipython"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
[[package]]
name = "importlib-resources"
-version = "5.9.0"
+version = "5.10.0"
description = "Read resources from Python packages"
category = "main"
optional = false
@@ -433,8 +451,8 @@ python-versions = ">=3.7"
zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
[package.extras]
-docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "jaraco.tidelift (>=1.4)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
+docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
[[package]]
name = "iniconfig"
@@ -444,6 +462,20 @@ category = "dev"
optional = false
python-versions = "*"
+[[package]]
+name = "isort"
+version = "5.10.1"
+description = "A Python utility / library to sort Python imports."
+category = "dev"
+optional = false
+python-versions = ">=3.6.1,<4.0"
+
+[package.extras]
+pipfile_deprecated_finder = ["pipreqs", "requirementslib"]
+requirements_deprecated_finder = ["pipreqs", "pip-api"]
+colors = ["colorama (>=0.4.3,<0.5.0)"]
+plugins = ["setuptools"]
+
[[package]]
name = "kiwisolver"
version = "1.4.4"
@@ -461,14 +493,14 @@ optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*"
[package.extras]
-cssselect = ["cssselect (>=0.7)"]
-html5 = ["html5lib"]
-htmlsoup = ["beautifulsoup4"]
source = ["Cython (>=0.29.7)"]
+htmlsoup = ["beautifulsoup4"]
+html5 = ["html5lib"]
+cssselect = ["cssselect (>=0.7)"]
[[package]]
name = "mako"
-version = "1.2.2"
+version = "1.2.3"
description = "A super-fast templating language that borrows the best ideas from the existing templating languages."
category = "main"
optional = false
@@ -492,22 +524,23 @@ python-versions = ">=3.7"
[[package]]
name = "matplotlib"
-version = "3.5.3"
+version = "3.6.1"
description = "Python plotting package"
category = "main"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
[package.dependencies]
+contourpy = ">=1.0.1"
cycler = ">=0.10"
fonttools = ">=4.22.0"
kiwisolver = ">=1.0.1"
-numpy = ">=1.17"
+numpy = ">=1.19"
packaging = ">=20.0"
pillow = ">=6.2.0"
pyparsing = ">=2.2.1"
python-dateutil = ">=2.7"
-setuptools_scm = ">=4,<7"
+setuptools_scm = ">=7"
[[package]]
name = "mypy"
@@ -580,7 +613,7 @@ et-xmlfile = "*"
[[package]]
name = "openpyxl-stubs"
-version = "0.1.22"
+version = "0.1.24"
description = "Type stubs for openpyxl"
category = "dev"
optional = false
@@ -602,6 +635,14 @@ python-versions = ">=3.6"
[package.dependencies]
pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
+[[package]]
+name = "pastel"
+version = "0.2.1"
+description = "Bring colors to your terminal."
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+
[[package]]
name = "pathspec"
version = "0.10.1"
@@ -646,6 +687,21 @@ python-versions = ">=3.6"
dev = ["pre-commit", "tox"]
testing = ["pytest", "pytest-benchmark"]
+[[package]]
+name = "poethepoet"
+version = "0.16.4"
+description = "A task runner that works well with poetry."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+pastel = ">=0.2.1,<0.3.0"
+tomli = ">=1.2.2"
+
+[package.extras]
+poetry_plugin = ["poetry (>=1.0,<2.0)"]
+
[[package]]
name = "py"
version = "1.11.0"
@@ -823,26 +879,32 @@ requests = "*"
[[package]]
name = "scipy"
-version = "1.9.1"
-description = "SciPy: Scientific Library for Python"
+version = "1.9.2"
+description = "Fundamental algorithms for scientific computing in Python"
category = "main"
optional = false
-python-versions = ">=3.8,<3.12"
+python-versions = ">=3.8"
[package.dependencies]
-numpy = ">=1.18.5,<1.25.0"
+numpy = ">=1.18.5,<1.26.0"
+
+[package.extras]
+test = ["pytest", "pytest-cov", "pytest-xdist", "asv", "mpmath", "gmpy2", "threadpoolctl", "scikit-umfpack"]
+doc = ["sphinx (!=4.1.0)", "pydata-sphinx-theme (==0.9.0)", "sphinx-panels (>=0.5.2)", "matplotlib (>2)", "numpydoc", "sphinx-tabs"]
+dev = ["mypy", "typing-extensions", "pycodestyle", "flake8"]
[[package]]
name = "setuptools-scm"
-version = "6.4.2"
+version = "7.0.5"
description = "the blessed package to manage your versions by scm tags"
category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
[package.dependencies]
packaging = ">=20.0"
tomli = ">=1.0.0"
+typing-extensions = "*"
[package.extras]
test = ["pytest (>=6.2)", "virtualenv (>20)"]
@@ -976,7 +1038,7 @@ python-versions = "*"
[[package]]
name = "types-requests"
-version = "2.28.10"
+version = "2.28.11.2"
description = "Typing stubs for requests"
category = "dev"
optional = false
@@ -987,7 +1049,7 @@ types-urllib3 = "<1.27"
[[package]]
name = "types-urllib3"
-version = "1.26.24"
+version = "1.26.25"
description = "Typing stubs for urllib3"
category = "dev"
optional = false
@@ -995,7 +1057,7 @@ python-versions = "*"
[[package]]
name = "typing-extensions"
-version = "4.3.0"
+version = "4.4.0"
description = "Backported and Experimental Type Hints for Python 3.7+"
category = "main"
optional = false
@@ -1071,15 +1133,15 @@ python-versions = ">=3.7"
[[package]]
name = "zipp"
-version = "3.8.1"
+version = "3.9.0"
description = "Backport of pathlib-compatible object wrapper for zip files"
category = "main"
optional = false
python-versions = ">=3.7"
[package.extras]
-docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "jaraco.tidelift (>=1.4)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.3)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
+docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "jaraco.itertools", "func-timeout", "jaraco.functools", "more-itertools", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
[extras]
pycurl = ["pycurl"]
@@ -1087,7 +1149,7 @@ pycurl = ["pycurl"]
[metadata]
lock-version = "1.1"
python-versions = "^3.8,<3.11"
-content-hash = "7b8b105ca83ef8e52fbe25b28598fe9ea7561a51c2d5b72b452e0e187b485c4e"
+content-hash = "9ab05116e413805c6164304403e5972b20d03c22b8efad5895a3b051d6785d51"
[metadata.files]
aiomysql = [
@@ -1109,17 +1171,238 @@ asgiref = [
]
atomicwrites = []
attrs = []
-authlib = []
-black = []
-certifi = []
-cffi = []
-charset-normalizer = []
+authlib = [
+ {file = "Authlib-1.1.0-py2.py3-none-any.whl", hash = "sha256:be4b6a1dea51122336c210a6945b27a105b9ac572baffd15b07bcff4376c1523"},
+ {file = "Authlib-1.1.0.tar.gz", hash = "sha256:0a270c91409fc2b7b0fbee6996e09f2ee3187358762111a9a4225c874b94e891"},
+]
+black = [
+ {file = "black-22.10.0-1fixedarch-cp310-cp310-macosx_11_0_x86_64.whl", hash = "sha256:5cc42ca67989e9c3cf859e84c2bf014f6633db63d1cbdf8fdb666dcd9e77e3fa"},
+ {file = "black-22.10.0-1fixedarch-cp311-cp311-macosx_11_0_x86_64.whl", hash = "sha256:5d8f74030e67087b219b032aa33a919fae8806d49c867846bfacde57f43972ef"},
+ {file = "black-22.10.0-1fixedarch-cp37-cp37m-macosx_10_16_x86_64.whl", hash = "sha256:197df8509263b0b8614e1df1756b1dd41be6738eed2ba9e9769f3880c2b9d7b6"},
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+ {file = "uvloop-0.17.0-cp38-cp38-macosx_10_9_universal2.whl", hash = "sha256:a4aee22ece20958888eedbad20e4dbb03c37533e010fb824161b4f05e641f738"},
+ {file = "uvloop-0.17.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:307958f9fc5c8bb01fad752d1345168c0abc5d62c1b72a4a8c6c06f042b45b20"},
+ {file = "uvloop-0.17.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:3ebeeec6a6641d0adb2ea71dcfb76017602ee2bfd8213e3fcc18d8f699c5104f"},
+ {file = "uvloop-0.17.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:1436c8673c1563422213ac6907789ecb2b070f5939b9cbff9ef7113f2b531595"},
+ {file = "uvloop-0.17.0-cp38-cp38-musllinux_1_1_aarch64.whl", hash = "sha256:8887d675a64cfc59f4ecd34382e5b4f0ef4ae1da37ed665adba0c2badf0d6578"},
+ {file = "uvloop-0.17.0-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:3db8de10ed684995a7f34a001f15b374c230f7655ae840964d51496e2f8a8474"},
+ {file = "uvloop-0.17.0-cp39-cp39-macosx_10_9_universal2.whl", hash = "sha256:7d37dccc7ae63e61f7b96ee2e19c40f153ba6ce730d8ba4d3b4e9738c1dccc1b"},
+ {file = "uvloop-0.17.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:cbbe908fda687e39afd6ea2a2f14c2c3e43f2ca88e3a11964b297822358d0e6c"},
+ {file = "uvloop-0.17.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:3d97672dc709fa4447ab83276f344a165075fd9f366a97b712bdd3fee05efae8"},
+ {file = "uvloop-0.17.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f1e507c9ee39c61bfddd79714e4f85900656db1aec4d40c6de55648e85c2799c"},
+ {file = "uvloop-0.17.0-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:c092a2c1e736086d59ac8e41f9c98f26bbf9b9222a76f21af9dfe949b99b2eb9"},
+ {file = "uvloop-0.17.0-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:30babd84706115626ea78ea5dbc7dd8d0d01a2e9f9b306d24ca4ed5796c66ded"},
+ {file = "uvloop-0.17.0.tar.gz", hash = "sha256:0ddf6baf9cf11a1a22c71487f39f15b2cf78eb5bde7e5b45fbb99e8a9d91b9e1"},
+]
watchgod = [
{file = "watchgod-0.8.2-py3-none-any.whl", hash = "sha256:2f3e8137d98f493ff58af54ea00f4d1433a6afe2ed08ab331a657df468c6bfce"},
{file = "watchgod-0.8.2.tar.gz", hash = "sha256:cb11ff66657befba94d828e3b622d5fb76f22fbda1376f355f3e6e51e97d9450"},
@@ -1479,4 +2187,7 @@ websockets = [
{file = "websockets-10.3-pp37-pypy37_pp73-win_amd64.whl", hash = "sha256:3eda1cb7e9da1b22588cefff09f0951771d6ee9fa8dbe66f5ae04cc5f26b2b55"},
{file = "websockets-10.3.tar.gz", hash = "sha256:fc06cc8073c8e87072138ba1e431300e2d408f054b27047d047b549455066ff4"},
]
-zipp = []
+zipp = [
+ {file = "zipp-3.9.0-py3-none-any.whl", hash = "sha256:972cfa31bc2fedd3fa838a51e9bc7e64b7fb725a8c00e7431554311f180e9980"},
+ {file = "zipp-3.9.0.tar.gz", hash = "sha256:3a7af91c3db40ec72dd9d154ae18e008c69efe8ca88dde4f9a731bb82fe2f9eb"},
+]
diff --git a/pyproject.toml b/pyproject.toml
index cf5d931e..4de69450 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,18 +38,20 @@ cryptography = "^36.0.2"
databases = {extras = ["mysql", "sqlite"], version = "^0.5.5"}
fastapi = "^0.75.0"
gunicorn = "^20.1.0"
+httpx = "0.22.0"
SQLAlchemy = "^1.4.32"
SQLAlchemy-Utc = "^0.14.0"
uvicorn = {extras = ["standard"], version = "^0.17.6"}
-httpx = "0.22.0"
[tool.poetry.dev-dependencies]
black = "^22.1.0"
+isort = "^5.10.1"
+mypy = "^0.941"
+poethepoet = "^0.16.0"
pytest = "^6.2.4"
pytest-cov = "^2.12.1"
safety = "^1.10.3"
-mypy = "^0.941"
# type hints
data-science-types = "^0.2.23"
openpyxl-stubs = "^0.1.19"
@@ -71,4 +73,20 @@ geomag-py = "geomagio.Controller:main"
magproc-prepfiles = "geomagio.processing.magproc:main"
make-cal = "geomagio.processing.make_cal:main"
geomag-filter = "geomagio.processing.filters:main"
-copy-absolutes = "geomagio.processing.copy_absolutes:main"
\ No newline at end of file
+copy-absolutes = "geomagio.processing.copy_absolutes:main"
+
+
+[tool.poe.tasks]
+# e.g. "poetry run poe lint"
+lint = [
+ { shell = "black --check ." },
+ # TODO: fix isort warnings then enable this check
+ # { shell = "isort --check ." },
+ # TODO: fix mypy warnings then enable this check
+ # { shell = "mypy ." }
+]
+test = [
+ { shell = "pytest --cov=geomagio --junitxml junit.xml test" },
+ { shell = "coverage html" },
+ { shell = "coverage xml" }
+]
--
GitLab
From f2c295348570c9298d160f62a68245f508082866 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Thu, 11 Aug 2022 22:33:22 -0600
Subject: [PATCH 086/142] Update default FROM_IMAGE to python 3.10
---
Dockerfile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Dockerfile b/Dockerfile
index 6dece3a7..4e4219ff 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-ARG FROM_IMAGE=usgs/python:3.9-obspy
+ARG FROM_IMAGE=code.usgs.gov:5001/devops/images/usgs/python:3.10-obspy
# build wheel
FROM ${FROM_IMAGE} as build
--
GitLab
From edd6fad37b2dc2d1bbccaf3aa1a1b80e3e33ddfe Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Thu, 11 Aug 2022 23:06:49 -0600
Subject: [PATCH 087/142] Update pipeline to use code.usgs.gov images
---
.gitignore | 11 +++++-----
.gitlab-ci.yml | 54 +++++++++++++++++++++++++++++++-------------------
pyproject.toml | 3 +++
3 files changed, 43 insertions(+), 25 deletions(-)
diff --git a/.gitignore b/.gitignore
index 574fe32b..024eb667 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,14 +1,15 @@
+__pycache__
.coverage
-cov.xml
.DS_Store
.eggs
-*.pyc
-coverage.xml
.ipynb_checkpoints*
.mypy_cache
.pytest_cache
-htmlcov
.vscode
+*.egg-info
+*.pyc
build
+coverage.xml
dist
-*.egg-info
\ No newline at end of file
+htmlcov
+junit.xml
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c7e28786..e6f77b92 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,4 +1,4 @@
-image: ${DEVOPS_REGISTRY}usgs/python:3.9-obspy
+image: code.usgs.gov:5001/devops/images/usgs/python:3.10-obspy
stages:
- init
@@ -28,7 +28,6 @@ workflow:
- IMAGE_NAME=usgs/${APP_NAME}:${CI_COMMIT_REF_SLUG}
- IMAGE_NAME=${IMAGE_NAME/:master/:latest}
- INTERNAL_IMAGE_NAME=${CODE_REGISTRY_IMAGE}/${IMAGE_NAME}
- - STACK_NAME=${APP_NAME}
.deploy:
extends:
@@ -90,6 +89,22 @@ workflow:
APP_DEPLOY_DIR: "/geomag/geomag-algorithms"
REQUIRED_PREFIX: "/geomag"
+# template for jobs that need docker-in-docker
+.dind:
+ # TODO: refactor Docker build to different runner
+ # before_script:
+ # - |
+ # echo "${CI_REGISTRY_PASSWORD}" | docker login \
+ # --username "${CI_REGISTRY_USER}" \
+ # --password-stdin \
+ # "${CI_REGISTRY}"
+ image: code.usgs.gov:5001/devops/images/usgs/docker:20
+ services:
+ - alias: docker
+ name: code.usgs.gov:5001/devops/images/usgs/docker:20-dind
+ variables:
+ DOCKER_DRIVER: overlay2
+
# rules to define which branches should trigger actions
.development-env: &development-env
if: $CI_PROJECT_PATH != $UPSTREAM_PATH
@@ -106,7 +121,7 @@ workflow:
.production-env: &production-env
if: >
$CI_PROJECT_PATH == $UPSTREAM_PATH
- && ( $CI_COMMIT_BRANCH == 'production' || $CI_COMMIT_TAG)
+ && ( $CI_COMMIT_BRANCH == 'production' || $CI_COMMIT_TAG )
variables:
ENVIRONMENT: production
@@ -127,7 +142,6 @@ Poetry:
# install into .venv for artifact
- poetry config virtualenvs.in-project true --local
- poetry install
- - poetry run safety check
stage: init
variables:
PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
@@ -136,21 +150,28 @@ Poetry:
# Test Stage
## --------------------------------------------------
-Python Build:
+Audit:
+ needs:
+ - Poetry
+ script:
+ - poetry run poe audit
+ stage: test
+
+Build:
needs:
- Poetry
script:
- poetry build
stage: test
-Python Lint:
+Lint:
needs:
- Poetry
script:
- - poetry run black --check .
+ - poetry run poe lint
stage: test
-Python Test:
+Test:
artifacts:
reports:
coverage_report:
@@ -160,8 +181,7 @@ Python Test:
needs:
- Poetry
script:
- - poetry run pytest --cov=geomagio --junitxml junit.xml
- - poetry run coverage xml
+ - poetry run poe test
stage: test
## --------------------------------------------------
@@ -171,9 +191,9 @@ Python Test:
Build Docker Image:
extends:
- .adjust_image_names
- image: ${DEVOPS_REGISTRY}docker:19.03-git
+ - .dind
needs:
- - Python Build
+ - Build
script:
- LOCAL_IMAGE="local/${IMAGE_NAME}"
## build image
@@ -186,8 +206,6 @@ Build Docker Image:
"."
## trivy scan before push
- - wget https://github.com/aquasecurity/trivy/releases/download/v${TRIVY_VERSION}/trivy_${TRIVY_VERSION}_Linux-64bit.tar.gz
- - tar zxvf trivy_${TRIVY_VERSION}_Linux-64bit.tar.gz
# fail LOW,MEDIUM vulnerabilities that have a fix available
- ./trivy image --exit-code 1 --ignore-unfixed --severity LOW,MEDIUM "${LOCAL_IMAGE}";
# fail HIGH,CRITICAL vulnerabilities
@@ -203,17 +221,13 @@ Build Docker Image:
docker tag "${LOCAL_IMAGE}" "${IMAGE}";
docker push "${IMAGE}";
done
- services:
- - alias: docker
- name: ${DEVOPS_REGISTRY}docker:19.03-dind
stage: integration
tags:
+ # TODO: refactor to separate build/publish steps
- build
variables:
APP_NAME: geomag-algorithms
- DOCKER_DRIVER: overlay2
- FROM_IMAGE: ${DEVOPS_REGISTRY}usgs/python:3.9-obspy
- TRIVY_VERSION: "0.27.1"
+ FROM_IMAGE: code.usgs.gov:5001/devops/images/usgs/python:3.10-obspy
## --------------------------------------------------
# Deploy Stage
diff --git a/pyproject.toml b/pyproject.toml
index 4de69450..41503ae5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -78,6 +78,9 @@ copy-absolutes = "geomagio.processing.copy_absolutes:main"
[tool.poe.tasks]
# e.g. "poetry run poe lint"
+audit = [
+ { shell = "safety check"}
+]
lint = [
{ shell = "black --check ." },
# TODO: fix isort warnings then enable this check
--
GitLab
From afb8d8fa3afa333054666ecc46bb8e717027e701 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Tue, 16 Aug 2022 01:35:06 -0600
Subject: [PATCH 088/142] Add SETUPTOOLS_USE_DISTUTILS to poetry job
---
.gitlab-ci.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index e6f77b92..2ac1b0c7 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -145,6 +145,7 @@ Poetry:
stage: init
variables:
PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
+ SETUPTOOLS_USE_DISTUTILS: stdlib
## --------------------------------------------------
# Test Stage
--
GitLab
From 60fcf6260a43f58df37874313e1b5c2478ee7b77 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Tue, 16 Aug 2022 01:46:14 -0600
Subject: [PATCH 089/142] pipeline: Update path to trivy
---
.gitlab-ci.yml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 2ac1b0c7..6884d32d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -208,9 +208,9 @@ Build Docker Image:
## trivy scan before push
# fail LOW,MEDIUM vulnerabilities that have a fix available
- - ./trivy image --exit-code 1 --ignore-unfixed --severity LOW,MEDIUM "${LOCAL_IMAGE}";
+ - trivy image --exit-code 1 --ignore-unfixed --severity LOW,MEDIUM "${LOCAL_IMAGE}";
# fail HIGH,CRITICAL vulnerabilities
- - ./trivy image --exit-code 1 --severity HIGH,CRITICAL "${LOCAL_IMAGE}";
+ - trivy image --exit-code 1 --severity HIGH,CRITICAL "${LOCAL_IMAGE}";
## push image
- if [ "${CI_PROJECT_PATH}" != "${UPSTREAM_PATH}" ]; then
--
GitLab
From 08e73910e42e3195ea2136261e60bc18e9f04fee Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Mon, 24 Oct 2022 14:02:54 -0600
Subject: [PATCH 090/142] Log session load exceptions
---
geomagio/api/secure/SessionMiddleware.py | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/geomagio/api/secure/SessionMiddleware.py b/geomagio/api/secure/SessionMiddleware.py
index 3bf0ea8e..3d455bad 100644
--- a/geomagio/api/secure/SessionMiddleware.py
+++ b/geomagio/api/secure/SessionMiddleware.py
@@ -1,6 +1,7 @@
import json
-from typing import Callable, Dict, Mapping
+import logging
import uuid
+from typing import Callable, Dict, Mapping
from cryptography.fernet import Fernet
from starlette.datastructures import MutableHeaders
@@ -73,6 +74,7 @@ class SessionMiddleware:
scope["session"] = await self.get_session(session_id)
initial_session_was_empty = False
except Exception:
+ logging.exception(f"Error loading session {session_id}")
scope["session"] = {}
else:
scope["session"] = {}
--
GitLab
From 7094c1c2a1464744d0b9cedc33a55920a6fe9dad Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Mon, 24 Oct 2022 14:03:41 -0600
Subject: [PATCH 091/142] pyproject.toml: pin sqlalchemy version to 1.4.41 to
fix session issue
---
poetry.lock | 517 +++++++++++++++++++++++++++++++++----------------
pyproject.toml | 7 +-
2 files changed, 357 insertions(+), 167 deletions(-)
diff --git a/poetry.lock b/poetry.lock
index f353b962..93c63aa9 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -43,7 +43,7 @@ tz = ["python-dateutil"]
[[package]]
name = "anyio"
-version = "3.6.1"
+version = "3.6.2"
description = "High level compatibility layer for multiple asynchronous event loop implementations"
category = "main"
optional = false
@@ -54,9 +54,9 @@ idna = ">=2.8"
sniffio = ">=1.1"
[package.extras]
-doc = ["packaging", "sphinx-rtd-theme", "sphinx-autodoc-typehints (>=1.2.0)"]
-test = ["coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "contextlib2", "uvloop (<0.15)", "mock (>=4)", "uvloop (>=0.15)"]
-trio = ["trio (>=0.16)"]
+doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
+test = ["contextlib2", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (<0.15)", "uvloop (>=0.15)"]
+trio = ["trio (>=0.16,<0.22)"]
[[package]]
name = "asgiref"
@@ -67,7 +67,7 @@ optional = false
python-versions = ">=3.7"
[package.extras]
-tests = ["pytest", "pytest-asyncio", "mypy (>=0.800)"]
+tests = ["mypy (>=0.800)", "pytest", "pytest-asyncio"]
[[package]]
name = "atomicwrites"
@@ -86,10 +86,10 @@ optional = false
python-versions = ">=3.5"
[package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
-docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "cloudpickle"]
+dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"]
+docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"]
+tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"]
+tests-no-zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"]
[[package]]
name = "authlib"
@@ -152,7 +152,7 @@ optional = false
python-versions = ">=3.6.0"
[package.extras]
-unicode_backport = ["unicodedata2"]
+unicode-backport = ["unicodedata2"]
[[package]]
name = "click"
@@ -185,11 +185,11 @@ python-versions = ">=3.7"
numpy = ">=1.16"
[package.extras]
-test-no-codebase = ["pillow", "matplotlib", "pytest"]
+bokeh = ["bokeh", "selenium"]
+docs = ["docutils (<0.18)", "sphinx", "sphinx-rtd-theme"]
+test = ["Pillow", "flake8", "isort", "matplotlib", "pytest"]
test-minimal = ["pytest"]
-test = ["isort", "flake8", "pillow", "matplotlib", "pytest"]
-docs = ["sphinx-rtd-theme", "sphinx", "docutils (<0.18)"]
-bokeh = ["selenium", "bokeh"]
+test-no-codebase = ["Pillow", "matplotlib", "pytest"]
[[package]]
name = "coverage"
@@ -214,12 +214,12 @@ python-versions = ">=3.6"
cffi = ">=1.12"
[package.extras]
-docs = ["sphinx (>=1.6.5,!=1.8.0,!=3.1.0,!=3.1.1)", "sphinx-rtd-theme"]
-docstest = ["pyenchant (>=1.6.11)", "twine (>=1.12.0)", "sphinxcontrib-spelling (>=4.0.1)"]
+docs = ["sphinx (>=1.6.5,!=1.8.0,!=3.1.0,!=3.1.1)", "sphinx_rtd_theme"]
+docstest = ["pyenchant (>=1.6.11)", "sphinxcontrib-spelling (>=4.0.1)", "twine (>=1.12.0)"]
pep8test = ["black", "flake8", "flake8-import-order", "pep8-naming"]
sdist = ["setuptools_rust (>=0.11.4)"]
ssh = ["bcrypt (>=3.1.5)"]
-test = ["pytest (>=6.2.0)", "pytest-cov", "pytest-subtests", "pytest-xdist", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,!=3.79.2)"]
+test = ["hypothesis (>=1.11.4,!=3.79.2)", "iso8601", "pretend", "pytest (>=6.2.0)", "pytest-cov", "pytest-subtests", "pytest-xdist", "pytz"]
[[package]]
name = "cycler"
@@ -255,9 +255,9 @@ sqlalchemy = ">=1.4,<1.5"
[package.extras]
mysql = ["aiomysql"]
-mysql_asyncmy = ["asyncmy"]
+mysql-asyncmy = ["asyncmy"]
postgresql = ["asyncpg"]
-postgresql_aiopg = ["aiopg"]
+postgresql-aiopg = ["aiopg"]
sqlite = ["aiosqlite"]
[[package]]
@@ -281,8 +281,8 @@ packaging = "*"
toml = "*"
[package.extras]
-pipenv = ["pipenv"]
conda = ["pyyaml"]
+pipenv = ["pipenv"]
[[package]]
name = "et-xmlfile"
@@ -305,23 +305,23 @@ pydantic = ">=1.6.2,<1.7 || >1.7,<1.7.1 || >1.7.1,<1.7.2 || >1.7.2,<1.7.3 || >1.
starlette = "0.17.1"
[package.extras]
-all = ["requests (>=2.24.0,<3.0.0)", "jinja2 (>=2.11.2,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "itsdangerous (>=1.1.0,<3.0.0)", "pyyaml (>=5.3.1,<7.0.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)", "orjson (>=3.2.1,<4.0.0)", "email_validator (>=1.1.1,<2.0.0)", "uvicorn[standard] (>=0.12.0,<0.18.0)"]
-dev = ["python-jose[cryptography] (>=3.3.0,<4.0.0)", "passlib[bcrypt] (>=1.7.2,<2.0.0)", "autoflake (>=1.4.0,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "uvicorn[standard] (>=0.12.0,<0.18.0)"]
-doc = ["mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "mdx-include (>=1.4.1,<2.0.0)", "mkdocs-markdownextradata-plugin (>=0.1.7,<0.3.0)", "typer (>=0.4.1,<0.5.0)", "pyyaml (>=5.3.1,<7.0.0)"]
-test = ["pytest (>=6.2.4,<7.0.0)", "pytest-cov (>=2.12.0,<4.0.0)", "mypy (==0.910)", "flake8 (>=3.8.3,<4.0.0)", "black (==22.3.0)", "isort (>=5.0.6,<6.0.0)", "requests (>=2.24.0,<3.0.0)", "httpx (>=0.14.0,<0.19.0)", "email_validator (>=1.1.1,<2.0.0)", "sqlalchemy (>=1.3.18,<1.5.0)", "peewee (>=3.13.3,<4.0.0)", "databases[sqlite] (>=0.3.2,<0.6.0)", "orjson (>=3.2.1,<4.0.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "flask (>=1.1.2,<3.0.0)", "anyio[trio] (>=3.2.1,<4.0.0)", "types-ujson (==4.2.1)", "types-orjson (==3.6.2)", "types-dataclasses (==0.6.5)"]
+all = ["email_validator (>=1.1.1,<2.0.0)", "itsdangerous (>=1.1.0,<3.0.0)", "jinja2 (>=2.11.2,<4.0.0)", "orjson (>=3.2.1,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "pyyaml (>=5.3.1,<7.0.0)", "requests (>=2.24.0,<3.0.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)", "uvicorn[standard] (>=0.12.0,<0.18.0)"]
+dev = ["autoflake (>=1.4.0,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "passlib[bcrypt] (>=1.7.2,<2.0.0)", "python-jose[cryptography] (>=3.3.0,<4.0.0)", "uvicorn[standard] (>=0.12.0,<0.18.0)"]
+doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-markdownextradata-plugin (>=0.1.7,<0.3.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "pyyaml (>=5.3.1,<7.0.0)", "typer (>=0.4.1,<0.5.0)"]
+test = ["anyio[trio] (>=3.2.1,<4.0.0)", "black (==22.3.0)", "databases[sqlite] (>=0.3.2,<0.6.0)", "email_validator (>=1.1.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "flask (>=1.1.2,<3.0.0)", "httpx (>=0.14.0,<0.19.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "orjson (>=3.2.1,<4.0.0)", "peewee (>=3.13.3,<4.0.0)", "pytest (>=6.2.4,<7.0.0)", "pytest-cov (>=2.12.0,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "requests (>=2.24.0,<3.0.0)", "sqlalchemy (>=1.3.18,<1.5.0)", "types-dataclasses (==0.6.5)", "types-orjson (==3.6.2)", "types-ujson (==4.2.1)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)"]
[[package]]
name = "fonttools"
-version = "4.37.4"
+version = "4.38.0"
description = "Tools to manipulate font files"
category = "main"
optional = false
python-versions = ">=3.7"
[package.extras]
-all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "uharfbuzz (>=0.23.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=14.0.0)", "xattr"]
+all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=14.0.0)", "xattr", "zopfli (>=0.1.4)"]
graphite = ["lz4 (>=1.7.4.2)"]
-interpolatable = ["scipy", "munkres"]
+interpolatable = ["munkres", "scipy"]
lxml = ["lxml (>=4.0,<5)"]
pathops = ["skia-pathops (>=0.5.0)"]
plot = ["matplotlib"]
@@ -330,7 +330,7 @@ symfont = ["sympy"]
type1 = ["xattr"]
ufo = ["fs (>=2.2.0,<3)"]
unicode = ["unicodedata2 (>=14.0.0)"]
-woff = ["zopfli (>=0.1.4)", "brotlicffi (>=0.8.0)", "brotli (>=1.0.1)"]
+woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
[[package]]
name = "greenlet"
@@ -341,7 +341,7 @@ optional = false
python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
[package.extras]
-docs = ["sphinx"]
+docs = ["Sphinx"]
[[package]]
name = "gunicorn"
@@ -351,6 +351,9 @@ category = "main"
optional = false
python-versions = ">=3.5"
+[package.dependencies]
+setuptools = ">=3.0"
+
[package.extras]
eventlet = ["eventlet (>=0.24.1)"]
gevent = ["gevent (>=1.4.0)"]
@@ -410,8 +413,8 @@ rfc3986 = {version = ">=1.3,<2", extras = ["idna2008"]}
sniffio = "*"
[package.extras]
-brotli = ["brotlicffi", "brotli"]
-cli = ["click (>=8.0.0,<9.0.0)", "rich (>=10.0.0,<11.0.0)", "pygments (>=2.0.0,<3.0.0)"]
+brotli = ["brotli", "brotlicffi"]
+cli = ["click (>=8.0.0,<9.0.0)", "pygments (>=2.0.0,<3.0.0)", "rich (>=10.0.0,<11.0.0)"]
http2 = ["h2 (>=3,<5)"]
socks = ["socksio (>=1.0.0,<2.0.0)"]
@@ -435,9 +438,9 @@ python-versions = ">=3.7"
zipp = ">=0.5"
[package.extras]
-docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
perf = ["ipython"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
+testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"]
[[package]]
name = "importlib-resources"
@@ -451,8 +454,8 @@ python-versions = ">=3.7"
zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
[package.extras]
-docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
+testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
[[package]]
name = "iniconfig"
@@ -471,10 +474,10 @@ optional = false
python-versions = ">=3.6.1,<4.0"
[package.extras]
-pipfile_deprecated_finder = ["pipreqs", "requirementslib"]
-requirements_deprecated_finder = ["pipreqs", "pip-api"]
colors = ["colorama (>=0.4.3,<0.5.0)"]
+pipfile-deprecated-finder = ["pipreqs", "requirementslib"]
plugins = ["setuptools"]
+requirements-deprecated-finder = ["pip-api", "pipreqs"]
[[package]]
name = "kiwisolver"
@@ -493,10 +496,10 @@ optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*"
[package.extras]
-source = ["Cython (>=0.29.7)"]
-htmlsoup = ["beautifulsoup4"]
-html5 = ["html5lib"]
cssselect = ["cssselect (>=0.7)"]
+html5 = ["html5lib"]
+htmlsoup = ["BeautifulSoup4"]
+source = ["Cython (>=0.29.7)"]
[[package]]
name = "mako"
@@ -510,7 +513,7 @@ python-versions = ">=3.7"
MarkupSafe = ">=0.9.2"
[package.extras]
-babel = ["babel"]
+babel = ["Babel"]
lingua = ["lingua"]
testing = ["pytest"]
@@ -570,7 +573,7 @@ python-versions = "*"
[[package]]
name = "numpy"
-version = "1.23.3"
+version = "1.23.4"
description = "NumPy is the fundamental package for array computing with Python."
category = "main"
optional = false
@@ -578,7 +581,7 @@ python-versions = ">=3.8"
[[package]]
name = "obspy"
-version = "1.3.0"
+version = "1.3.1"
description = "ObsPy - a Python framework for seismological observatories."
category = "main"
optional = false
@@ -591,13 +594,14 @@ matplotlib = ">=3.2.0"
numpy = ">=1.15.0"
requests = "*"
scipy = ">=1.0.0"
+setuptools = "*"
sqlalchemy = "*"
[package.extras]
-all = ["packaging", "pyproj", "pytest", "pytest-json-report", "geographiclib", "cartopy", "pyshp"]
+all = ["cartopy", "geographiclib", "packaging", "pyproj", "pyshp", "pytest", "pytest-json-report"]
geo = ["geographiclib"]
imaging = ["cartopy"]
-"io.shapefile" = ["pyshp"]
+io-shapefile = ["pyshp"]
tests = ["packaging", "pyproj", "pytest", "pytest-json-report"]
[[package]]
@@ -672,8 +676,8 @@ optional = false
python-versions = ">=3.7"
[package.extras]
-docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)", "sphinx (>=4)"]
-test = ["appdirs (==1.4.4)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)", "pytest (>=6)"]
+docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx (>=4)", "sphinx-autodoc-typehints (>=1.12)"]
+test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"]
[[package]]
name = "pluggy"
@@ -700,7 +704,7 @@ pastel = ">=0.2.1,<0.3.0"
tomli = ">=1.2.2"
[package.extras]
-poetry_plugin = ["poetry (>=1.0,<2.0)"]
+poetry-plugin = ["poetry (>=1.0,<2.0)"]
[[package]]
name = "py"
@@ -762,7 +766,7 @@ optional = false
python-versions = ">=3.6.8"
[package.extras]
-diagrams = ["railroad-diagrams", "jinja2"]
+diagrams = ["jinja2", "railroad-diagrams"]
[[package]]
name = "pytest"
@@ -799,7 +803,7 @@ pytest = ">=4.6"
toml = "*"
[package.extras]
-testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"]
+testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
[[package]]
name = "python-dateutil"
@@ -847,7 +851,7 @@ urllib3 = ">=1.21.1,<1.27"
[package.extras]
socks = ["PySocks (>=1.5.6,!=1.5.7)"]
-use_chardet_on_py3 = ["chardet (>=3.0.2,<6)"]
+use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
[[package]]
name = "rfc3986"
@@ -876,10 +880,11 @@ Click = ">=6.0"
dparse = ">=0.5.1"
packaging = "*"
requests = "*"
+setuptools = "*"
[[package]]
name = "scipy"
-version = "1.9.2"
+version = "1.9.3"
description = "Fundamental algorithms for scientific computing in Python"
category = "main"
optional = false
@@ -889,9 +894,22 @@ python-versions = ">=3.8"
numpy = ">=1.18.5,<1.26.0"
[package.extras]
-test = ["pytest", "pytest-cov", "pytest-xdist", "asv", "mpmath", "gmpy2", "threadpoolctl", "scikit-umfpack"]
-doc = ["sphinx (!=4.1.0)", "pydata-sphinx-theme (==0.9.0)", "sphinx-panels (>=0.5.2)", "matplotlib (>2)", "numpydoc", "sphinx-tabs"]
-dev = ["mypy", "typing-extensions", "pycodestyle", "flake8"]
+dev = ["flake8", "mypy", "pycodestyle", "typing_extensions"]
+doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-panels (>=0.5.2)", "sphinx-tabs"]
+test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
+
+[[package]]
+name = "setuptools"
+version = "65.5.0"
+description = "Easily download, build, install, upgrade, and uninstall Python packages"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mock", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
[[package]]
name = "setuptools-scm"
@@ -903,6 +921,7 @@ python-versions = ">=3.7"
[package.dependencies]
packaging = ">=20.0"
+setuptools = "*"
tomli = ">=1.0.0"
typing-extensions = "*"
@@ -938,25 +957,25 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"}
[package.extras]
-aiomysql = ["greenlet (!=0.4.17)", "aiomysql"]
-aiosqlite = ["typing_extensions (!=3.10.0.1)", "greenlet (!=0.4.17)", "aiosqlite"]
+aiomysql = ["aiomysql", "greenlet (!=0.4.17)"]
+aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"]
asyncio = ["greenlet (!=0.4.17)"]
-asyncmy = ["greenlet (!=0.4.17)", "asyncmy (>=0.2.3,!=0.2.4)"]
-mariadb_connector = ["mariadb (>=1.0.1,!=1.1.2)"]
+asyncmy = ["asyncmy (>=0.2.3,!=0.2.4)", "greenlet (!=0.4.17)"]
+mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2)"]
mssql = ["pyodbc"]
-mssql_pymssql = ["pymssql"]
-mssql_pyodbc = ["pyodbc"]
-mypy = ["sqlalchemy2-stubs", "mypy (>=0.910)"]
-mysql = ["mysqlclient (>=1.4.0,<2)", "mysqlclient (>=1.4.0)"]
-mysql_connector = ["mysql-connector-python"]
-oracle = ["cx_oracle (>=7,<8)", "cx_oracle (>=7)"]
+mssql-pymssql = ["pymssql"]
+mssql-pyodbc = ["pyodbc"]
+mypy = ["mypy (>=0.910)", "sqlalchemy2-stubs"]
+mysql = ["mysqlclient (>=1.4.0)", "mysqlclient (>=1.4.0,<2)"]
+mysql-connector = ["mysql-connector-python"]
+oracle = ["cx_oracle (>=7)", "cx_oracle (>=7,<8)"]
postgresql = ["psycopg2 (>=2.7)"]
-postgresql_asyncpg = ["greenlet (!=0.4.17)", "asyncpg"]
-postgresql_pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)"]
-postgresql_psycopg2binary = ["psycopg2-binary"]
-postgresql_psycopg2cffi = ["psycopg2cffi"]
-pymysql = ["pymysql (<1)", "pymysql"]
-sqlcipher = ["sqlcipher3-binary"]
+postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
+postgresql-pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)"]
+postgresql-psycopg2binary = ["psycopg2-binary"]
+postgresql-psycopg2cffi = ["psycopg2cffi"]
+pymysql = ["pymysql", "pymysql (<1)"]
+sqlcipher = ["sqlcipher3_binary"]
[[package]]
name = "sqlalchemy-stubs"
@@ -979,6 +998,7 @@ optional = false
python-versions = "*"
[package.dependencies]
+setuptools = "*"
SQLAlchemy = ">=0.9.0"
[[package]]
@@ -1023,10 +1043,10 @@ python-versions = ">=3.6"
click = ">=7.1.1,<9.0.0"
[package.extras]
-test = ["isort (>=5.0.6,<6.0.0)", "black (>=22.3.0,<23.0.0)", "mypy (==0.910)", "pytest-sugar (>=0.9.4,<0.10.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "coverage (>=5.2,<6.0)", "pytest-cov (>=2.10.0,<3.0.0)", "pytest (>=4.4.0,<5.4.0)", "shellingham (>=1.3.0,<2.0.0)"]
-doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "mkdocs (>=1.1.2,<2.0.0)"]
-dev = ["pre-commit (>=2.17.0,<3.0.0)", "flake8 (>=3.8.3,<4.0.0)", "autoflake (>=1.3.1,<2.0.0)"]
-all = ["shellingham (>=1.3.0,<2.0.0)", "colorama (>=0.4.3,<0.5.0)"]
+all = ["colorama (>=0.4.3,<0.5.0)", "shellingham (>=1.3.0,<2.0.0)"]
+dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "pre-commit (>=2.17.0,<3.0.0)"]
+doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)"]
+test = ["black (>=22.3.0,<23.0.0)", "coverage (>=5.2,<6.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "shellingham (>=1.3.0,<2.0.0)"]
[[package]]
name = "types-python-dateutil"
@@ -1049,7 +1069,7 @@ types-urllib3 = "<1.27"
[[package]]
name = "types-urllib3"
-version = "1.26.25"
+version = "1.26.25.1"
description = "Typing stubs for urllib3"
category = "dev"
optional = false
@@ -1072,8 +1092,8 @@ optional = false
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@@ -1982,29 +2157,36 @@ safety = [
{file = "safety-1.10.3.tar.gz", hash = "sha256:30e394d02a20ac49b7f65292d19d38fa927a8f9582cdfd3ad1adbbc66c641ad5"},
]
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+ {file = "scipy-1.9.3-cp39-cp39-win_amd64.whl", hash = "sha256:5b88e6d91ad9d59478fafe92a7c757d00c59e3bdc3331be8ada76a4f8d683f58"},
+ {file = "scipy-1.9.3.tar.gz", hash = "sha256:fbc5c05c85c1a02be77b1ff591087c83bc44579c6d2bd9fb798bb64ea5e1a027"},
+]
+setuptools = [
+ {file = "setuptools-65.5.0-py3-none-any.whl", hash = "sha256:f62ea9da9ed6289bfe868cd6845968a2c854d1427f8548d52cae02a42b4f0356"},
+ {file = "setuptools-65.5.0.tar.gz", hash = "sha256:512e5536220e38146176efb833d4a62aa726b7bbff82cfbc8ba9eaa3996e0b17"},
+]
+setuptools-scm = [
+ {file = "setuptools_scm-7.0.5-py3-none-any.whl", hash = "sha256:7930f720905e03ccd1e1d821db521bff7ec2ac9cf0ceb6552dd73d24a45d3b02"},
+ {file = "setuptools_scm-7.0.5.tar.gz", hash = "sha256:031e13af771d6f892b941adb6ea04545bbf91ebc5ce68c78aaf3fff6e1fb4844"},
+]
six = [
{file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
{file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
@@ -2076,7 +2258,10 @@ tomli = [
{file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
{file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
]
-typer = []
+typer = [
+ {file = "typer-0.4.2-py3-none-any.whl", hash = "sha256:023bae00d1baf358a6cc7cea45851639360bb716de687b42b0a4641cd99173f1"},
+ {file = "typer-0.4.2.tar.gz", hash = "sha256:b8261c6c0152dd73478b5ba96ba677e5d6948c715c310f7c91079f311f62ec03"},
+]
types-python-dateutil = [
{file = "types-python-dateutil-0.1.6.tar.gz", hash = "sha256:b02de39a54ce6e3fadfdc7dba77d8519fbfb6ca049920e190b5f89c74d5f9de6"},
{file = "types_python_dateutil-0.1.6-py3-none-any.whl", hash = "sha256:5b6241ea9fca2d8878cc152017d9524da62a7a856b98e31006e68b02aab47442"},
@@ -2086,8 +2271,8 @@ types-requests = [
{file = "types_requests-2.28.11.2-py3-none-any.whl", hash = "sha256:14941f8023a80b16441b3b46caffcbfce5265fd14555844d6029697824b5a2ef"},
]
types-urllib3 = [
- {file = "types-urllib3-1.26.25.tar.gz", hash = "sha256:5aef0e663724eef924afa8b320b62ffef2c1736c1fa6caecfc9bc6c8ae2c3def"},
- {file = "types_urllib3-1.26.25-py3-none-any.whl", hash = "sha256:c1d78cef7bd581e162e46c20a57b2e1aa6ebecdcf01fd0713bb90978ff3e3427"},
+ {file = "types-urllib3-1.26.25.1.tar.gz", hash = "sha256:a948584944b2412c9a74b9cf64f6c48caf8652cb88b38361316f6d15d8a184cd"},
+ {file = "types_urllib3-1.26.25.1-py3-none-any.whl", hash = "sha256:f6422596cc9ee5fdf68f9d547f541096a20c2dcfd587e37c804c9ea720bf5cb2"},
]
typing-extensions = [
{file = "typing_extensions-4.4.0-py3-none-any.whl", hash = "sha256:16fa4864408f655d35ec496218b85f79b3437c829e93320c7c9215ccfd92489e"},
@@ -2188,6 +2373,6 @@ websockets = [
{file = "websockets-10.3.tar.gz", hash = "sha256:fc06cc8073c8e87072138ba1e431300e2d408f054b27047d047b549455066ff4"},
]
zipp = [
- {file = "zipp-3.9.0-py3-none-any.whl", hash = "sha256:972cfa31bc2fedd3fa838a51e9bc7e64b7fb725a8c00e7431554311f180e9980"},
- {file = "zipp-3.9.0.tar.gz", hash = "sha256:3a7af91c3db40ec72dd9d154ae18e008c69efe8ca88dde4f9a731bb82fe2f9eb"},
+ {file = "zipp-3.10.0-py3-none-any.whl", hash = "sha256:4fcb6f278987a6605757302a6e40e896257570d11c51628968ccb2a47e80c6c1"},
+ {file = "zipp-3.10.0.tar.gz", hash = "sha256:7a7262fd930bd3e36c50b9a64897aec3fafff3dfdeec9623ae22b40e93f99bb8"},
]
diff --git a/pyproject.toml b/pyproject.toml
index 41503ae5..aad1874a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,7 +39,9 @@ databases = {extras = ["mysql", "sqlite"], version = "^0.5.5"}
fastapi = "^0.75.0"
gunicorn = "^20.1.0"
httpx = "0.22.0"
-SQLAlchemy = "^1.4.32"
+# 2022-10-24 pin sqlalchemy to 1.4.41 for now
+# 1.4.42 seems to cause issues with databases (https://stackoverflow.com/a/74102692)
+SQLAlchemy = "1.4.41"
SQLAlchemy-Utc = "^0.14.0"
uvicorn = {extras = ["standard"], version = "^0.17.6"}
@@ -93,3 +95,6 @@ test = [
{ shell = "coverage html" },
{ shell = "coverage xml" }
]
+webservice = [
+ { shell = "uvicorn geomagio.api:app" }
+]
--
GitLab
From 10bbdb98e9c83b445848abd3fc7ef502b282758c Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Mon, 24 Oct 2022 14:19:06 -0600
Subject: [PATCH 092/142] api: logging environment variable for webservice
---
geomagio/api/app.py | 10 ++++++++--
1 file changed, 8 insertions(+), 2 deletions(-)
diff --git a/geomagio/api/app.py b/geomagio/api/app.py
index e206d680..47fb64a4 100644
--- a/geomagio/api/app.py
+++ b/geomagio/api/app.py
@@ -6,13 +6,19 @@ and can be run using uvicorn, or any other ASGI server:
uvicorn geomagio.api:app
"""
+import logging
+import os
+
from fastapi import FastAPI
from starlette.responses import RedirectResponse
+from . import secure, ws
from .db import database
-from . import secure
-from . import ws
+# configure logging
+DEBUG = os.getenv('DEBUG', 'false')
+LOG_LEVEL = logging.DEBUG if DEBUG == "true" else logging.INFO
+logging.basicConfig(level=LOG_LEVEL)
app = FastAPI()
app.mount("/ws/secure", secure.app)
--
GitLab
From c8932213ae0e98eef580a9d138c920b2258927df Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Mon, 24 Oct 2022 14:34:31 -0600
Subject: [PATCH 093/142] Update other dependencies to latest versions
---
poetry.lock | 286 ++++++++++++++++++++++++-------------------------
pyproject.toml | 44 ++++----
2 files changed, 165 insertions(+), 165 deletions(-)
diff --git a/poetry.lock b/poetry.lock
index 93c63aa9..7445e01a 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -58,25 +58,6 @@ doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
test = ["contextlib2", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (<0.15)", "uvloop (>=0.15)"]
trio = ["trio (>=0.16,<0.22)"]
-[[package]]
-name = "asgiref"
-version = "3.5.2"
-description = "ASGI specs, helper code, and adapters"
-category = "main"
-optional = false
-python-versions = ">=3.7"
-
-[package.extras]
-tests = ["mypy (>=0.800)", "pytest", "pytest-asyncio"]
-
-[[package]]
-name = "atomicwrites"
-version = "1.4.1"
-description = "Atomic file writes."
-category = "dev"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-
[[package]]
name = "attrs"
version = "22.1.0"
@@ -199,12 +180,15 @@ category = "dev"
optional = false
python-versions = ">=3.7"
+[package.dependencies]
+tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}
+
[package.extras]
toml = ["tomli"]
[[package]]
name = "cryptography"
-version = "36.0.2"
+version = "38.0.1"
description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
category = "main"
optional = false
@@ -214,12 +198,12 @@ python-versions = ">=3.6"
cffi = ">=1.12"
[package.extras]
-docs = ["sphinx (>=1.6.5,!=1.8.0,!=3.1.0,!=3.1.1)", "sphinx_rtd_theme"]
+docs = ["sphinx (>=1.6.5,!=1.8.0,!=3.1.0,!=3.1.1)", "sphinx-rtd-theme"]
docstest = ["pyenchant (>=1.6.11)", "sphinxcontrib-spelling (>=4.0.1)", "twine (>=1.12.0)"]
pep8test = ["black", "flake8", "flake8-import-order", "pep8-naming"]
-sdist = ["setuptools_rust (>=0.11.4)"]
+sdist = ["setuptools-rust (>=0.11.4)"]
ssh = ["bcrypt (>=3.1.5)"]
-test = ["hypothesis (>=1.11.4,!=3.79.2)", "iso8601", "pretend", "pytest (>=6.2.0)", "pytest-cov", "pytest-subtests", "pytest-xdist", "pytz"]
+test = ["hypothesis (>=1.11.4,!=3.79.2)", "iso8601", "pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-subtests", "pytest-xdist", "pytz"]
[[package]]
name = "cycler"
@@ -242,11 +226,11 @@ dev = ["black", "flake8", "flake8-pyi", "matplotlib", "mypy (==0.770)", "numpy",
[[package]]
name = "databases"
-version = "0.5.5"
+version = "0.6.1"
description = "Async database support for Python."
category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
[package.dependencies]
aiomysql = {version = "*", optional = true, markers = "extra == \"mysql\""}
@@ -254,10 +238,13 @@ aiosqlite = {version = "*", optional = true, markers = "extra == \"sqlite\""}
sqlalchemy = ">=1.4,<1.5"
[package.extras]
+aiomysql = ["aiomysql"]
+aiopg = ["aiopg"]
+aiosqlite = ["aiosqlite"]
+asyncmy = ["asyncmy"]
+asyncpg = ["asyncpg"]
mysql = ["aiomysql"]
-mysql-asyncmy = ["asyncmy"]
postgresql = ["asyncpg"]
-postgresql-aiopg = ["aiopg"]
sqlite = ["aiosqlite"]
[[package]]
@@ -294,21 +281,21 @@ python-versions = ">=3.6"
[[package]]
name = "fastapi"
-version = "0.75.2"
+version = "0.85.1"
description = "FastAPI framework, high performance, easy to learn, fast to code, ready for production"
category = "main"
optional = false
-python-versions = ">=3.6.1"
+python-versions = ">=3.7"
[package.dependencies]
pydantic = ">=1.6.2,<1.7 || >1.7,<1.7.1 || >1.7.1,<1.7.2 || >1.7.2,<1.7.3 || >1.7.3,<1.8 || >1.8,<1.8.1 || >1.8.1,<2.0.0"
-starlette = "0.17.1"
+starlette = "0.20.4"
[package.extras]
-all = ["email_validator (>=1.1.1,<2.0.0)", "itsdangerous (>=1.1.0,<3.0.0)", "jinja2 (>=2.11.2,<4.0.0)", "orjson (>=3.2.1,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "pyyaml (>=5.3.1,<7.0.0)", "requests (>=2.24.0,<3.0.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)", "uvicorn[standard] (>=0.12.0,<0.18.0)"]
-dev = ["autoflake (>=1.4.0,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "passlib[bcrypt] (>=1.7.2,<2.0.0)", "python-jose[cryptography] (>=3.3.0,<4.0.0)", "uvicorn[standard] (>=0.12.0,<0.18.0)"]
-doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-markdownextradata-plugin (>=0.1.7,<0.3.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "pyyaml (>=5.3.1,<7.0.0)", "typer (>=0.4.1,<0.5.0)"]
-test = ["anyio[trio] (>=3.2.1,<4.0.0)", "black (==22.3.0)", "databases[sqlite] (>=0.3.2,<0.6.0)", "email_validator (>=1.1.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "flask (>=1.1.2,<3.0.0)", "httpx (>=0.14.0,<0.19.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "orjson (>=3.2.1,<4.0.0)", "peewee (>=3.13.3,<4.0.0)", "pytest (>=6.2.4,<7.0.0)", "pytest-cov (>=2.12.0,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "requests (>=2.24.0,<3.0.0)", "sqlalchemy (>=1.3.18,<1.5.0)", "types-dataclasses (==0.6.5)", "types-orjson (==3.6.2)", "types-ujson (==4.2.1)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)"]
+all = ["email-validator (>=1.1.1,<2.0.0)", "itsdangerous (>=1.1.0,<3.0.0)", "jinja2 (>=2.11.2,<4.0.0)", "orjson (>=3.2.1,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "pyyaml (>=5.3.1,<7.0.0)", "requests (>=2.24.0,<3.0.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)", "uvicorn[standard] (>=0.12.0,<0.19.0)"]
+dev = ["autoflake (>=1.4.0,<2.0.0)", "flake8 (>=3.8.3,<6.0.0)", "pre-commit (>=2.17.0,<3.0.0)", "uvicorn[standard] (>=0.12.0,<0.19.0)"]
+doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-markdownextradata-plugin (>=0.1.7,<0.3.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "pyyaml (>=5.3.1,<7.0.0)", "typer (>=0.4.1,<0.7.0)"]
+test = ["anyio[trio] (>=3.2.1,<4.0.0)", "black (==22.8.0)", "databases[sqlite] (>=0.3.2,<0.7.0)", "email-validator (>=1.1.1,<2.0.0)", "flake8 (>=3.8.3,<6.0.0)", "flask (>=1.1.2,<3.0.0)", "httpx (>=0.23.0,<0.24.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.971)", "orjson (>=3.2.1,<4.0.0)", "passlib[bcrypt] (>=1.7.2,<2.0.0)", "peewee (>=3.13.3,<4.0.0)", "pytest (>=7.1.3,<8.0.0)", "pytest-cov (>=2.12.0,<4.0.0)", "python-jose[cryptography] (>=3.3.0,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "pyyaml (>=5.3.1,<7.0.0)", "requests (>=2.24.0,<3.0.0)", "sqlalchemy (>=1.3.18,<1.5.0)", "types-orjson (==3.6.2)", "types-ujson (==5.4.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)"]
[[package]]
name = "fonttools"
@@ -370,11 +357,11 @@ python-versions = ">=3.6"
[[package]]
name = "httpcore"
-version = "0.14.7"
+version = "0.15.0"
description = "A minimal low-level HTTP client."
category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
[package.dependencies]
anyio = ">=3.0.0,<4.0.0"
@@ -399,22 +386,21 @@ test = ["Cython (>=0.29.24,<0.30.0)"]
[[package]]
name = "httpx"
-version = "0.22.0"
+version = "0.23.0"
description = "The next generation HTTP client."
category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
[package.dependencies]
certifi = "*"
-charset-normalizer = "*"
-httpcore = ">=0.14.5,<0.15.0"
+httpcore = ">=0.15.0,<0.16.0"
rfc3986 = {version = ">=1.3,<2", extras = ["idna2008"]}
sniffio = "*"
[package.extras]
brotli = ["brotli", "brotlicffi"]
-cli = ["click (>=8.0.0,<9.0.0)", "pygments (>=2.0.0,<3.0.0)", "rich (>=10.0.0,<11.0.0)"]
+cli = ["click (>=8.0.0,<9.0.0)", "pygments (>=2.0.0,<3.0.0)", "rich (>=10,<13)"]
http2 = ["h2 (>=3,<5)"]
socks = ["socksio (>=1.0.0,<2.0.0)"]
@@ -547,15 +533,15 @@ setuptools_scm = ">=7"
[[package]]
name = "mypy"
-version = "0.941"
+version = "0.982"
description = "Optional static typing for Python"
category = "dev"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
[package.dependencies]
mypy-extensions = ">=0.4.3"
-tomli = ">=1.1.0"
+tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
typing-extensions = ">=3.10"
[package.extras]
@@ -770,37 +756,35 @@ diagrams = ["jinja2", "railroad-diagrams"]
[[package]]
name = "pytest"
-version = "6.2.5"
+version = "7.1.3"
description = "pytest: simple powerful testing with Python"
category = "dev"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
[package.dependencies]
-atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
attrs = ">=19.2.0"
colorama = {version = "*", markers = "sys_platform == \"win32\""}
iniconfig = "*"
packaging = "*"
pluggy = ">=0.12,<2.0"
py = ">=1.8.2"
-toml = "*"
+tomli = ">=1.0.0"
[package.extras]
-testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
+testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"]
[[package]]
name = "pytest-cov"
-version = "2.12.1"
+version = "4.0.0"
description = "Pytest plugin for measuring coverage."
category = "dev"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.6"
[package.dependencies]
-coverage = ">=5.2.1"
+coverage = {version = ">=5.2.1", extras = ["toml"]}
pytest = ">=4.6"
-toml = "*"
[package.extras]
testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
@@ -1003,14 +987,15 @@ SQLAlchemy = ">=0.9.0"
[[package]]
name = "starlette"
-version = "0.17.1"
+version = "0.20.4"
description = "The little ASGI library that shines."
category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
[package.dependencies]
-anyio = ">=3.0.0,<4"
+anyio = ">=3.4.0,<5"
+typing-extensions = {version = ">=3.10.0", markers = "python_version < \"3.10\""}
[package.extras]
full = ["itsdangerous", "jinja2", "python-multipart", "pyyaml", "requests"]
@@ -1033,7 +1018,7 @@ python-versions = ">=3.7"
[[package]]
name = "typer"
-version = "0.4.2"
+version = "0.6.1"
description = "Typer, build great CLIs. Easy to code. Based on Python type hints."
category = "main"
optional = false
@@ -1043,14 +1028,14 @@ python-versions = ">=3.6"
click = ">=7.1.1,<9.0.0"
[package.extras]
-all = ["colorama (>=0.4.3,<0.5.0)", "shellingham (>=1.3.0,<2.0.0)"]
+all = ["colorama (>=0.4.3,<0.5.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"]
dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "pre-commit (>=2.17.0,<3.0.0)"]
doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)"]
-test = ["black (>=22.3.0,<23.0.0)", "coverage (>=5.2,<6.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "shellingham (>=1.3.0,<2.0.0)"]
+test = ["black (>=22.3.0,<23.0.0)", "coverage (>=5.2,<6.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"]
[[package]]
name = "types-python-dateutil"
-version = "0.1.6"
+version = "2.8.19.2"
description = "Typing stubs for python-dateutil"
category = "dev"
optional = false
@@ -1098,26 +1083,25 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
[[package]]
name = "uvicorn"
-version = "0.17.6"
+version = "0.19.0"
description = "The lightning-fast ASGI server."
category = "main"
optional = false
python-versions = ">=3.7"
[package.dependencies]
-asgiref = ">=3.4.0"
click = ">=7.0"
colorama = {version = ">=0.4", optional = true, markers = "sys_platform == \"win32\" and extra == \"standard\""}
h11 = ">=0.8"
-httptools = {version = ">=0.4.0", optional = true, markers = "extra == \"standard\""}
+httptools = {version = ">=0.5.0", optional = true, markers = "extra == \"standard\""}
python-dotenv = {version = ">=0.13", optional = true, markers = "extra == \"standard\""}
-PyYAML = {version = ">=5.1", optional = true, markers = "extra == \"standard\""}
+pyyaml = {version = ">=5.1", optional = true, markers = "extra == \"standard\""}
uvloop = {version = ">=0.14.0,<0.15.0 || >0.15.0,<0.15.1 || >0.15.1", optional = true, markers = "sys_platform != \"win32\" and sys_platform != \"cygwin\" and platform_python_implementation != \"PyPy\" and extra == \"standard\""}
-watchgod = {version = ">=0.6", optional = true, markers = "extra == \"standard\""}
+watchfiles = {version = ">=0.13", optional = true, markers = "extra == \"standard\""}
websockets = {version = ">=10.0", optional = true, markers = "extra == \"standard\""}
[package.extras]
-standard = ["PyYAML (>=5.1)", "colorama (>=0.4)", "httptools (>=0.4.0)", "python-dotenv (>=0.13)", "uvloop (>=0.14.0,!=0.15.0,!=0.15.1)", "watchgod (>=0.6)", "websockets (>=10.0)"]
+standard = ["colorama (>=0.4)", "httptools (>=0.5.0)", "python-dotenv (>=0.13)", "pyyaml (>=5.1)", "uvloop (>=0.14.0,!=0.15.0,!=0.15.1)", "watchfiles (>=0.13)", "websockets (>=10.0)"]
[[package]]
name = "uvloop"
@@ -1133,9 +1117,9 @@ docs = ["Sphinx (>=4.1.2,<4.2.0)", "sphinx-rtd-theme (>=0.5.2,<0.6.0)", "sphinxc
test = ["Cython (>=0.29.32,<0.30.0)", "aiohttp", "flake8 (>=3.9.2,<3.10.0)", "mypy (>=0.800)", "psutil", "pyOpenSSL (>=22.0.0,<22.1.0)", "pycodestyle (>=2.7.0,<2.8.0)"]
[[package]]
-name = "watchgod"
-version = "0.8.2"
-description = "Simple, modern file watching and code reload in python."
+name = "watchfiles"
+version = "0.18.0"
+description = "Simple, modern and high performance file watching and code reload in python."
category = "main"
optional = false
python-versions = ">=3.7"
@@ -1169,7 +1153,7 @@ pycurl = ["pycurl"]
[metadata]
lock-version = "1.1"
python-versions = "^3.8,<3.11"
-content-hash = "9ed6469202039ba553d51353dae078254227da3749f27c42886ca6c1368a54b6"
+content-hash = "5fa530d09cec90a394b1a69cebbf7d7744f7dcbeadeae5d3005af83c786c2231"
[metadata.files]
aiomysql = [
@@ -1188,13 +1172,6 @@ anyio = [
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{file = "anyio-3.6.2.tar.gz", hash = "sha256:25ea0d673ae30af41a0c442f81cf3b38c7e79fdc7b60335a4c14e05eb0947421"},
]
-asgiref = [
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- {file = "asgiref-3.5.2.tar.gz", hash = "sha256:4a29362a6acebe09bf1d6640db38c1dc3d9217c68e6f9f6204d72667fc19a424"},
-]
-atomicwrites = [
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attrs = [
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@@ -1432,26 +1409,32 @@ coverage = [
{file = "coverage-6.5.0.tar.gz", hash = "sha256:f642e90754ee3e06b0e7e51bce3379590e76b7f76b708e1a71ff043f87025c84"},
]
cryptography = [
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+ {file = "mypy-0.982-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:75838c649290d83a2b83a88288c1eb60fe7a05b36d46cbea9d22efc790002146"},
+ {file = "mypy-0.982-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:91781eff1f3f2607519c8b0e8518aad8498af1419e8442d5d0afb108059881fc"},
+ {file = "mypy-0.982-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:eaa97b9ddd1dd9901a22a879491dbb951b5dec75c3b90032e2baa7336777363b"},
+ {file = "mypy-0.982-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:a692a8e7d07abe5f4b2dd32d731812a0175626a90a223d4b58f10f458747dd8a"},
+ {file = "mypy-0.982-cp39-cp39-win_amd64.whl", hash = "sha256:eb7a068e503be3543c4bd329c994103874fa543c1727ba5288393c21d912d795"},
+ {file = "mypy-0.982-py3-none-any.whl", hash = "sha256:1021c241e8b6e1ca5a47e4d52601274ac078a89845cfde66c6d5f769819ffa1d"},
+ {file = "mypy-0.982.tar.gz", hash = "sha256:85f7a343542dc8b1ed0a888cdd34dca56462654ef23aa673907305b260b3d746"},
]
mypy-extensions = [
{file = "mypy_extensions-0.4.3-py2.py3-none-any.whl", hash = "sha256:090fedd75945a69ae91ce1303b5824f428daf5a028d2f6ab8a299250a846f15d"},
@@ -2087,12 +2071,12 @@ pyparsing = [
{file = "pyparsing-3.0.9.tar.gz", hash = "sha256:2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb"},
]
pytest = [
- {file = "pytest-6.2.5-py3-none-any.whl", hash = "sha256:7310f8d27bc79ced999e760ca304d69f6ba6c6649c0b60fb0e04a4a77cacc134"},
- {file = "pytest-6.2.5.tar.gz", hash = "sha256:131b36680866a76e6781d13f101efb86cf674ebb9762eb70d3082b6f29889e89"},
+ {file = "pytest-7.1.3-py3-none-any.whl", hash = "sha256:1377bda3466d70b55e3f5cecfa55bb7cfcf219c7964629b967c37cf0bda818b7"},
+ {file = "pytest-7.1.3.tar.gz", hash = "sha256:4f365fec2dff9c1162f834d9f18af1ba13062db0c708bf7b946f8a5c76180c39"},
]
pytest-cov = [
- {file = "pytest-cov-2.12.1.tar.gz", hash = "sha256:261ceeb8c227b726249b376b8526b600f38667ee314f910353fa318caa01f4d7"},
- {file = "pytest_cov-2.12.1-py2.py3-none-any.whl", hash = "sha256:261bb9e47e65bd099c89c3edf92972865210c36813f80ede5277dceb77a4a62a"},
+ {file = "pytest-cov-4.0.0.tar.gz", hash = "sha256:996b79efde6433cdbd0088872dbc5fb3ed7fe1578b68cdbba634f14bb8dd0470"},
+ {file = "pytest_cov-4.0.0-py3-none-any.whl", hash = "sha256:2feb1b751d66a8bd934e5edfa2e961d11309dc37b73b0eabe73b5945fee20f6b"},
]
python-dateutil = [
{file = "python-dateutil-2.8.2.tar.gz", hash = "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86"},
@@ -2247,8 +2231,8 @@ sqlalchemy-utc = [
{file = "SQLAlchemy_Utc-0.14.0-py2.py3-none-any.whl", hash = "sha256:d2379eed5cce372128b5e744ce382decd262b2c742ab31f7f22ca11c6647f60b"},
]
starlette = [
- {file = "starlette-0.17.1-py3-none-any.whl", hash = "sha256:26a18cbda5e6b651c964c12c88b36d9898481cd428ed6e063f5f29c418f73050"},
- {file = "starlette-0.17.1.tar.gz", hash = "sha256:57eab3cc975a28af62f6faec94d355a410634940f10b30d68d31cb5ec1b44ae8"},
+ {file = "starlette-0.20.4-py3-none-any.whl", hash = "sha256:c0414d5a56297d37f3db96a84034d61ce29889b9eaccf65eb98a0b39441fcaa3"},
+ {file = "starlette-0.20.4.tar.gz", hash = "sha256:42fcf3122f998fefce3e2c5ad7e5edbf0f02cf685d646a83a08d404726af5084"},
]
toml = [
{file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"},
@@ -2259,12 +2243,12 @@ tomli = [
{file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
]
typer = [
- {file = "typer-0.4.2-py3-none-any.whl", hash = "sha256:023bae00d1baf358a6cc7cea45851639360bb716de687b42b0a4641cd99173f1"},
- {file = "typer-0.4.2.tar.gz", hash = "sha256:b8261c6c0152dd73478b5ba96ba677e5d6948c715c310f7c91079f311f62ec03"},
+ {file = "typer-0.6.1-py3-none-any.whl", hash = "sha256:54b19e5df18654070a82f8c2aa1da456a4ac16a2a83e6dcd9f170e291c56338e"},
+ {file = "typer-0.6.1.tar.gz", hash = "sha256:2d5720a5e63f73eaf31edaa15f6ab87f35f0690f8ca233017d7d23d743a91d73"},
]
types-python-dateutil = [
- {file = "types-python-dateutil-0.1.6.tar.gz", hash = "sha256:b02de39a54ce6e3fadfdc7dba77d8519fbfb6ca049920e190b5f89c74d5f9de6"},
- {file = "types_python_dateutil-0.1.6-py3-none-any.whl", hash = "sha256:5b6241ea9fca2d8878cc152017d9524da62a7a856b98e31006e68b02aab47442"},
+ {file = "types-python-dateutil-2.8.19.2.tar.gz", hash = "sha256:e6e32ce18f37765b08c46622287bc8d8136dc0c562d9ad5b8fd158c59963d7a7"},
+ {file = "types_python_dateutil-2.8.19.2-py3-none-any.whl", hash = "sha256:3f4dbe465e7e0c6581db11fd7a4855d1355b78712b3f292bd399cd332247e9c0"},
]
types-requests = [
{file = "types-requests-2.28.11.2.tar.gz", hash = "sha256:fdcd7bd148139fb8eef72cf4a41ac7273872cad9e6ada14b11ff5dfdeee60ed3"},
@@ -2283,8 +2267,8 @@ urllib3 = [
{file = "urllib3-1.26.12.tar.gz", hash = "sha256:3fa96cf423e6987997fc326ae8df396db2a8b7c667747d47ddd8ecba91f4a74e"},
]
uvicorn = [
- {file = "uvicorn-0.17.6-py3-none-any.whl", hash = "sha256:19e2a0e96c9ac5581c01eb1a79a7d2f72bb479691acd2b8921fce48ed5b961a6"},
- {file = "uvicorn-0.17.6.tar.gz", hash = "sha256:5180f9d059611747d841a4a4c4ab675edf54c8489e97f96d0583ee90ac3bfc23"},
+ {file = "uvicorn-0.19.0-py3-none-any.whl", hash = "sha256:cc277f7e73435748e69e075a721841f7c4a95dba06d12a72fe9874acced16f6f"},
+ {file = "uvicorn-0.19.0.tar.gz", hash = "sha256:cf538f3018536edb1f4a826311137ab4944ed741d52aeb98846f52215de57f25"},
]
uvloop = [
{file = "uvloop-0.17.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:ce9f61938d7155f79d3cb2ffa663147d4a76d16e08f65e2c66b77bd41b356718"},
@@ -2318,9 +2302,25 @@ uvloop = [
{file = "uvloop-0.17.0-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:30babd84706115626ea78ea5dbc7dd8d0d01a2e9f9b306d24ca4ed5796c66ded"},
{file = "uvloop-0.17.0.tar.gz", hash = "sha256:0ddf6baf9cf11a1a22c71487f39f15b2cf78eb5bde7e5b45fbb99e8a9d91b9e1"},
]
-watchgod = [
- {file = "watchgod-0.8.2-py3-none-any.whl", hash = "sha256:2f3e8137d98f493ff58af54ea00f4d1433a6afe2ed08ab331a657df468c6bfce"},
- {file = "watchgod-0.8.2.tar.gz", hash = "sha256:cb11ff66657befba94d828e3b622d5fb76f22fbda1376f355f3e6e51e97d9450"},
+watchfiles = [
+ {file = "watchfiles-0.18.0-cp37-abi3-macosx_10_7_x86_64.whl", hash = "sha256:76a4c4a8e25a2c9a4f7fa3d373bbaf5558c17b97b4cf8411d33de368fe6b68a9"},
+ {file = "watchfiles-0.18.0-cp37-abi3-macosx_11_0_arm64.whl", hash = "sha256:d5d799614d4c56d29c5ba56f4f619f967210dc10a0d6965b62d326b9e2f72c9e"},
+ {file = "watchfiles-0.18.0-cp37-abi3-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:39b932b044fef6c43e813e0bef908e0edf185bf7b5d8d53246651cb7ac9efe79"},
+ {file = "watchfiles-0.18.0-cp37-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1686bc4ac40ffde7256b6543b0f9a2cc8b531ae45243786f1d3f1dda2fe39e24"},
+ {file = "watchfiles-0.18.0-cp37-abi3-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:320bcde0adaa972403ed3b70f784409437325a1a4df2de54ba0672203d8847e5"},
+ {file = "watchfiles-0.18.0-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:4ba6d8c2f957cae3e888bc250bc60ed09fe869b3f55f09d020ed3fecbefb6a4c"},
+ {file = "watchfiles-0.18.0-cp37-abi3-musllinux_1_1_aarch64.whl", hash = "sha256:fd4215badad1e3d1ad5fb79f21432dd5157e2e7b0765d27a19dc2a28580c6979"},
+ {file = "watchfiles-0.18.0-cp37-abi3-musllinux_1_1_x86_64.whl", hash = "sha256:cfdbfc4b6797c28dd1a8524581fed00ca333971b4111af8cd42fb7a92dcdc227"},
+ {file = "watchfiles-0.18.0-cp37-abi3-win32.whl", hash = "sha256:8eddc2d19bf6f49aee224072ec0f4f3258125a49f11b5dcff1448e68718a745e"},
+ {file = "watchfiles-0.18.0-cp37-abi3-win_amd64.whl", hash = "sha256:be87c9b1fe2b02105a9ac6d9df7500a110652bbd97cf46b13964eeaef9a6c89c"},
+ {file = "watchfiles-0.18.0-cp37-abi3-win_arm64.whl", hash = "sha256:184799818c4fa7dbc6a1e4ca20bcbc6b85e4e0db07ce4554ea2f29b75ccd0cdc"},
+ {file = "watchfiles-0.18.0-pp38-pypy38_pp73-macosx_10_7_x86_64.whl", hash = "sha256:7f39fcdac5d5b9815a0c2ab9005d39854296b11fa15386a9a69c09cbbc5dde2c"},
+ {file = "watchfiles-0.18.0-pp38-pypy38_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:78b1e7c29b92dfc8fc32f15949019232b493767d236c2bff31848df13fdb9e8a"},
+ {file = "watchfiles-0.18.0-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:27d64a6ed5e0aebef97c70fa3899a6958d4f7f049effc659e7dc3e81f3170a7b"},
+ {file = "watchfiles-0.18.0-pp39-pypy39_pp73-macosx_10_7_x86_64.whl", hash = "sha256:4bbc8bfa0f3871b1867af42837a5635a9c1cbb2b68d039754b4750642c34aaee"},
+ {file = "watchfiles-0.18.0-pp39-pypy39_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:9d3a12e4de5446fb6e286b720d0cb3a080811caf0ef43e556c2db5fe10ef0342"},
+ {file = "watchfiles-0.18.0-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9e611a90482ac14ef3ec234c1604ed921d1b0c68970eba82f1cf0d59a3e4eb76"},
+ {file = "watchfiles-0.18.0.tar.gz", hash = "sha256:bbe10d134eef1666451382015e48f092c941a6d4562a98ffa1a288f79a897c46"},
]
websockets = [
{file = "websockets-10.3-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:661f641b44ed315556a2fa630239adfd77bd1b11cb0b9d96ed8ad90b0b1e4978"},
diff --git a/pyproject.toml b/pyproject.toml
index aad1874a..66fb3bd6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,43 +23,43 @@ version = "1.5.3"
[tool.poetry.dependencies]
python = "^3.8,<3.11"
# core
-numpy = "^1.22.3"
-obspy = "^1.3.0"
-openpyxl = "^3.0.9"
+numpy = "^1.23.4"
+obspy = "^1.3.1"
+openpyxl = "^3.0.10"
pycurl = {version = "^7.45.1", optional = true}
-pydantic = "^1.9.0"
-requests = "^2.27.1"
-scipy = "^1.8.0"
-typer = "^0.4.0"
+pydantic = "^1.10.2"
+requests = "^2.28.1"
+scipy = "^1.9.3"
+typer = "^0.6.1"
# webservice
-alembic = "^1.8.0"
-Authlib = "^1.0.0"
-cryptography = "^36.0.2"
-databases = {extras = ["mysql", "sqlite"], version = "^0.5.5"}
-fastapi = "^0.75.0"
+alembic = "^1.8.1"
+Authlib = "^1.1.0"
+cryptography = "^38.0.1"
+databases = {extras = ["mysql", "sqlite"], version = "^0.6.1"}
+fastapi = "^0.85.1"
gunicorn = "^20.1.0"
-httpx = "0.22.0"
+httpx = "0.23.0"
# 2022-10-24 pin sqlalchemy to 1.4.41 for now
# 1.4.42 seems to cause issues with databases (https://stackoverflow.com/a/74102692)
SQLAlchemy = "1.4.41"
SQLAlchemy-Utc = "^0.14.0"
-uvicorn = {extras = ["standard"], version = "^0.17.6"}
+uvicorn = {extras = ["standard"], version = "^0.19.0"}
[tool.poetry.dev-dependencies]
-black = "^22.1.0"
+black = "^22.10.0"
isort = "^5.10.1"
-mypy = "^0.941"
-poethepoet = "^0.16.0"
-pytest = "^6.2.4"
-pytest-cov = "^2.12.1"
+mypy = "^0.982"
+poethepoet = "^0.16.4"
+pytest = "^7.1.3"
+pytest-cov = "^4.0.0"
safety = "^1.10.3"
# type hints
data-science-types = "^0.2.23"
-openpyxl-stubs = "^0.1.19"
+openpyxl-stubs = "^0.1.24"
sqlalchemy-stubs = "^0.4"
-types-python-dateutil = "^0.1.6"
-types-requests = "^2.25.6"
+types-python-dateutil = "^2.8.19.2"
+types-requests = "^2.28.11.2"
[tool.poetry.extras]
--
GitLab
From 0a588c389b3f0c70bb99e77cfd07dbf67a49b054 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Mon, 24 Oct 2022 14:40:41 -0600
Subject: [PATCH 094/142] Bump version to 1.5.4
---
code.json | 4 ++--
pyproject.toml | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/code.json b/code.json
index e53c03f2..ea62f29c 100644
--- a/code.json
+++ b/code.json
@@ -3,7 +3,7 @@
"name": "geomag-algorithms",
"organization": "U.S. Geological Survey",
"description": "Library for processing Geomagnetic timeseries data.",
- "version": "1.5.3",
+ "version": "1.5.4",
"status": "Development",
"permissions": {
@@ -34,7 +34,7 @@
},
"date": {
- "metadataLastUpdated": "2022-06-01"
+ "metadataLastUpdated": "2022-10-24"
}
}
]
diff --git a/pyproject.toml b/pyproject.toml
index 66fb3bd6..fb903103 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ packages = [
{include = "geomagio" }
]
repository="https://code.usgs.gov/ghsc/geomag/geomag-algorithms"
-version = "1.5.3"
+version = "1.5.4"
[tool.poetry.dependencies]
--
GitLab
From e5c19b6e8d2833619114403dd857bd01da607d87 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Mon, 24 Oct 2022 15:47:17 -0600
Subject: [PATCH 095/142] Update logging configuration
---
docker-entrypoint.sh | 3 +++
geomagio/api/app.py | 8 ++++----
2 files changed, 7 insertions(+), 4 deletions(-)
diff --git a/docker-entrypoint.sh b/docker-entrypoint.sh
index 7c05ad6e..0f95ec97 100755
--- a/docker-entrypoint.sh
+++ b/docker-entrypoint.sh
@@ -9,10 +9,13 @@ if [ "${WEBSERVICE}" = "false" ]; then
# run arguments as command, or bash prompt if no arguments
exec "${@:-/bin/bash}"
else
+ export LOG_BASIC_CONFIG="${LOG_BASIC_CONFIG:-true}"
+ export LOG_LEVEL="${LOG_LEVEL:-INFO}"
# run gunicorn server for web service
exec gunicorn \
--access-logfile - \
--bind 0.0.0.0:8000 \
+ --log-level "${LOG_LEVEL}" \
--threads 2 \
--workers 2 \
--worker-class uvicorn.workers.UvicornWorker \
diff --git a/geomagio/api/app.py b/geomagio/api/app.py
index 47fb64a4..618fe8ed 100644
--- a/geomagio/api/app.py
+++ b/geomagio/api/app.py
@@ -15,10 +15,10 @@ from starlette.responses import RedirectResponse
from . import secure, ws
from .db import database
-# configure logging
-DEBUG = os.getenv('DEBUG', 'false')
-LOG_LEVEL = logging.DEBUG if DEBUG == "true" else logging.INFO
-logging.basicConfig(level=LOG_LEVEL)
+LOG_BASIC_CONFIG = os.getenv("LOG_BASIC_CONFIG", "false")
+LOG_LEVEL = os.getenv("LOG_LEVEL", "INFO")
+if LOG_BASIC_CONFIG == "true":
+ logging.basicConfig(level=LOG_LEVEL)
app = FastAPI()
app.mount("/ws/secure", secure.app)
--
GitLab
From ab304c37f2159aac7a5b9bd70036bd9affe7ecd5 Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Tue, 1 Nov 2022 12:40:25 -0600
Subject: [PATCH 096/142] Changed dst_tot to calculate average regardless of
nan values and added a new stream that counts available observatories
pertimestep
---
geomagio/algorithm/AverageAlgorithm.py | 23 ++++++++++++--------
test/algorithm_test/AverageAlgorithm_test.py | 15 +++++++------
2 files changed, 22 insertions(+), 16 deletions(-)
diff --git a/geomagio/algorithm/AverageAlgorithm.py b/geomagio/algorithm/AverageAlgorithm.py
index d6536c76..9dbf6f7b 100644
--- a/geomagio/algorithm/AverageAlgorithm.py
+++ b/geomagio/algorithm/AverageAlgorithm.py
@@ -63,18 +63,14 @@ class AverageAlgorithm(Algorithm):
if ts.stats.npts != self._npts:
raise AlgorithmException("Received timeseries have different lengths")
- if numpy.isnan(ts.data).all():
- raise AlgorithmException(
- "Trace for %s observatory is completely empty." % (ts.stats.station)
- )
-
if ts.stats.starttime != self._stt:
raise AlgorithmException(
"Received timeseries have different starttimes"
)
def process(self, timeseries):
- """averages a channel across multiple stations
+ """averages a channel across multiple stations and counts available
+ observatories per timestep
Parameters
----------
@@ -82,7 +78,7 @@ class AverageAlgorithm(Algorithm):
Returns
-------
out_stream:
- new stream object containing the averaged values.
+ new stream object containing the averaged values and available observatories.
"""
self.observatories = self.observatories or [t.stats.station for t in timeseries]
@@ -116,9 +112,13 @@ class AverageAlgorithm(Algorithm):
combined.append(ts.data * latcorr)
# after looping over stations, compute average
- dst_tot = numpy.mean(combined, axis=0)
+ dst_tot = numpy.nanmean(combined, axis=0)
- # Create a stream from the trace function
+ # Stack timeseries and count non-nan values per timestep
+ ts_counter = numpy.column_stack(timeseries)
+ channel_count = numpy.count_nonzero(~numpy.isnan(ts_counter), axis=1)
+
+ # create metadata
new_stats = obspy.core.Stats()
new_stats.station = "USGS"
new_stats.channel = self.outchannel
@@ -127,7 +127,12 @@ class AverageAlgorithm(Algorithm):
new_stats.starttime = timeseries[0].stats.starttime
new_stats.npts = timeseries[0].stats.npts
new_stats.delta = timeseries[0].stats.delta
+ new_stats2 = new_stats.copy()
+ new_stats2.channel = new_stats.channel + "_count"
+
+ # create streams from the trace function
stream = obspy.core.Stream((obspy.core.Trace(dst_tot, new_stats),))
+ stream += obspy.core.Trace(numpy.asarray(channel_count), new_stats2)
# return averaged values as a stream
return stream
diff --git a/test/algorithm_test/AverageAlgorithm_test.py b/test/algorithm_test/AverageAlgorithm_test.py
index a93540cd..1a003812 100644
--- a/test/algorithm_test/AverageAlgorithm_test.py
+++ b/test/algorithm_test/AverageAlgorithm_test.py
@@ -8,18 +8,19 @@ from numpy.testing import assert_array_equal, assert_equal
def test_process():
"""AverageAlgorithm_test.test_process()
- confirms that the output of the algorithm is the average of three
- different stations.
+ confirms that the output of the algorithm is the average of two
+ stations and ignores the third.
"""
- # Make three test data arrays of 1's, 3's, and 5's
- # the average of the three arrays should be 3
- test_data1 = np.ones(5)
+ # Make three test data arrays of NAN's, 3's, and 5's
+ # the average of the three arrays should be 4
+ test_data1 = np.zeros(5)
+ test_data1[:] = np.nan
test_data2 = np.ones(5) * 5
test_data3 = np.ones(5) * 3
- # Create expected solution array of 3's
- expected_solution = np.ones(5) * 3
+ # Create expected solution array of 4's
+ expected_solution = np.ones(5) * 4
# Create timeseries with first trace that uses test_data1
timeseries = Stream()
--
GitLab
From a05b770f6540ad11dedeb8a84541feb0daf6cb1a Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Tue, 1 Nov 2022 13:57:45 -0600
Subject: [PATCH 097/142] Fixed linting errors
---
geomagio/algorithm/AverageAlgorithm.py | 2 +-
test/algorithm_test/AverageAlgorithm_test.py | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/geomagio/algorithm/AverageAlgorithm.py b/geomagio/algorithm/AverageAlgorithm.py
index 9dbf6f7b..16eafdf9 100644
--- a/geomagio/algorithm/AverageAlgorithm.py
+++ b/geomagio/algorithm/AverageAlgorithm.py
@@ -69,7 +69,7 @@ class AverageAlgorithm(Algorithm):
)
def process(self, timeseries):
- """averages a channel across multiple stations and counts available
+ """averages a channel across multiple stations and counts available
observatories per timestep
Parameters
diff --git a/test/algorithm_test/AverageAlgorithm_test.py b/test/algorithm_test/AverageAlgorithm_test.py
index 1a003812..43cd48d0 100644
--- a/test/algorithm_test/AverageAlgorithm_test.py
+++ b/test/algorithm_test/AverageAlgorithm_test.py
@@ -8,7 +8,7 @@ from numpy.testing import assert_array_equal, assert_equal
def test_process():
"""AverageAlgorithm_test.test_process()
- confirms that the output of the algorithm is the average of two
+ confirms that the output of the algorithm is the average of two
stations and ignores the third.
"""
--
GitLab
From f672b9517d739dbe07e94c3987cabaa3d96e8e4c Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Tue, 1 Nov 2022 14:17:24 -0600
Subject: [PATCH 098/142] Updating poetry.lock
---
poetry.lock | 684 +++++++++++++++++++++++++++++++++-------------------
1 file changed, 439 insertions(+), 245 deletions(-)
diff --git a/poetry.lock b/poetry.lock
index 7445e01a..ceed07f6 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -10,8 +10,8 @@ python-versions = ">=3.7"
PyMySQL = ">=1.0"
[package.extras]
-rsa = ["PyMySQL[rsa] (>=1.0)"]
sa = ["sqlalchemy (>=1.0,<1.4)"]
+rsa = ["PyMySQL[rsa] (>=1.0)"]
[[package]]
name = "aiosqlite"
@@ -148,15 +148,15 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
[[package]]
name = "colorama"
-version = "0.4.5"
+version = "0.4.6"
description = "Cross-platform colored terminal text."
category = "main"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
[[package]]
name = "contourpy"
-version = "1.0.5"
+version = "1.0.6"
description = "Python library for calculating contours of 2D quadrilateral grids"
category = "main"
optional = false
@@ -167,10 +167,17 @@ numpy = ">=1.16"
[package.extras]
bokeh = ["bokeh", "selenium"]
+<<<<<<< HEAD
docs = ["docutils (<0.18)", "sphinx", "sphinx-rtd-theme"]
test = ["Pillow", "flake8", "isort", "matplotlib", "pytest"]
test-minimal = ["pytest"]
test-no-codebase = ["Pillow", "matplotlib", "pytest"]
+=======
+docs = ["docutils (<0.18)", "sphinx (<=5.2.0)", "sphinx-rtd-theme"]
+test = ["pytest", "matplotlib", "pillow", "flake8", "isort"]
+test-minimal = ["pytest"]
+test-no-codebase = ["pytest", "matplotlib", "pillow"]
+>>>>>>> Updating poetry.lock
[[package]]
name = "coverage"
@@ -238,6 +245,7 @@ aiosqlite = {version = "*", optional = true, markers = "extra == \"sqlite\""}
sqlalchemy = ">=1.4,<1.5"
[package.extras]
+<<<<<<< HEAD
aiomysql = ["aiomysql"]
aiopg = ["aiopg"]
aiosqlite = ["aiosqlite"]
@@ -245,7 +253,13 @@ asyncmy = ["asyncmy"]
asyncpg = ["asyncpg"]
mysql = ["aiomysql"]
postgresql = ["asyncpg"]
+=======
+>>>>>>> Updating poetry.lock
sqlite = ["aiosqlite"]
+postgresql_aiopg = ["aiopg"]
+postgresql = ["asyncpg"]
+mysql_asyncmy = ["asyncmy"]
+mysql = ["aiomysql"]
[[package]]
name = "decorator"
@@ -321,14 +335,19 @@ woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
[[package]]
name = "greenlet"
-version = "1.1.3.post0"
+version = "2.0.0"
description = "Lightweight in-process concurrent programming"
category = "main"
optional = false
python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
[package.extras]
+<<<<<<< HEAD
docs = ["Sphinx"]
+=======
+docs = ["sphinx", "docutils (<0.18)"]
+test = ["objgraph", "faulthandler"]
+>>>>>>> Updating poetry.lock
[[package]]
name = "gunicorn"
@@ -484,7 +503,11 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*"
[package.extras]
cssselect = ["cssselect (>=0.7)"]
html5 = ["html5lib"]
+<<<<<<< HEAD
htmlsoup = ["BeautifulSoup4"]
+=======
+htmlsoup = ["beautifulsoup4"]
+>>>>>>> Updating poetry.lock
source = ["Cython (>=0.29.7)"]
[[package]]
@@ -643,7 +666,7 @@ python-versions = ">=3.7"
[[package]]
name = "pillow"
-version = "9.2.0"
+version = "9.3.0"
description = "Python Imaging Library (Fork)"
category = "main"
optional = false
@@ -674,8 +697,8 @@ optional = false
python-versions = ">=3.6"
[package.extras]
-dev = ["pre-commit", "tox"]
-testing = ["pytest", "pytest-benchmark"]
+testing = ["pytest-benchmark", "pytest"]
+dev = ["tox", "pre-commit"]
[[package]]
name = "poethepoet"
@@ -740,8 +763,8 @@ optional = false
python-versions = ">=3.6"
[package.extras]
-ed25519 = ["PyNaCl (>=1.4.0)"]
rsa = ["cryptography"]
+ed25519 = ["PyNaCl (>=1.4.0)"]
[[package]]
name = "pyparsing"
@@ -852,19 +875,50 @@ idna = {version = "*", optional = true, markers = "extra == \"idna2008\""}
idna2008 = ["idna"]
[[package]]
-name = "safety"
-version = "1.10.3"
-description = "Checks installed dependencies for known vulnerabilities."
+name = "ruamel.yaml"
+version = "0.17.21"
+description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order"
+category = "dev"
+optional = false
+python-versions = ">=3"
+
+[package.dependencies]
+"ruamel.yaml.clib" = {version = ">=0.2.6", markers = "platform_python_implementation == \"CPython\" and python_version < \"3.11\""}
+
+[package.extras]
+docs = ["ryd"]
+jinja2 = ["ruamel.yaml.jinja2 (>=0.2)"]
+
+[[package]]
+name = "ruamel.yaml.clib"
+version = "0.2.7"
+description = "C version of reader, parser and emitter for ruamel.yaml derived from libyaml"
category = "dev"
optional = false
python-versions = ">=3.5"
+[[package]]
+name = "safety"
+version = "2.3.1"
+description = "Checks installed dependencies for known vulnerabilities and licenses."
+category = "dev"
+optional = false
+python-versions = "*"
+
[package.dependencies]
-Click = ">=6.0"
-dparse = ">=0.5.1"
-packaging = "*"
+Click = ">=8.0.2"
+dparse = ">=0.6.2"
+packaging = ">=21.0"
requests = "*"
+<<<<<<< HEAD
setuptools = "*"
+=======
+"ruamel.yaml" = ">=0.17.21"
+
+[package.extras]
+github = ["pygithub (>=1.43.3)", "jinja2 (>=3.1.0)"]
+gitlab = ["python-gitlab (>=1.3.0)"]
+>>>>>>> Updating poetry.lock
[[package]]
name = "scipy"
@@ -931,7 +985,7 @@ python-versions = ">=3.7"
[[package]]
name = "sqlalchemy"
-version = "1.4.41"
+version = "1.4.42"
description = "Database Abstraction Library"
category = "main"
optional = false
@@ -1028,10 +1082,17 @@ python-versions = ">=3.6"
click = ">=7.1.1,<9.0.0"
[package.extras]
+<<<<<<< HEAD
all = ["colorama (>=0.4.3,<0.5.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"]
dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "pre-commit (>=2.17.0,<3.0.0)"]
doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)"]
test = ["black (>=22.3.0,<23.0.0)", "coverage (>=5.2,<6.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"]
+=======
+all = ["colorama (>=0.4.3,<0.5.0)", "shellingham (>=1.3.0,<2.0.0)"]
+dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "pre-commit (>=2.17.0,<3.0.0)"]
+doc = ["mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "mdx-include (>=1.4.1,<2.0.0)"]
+test = ["shellingham (>=1.3.0,<2.0.0)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "coverage (>=5.2,<6.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "mypy (==0.910)", "black (>=22.3.0,<23.0.0)", "isort (>=5.0.6,<6.0.0)"]
+>>>>>>> Updating poetry.lock
[[package]]
name = "types-python-dateutil"
@@ -1129,7 +1190,7 @@ anyio = ">=3.0.0,<4"
[[package]]
name = "websockets"
-version = "10.3"
+version = "10.4"
description = "An implementation of the WebSocket Protocol (RFC 6455 & 7692)"
category = "main"
optional = false
@@ -1153,7 +1214,11 @@ pycurl = ["pycurl"]
[metadata]
lock-version = "1.1"
python-versions = "^3.8,<3.11"
+<<<<<<< HEAD
content-hash = "5fa530d09cec90a394b1a69cebbf7d7744f7dcbeadeae5d3005af83c786c2231"
+=======
+content-hash = "b422f9654f545a2922de39a470862060db8ad5e1e484bbf75b46b4223c31a364"
+>>>>>>> Updating poetry.lock
[metadata.files]
aiomysql = [
@@ -1176,6 +1241,16 @@ attrs = [
{file = "attrs-22.1.0-py2.py3-none-any.whl", hash = "sha256:86efa402f67bf2df34f51a335487cf46b1ec130d02b8d39fd248abfd30da551c"},
{file = "attrs-22.1.0.tar.gz", hash = "sha256:29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6"},
]
+<<<<<<< HEAD
+=======
+atomicwrites = [
+ {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"},
+]
+attrs = [
+ {file = "attrs-22.1.0-py2.py3-none-any.whl", hash = "sha256:86efa402f67bf2df34f51a335487cf46b1ec130d02b8d39fd248abfd30da551c"},
+ {file = "attrs-22.1.0.tar.gz", hash = "sha256:29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6"},
+]
+>>>>>>> Updating poetry.lock
authlib = [
{file = "Authlib-1.1.0-py2.py3-none-any.whl", hash = "sha256:be4b6a1dea51122336c210a6945b27a105b9ac572baffd15b07bcff4376c1523"},
{file = "Authlib-1.1.0.tar.gz", hash = "sha256:0a270c91409fc2b7b0fbee6996e09f2ee3187358762111a9a4225c874b94e891"},
@@ -1282,79 +1357,79 @@ click = [
{file = "click-8.1.3.tar.gz", hash = "sha256:7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e"},
]
colorama = [
- {file = "colorama-0.4.5-py2.py3-none-any.whl", hash = "sha256:854bf444933e37f5824ae7bfc1e98d5bce2ebe4160d46b5edf346a89358e99da"},
- {file = "colorama-0.4.5.tar.gz", hash = "sha256:e6c6b4334fc50988a639d9b98aa429a0b57da6e17b9a44f0451f930b6967b7a4"},
+ {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
+ {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
]
contourpy = [
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+>>>>>>> Updating poetry.lock
]
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]
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+<<<<<<< HEAD
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]
+=======
+>>>>>>> Updating poetry.lock
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+ {file = "websockets-10.4-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:05a7233089f8bd355e8cbe127c2e8ca0b4ea55467861906b80d2ebc7db4d6b72"},
+ {file = "websockets-10.4.tar.gz", hash = "sha256:eef610b23933c54d5d921c92578ae5f89813438fded840c2e9809d378dc765d3"},
]
zipp = [
{file = "zipp-3.10.0-py3-none-any.whl", hash = "sha256:4fcb6f278987a6605757302a6e40e896257570d11c51628968ccb2a47e80c6c1"},
--
GitLab
From cce7756289ca630f4830487dd6c17fc59bc2b219 Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Tue, 1 Nov 2022 15:50:46 -0600
Subject: [PATCH 099/142] Fixed test_gaps function
---
test/algorithm_test/AverageAlgorithm_test.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/test/algorithm_test/AverageAlgorithm_test.py b/test/algorithm_test/AverageAlgorithm_test.py
index 43cd48d0..88ca37e0 100644
--- a/test/algorithm_test/AverageAlgorithm_test.py
+++ b/test/algorithm_test/AverageAlgorithm_test.py
@@ -80,8 +80,8 @@ def test_gaps():
# Run timeseries through the average process
outstream = alg.process(timeseries)
- # The gaps should not be changed and should remain 'nan'
- assert_array_equal(outstream[0].data, [1, 1, np.nan, np.nan, 1, 1])
+ # The gaps should not be ignored
+ assert_array_equal(outstream[0].data, [1, 1, 1, 1, 1, 1])
def test_metadata():
--
GitLab
From d9a9d89b4db4b2845a6828e18128c0b55af44150 Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Wed, 2 Nov 2022 11:37:15 -0600
Subject: [PATCH 100/142] Renamed variables and put into paragraphs. Asserted
that the count correctly shows where there are fewer input data.
---
geomagio/algorithm/AverageAlgorithm.py | 46 ++++++++++----------
test/algorithm_test/AverageAlgorithm_test.py | 2 +
2 files changed, 25 insertions(+), 23 deletions(-)
diff --git a/geomagio/algorithm/AverageAlgorithm.py b/geomagio/algorithm/AverageAlgorithm.py
index 16eafdf9..2b07bda4 100644
--- a/geomagio/algorithm/AverageAlgorithm.py
+++ b/geomagio/algorithm/AverageAlgorithm.py
@@ -111,30 +111,30 @@ class AverageAlgorithm(Algorithm):
ts = timeseries.select(station=obsy)[0]
combined.append(ts.data * latcorr)
- # after looping over stations, compute average
- dst_tot = numpy.nanmean(combined, axis=0)
-
- # Stack timeseries and count non-nan values per timestep
+ # calculate averages
+ average_data = numpy.nanmean(combined, axis=0)
+ average_stats = obspy.core.Stats()
+ average_stats.station = "USGS"
+ average_stats.channel = self.outchannel
+ average_stats.network = "NT"
+ average_stats.location = self.outlocation
+ average_stats.starttime = timeseries[0].stats.starttime
+ average_stats.npts = timeseries[0].stats.npts
+ average_stats.delta = timeseries[0].stats.delta
+
+ # calculate counts
ts_counter = numpy.column_stack(timeseries)
- channel_count = numpy.count_nonzero(~numpy.isnan(ts_counter), axis=1)
-
- # create metadata
- new_stats = obspy.core.Stats()
- new_stats.station = "USGS"
- new_stats.channel = self.outchannel
- new_stats.network = "NT"
- new_stats.location = self.outlocation
- new_stats.starttime = timeseries[0].stats.starttime
- new_stats.npts = timeseries[0].stats.npts
- new_stats.delta = timeseries[0].stats.delta
- new_stats2 = new_stats.copy()
- new_stats2.channel = new_stats.channel + "_count"
-
- # create streams from the trace function
- stream = obspy.core.Stream((obspy.core.Trace(dst_tot, new_stats),))
- stream += obspy.core.Trace(numpy.asarray(channel_count), new_stats2)
-
- # return averaged values as a stream
+ count_data = numpy.count_nonzero(~numpy.isnan(ts_counter), axis=1)
+ count_stats = average_stats.copy()
+ count_stats.channel = average_stats.channel + "_count"
+
+ # return stream
+ stream = obspy.core.Stream(
+ (
+ obspy.core.Trace(average_data, average_stats),
+ obspy.core.Trace(numpy.asarray(count_data), count_stats),
+ )
+ )
return stream
@classmethod
diff --git a/test/algorithm_test/AverageAlgorithm_test.py b/test/algorithm_test/AverageAlgorithm_test.py
index 88ca37e0..2480f655 100644
--- a/test/algorithm_test/AverageAlgorithm_test.py
+++ b/test/algorithm_test/AverageAlgorithm_test.py
@@ -82,6 +82,8 @@ def test_gaps():
# The gaps should not be ignored
assert_array_equal(outstream[0].data, [1, 1, 1, 1, 1, 1])
+ # Counts should show where there are fewer input data
+ assert_array_equal(outstream[1].data, [2, 2, 1, 1, 2, 2])
def test_metadata():
--
GitLab
From 6cad83d2f793197540d06da95ccebeb3a8d034f4 Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Wed, 2 Nov 2022 15:07:29 -0600
Subject: [PATCH 101/142] Fixing poetry.lock and pyproject.toml files
---
poetry.lock | 447 +++++++++++++++++--------------------------------
pyproject.toml | 2 +-
2 files changed, 153 insertions(+), 296 deletions(-)
diff --git a/poetry.lock b/poetry.lock
index ceed07f6..0207bf94 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -54,8 +54,8 @@ idna = ">=2.8"
sniffio = ">=1.1"
[package.extras]
-doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
-test = ["contextlib2", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (<0.15)", "uvloop (>=0.15)"]
+doc = ["packaging", "sphinx-rtd-theme", "sphinx-autodoc-typehints (>=1.2.0)"]
+test = ["coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "contextlib2", "uvloop (<0.15)", "mock (>=4)", "uvloop (>=0.15)"]
trio = ["trio (>=0.16,<0.22)"]
[[package]]
@@ -67,10 +67,10 @@ optional = false
python-versions = ">=3.5"
[package.extras]
-dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"]
-docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"]
-tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"]
-tests-no-zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
+docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "cloudpickle"]
[[package]]
name = "authlib"
@@ -133,7 +133,7 @@ optional = false
python-versions = ">=3.6.0"
[package.extras]
-unicode-backport = ["unicodedata2"]
+unicode_backport = ["unicodedata2"]
[[package]]
name = "click"
@@ -167,17 +167,10 @@ numpy = ">=1.16"
[package.extras]
bokeh = ["bokeh", "selenium"]
-<<<<<<< HEAD
-docs = ["docutils (<0.18)", "sphinx", "sphinx-rtd-theme"]
-test = ["Pillow", "flake8", "isort", "matplotlib", "pytest"]
-test-minimal = ["pytest"]
-test-no-codebase = ["Pillow", "matplotlib", "pytest"]
-=======
docs = ["docutils (<0.18)", "sphinx (<=5.2.0)", "sphinx-rtd-theme"]
test = ["pytest", "matplotlib", "pillow", "flake8", "isort"]
test-minimal = ["pytest"]
test-no-codebase = ["pytest", "matplotlib", "pillow"]
->>>>>>> Updating poetry.lock
[[package]]
name = "coverage"
@@ -195,7 +188,7 @@ toml = ["tomli"]
[[package]]
name = "cryptography"
-version = "38.0.1"
+version = "38.0.3"
description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
category = "main"
optional = false
@@ -206,11 +199,11 @@ cffi = ">=1.12"
[package.extras]
docs = ["sphinx (>=1.6.5,!=1.8.0,!=3.1.0,!=3.1.1)", "sphinx-rtd-theme"]
-docstest = ["pyenchant (>=1.6.11)", "sphinxcontrib-spelling (>=4.0.1)", "twine (>=1.12.0)"]
+docstest = ["pyenchant (>=1.6.11)", "twine (>=1.12.0)", "sphinxcontrib-spelling (>=4.0.1)"]
pep8test = ["black", "flake8", "flake8-import-order", "pep8-naming"]
sdist = ["setuptools-rust (>=0.11.4)"]
ssh = ["bcrypt (>=3.1.5)"]
-test = ["hypothesis (>=1.11.4,!=3.79.2)", "iso8601", "pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-subtests", "pytest-xdist", "pytz"]
+test = ["pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-subtests", "pytest-xdist", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,!=3.79.2)"]
[[package]]
name = "cycler"
@@ -245,7 +238,6 @@ aiosqlite = {version = "*", optional = true, markers = "extra == \"sqlite\""}
sqlalchemy = ">=1.4,<1.5"
[package.extras]
-<<<<<<< HEAD
aiomysql = ["aiomysql"]
aiopg = ["aiopg"]
aiosqlite = ["aiosqlite"]
@@ -253,13 +245,7 @@ asyncmy = ["asyncmy"]
asyncpg = ["asyncpg"]
mysql = ["aiomysql"]
postgresql = ["asyncpg"]
-=======
->>>>>>> Updating poetry.lock
sqlite = ["aiosqlite"]
-postgresql_aiopg = ["aiopg"]
-postgresql = ["asyncpg"]
-mysql_asyncmy = ["asyncmy"]
-mysql = ["aiomysql"]
[[package]]
name = "decorator"
@@ -293,9 +279,20 @@ category = "main"
optional = false
python-versions = ">=3.6"
+[[package]]
+name = "exceptiongroup"
+version = "1.0.0"
+description = "Backport of PEP 654 (exception groups)"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+test = ["pytest (>=6)"]
+
[[package]]
name = "fastapi"
-version = "0.85.1"
+version = "0.85.2"
description = "FastAPI framework, high performance, easy to learn, fast to code, ready for production"
category = "main"
optional = false
@@ -308,8 +305,8 @@ starlette = "0.20.4"
[package.extras]
all = ["email-validator (>=1.1.1,<2.0.0)", "itsdangerous (>=1.1.0,<3.0.0)", "jinja2 (>=2.11.2,<4.0.0)", "orjson (>=3.2.1,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "pyyaml (>=5.3.1,<7.0.0)", "requests (>=2.24.0,<3.0.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)", "uvicorn[standard] (>=0.12.0,<0.19.0)"]
dev = ["autoflake (>=1.4.0,<2.0.0)", "flake8 (>=3.8.3,<6.0.0)", "pre-commit (>=2.17.0,<3.0.0)", "uvicorn[standard] (>=0.12.0,<0.19.0)"]
-doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-markdownextradata-plugin (>=0.1.7,<0.3.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "pyyaml (>=5.3.1,<7.0.0)", "typer (>=0.4.1,<0.7.0)"]
-test = ["anyio[trio] (>=3.2.1,<4.0.0)", "black (==22.8.0)", "databases[sqlite] (>=0.3.2,<0.7.0)", "email-validator (>=1.1.1,<2.0.0)", "flake8 (>=3.8.3,<6.0.0)", "flask (>=1.1.2,<3.0.0)", "httpx (>=0.23.0,<0.24.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.971)", "orjson (>=3.2.1,<4.0.0)", "passlib[bcrypt] (>=1.7.2,<2.0.0)", "peewee (>=3.13.3,<4.0.0)", "pytest (>=7.1.3,<8.0.0)", "pytest-cov (>=2.12.0,<4.0.0)", "python-jose[cryptography] (>=3.3.0,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "pyyaml (>=5.3.1,<7.0.0)", "requests (>=2.24.0,<3.0.0)", "sqlalchemy (>=1.3.18,<1.5.0)", "types-orjson (==3.6.2)", "types-ujson (==5.4.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)"]
+doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs-markdownextradata-plugin (>=0.1.7,<0.3.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "pyyaml (>=5.3.1,<7.0.0)", "typer[all] (>=0.6.1,<0.7.0)"]
+test = ["anyio[trio] (>=3.2.1,<4.0.0)", "black (==22.8.0)", "databases[sqlite] (>=0.3.2,<0.7.0)", "email-validator (>=1.1.1,<2.0.0)", "flake8 (>=3.8.3,<6.0.0)", "flask (>=1.1.2,<3.0.0)", "httpx (>=0.23.0,<0.24.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.982)", "orjson (>=3.2.1,<4.0.0)", "passlib[bcrypt] (>=1.7.2,<2.0.0)", "peewee (>=3.13.3,<4.0.0)", "pytest-cov (>=2.12.0,<5.0.0)", "pytest (>=7.1.3,<8.0.0)", "python-jose[cryptography] (>=3.3.0,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "pyyaml (>=5.3.1,<7.0.0)", "requests (>=2.24.0,<3.0.0)", "sqlalchemy (>=1.3.18,<=1.4.41)", "types-orjson (==3.6.2)", "types-ujson (==5.5.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)"]
[[package]]
name = "fonttools"
@@ -320,9 +317,9 @@ optional = false
python-versions = ">=3.7"
[package.extras]
-all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=14.0.0)", "xattr", "zopfli (>=0.1.4)"]
+all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "uharfbuzz (>=0.23.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=14.0.0)", "xattr"]
graphite = ["lz4 (>=1.7.4.2)"]
-interpolatable = ["munkres", "scipy"]
+interpolatable = ["scipy", "munkres"]
lxml = ["lxml (>=4.0,<5)"]
pathops = ["skia-pathops (>=0.5.0)"]
plot = ["matplotlib"]
@@ -331,7 +328,7 @@ symfont = ["sympy"]
type1 = ["xattr"]
ufo = ["fs (>=2.2.0,<3)"]
unicode = ["unicodedata2 (>=14.0.0)"]
-woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
+woff = ["zopfli (>=0.1.4)", "brotlicffi (>=0.8.0)", "brotli (>=1.0.1)"]
[[package]]
name = "greenlet"
@@ -342,12 +339,8 @@ optional = false
python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
[package.extras]
-<<<<<<< HEAD
-docs = ["Sphinx"]
-=======
docs = ["sphinx", "docutils (<0.18)"]
test = ["objgraph", "faulthandler"]
->>>>>>> Updating poetry.lock
[[package]]
name = "gunicorn"
@@ -357,9 +350,6 @@ category = "main"
optional = false
python-versions = ">=3.5"
-[package.dependencies]
-setuptools = ">=3.0"
-
[package.extras]
eventlet = ["eventlet (>=0.24.1)"]
gevent = ["gevent (>=1.4.0)"]
@@ -418,8 +408,8 @@ rfc3986 = {version = ">=1.3,<2", extras = ["idna2008"]}
sniffio = "*"
[package.extras]
-brotli = ["brotli", "brotlicffi"]
-cli = ["click (>=8.0.0,<9.0.0)", "pygments (>=2.0.0,<3.0.0)", "rich (>=10,<13)"]
+brotli = ["brotlicffi", "brotli"]
+cli = ["click (>=8.0.0,<9.0.0)", "rich (>=10,<13)", "pygments (>=2.0.0,<3.0.0)"]
http2 = ["h2 (>=3,<5)"]
socks = ["socksio (>=1.0.0,<2.0.0)"]
@@ -443,9 +433,9 @@ python-versions = ">=3.7"
zipp = ">=0.5"
[package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
+docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
perf = ["ipython"]
-testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
[[package]]
name = "importlib-resources"
@@ -459,8 +449,8 @@ python-versions = ">=3.7"
zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
[package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
-testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
[[package]]
name = "iniconfig"
@@ -479,10 +469,10 @@ optional = false
python-versions = ">=3.6.1,<4.0"
[package.extras]
+pipfile_deprecated_finder = ["pipreqs", "requirementslib"]
+requirements_deprecated_finder = ["pipreqs", "pip-api"]
colors = ["colorama (>=0.4.3,<0.5.0)"]
-pipfile-deprecated-finder = ["pipreqs", "requirementslib"]
plugins = ["setuptools"]
-requirements-deprecated-finder = ["pip-api", "pipreqs"]
[[package]]
name = "kiwisolver"
@@ -503,11 +493,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*"
[package.extras]
cssselect = ["cssselect (>=0.7)"]
html5 = ["html5lib"]
-<<<<<<< HEAD
-htmlsoup = ["BeautifulSoup4"]
-=======
htmlsoup = ["beautifulsoup4"]
->>>>>>> Updating poetry.lock
source = ["Cython (>=0.29.7)"]
[[package]]
@@ -522,7 +508,7 @@ python-versions = ">=3.7"
MarkupSafe = ">=0.9.2"
[package.extras]
-babel = ["Babel"]
+babel = ["babel"]
lingua = ["lingua"]
testing = ["pytest"]
@@ -603,14 +589,13 @@ matplotlib = ">=3.2.0"
numpy = ">=1.15.0"
requests = "*"
scipy = ">=1.0.0"
-setuptools = "*"
sqlalchemy = "*"
[package.extras]
-all = ["cartopy", "geographiclib", "packaging", "pyproj", "pyshp", "pytest", "pytest-json-report"]
+all = ["packaging", "pyproj", "pytest", "pytest-json-report", "geographiclib", "cartopy", "pyshp"]
geo = ["geographiclib"]
imaging = ["cartopy"]
-io-shapefile = ["pyshp"]
+"io.shapefile" = ["pyshp"]
tests = ["packaging", "pyproj", "pytest", "pytest-json-report"]
[[package]]
@@ -685,8 +670,8 @@ optional = false
python-versions = ">=3.7"
[package.extras]
-docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx (>=4)", "sphinx-autodoc-typehints (>=1.12)"]
-test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"]
+docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)", "sphinx (>=4)"]
+test = ["appdirs (==1.4.4)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)", "pytest (>=6)"]
[[package]]
name = "pluggy"
@@ -713,15 +698,7 @@ pastel = ">=0.2.1,<0.3.0"
tomli = ">=1.2.2"
[package.extras]
-poetry-plugin = ["poetry (>=1.0,<2.0)"]
-
-[[package]]
-name = "py"
-version = "1.11.0"
-description = "library with cross-python path, ini-parsing, io, code, log facilities"
-category = "dev"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+poetry_plugin = ["poetry (>=1.0,<2.0)"]
[[package]]
name = "pycparser"
@@ -775,11 +752,11 @@ optional = false
python-versions = ">=3.6.8"
[package.extras]
-diagrams = ["jinja2", "railroad-diagrams"]
+diagrams = ["railroad-diagrams", "jinja2"]
[[package]]
name = "pytest"
-version = "7.1.3"
+version = "7.2.0"
description = "pytest: simple powerful testing with Python"
category = "dev"
optional = false
@@ -788,11 +765,11 @@ python-versions = ">=3.7"
[package.dependencies]
attrs = ">=19.2.0"
colorama = {version = "*", markers = "sys_platform == \"win32\""}
+exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
iniconfig = "*"
packaging = "*"
pluggy = ">=0.12,<2.0"
-py = ">=1.8.2"
-tomli = ">=1.0.0"
+tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
[package.extras]
testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"]
@@ -810,7 +787,7 @@ coverage = {version = ">=5.2.1", extras = ["toml"]}
pytest = ">=4.6"
[package.extras]
-testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
+testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"]
[[package]]
name = "python-dateutil"
@@ -858,7 +835,7 @@ urllib3 = ">=1.21.1,<1.27"
[package.extras]
socks = ["PySocks (>=1.5.6,!=1.5.7)"]
-use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
+use_chardet_on_py3 = ["chardet (>=3.0.2,<6)"]
[[package]]
name = "rfc3986"
@@ -910,15 +887,11 @@ Click = ">=8.0.2"
dparse = ">=0.6.2"
packaging = ">=21.0"
requests = "*"
-<<<<<<< HEAD
-setuptools = "*"
-=======
"ruamel.yaml" = ">=0.17.21"
[package.extras]
github = ["pygithub (>=1.43.3)", "jinja2 (>=3.1.0)"]
gitlab = ["python-gitlab (>=1.3.0)"]
->>>>>>> Updating poetry.lock
[[package]]
name = "scipy"
@@ -932,22 +905,9 @@ python-versions = ">=3.8"
numpy = ">=1.18.5,<1.26.0"
[package.extras]
-dev = ["flake8", "mypy", "pycodestyle", "typing_extensions"]
-doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-panels (>=0.5.2)", "sphinx-tabs"]
-test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
-
-[[package]]
-name = "setuptools"
-version = "65.5.0"
-description = "Easily download, build, install, upgrade, and uninstall Python packages"
-category = "main"
-optional = false
-python-versions = ">=3.7"
-
-[package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mock", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
-testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
+test = ["pytest", "pytest-cov", "pytest-xdist", "asv", "mpmath", "gmpy2", "threadpoolctl", "scikit-umfpack"]
+doc = ["sphinx (!=4.1.0)", "pydata-sphinx-theme (==0.9.0)", "sphinx-panels (>=0.5.2)", "matplotlib (>2)", "numpydoc", "sphinx-tabs"]
+dev = ["mypy", "typing-extensions", "pycodestyle", "flake8"]
[[package]]
name = "setuptools-scm"
@@ -959,7 +919,6 @@ python-versions = ">=3.7"
[package.dependencies]
packaging = ">=20.0"
-setuptools = "*"
tomli = ">=1.0.0"
typing-extensions = "*"
@@ -985,7 +944,7 @@ python-versions = ">=3.7"
[[package]]
name = "sqlalchemy"
-version = "1.4.42"
+version = "1.4.41"
description = "Database Abstraction Library"
category = "main"
optional = false
@@ -995,25 +954,25 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"}
[package.extras]
-aiomysql = ["aiomysql", "greenlet (!=0.4.17)"]
-aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"]
+aiomysql = ["greenlet (!=0.4.17)", "aiomysql"]
+aiosqlite = ["typing_extensions (!=3.10.0.1)", "greenlet (!=0.4.17)", "aiosqlite"]
asyncio = ["greenlet (!=0.4.17)"]
-asyncmy = ["asyncmy (>=0.2.3,!=0.2.4)", "greenlet (!=0.4.17)"]
-mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2)"]
+asyncmy = ["greenlet (!=0.4.17)", "asyncmy (>=0.2.3,!=0.2.4)"]
+mariadb_connector = ["mariadb (>=1.0.1,!=1.1.2)"]
mssql = ["pyodbc"]
-mssql-pymssql = ["pymssql"]
-mssql-pyodbc = ["pyodbc"]
-mypy = ["mypy (>=0.910)", "sqlalchemy2-stubs"]
-mysql = ["mysqlclient (>=1.4.0)", "mysqlclient (>=1.4.0,<2)"]
-mysql-connector = ["mysql-connector-python"]
-oracle = ["cx_oracle (>=7)", "cx_oracle (>=7,<8)"]
+mssql_pymssql = ["pymssql"]
+mssql_pyodbc = ["pyodbc"]
+mypy = ["sqlalchemy2-stubs", "mypy (>=0.910)"]
+mysql = ["mysqlclient (>=1.4.0,<2)", "mysqlclient (>=1.4.0)"]
+mysql_connector = ["mysql-connector-python"]
+oracle = ["cx_oracle (>=7,<8)", "cx_oracle (>=7)"]
postgresql = ["psycopg2 (>=2.7)"]
-postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
-postgresql-pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)"]
-postgresql-psycopg2binary = ["psycopg2-binary"]
-postgresql-psycopg2cffi = ["psycopg2cffi"]
-pymysql = ["pymysql", "pymysql (<1)"]
-sqlcipher = ["sqlcipher3_binary"]
+postgresql_asyncpg = ["greenlet (!=0.4.17)", "asyncpg"]
+postgresql_pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)"]
+postgresql_psycopg2binary = ["psycopg2-binary"]
+postgresql_psycopg2cffi = ["psycopg2cffi"]
+pymysql = ["pymysql (<1)", "pymysql"]
+sqlcipher = ["sqlcipher3-binary"]
[[package]]
name = "sqlalchemy-stubs"
@@ -1036,7 +995,6 @@ optional = false
python-versions = "*"
[package.dependencies]
-setuptools = "*"
SQLAlchemy = ">=0.9.0"
[[package]]
@@ -1082,17 +1040,10 @@ python-versions = ">=3.6"
click = ">=7.1.1,<9.0.0"
[package.extras]
-<<<<<<< HEAD
-all = ["colorama (>=0.4.3,<0.5.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"]
-dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "pre-commit (>=2.17.0,<3.0.0)"]
-doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)"]
-test = ["black (>=22.3.0,<23.0.0)", "coverage (>=5.2,<6.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"]
-=======
-all = ["colorama (>=0.4.3,<0.5.0)", "shellingham (>=1.3.0,<2.0.0)"]
+all = ["colorama (>=0.4.3,<0.5.0)", "shellingham (>=1.3.0,<2.0.0)", "rich (>=10.11.0,<13.0.0)"]
dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "pre-commit (>=2.17.0,<3.0.0)"]
doc = ["mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "mdx-include (>=1.4.1,<2.0.0)"]
-test = ["shellingham (>=1.3.0,<2.0.0)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "coverage (>=5.2,<6.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "mypy (==0.910)", "black (>=22.3.0,<23.0.0)", "isort (>=5.0.6,<6.0.0)"]
->>>>>>> Updating poetry.lock
+test = ["shellingham (>=1.3.0,<2.0.0)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "coverage (>=5.2,<6.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "mypy (==0.910)", "black (>=22.3.0,<23.0.0)", "isort (>=5.0.6,<6.0.0)", "rich (>=10.11.0,<13.0.0)"]
[[package]]
name = "types-python-dateutil"
@@ -1138,8 +1089,8 @@ optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, <4"
[package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
-secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
+brotli = ["brotlicffi (>=0.8.0)", "brotli (>=1.0.9)", "brotlipy (>=0.6.0)"]
+secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "urllib3-secure-extra", "ipaddress"]
socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
[[package]]
@@ -1173,9 +1124,9 @@ optional = false
python-versions = ">=3.7"
[package.extras]
-dev = ["Cython (>=0.29.32,<0.30.0)", "Sphinx (>=4.1.2,<4.2.0)", "aiohttp", "flake8 (>=3.9.2,<3.10.0)", "mypy (>=0.800)", "psutil", "pyOpenSSL (>=22.0.0,<22.1.0)", "pycodestyle (>=2.7.0,<2.8.0)", "pytest (>=3.6.0)", "sphinx-rtd-theme (>=0.5.2,<0.6.0)", "sphinxcontrib-asyncio (>=0.3.0,<0.4.0)"]
-docs = ["Sphinx (>=4.1.2,<4.2.0)", "sphinx-rtd-theme (>=0.5.2,<0.6.0)", "sphinxcontrib-asyncio (>=0.3.0,<0.4.0)"]
-test = ["Cython (>=0.29.32,<0.30.0)", "aiohttp", "flake8 (>=3.9.2,<3.10.0)", "mypy (>=0.800)", "psutil", "pyOpenSSL (>=22.0.0,<22.1.0)", "pycodestyle (>=2.7.0,<2.8.0)"]
+dev = ["Cython (>=0.29.32,<0.30.0)", "pytest (>=3.6.0)", "Sphinx (>=4.1.2,<4.2.0)", "sphinxcontrib-asyncio (>=0.3.0,<0.4.0)", "sphinx-rtd-theme (>=0.5.2,<0.6.0)", "flake8 (>=3.9.2,<3.10.0)", "psutil", "pycodestyle (>=2.7.0,<2.8.0)", "pyOpenSSL (>=22.0.0,<22.1.0)", "mypy (>=0.800)", "aiohttp"]
+docs = ["Sphinx (>=4.1.2,<4.2.0)", "sphinxcontrib-asyncio (>=0.3.0,<0.4.0)", "sphinx-rtd-theme (>=0.5.2,<0.6.0)"]
+test = ["flake8 (>=3.9.2,<3.10.0)", "psutil", "pycodestyle (>=2.7.0,<2.8.0)", "pyOpenSSL (>=22.0.0,<22.1.0)", "mypy (>=0.800)", "Cython (>=0.29.32,<0.30.0)", "aiohttp"]
[[package]]
name = "watchfiles"
@@ -1205,8 +1156,8 @@ optional = false
python-versions = ">=3.7"
[package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
-testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "jaraco.itertools", "func-timeout", "jaraco.functools", "more-itertools", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
[extras]
pycurl = ["pycurl"]
@@ -1214,11 +1165,7 @@ pycurl = ["pycurl"]
[metadata]
lock-version = "1.1"
python-versions = "^3.8,<3.11"
-<<<<<<< HEAD
-content-hash = "5fa530d09cec90a394b1a69cebbf7d7744f7dcbeadeae5d3005af83c786c2231"
-=======
-content-hash = "b422f9654f545a2922de39a470862060db8ad5e1e484bbf75b46b4223c31a364"
->>>>>>> Updating poetry.lock
+content-hash = "7f5183b6cc148a8931464f59583f2786977958cf74541a6b3c6555cf89adceca"
[metadata.files]
aiomysql = [
@@ -1241,16 +1188,6 @@ attrs = [
{file = "attrs-22.1.0-py2.py3-none-any.whl", hash = "sha256:86efa402f67bf2df34f51a335487cf46b1ec130d02b8d39fd248abfd30da551c"},
{file = "attrs-22.1.0.tar.gz", hash = "sha256:29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6"},
]
-<<<<<<< HEAD
-=======
-atomicwrites = [
- {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"},
-]
-attrs = [
- {file = "attrs-22.1.0-py2.py3-none-any.whl", hash = "sha256:86efa402f67bf2df34f51a335487cf46b1ec130d02b8d39fd248abfd30da551c"},
- {file = "attrs-22.1.0.tar.gz", hash = "sha256:29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6"},
-]
->>>>>>> Updating poetry.lock
authlib = [
{file = "Authlib-1.1.0-py2.py3-none-any.whl", hash = "sha256:be4b6a1dea51122336c210a6945b27a105b9ac572baffd15b07bcff4376c1523"},
{file = "Authlib-1.1.0.tar.gz", hash = "sha256:0a270c91409fc2b7b0fbee6996e09f2ee3187358762111a9a4225c874b94e891"},
@@ -1484,32 +1421,32 @@ coverage = [
{file = "coverage-6.5.0.tar.gz", hash = "sha256:f642e90754ee3e06b0e7e51bce3379590e76b7f76b708e1a71ff043f87025c84"},
]
cryptography = [
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- {file = "cryptography-38.0.1-cp36-abi3-macosx_10_10_x86_64.whl", hash = "sha256:3fc26e22840b77326a764ceb5f02ca2d342305fba08f002a8c1f139540cdfaad"},
- {file = "cryptography-38.0.1-cp36-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.manylinux_2_24_aarch64.whl", hash = "sha256:3b72c360427889b40f36dc214630e688c2fe03e16c162ef0aa41da7ab1455153"},
- {file = "cryptography-38.0.1-cp36-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:194044c6b89a2f9f169df475cc167f6157eb9151cc69af8a2a163481d45cc407"},
- {file = "cryptography-38.0.1-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ca9f6784ea96b55ff41708b92c3f6aeaebde4c560308e5fbbd3173fbc466e94e"},
- {file = "cryptography-38.0.1-cp36-abi3-manylinux_2_24_x86_64.whl", hash = "sha256:16fa61e7481f4b77ef53991075de29fc5bacb582a1244046d2e8b4bb72ef66d0"},
- {file = "cryptography-38.0.1-cp36-abi3-manylinux_2_28_aarch64.whl", hash = "sha256:d4ef6cc305394ed669d4d9eebf10d3a101059bdcf2669c366ec1d14e4fb227bd"},
- {file = "cryptography-38.0.1-cp36-abi3-manylinux_2_28_x86_64.whl", hash = "sha256:3261725c0ef84e7592597606f6583385fed2a5ec3909f43bc475ade9729a41d6"},
- {file = "cryptography-38.0.1-cp36-abi3-musllinux_1_1_aarch64.whl", hash = "sha256:0297ffc478bdd237f5ca3a7dc96fc0d315670bfa099c04dc3a4a2172008a405a"},
- {file = "cryptography-38.0.1-cp36-abi3-musllinux_1_1_x86_64.whl", hash = "sha256:89ed49784ba88c221756ff4d4755dbc03b3c8d2c5103f6d6b4f83a0fb1e85294"},
- {file = "cryptography-38.0.1-cp36-abi3-win32.whl", hash = "sha256:ac7e48f7e7261207d750fa7e55eac2d45f720027d5703cd9007e9b37bbb59ac0"},
- {file = "cryptography-38.0.1-cp36-abi3-win_amd64.whl", hash = "sha256:ad7353f6ddf285aeadfaf79e5a6829110106ff8189391704c1d8801aa0bae45a"},
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->>>>>>> Updating poetry.lock
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-=======
->>>>>>> Updating poetry.lock
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+ {file = "SQLAlchemy-1.4.41-cp39-cp39-win_amd64.whl", hash = "sha256:f5fa526d027d804b1f85cdda1eb091f70bde6fb7d87892f6dd5a48925bc88898"},
+ {file = "SQLAlchemy-1.4.41.tar.gz", hash = "sha256:0292f70d1797e3c54e862e6f30ae474014648bc9c723e14a2fda730adb0a9791"},
]
sqlalchemy-stubs = [
{file = "sqlalchemy-stubs-0.4.tar.gz", hash = "sha256:c665d6dd4482ef642f01027fa06c3d5e91befabb219dc71fc2a09e7d7695f7ae"},
@@ -2411,13 +2273,8 @@ tomli = [
{file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
]
typer = [
-<<<<<<< HEAD
{file = "typer-0.6.1-py3-none-any.whl", hash = "sha256:54b19e5df18654070a82f8c2aa1da456a4ac16a2a83e6dcd9f170e291c56338e"},
{file = "typer-0.6.1.tar.gz", hash = "sha256:2d5720a5e63f73eaf31edaa15f6ab87f35f0690f8ca233017d7d23d743a91d73"},
-=======
- {file = "typer-0.4.2-py3-none-any.whl", hash = "sha256:023bae00d1baf358a6cc7cea45851639360bb716de687b42b0a4641cd99173f1"},
- {file = "typer-0.4.2.tar.gz", hash = "sha256:b8261c6c0152dd73478b5ba96ba677e5d6948c715c310f7c91079f311f62ec03"},
->>>>>>> Updating poetry.lock
]
types-python-dateutil = [
{file = "types-python-dateutil-2.8.19.2.tar.gz", hash = "sha256:e6e32ce18f37765b08c46622287bc8d8136dc0c562d9ad5b8fd158c59963d7a7"},
diff --git a/pyproject.toml b/pyproject.toml
index fb903103..85f5fd12 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -53,7 +53,7 @@ mypy = "^0.982"
poethepoet = "^0.16.4"
pytest = "^7.1.3"
pytest-cov = "^4.0.0"
-safety = "^1.10.3"
+safety = "^2.2.0"
# type hints
data-science-types = "^0.2.23"
openpyxl-stubs = "^0.1.24"
--
GitLab
From f1b305e40951bed9c7ab9f24385ed6b77a8e83cc Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Wed, 9 Nov 2022 16:49:39 -0700
Subject: [PATCH 102/142] Add --average-min-count option to AverageAlgorithm
- added a `min_count` keyword to the AvergeAlgorithm's __init__() method;
- added a --average-min-count option via the add_arguments() classmethod;
- set `self.min_count = arguments.average_min_count` in configure() method;
- refactored process() method to respect `min_count`, but now it defaults
to a requirement that all inputs be valid (this modified a recent merge
by @awernle that only required that any inputs be valid;
- modified AverageAlgorithm_test.py to properly assess things in light
of the change to default behavior just mentioned.
---
geomagio/algorithm/AverageAlgorithm.py | 40 ++++++++++++++++----
test/algorithm_test/AverageAlgorithm_test.py | 4 +-
2 files changed, 35 insertions(+), 9 deletions(-)
diff --git a/geomagio/algorithm/AverageAlgorithm.py b/geomagio/algorithm/AverageAlgorithm.py
index 2b07bda4..75ee9170 100644
--- a/geomagio/algorithm/AverageAlgorithm.py
+++ b/geomagio/algorithm/AverageAlgorithm.py
@@ -18,7 +18,14 @@ class AverageAlgorithm(Algorithm):
"""
- def __init__(self, observatories=None, channel=None, location=None, scales=None):
+ def __init__(
+ self,
+ observatories=None,
+ channel=None,
+ location=None,
+ scales=None,
+ min_count=None,
+ ):
Algorithm.__init__(self)
self._npts = -1
self._stt = -1
@@ -27,6 +34,7 @@ class AverageAlgorithm(Algorithm):
self.observatories = observatories
self.outchannel = channel
self.outlocation = location
+ self.min_count = min_count
self.observatoryMetadata = ObservatoryMetadata()
def check_stream(self, timeseries):
@@ -86,6 +94,8 @@ class AverageAlgorithm(Algorithm):
self.outlocation = self.outlocation or timeseries[0].stats.location
+ self.min_count = self.min_count or len(timeseries)
+
scale_values = self.scales or ([1] * len(timeseries))
lat_corr = {}
i = 0
@@ -111,8 +121,18 @@ class AverageAlgorithm(Algorithm):
ts = timeseries.select(station=obsy)[0]
combined.append(ts.data * latcorr)
+ # calculate counts
+ count_data = numpy.count_nonzero(
+ ~numpy.isnan(numpy.column_stack(timeseries)), axis=1
+ )
+
# calculate averages
- average_data = numpy.nanmean(combined, axis=0)
+ average_data = numpy.nansum(combined, axis=0) / count_data
+
+ # apply min_count
+ average_data[count_data < self.min_count] = numpy.nan
+
+ # create first output trace metadata
average_stats = obspy.core.Stats()
average_stats.station = "USGS"
average_stats.channel = self.outchannel
@@ -121,10 +141,7 @@ class AverageAlgorithm(Algorithm):
average_stats.starttime = timeseries[0].stats.starttime
average_stats.npts = timeseries[0].stats.npts
average_stats.delta = timeseries[0].stats.delta
-
- # calculate counts
- ts_counter = numpy.column_stack(timeseries)
- count_data = numpy.count_nonzero(~numpy.isnan(ts_counter), axis=1)
+ # create second output trace metadata
count_stats = average_stats.copy()
count_stats.channel = average_stats.channel + "_count"
@@ -132,7 +149,7 @@ class AverageAlgorithm(Algorithm):
stream = obspy.core.Stream(
(
obspy.core.Trace(average_data, average_stats),
- obspy.core.Trace(numpy.asarray(count_data), count_stats),
+ obspy.core.Trace(count_data, count_stats),
)
)
return stream
@@ -154,6 +171,13 @@ class AverageAlgorithm(Algorithm):
nargs="*",
type=float,
)
+ parser.add_argument(
+ "--average-min-count",
+ default=None,
+ help="Minimum number of inputs required to calculate average",
+ nargs="*",
+ type=int,
+ )
def configure(self, arguments):
"""Configure algorithm using comand line arguments.
@@ -178,3 +202,5 @@ class AverageAlgorithm(Algorithm):
)
self.outlocation = arguments.outlocationcode or arguments.locationcode
+
+ self.min_count = arguments.average_min_count
diff --git a/test/algorithm_test/AverageAlgorithm_test.py b/test/algorithm_test/AverageAlgorithm_test.py
index 2480f655..1c3a8800 100644
--- a/test/algorithm_test/AverageAlgorithm_test.py
+++ b/test/algorithm_test/AverageAlgorithm_test.py
@@ -39,7 +39,7 @@ def test_process():
timeseries[2].stats.station = "SJG"
# initialize the algorithm factory with Observatories and Channel
- a = AverageAlgorithm(("HON", "GUA", "SJG"), "H")
+ a = AverageAlgorithm(("HON", "GUA", "SJG"), "H", min_count=1)
outstream = a.process(timeseries)
# Ensure the average of two
np.testing.assert_array_equal(outstream[0].data, expected_solution)
@@ -76,7 +76,7 @@ def test_gaps():
timeseries += gap_trace
timeseries += full_trace
# Initialize the AverageAlgorithm factory with observatories and channel
- alg = AverageAlgorithm(("HON", "SJG"), "H")
+ alg = AverageAlgorithm(("HON", "SJG"), "H", min_count=1)
# Run timeseries through the average process
outstream = alg.process(timeseries)
--
GitLab
From f9e88924435a480e7017674eb26689e09bbbb592 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Mon, 14 Nov 2022 09:07:24 -0700
Subject: [PATCH 103/142] Fix __create_trace() in StreamConverter_test.py
A "feature" in obspy is that the stats.npts metadata object is not
automatically calculated if a Trace is created by passing in a Stats
object (instead of a simple dictionary). The Trace still contained
the data array, which is probably why this issue wasn't discovered
sooner, but something as simple as trace.times() is broken if npts
is not specified. It's amazing this wasn't discovered sooner, given
how many times traces get "created" throughout geomag-algoriothms.
Probably, we should survey the codebase to make sure this isn't a
problem elsewhere.
---
test/StreamConverter_test.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/test/StreamConverter_test.py b/test/StreamConverter_test.py
index 0c8b4207..446a4b55 100644
--- a/test/StreamConverter_test.py
+++ b/test/StreamConverter_test.py
@@ -362,6 +362,7 @@ def __create_trace(channel, data, decbase=0):
stats = obspy.core.Stats()
stats.starttime = STARTTIME
stats.delta = 60
+ stats.npts = len(data)
stats.declination_base = decbase
stats.channel = channel
numpy_data = numpy.array(data, dtype=numpy.float64)
--
GitLab
From 46cc142589417f71677a8ce71a0fdf6bf8cb301a Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Mon, 14 Nov 2022 09:50:51 -0700
Subject: [PATCH 104/142] Add start/end options AverageAlgorithm's min_count
The recently added `min_count` option to AverageAlgorithm.py leads to some
undesirable behavior when realtime data, with asynchronous inputs, are being
processed. By adding the ability to specify an interval over which `min_count`
is applied, some of this undesirable behavior can be mitigated.
In particular, if the `realtime` option is specified via the controller, and
`min_count` is defined, the minimum number of inputs will be allowed only for
time steps prior to `(UTCDateTime.now() - realtime)`; the full complement of
inputs will be required to calculate averages more recent than that. One
drawback is that if an input observatory goes offline for an extended period,
the Dst index will be calculated with a persistent lag `realtime` seconds long.
A user can always override this admittedly ad-hoc default behavior using the
`min_count_start` and `min_count_end` options.
---
geomagio/algorithm/AverageAlgorithm.py | 70 +++++++++++++++++++-
test/algorithm_test/AverageAlgorithm_test.py | 12 ++++
2 files changed, 80 insertions(+), 2 deletions(-)
diff --git a/geomagio/algorithm/AverageAlgorithm.py b/geomagio/algorithm/AverageAlgorithm.py
index 75ee9170..3a087918 100644
--- a/geomagio/algorithm/AverageAlgorithm.py
+++ b/geomagio/algorithm/AverageAlgorithm.py
@@ -11,10 +11,34 @@ import obspy.core
class AverageAlgorithm(Algorithm):
- """Algorithm that creates an averaged Dst.
+ """Algorithm that creates an average of multiple inputs of same channel (i.e., Dst index).
Parameters
----------
+ observatories: array_like
+ strings specifying multiple observatories to average
+ channel: string
+ specifies the channel to be processed.
+ location: string
+ location code for output
+ scales: array_like
+ floats that scale the corresponding observatories
+ min_count: integer
+ minimum number of observatories required for valid average
+ min_count_start: UTCDateTime
+ the beginning of an interval over which to apply min_count
+ min_count_end: UTCDateTime
+ the end of an interval over which to apply min_count
+
+ Notes
+ -----
+ The original version of this algorithm allowed no missing inputs. But,
+ allowing missing inputs is problematic as one gets nearer to realtime,
+ and input streams have differing latencies. So, min_count was added to
+ require a minimum number of observatories (more than 1), and the related
+ min_count_start and min_count_end were added to allow min_count to be
+ applied to a sub-interval (most likely something lagging realtime by
+ a sufficient interval to prevent frequent DC shifts in the output)
"""
@@ -25,6 +49,8 @@ class AverageAlgorithm(Algorithm):
location=None,
scales=None,
min_count=None,
+ min_count_start=None,
+ min_count_end=None,
):
Algorithm.__init__(self)
self._npts = -1
@@ -35,6 +61,8 @@ class AverageAlgorithm(Algorithm):
self.outchannel = channel
self.outlocation = location
self.min_count = min_count
+ self.min_count_start = min_count_start
+ self.min_count_end = min_count_end
self.observatoryMetadata = ObservatoryMetadata()
def check_stream(self, timeseries):
@@ -95,6 +123,8 @@ class AverageAlgorithm(Algorithm):
self.outlocation = self.outlocation or timeseries[0].stats.location
self.min_count = self.min_count or len(timeseries)
+ self.min_count_start = self.min_count_start or timeseries[0].stats.starttime
+ self.min_count_end = self.min_count_end or timeseries[0].stats.endtime
scale_values = self.scales or ([1] * len(timeseries))
lat_corr = {}
@@ -132,6 +162,18 @@ class AverageAlgorithm(Algorithm):
# apply min_count
average_data[count_data < self.min_count] = numpy.nan
+ # apply min_count_start and min_count_end
+ # NOTE: the logic here is not very intuitive, but it works as intended
+ utc_datetimes = numpy.array(
+ [timeseries[0].stats.starttime + t for t in timeseries[0].times()]
+ )
+ average_data[
+ (count_data < timeseries.count()) & (utc_datetimes > self.min_count_end)
+ ] = numpy.nan
+ average_data[
+ (count_data < timeseries.count()) & (utc_datetimes < self.min_count_start)
+ ] = numpy.nan
+
# create first output trace metadata
average_stats = obspy.core.Stats()
average_stats.station = "USGS"
@@ -175,8 +217,22 @@ class AverageAlgorithm(Algorithm):
"--average-min-count",
default=None,
help="Minimum number of inputs required to calculate average",
- nargs="*",
type=int,
+ metavar="N",
+ )
+ parser.add_argument(
+ "--average-min-count-start",
+ default=None,
+ help="First UTC date time to apply min_count to YYYY-MM-DDTHH:MM:SS",
+ metavar="ISO8601",
+ type=obspy.core.UTCDateTime,
+ )
+ parser.add_argument(
+ "--average-min-count-end",
+ default=None,
+ help="Last UTC date time to apply min_count to YYYY-MM-DDTHH:MM:SS",
+ metavar="ISO8601",
+ type=obspy.core.UTCDateTime,
)
def configure(self, arguments):
@@ -204,3 +260,13 @@ class AverageAlgorithm(Algorithm):
self.outlocation = arguments.outlocationcode or arguments.locationcode
self.min_count = arguments.average_min_count
+ self.min_count_start = arguments.average_min_count_start
+ self.min_count_end = arguments.average_min_count_end
+
+ if arguments.realtime and not self.min_count_end:
+ # if the realtime parameter is defined in arguments (i.e., it is
+ # set via the controller), but min_count_end is not, then assume
+ # the most recent interval should NOT allow fewer than the full
+ # complement of inputs in order to calculate an average (previous
+ # "update" intervals will allow fewer than the full complement)
+ self.min_count_end = arguments.starttime
diff --git a/test/algorithm_test/AverageAlgorithm_test.py b/test/algorithm_test/AverageAlgorithm_test.py
index 1c3a8800..bbe377e7 100644
--- a/test/algorithm_test/AverageAlgorithm_test.py
+++ b/test/algorithm_test/AverageAlgorithm_test.py
@@ -44,6 +44,18 @@ def test_process():
# Ensure the average of two
np.testing.assert_array_equal(outstream[0].data, expected_solution)
+ # repeat process with min_count_end set
+ a.min_count_end = timeseries[0].stats.starttime + timeseries[0].stats.delta * 2
+ expected_solution[3:] = np.nan
+ outstream = a.process(timeseries)
+ np.testing.assert_array_equal(outstream[0].data, expected_solution)
+
+ # repeat process with min_count_start set
+ a.min_count_start = timeseries[0].stats.starttime + timeseries[0].stats.delta * 2
+ expected_solution[:2] = np.nan
+ outstream = a.process(timeseries)
+ np.testing.assert_array_equal(outstream[0].data, expected_solution)
+
def test_gaps():
"""AverageAlgorithm_test.test_gaps()
--
GitLab
From 0ac272854f76cf09a2ff7fe88af52ddfa270aeac Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Mon, 14 Nov 2022 12:57:00 -0700
Subject: [PATCH 105/142] Use self.observatories to determine number of inputs
Previously use the number of traces in the input Stream. This could
be fewer than the number of desired observatories if a given input's
data was completely missing.
---
geomagio/algorithm/AverageAlgorithm.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/geomagio/algorithm/AverageAlgorithm.py b/geomagio/algorithm/AverageAlgorithm.py
index 3a087918..1787ad19 100644
--- a/geomagio/algorithm/AverageAlgorithm.py
+++ b/geomagio/algorithm/AverageAlgorithm.py
@@ -122,7 +122,7 @@ class AverageAlgorithm(Algorithm):
self.outlocation = self.outlocation or timeseries[0].stats.location
- self.min_count = self.min_count or len(timeseries)
+ self.min_count = self.min_count or len(self.observatories)
self.min_count_start = self.min_count_start or timeseries[0].stats.starttime
self.min_count_end = self.min_count_end or timeseries[0].stats.endtime
--
GitLab
From 2f8428cf3ccf3668dce01bedf5871119992f33d6 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Tue, 15 Nov 2022 15:05:14 -0700
Subject: [PATCH 106/142] Better way to create array of UTCDateTimes
---
geomagio/algorithm/AverageAlgorithm.py | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/geomagio/algorithm/AverageAlgorithm.py b/geomagio/algorithm/AverageAlgorithm.py
index 1787ad19..b065f51f 100644
--- a/geomagio/algorithm/AverageAlgorithm.py
+++ b/geomagio/algorithm/AverageAlgorithm.py
@@ -164,9 +164,7 @@ class AverageAlgorithm(Algorithm):
# apply min_count_start and min_count_end
# NOTE: the logic here is not very intuitive, but it works as intended
- utc_datetimes = numpy.array(
- [timeseries[0].stats.starttime + t for t in timeseries[0].times()]
- )
+ utc_datetimes = timeseries[0].times(type="utcdatetime")
average_data[
(count_data < timeseries.count()) & (utc_datetimes > self.min_count_end)
] = numpy.nan
--
GitLab
From a61ffa143d7a52f1ecc1d61b475648627fc380ad Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Tue, 15 Nov 2022 18:29:39 -0700
Subject: [PATCH 107/142] Don't modify algorithm state inside process() method
---
geomagio/algorithm/AverageAlgorithm.py | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/geomagio/algorithm/AverageAlgorithm.py b/geomagio/algorithm/AverageAlgorithm.py
index b065f51f..692ff5c8 100644
--- a/geomagio/algorithm/AverageAlgorithm.py
+++ b/geomagio/algorithm/AverageAlgorithm.py
@@ -122,9 +122,9 @@ class AverageAlgorithm(Algorithm):
self.outlocation = self.outlocation or timeseries[0].stats.location
- self.min_count = self.min_count or len(self.observatories)
- self.min_count_start = self.min_count_start or timeseries[0].stats.starttime
- self.min_count_end = self.min_count_end or timeseries[0].stats.endtime
+ min_count = self.min_count or len(self.observatories)
+ min_count_start = self.min_count_start or timeseries[0].stats.starttime
+ min_count_end = self.min_count_end or timeseries[0].stats.endtime
scale_values = self.scales or ([1] * len(timeseries))
lat_corr = {}
@@ -160,16 +160,16 @@ class AverageAlgorithm(Algorithm):
average_data = numpy.nansum(combined, axis=0) / count_data
# apply min_count
- average_data[count_data < self.min_count] = numpy.nan
+ average_data[count_data < min_count] = numpy.nan
# apply min_count_start and min_count_end
# NOTE: the logic here is not very intuitive, but it works as intended
utc_datetimes = timeseries[0].times(type="utcdatetime")
average_data[
- (count_data < timeseries.count()) & (utc_datetimes > self.min_count_end)
+ (count_data < timeseries.count()) & (utc_datetimes > min_count_end)
] = numpy.nan
average_data[
- (count_data < timeseries.count()) & (utc_datetimes < self.min_count_start)
+ (count_data < timeseries.count()) & (utc_datetimes < min_count_start)
] = numpy.nan
# create first output trace metadata
--
GitLab
From 22c4a0ac2ab007c82663d41107a0c4bb6f1ff7d3 Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Tue, 18 Oct 2022 15:36:50 -0600
Subject: [PATCH 108/142] Imported Enum to define a CLI parameter with a
predefined set of values to choose from. Created a spreadsheets_dir option
and factory option.
---
geomagio/processing/copy_absolutes.py | 37 ++++++++++++++++++---------
1 file changed, 25 insertions(+), 12 deletions(-)
diff --git a/geomagio/processing/copy_absolutes.py b/geomagio/processing/copy_absolutes.py
index f60c214f..6d45442f 100644
--- a/geomagio/processing/copy_absolutes.py
+++ b/geomagio/processing/copy_absolutes.py
@@ -10,14 +10,20 @@ from datetime import date, datetime, time, timedelta
from typing import List
import typer
+from enum import Enum
from obspy import UTCDateTime
-from ..metadata import Metadata, MetadataCategory, MetadataFactory
-from ..residual import Reading, WebAbsolutesFactory
+from ..metadata import Metadata, MetadataFactory, MetadataCategory
+from ..residual import Reading, WebAbsolutesFactory, SpreadsheetAbsolutesFactory
TODAY = datetime.combine(date.today(), time(0, 0, 0))
+class factories(str, Enum):
+ web_absolutes_factory = "web_absolutes_factory"
+ spreadsheet_factory = "spreadsheet_factory"
+
+
def copy_absolutes(
observatory: str = typer.Option(..., help="Observatory code"),
starttime: datetime = typer.Option(
@@ -40,12 +46,22 @@ def copy_absolutes(
help="URL to web absolutes service",
metavar="URL",
),
+ spreadsheets_dir: str = typer.Option(
+ default="---", help="Directory to residual spreadsheets", metavar="DIR"
+ ),
+ # I am not sure what to specify as the default directory, I was using a local directory as a test
+ factory: factories = factories.web_absolutes_factory,
):
- """Copy absolutes from the web absolutes service into the metadata service."""
- # read readings from web absolutes
- web_absolutes_factory = WebAbsolutesFactory(url=web_absolutes_url)
+ """Copy absolutes from the web absolutes service OR residual spreadsheets into the metadata service."""
+ print(f"Using factory: {factory.value}")
+
+ if factory.value == factories.web_absolutes_factory:
+ factory = WebAbsolutesFactory(url=web_absolutes_url)
+ else:
+ factory = SpreadsheetAbsolutesFactory(base_directory=spreadsheets_dir)
+
readings = get_readings(
- factory=web_absolutes_factory,
+ factory=factory,
observatory=observatory,
starttime=UTCDateTime(starttime),
endtime=UTCDateTime(endtime),
@@ -88,17 +104,14 @@ def create_reading_metadata(reading: Reading) -> Metadata:
def get_readings(
- factory: WebAbsolutesFactory,
- observatory: str,
- starttime: UTCDateTime,
- endtime: UTCDateTime,
+ factory: factories, observatory: str, starttime: UTCDateTime, endtime: UTCDateTime
) -> List[Reading]:
- """Get readings from web absolutes.
+ """Get readings from web absolutes or residual spreadsheets.
Parameters
----------
factory
- configured WebAbsolutesFactory
+ configured WebAbsolutesFactory or SpreadsheetAbsolutesFactory
observatory
search observatory
starttime
--
GitLab
From ff40062538cd8a8cb2b3a4fc2cf2bfa84005ccdc Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Fri, 21 Oct 2022 11:03:54 -0600
Subject: [PATCH 109/142] Working on Jeremy's comments
---
geomagio/processing/copy_absolutes.py | 34 +++++++++++++++++----------
1 file changed, 21 insertions(+), 13 deletions(-)
diff --git a/geomagio/processing/copy_absolutes.py b/geomagio/processing/copy_absolutes.py
index 6d45442f..ffbfbcb2 100644
--- a/geomagio/processing/copy_absolutes.py
+++ b/geomagio/processing/copy_absolutes.py
@@ -7,7 +7,8 @@ Created on Thu Jul 7 11:05:19 2022
import json
import os
from datetime import date, datetime, time, timedelta
-from typing import List
+from typing import List, Optional
+from pathlib import Path
import typer
from enum import Enum
@@ -19,9 +20,9 @@ from ..residual import Reading, WebAbsolutesFactory, SpreadsheetAbsolutesFactory
TODAY = datetime.combine(date.today(), time(0, 0, 0))
-class factories(str, Enum):
- web_absolutes_factory = "web_absolutes_factory"
- spreadsheet_factory = "spreadsheet_factory"
+class ResidualFactory(str, Enum):
+ SPREADSHEET = "spreadsheet"
+ WEB_ABSOLUTES = "webabsolutes"
def copy_absolutes(
@@ -46,19 +47,23 @@ def copy_absolutes(
help="URL to web absolutes service",
metavar="URL",
),
- spreadsheets_dir: str = typer.Option(
- default="---", help="Directory to residual spreadsheets", metavar="DIR"
+ directory: Optional[Path] = typer.Option(
+ None,
+ exists=True,
+ file_okay=False,
+ dir_okay=True,
+ writable=False,
+ readable=False,
+ resolve_path=True,
+ help="Residual spreadsheet directory",
),
- # I am not sure what to specify as the default directory, I was using a local directory as a test
- factory: factories = factories.web_absolutes_factory,
+ factory: ResidualFactory = ResidualFactory.WEB_ABSOLUTES,
):
"""Copy absolutes from the web absolutes service OR residual spreadsheets into the metadata service."""
- print(f"Using factory: {factory.value}")
-
- if factory.value == factories.web_absolutes_factory:
+ if factory.value == ResidualFactory.WEB_ABSOLUTES:
factory = WebAbsolutesFactory(url=web_absolutes_url)
else:
- factory = SpreadsheetAbsolutesFactory(base_directory=spreadsheets_dir)
+ factory = SpreadsheetAbsolutesFactory(base_directory=directory)
readings = get_readings(
factory=factory,
@@ -104,7 +109,10 @@ def create_reading_metadata(reading: Reading) -> Metadata:
def get_readings(
- factory: factories, observatory: str, starttime: UTCDateTime, endtime: UTCDateTime
+ factory: ResidualFactory,
+ observatory: str,
+ starttime: UTCDateTime,
+ endtime: UTCDateTime,
) -> List[Reading]:
"""Get readings from web absolutes or residual spreadsheets.
--
GitLab
From dbc8b2f652bbbd9ce956ba5ea7139a339ce0f4ca Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Tue, 15 Nov 2022 14:51:06 -0700
Subject: [PATCH 110/142] Added confirm method as a check to user
---
geomagio/processing/copy_absolutes.py | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/geomagio/processing/copy_absolutes.py b/geomagio/processing/copy_absolutes.py
index ffbfbcb2..b2398b02 100644
--- a/geomagio/processing/copy_absolutes.py
+++ b/geomagio/processing/copy_absolutes.py
@@ -71,7 +71,15 @@ def copy_absolutes(
starttime=UTCDateTime(starttime),
endtime=UTCDateTime(endtime),
)
+
+ # confirm whether or not to copy absolutes
print(f"Found {len(readings)} absolutes")
+ copy = typer.confirm(f"Are you sure you want to copy {len(readings)} absolutes?")
+ if not copy:
+ print("Not copying absolutes")
+ raise typer.Abort()
+ print("Copying over absolutes")
+
# write readings to metadata service
metadata_factory = MetadataFactory(token=metadata_token, url=metadata_url)
with typer.progressbar(
--
GitLab
From 03998e3d926c8769d796a66ee72122ce4618e606 Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Wed, 16 Nov 2022 12:27:19 -0700
Subject: [PATCH 111/142] Added force option to force skip the typer.confirm
check
---
geomagio/processing/copy_absolutes.py | 15 +++++++++------
1 file changed, 9 insertions(+), 6 deletions(-)
diff --git a/geomagio/processing/copy_absolutes.py b/geomagio/processing/copy_absolutes.py
index b2398b02..86d0748c 100644
--- a/geomagio/processing/copy_absolutes.py
+++ b/geomagio/processing/copy_absolutes.py
@@ -58,6 +58,10 @@ def copy_absolutes(
help="Residual spreadsheet directory",
),
factory: ResidualFactory = ResidualFactory.WEB_ABSOLUTES,
+ force: bool = typer.Option(
+ default=False,
+ help="Force skip the check to copy absolutes",
+ ),
):
"""Copy absolutes from the web absolutes service OR residual spreadsheets into the metadata service."""
if factory.value == ResidualFactory.WEB_ABSOLUTES:
@@ -73,12 +77,11 @@ def copy_absolutes(
)
# confirm whether or not to copy absolutes
- print(f"Found {len(readings)} absolutes")
- copy = typer.confirm(f"Are you sure you want to copy {len(readings)} absolutes?")
- if not copy:
- print("Not copying absolutes")
- raise typer.Abort()
- print("Copying over absolutes")
+ if not force:
+ typer.confirm(
+ f"Are you sure you want to copy {len(readings)} absolutes?", abort=True
+ )
+ print("Copying over absolutes")
# write readings to metadata service
metadata_factory = MetadataFactory(token=metadata_token, url=metadata_url)
--
GitLab
From 45b057f94770c62312991d4fcef0133c243a5e20 Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Wed, 16 Nov 2022 13:38:43 -0700
Subject: [PATCH 112/142] Updating the version number to 1.6.0
---
code.json | 25 +++++++++++++------------
pyproject.toml | 2 +-
2 files changed, 14 insertions(+), 13 deletions(-)
diff --git a/code.json b/code.json
index ea62f29c..20cf9c88 100644
--- a/code.json
+++ b/code.json
@@ -3,9 +3,8 @@
"name": "geomag-algorithms",
"organization": "U.S. Geological Survey",
"description": "Library for processing Geomagnetic timeseries data.",
- "version": "1.5.4",
+ "version": "1.6.0",
"status": "Development",
-
"permissions": {
"usageType": "openSource",
"licenses": [
@@ -15,26 +14,28 @@
}
]
},
-
"homepageURL": "https://code.usgs.gov/ghsc/geomag/geomag-algorithms",
"downloadURL": "https://code.usgs.gov/ghsc/geomag/geomag-algorithms/-/archive/master/geomag-algorithms-master.zip",
"disclaimerURL": "https://code.usgs.gov/ghsc/geomag/geomag-algorithms/raw/master/DISCLAIMER.md",
"repositoryURL": "https://code.usgs.gov/ghsc/geomag/geomag-algorithms.git",
"vcs": "git",
-
"laborHours": 0,
-
- "tags": ["usgs", "geomagnetism", "timeseries", "processing"],
-
- "languages": ["Shell", "Python"],
-
+ "tags": [
+ "usgs",
+ "geomagnetism",
+ "timeseries",
+ "processing"
+ ],
+ "languages": [
+ "Shell",
+ "Python"
+ ],
"contact": {
"name": "HazDev Team",
"email": "gs-haz_dev_team_group@usgs.gov"
},
-
"date": {
- "metadataLastUpdated": "2022-10-24"
+ "metadataLastUpdated": "2022-11-16"
}
}
-]
+]
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 85f5fd12..84da83fe 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ packages = [
{include = "geomagio" }
]
repository="https://code.usgs.gov/ghsc/geomag/geomag-algorithms"
-version = "1.5.4"
+version = "1.6.0"
[tool.poetry.dependencies]
--
GitLab
From 5d4f84db5aa28d248b364b26daca49d167e1434d Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Fri, 18 Nov 2022 15:57:19 -0700
Subject: [PATCH 113/142] Make AverageAlgorithm require **any** inputs
Recent attempts to change the AverageAlgorithm to allow fewer than the full
complement of inputs when calculating a mutli-station average were thwarted
by the default can_produce_data() method in the parent Algorithm class, which
required all inputs to be present, when what we now want is **any** inputs to
be present.
---
geomagio/algorithm/AverageAlgorithm.py | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
diff --git a/geomagio/algorithm/AverageAlgorithm.py b/geomagio/algorithm/AverageAlgorithm.py
index 692ff5c8..fe970d63 100644
--- a/geomagio/algorithm/AverageAlgorithm.py
+++ b/geomagio/algorithm/AverageAlgorithm.py
@@ -6,6 +6,7 @@ from __future__ import absolute_import
from .Algorithm import Algorithm
from .AlgorithmException import AlgorithmException
from ..ObservatoryMetadata import ObservatoryMetadata
+from .. import TimeseriesUtility
import numpy
import obspy.core
@@ -65,6 +66,24 @@ class AverageAlgorithm(Algorithm):
self.min_count_end = min_count_end
self.observatoryMetadata = ObservatoryMetadata()
+ def can_produce_data(self, starttime, endtime, stream):
+ """Can Produce data
+
+ By default require all channels to have data at the same time.
+
+ Parameters
+ ----------
+ starttime: UTCDateTime
+ start time of requested output
+ end : UTCDateTime
+ end time of requested output
+ stream: obspy.core.Stream
+ The input stream we want to make certain has data for the algorithm
+ """
+ return TimeseriesUtility.has_any_channels(
+ stream, self.get_required_channels(), starttime, endtime
+ )
+
def check_stream(self, timeseries):
"""checks a stream to make certain the required data
exists.
--
GitLab
From e9cb25aa6949305de18a24e5facc666bc0f110fc Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Fri, 18 Nov 2022 17:24:18 -0700
Subject: [PATCH 114/142] Check for gaps in multi-observatory Stream
The method TimeseriesUtility.get_stream_gaps() would over-write gaps[channel] if
there were multiple Traces in a stream that were the same channel, but different
observatories. This is a typical situation when using the AverageAlgorithm.
---
geomagio/TimeseriesUtility.py | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/geomagio/TimeseriesUtility.py b/geomagio/TimeseriesUtility.py
index 35716142..2797b938 100644
--- a/geomagio/TimeseriesUtility.py
+++ b/geomagio/TimeseriesUtility.py
@@ -205,7 +205,10 @@ def get_stream_gaps(stream, channels=None):
channel = trace.stats.channel
if channels is not None and channel not in channels:
continue
- gaps[channel] = get_trace_gaps(trace)
+ if channel in gaps:
+ gaps[channel].extend(get_trace_gaps(trace))
+ else:
+ gaps[channel] = get_trace_gaps(trace)
return gaps
--
GitLab
From 5b76f9f45174190f71639685d9a27b43a3f33214 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Tue, 22 Nov 2022 11:05:21 -0700
Subject: [PATCH 115/142] Now process inchannels, not outchannels
The original version of AverageAlgorithm.py seemed to be written
to process the Controller's `--outchannels`. It "worked" for several
years because `--outchannels` defaulted to `--inchannels`. But what
we actually always wanted was to process `--inchannels`.
Mostly this was just a matter of semantics, but when I recently added
the ability to average fewer than the full complement of inputs, it
was also necessary to change the `can_produce_data()` method to check
for "any" instead of "all" channels, which in turn required that the
AverageAlgorithm class properly instantiate its `_inchannels` and
`_outchannels` class variables, instead of just set them to `None`.
To briefly explain the different changes in this commit:
- added `Algorithm.__init__(self, inchannels=[channel])` to ensure that
can_produce_data() would work when run via programmatic interface.
- added `Algorithm.configure(self, arguments)` to AverageAlgorithm.configure()
to ensure that can_produce_data() would work when run via Controller.py.
- changed all variations of `outchannel` to `inchannel`
- cleaned up where class variables were modified inside process() method
---
geomagio/algorithm/AverageAlgorithm.py | 29 +++++++++++++-------------
1 file changed, 15 insertions(+), 14 deletions(-)
diff --git a/geomagio/algorithm/AverageAlgorithm.py b/geomagio/algorithm/AverageAlgorithm.py
index fe970d63..065e674a 100644
--- a/geomagio/algorithm/AverageAlgorithm.py
+++ b/geomagio/algorithm/AverageAlgorithm.py
@@ -53,13 +53,13 @@ class AverageAlgorithm(Algorithm):
min_count_start=None,
min_count_end=None,
):
- Algorithm.__init__(self)
+ Algorithm.__init__(self, inchannels=[channel])
self._npts = -1
self._stt = -1
self._stats = None
self.scales = scales
self.observatories = observatories
- self.outchannel = channel
+ self.inchannel = channel
self.outlocation = location
self.min_count = min_count
self.min_count_start = min_count_start
@@ -135,11 +135,11 @@ class AverageAlgorithm(Algorithm):
out_stream:
new stream object containing the averaged values and available observatories.
"""
- self.observatories = self.observatories or [t.stats.station for t in timeseries]
+ observatories = self.observatories or [t.stats.station for t in timeseries]
- self.outchannel = self.outchannel or timeseries[0].stats.channel
+ inchannel = self.inchannel or timeseries[0].stats.channel
- self.outlocation = self.outlocation or timeseries[0].stats.location
+ outlocation = self.outlocation or timeseries[0].stats.location
min_count = self.min_count or len(self.observatories)
min_count_start = self.min_count_start or timeseries[0].stats.starttime
@@ -148,7 +148,7 @@ class AverageAlgorithm(Algorithm):
scale_values = self.scales or ([1] * len(timeseries))
lat_corr = {}
i = 0
- for obs in self.observatories:
+ for obs in observatories:
new_obs = {str(obs): scale_values[i]}
lat_corr.update(new_obs)
i += 1
@@ -159,7 +159,7 @@ class AverageAlgorithm(Algorithm):
# initialize array for data to be appended
combined = []
# loop over stations
- for obsy in self.observatories:
+ for obsy in observatories:
# lookup latitude correction factor, default = 1.0
if obsy in lat_corr:
@@ -194,9 +194,9 @@ class AverageAlgorithm(Algorithm):
# create first output trace metadata
average_stats = obspy.core.Stats()
average_stats.station = "USGS"
- average_stats.channel = self.outchannel
+ average_stats.channel = inchannel
average_stats.network = "NT"
- average_stats.location = self.outlocation
+ average_stats.location = outlocation
average_stats.starttime = timeseries[0].stats.starttime
average_stats.npts = timeseries[0].stats.npts
average_stats.delta = timeseries[0].stats.delta
@@ -260,13 +260,14 @@ class AverageAlgorithm(Algorithm):
arguments: Namespace
parsed command line arguments
"""
+ Algorithm.configure(self, arguments)
- self.observatories = arguments.observatory
- if arguments.outchannels:
- if len(arguments.outchannels) > 1:
- raise AlgorithmException("Only 1 channel can be specified")
- self.outchannel = arguments.outchannels[0]
+ if self._inchannels:
+ if len(self._inchannels) > 1:
+ raise AlgorithmException("Only 1 input channel can be specified")
+ self.inchannel = self._inchannels
+ self.observatories = arguments.observatory
self.scales = arguments.average_observatory_scale
if self.scales:
if len(self.observatories) != len(self.scales):
--
GitLab
From b2a95307f8ace7ae5d2b732f69cde3776e849074 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Tue, 22 Nov 2022 15:30:31 -0700
Subject: [PATCH 116/142] Small fix requiring a length-1 list to be indexed
Writing unit tests for Controller configurations is tricky, so I
didn't do it, and this tiny-but-impactful bug slipped in. I did
test this on the stagin server this time, and the processing pipe-
line should work after this is deployed.
---
geomagio/algorithm/AverageAlgorithm.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/geomagio/algorithm/AverageAlgorithm.py b/geomagio/algorithm/AverageAlgorithm.py
index 065e674a..15927447 100644
--- a/geomagio/algorithm/AverageAlgorithm.py
+++ b/geomagio/algorithm/AverageAlgorithm.py
@@ -265,7 +265,7 @@ class AverageAlgorithm(Algorithm):
if self._inchannels:
if len(self._inchannels) > 1:
raise AlgorithmException("Only 1 input channel can be specified")
- self.inchannel = self._inchannels
+ self.inchannel = self._inchannels[0]
self.observatories = arguments.observatory
self.scales = arguments.average_observatory_scale
--
GitLab
From 7c43467e6f4977c50589437c2db5b1bc958c21c8 Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Tue, 29 Nov 2022 09:24:44 -0700
Subject: [PATCH 117/142] Updating version to v1.6.1 for bug fix
---
code.json | 4 ++--
pyproject.toml | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/code.json b/code.json
index 20cf9c88..960eec17 100644
--- a/code.json
+++ b/code.json
@@ -3,7 +3,7 @@
"name": "geomag-algorithms",
"organization": "U.S. Geological Survey",
"description": "Library for processing Geomagnetic timeseries data.",
- "version": "1.6.0",
+ "version": "1.6.1",
"status": "Development",
"permissions": {
"usageType": "openSource",
@@ -35,7 +35,7 @@
"email": "gs-haz_dev_team_group@usgs.gov"
},
"date": {
- "metadataLastUpdated": "2022-11-16"
+ "metadataLastUpdated": "2022-11-29"
}
}
]
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 84da83fe..009abf96 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ packages = [
{include = "geomagio" }
]
repository="https://code.usgs.gov/ghsc/geomag/geomag-algorithms"
-version = "1.6.0"
+version = "1.6.1"
[tool.poetry.dependencies]
--
GitLab
From f87814035ff345526c29ebdeb90f16a0f5c67fb7 Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Tue, 29 Nov 2022 13:54:11 -0700
Subject: [PATCH 118/142] Added trivyignore file
---
.trivyignore | 2 ++
1 file changed, 2 insertions(+)
create mode 100644 .trivyignore
diff --git a/.trivyignore b/.trivyignore
new file mode 100644
index 00000000..1103d180
--- /dev/null
+++ b/.trivyignore
@@ -0,0 +1,2 @@
+# Not using the Cleo library 11/29/22
+CVE-2022-42966
\ No newline at end of file
--
GitLab
From 4d10aa154fdac041c5f3e67d795986b8f5836806 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Wed, 7 Dec 2022 19:42:54 -0700
Subject: [PATCH 119/142] Fix has_any_channels method
The has_any_channels method in TimeseriesUtility.py did not properly
handle streams with multiple traces with the same channel, but different
stations (or networks, or locations). It should work now.
---
geomagio/TimeseriesUtility.py | 25 ++++++++++++++-----------
1 file changed, 14 insertions(+), 11 deletions(-)
diff --git a/geomagio/TimeseriesUtility.py b/geomagio/TimeseriesUtility.py
index 2797b938..c54d7498 100644
--- a/geomagio/TimeseriesUtility.py
+++ b/geomagio/TimeseriesUtility.py
@@ -388,17 +388,20 @@ def has_any_channels(stream, channels, starttime, endtime):
bool: True if any data found between starttime/endtime
"""
# process if any channels have data not covering the time range
- input_gaps = get_stream_gaps(stream=stream, channels=channels)
- for channel in channels:
- if channel not in input_gaps:
- continue
- channel_gaps = input_gaps[channel]
- if len(channel_gaps) == 0:
- # no gaps in channel
- return True
- for gap in channel_gaps:
- if not (starttime >= gap[0] and starttime <= gap[1] and endtime < gap[2]):
- # gap doesn't span channel
+ for trace in stream:
+ if trace.stats.channel in channels:
+ gaps = get_trace_gaps(trace)
+ if len(gaps) == 0:
+ # no gaps in trace;
+ # "any" critierion achieved for stream
+ return True
+ nodata = [
+ (starttime >= gap[0] and starttime <= gap[1] and endtime < gap[2])
+ for gap in gaps
+ ]
+ if not any(nodata):
+ # no gaps in trace span interval;
+ # "any" criterion achieved for stream
return True
# didn't find any data
return False
--
GitLab
From a4319095bf1638e64aaeadf6d6e184e1c8db09ef Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Wed, 7 Dec 2022 19:47:54 -0700
Subject: [PATCH 120/142] Set min_count_end to starttime - delta
I was lazy the first time and didn't subtract delta from starttime
when setting the default min_count_end in the configure method. This
led to "flakiness" in Dst when long gaps were encountered in input
observatories...exactly the kind of issue min_count_end was intended
to mitigate. It should work correctly now.
---
geomagio/algorithm/AverageAlgorithm.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/geomagio/algorithm/AverageAlgorithm.py b/geomagio/algorithm/AverageAlgorithm.py
index 15927447..70588de8 100644
--- a/geomagio/algorithm/AverageAlgorithm.py
+++ b/geomagio/algorithm/AverageAlgorithm.py
@@ -287,4 +287,5 @@ class AverageAlgorithm(Algorithm):
# the most recent interval should NOT allow fewer than the full
# complement of inputs in order to calculate an average (previous
# "update" intervals will allow fewer than the full complement)
- self.min_count_end = arguments.starttime
+ delta = TimeseriesUtility.get_delta_from_interval(arguments.interval)
+ self.min_count_end = arguments.starttime - delta
--
GitLab
From 994da7540a922ed7655ae830fad9a1bdf47acc31 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Wed, 7 Dec 2022 19:54:26 -0700
Subject: [PATCH 121/142] Update metadata
- code.json
- pyproject.toml
---
code.json | 4 ++--
pyproject.toml | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/code.json b/code.json
index 960eec17..5056bd55 100644
--- a/code.json
+++ b/code.json
@@ -3,7 +3,7 @@
"name": "geomag-algorithms",
"organization": "U.S. Geological Survey",
"description": "Library for processing Geomagnetic timeseries data.",
- "version": "1.6.1",
+ "version": "1.6.2",
"status": "Development",
"permissions": {
"usageType": "openSource",
@@ -35,7 +35,7 @@
"email": "gs-haz_dev_team_group@usgs.gov"
},
"date": {
- "metadataLastUpdated": "2022-11-29"
+ "metadataLastUpdated": "2022-12-07"
}
}
]
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 009abf96..1e83497e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ packages = [
{include = "geomagio" }
]
repository="https://code.usgs.gov/ghsc/geomag/geomag-algorithms"
-version = "1.6.1"
+version = "1.6.2"
[tool.poetry.dependencies]
--
GitLab
From c3f094773a8596952397956d7408fd5452f4ba33 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Wed, 7 Dec 2022 21:30:46 -0700
Subject: [PATCH 122/142] Update dependencies in poetry.lock
I ran `poetry update`, which fixed several vulnerabilities. HOWEVER,
there were a couple that didn't get fixed, including the wheel package.
I ran `poetry run pip install -U wheel` to update wheel in my own virtual
environmenet instead of adding it to pyproject.toml. This is because I
read something that indicated that wheel is a rather special package that
either should be, or actually cannot be, handled via pyrpoject.toml. I
*believe* that the Gitlab pipeline will create an entirely new virtual
environemnt, and that this will not be an issue, but we'll see.
---
poetry.lock | 1239 +++++----------------------------------------------
1 file changed, 106 insertions(+), 1133 deletions(-)
diff --git a/poetry.lock b/poetry.lock
index 0207bf94..d29f2a27 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -10,8 +10,8 @@ python-versions = ">=3.7"
PyMySQL = ">=1.0"
[package.extras]
-sa = ["sqlalchemy (>=1.0,<1.4)"]
rsa = ["PyMySQL[rsa] (>=1.0)"]
+sa = ["sqlalchemy (>=1.0,<1.4)"]
[[package]]
name = "aiosqlite"
@@ -74,7 +74,7 @@ tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>
[[package]]
name = "authlib"
-version = "1.1.0"
+version = "1.2.0"
description = "The ultimate Python library in building OAuth and OpenID Connect servers and clients."
category = "main"
optional = false
@@ -107,7 +107,7 @@ uvloop = ["uvloop (>=0.15.2)"]
[[package]]
name = "certifi"
-version = "2022.9.24"
+version = "2022.12.7"
description = "Python package for providing Mozilla's CA Bundle."
category = "main"
optional = false
@@ -188,7 +188,7 @@ toml = ["tomli"]
[[package]]
name = "cryptography"
-version = "38.0.3"
+version = "38.0.4"
description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
category = "main"
optional = false
@@ -226,7 +226,7 @@ dev = ["black", "flake8", "flake8-pyi", "matplotlib", "mypy (==0.770)", "numpy",
[[package]]
name = "databases"
-version = "0.6.1"
+version = "0.6.2"
description = "Async database support for Python."
category = "main"
optional = false
@@ -235,7 +235,7 @@ python-versions = ">=3.7"
[package.dependencies]
aiomysql = {version = "*", optional = true, markers = "extra == \"mysql\""}
aiosqlite = {version = "*", optional = true, markers = "extra == \"sqlite\""}
-sqlalchemy = ">=1.4,<1.5"
+sqlalchemy = ">=1.4,<=1.4.41"
[package.extras]
aiomysql = ["aiomysql"]
@@ -281,7 +281,7 @@ python-versions = ">=3.6"
[[package]]
name = "exceptiongroup"
-version = "1.0.0"
+version = "1.0.4"
description = "Backport of PEP 654 (exception groups)"
category = "dev"
optional = false
@@ -332,7 +332,7 @@ woff = ["zopfli (>=0.1.4)", "brotlicffi (>=0.8.0)", "brotli (>=1.0.1)"]
[[package]]
name = "greenlet"
-version = "2.0.0"
+version = "2.0.1"
description = "Lightweight in-process concurrent programming"
category = "main"
optional = false
@@ -340,7 +340,7 @@ python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
[package.extras]
docs = ["sphinx", "docutils (<0.18)"]
-test = ["objgraph", "faulthandler"]
+test = ["objgraph", "psutil", "faulthandler"]
[[package]]
name = "gunicorn"
@@ -423,7 +423,7 @@ python-versions = ">=3.5"
[[package]]
name = "importlib-metadata"
-version = "5.0.0"
+version = "5.1.0"
description = "Read metadata from Python packages"
category = "main"
optional = false
@@ -435,11 +435,11 @@ zipp = ">=0.5"
[package.extras]
docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
perf = ["ipython"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "pytest-flake8", "importlib-resources (>=1.3)"]
[[package]]
name = "importlib-resources"
-version = "5.10.0"
+version = "5.10.1"
description = "Read resources from Python packages"
category = "main"
optional = false
@@ -450,7 +450,7 @@ zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
[package.extras]
docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "pytest-flake8"]
[[package]]
name = "iniconfig"
@@ -498,7 +498,7 @@ source = ["Cython (>=0.29.7)"]
[[package]]
name = "mako"
-version = "1.2.3"
+version = "1.2.4"
description = "A super-fast templating language that borrows the best ideas from the existing templating languages."
category = "main"
optional = false
@@ -522,7 +522,7 @@ python-versions = ">=3.7"
[[package]]
name = "matplotlib"
-version = "3.6.1"
+version = "3.6.2"
description = "Python plotting package"
category = "main"
optional = false
@@ -568,7 +568,7 @@ python-versions = "*"
[[package]]
name = "numpy"
-version = "1.23.4"
+version = "1.23.5"
description = "NumPy is the fundamental package for array computing with Python."
category = "main"
optional = false
@@ -576,19 +576,19 @@ python-versions = ">=3.8"
[[package]]
name = "obspy"
-version = "1.3.1"
+version = "1.4.0"
description = "ObsPy - a Python framework for seismological observatories."
category = "main"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
[package.dependencies]
decorator = "*"
lxml = "*"
-matplotlib = ">=3.2.0"
-numpy = ">=1.15.0"
+matplotlib = ">=3.3"
+numpy = ">=1.20"
requests = "*"
-scipy = ">=1.0.0"
+scipy = ">=1.7"
sqlalchemy = "*"
[package.extras]
@@ -624,14 +624,11 @@ typing-extensions = ">=3.7.4"
[[package]]
name = "packaging"
-version = "21.3"
+version = "22.0"
description = "Core utilities for Python packages"
category = "main"
optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
+python-versions = ">=3.7"
[[package]]
name = "pastel"
@@ -643,7 +640,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[[package]]
name = "pathspec"
-version = "0.10.1"
+version = "0.10.2"
description = "Utility library for gitignore style pattern matching of file paths."
category = "dev"
optional = false
@@ -663,15 +660,15 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa
[[package]]
name = "platformdirs"
-version = "2.5.2"
-description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+version = "2.6.0"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
category = "dev"
optional = false
python-versions = ">=3.7"
[package.extras]
-docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)", "sphinx (>=4)"]
-test = ["appdirs (==1.4.4)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)", "pytest (>=6)"]
+docs = ["furo (>=2022.9.29)", "proselint (>=0.13)", "sphinx-autodoc-typehints (>=1.19.4)", "sphinx (>=5.3)"]
+test = ["appdirs (==1.4.4)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest (>=7.2)"]
[[package]]
name = "pluggy"
@@ -682,12 +679,12 @@ optional = false
python-versions = ">=3.6"
[package.extras]
-testing = ["pytest-benchmark", "pytest"]
-dev = ["tox", "pre-commit"]
+dev = ["pre-commit", "tox"]
+testing = ["pytest", "pytest-benchmark"]
[[package]]
name = "poethepoet"
-version = "0.16.4"
+version = "0.16.5"
description = "A task runner that works well with poetry."
category = "dev"
optional = false
@@ -698,7 +695,7 @@ pastel = ">=0.2.1,<0.3.0"
tomli = ">=1.2.2"
[package.extras]
-poetry_plugin = ["poetry (>=1.0,<2.0)"]
+poetry-plugin = ["poetry (>=1.0,<2.0)"]
[[package]]
name = "pycparser"
@@ -740,8 +737,8 @@ optional = false
python-versions = ">=3.6"
[package.extras]
-rsa = ["cryptography"]
ed25519 = ["PyNaCl (>=1.4.0)"]
+rsa = ["cryptography"]
[[package]]
name = "pyparsing"
@@ -876,7 +873,7 @@ python-versions = ">=3.5"
[[package]]
name = "safety"
-version = "2.3.1"
+version = "2.3.4"
description = "Checks installed dependencies for known vulnerabilities and licenses."
category = "dev"
optional = false
@@ -1047,7 +1044,7 @@ test = ["shellingham (>=1.3.0,<2.0.0)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (
[[package]]
name = "types-python-dateutil"
-version = "2.8.19.2"
+version = "2.8.19.4"
description = "Typing stubs for python-dateutil"
category = "dev"
optional = false
@@ -1055,7 +1052,7 @@ python-versions = "*"
[[package]]
name = "types-requests"
-version = "2.28.11.2"
+version = "2.28.11.5"
description = "Typing stubs for requests"
category = "dev"
optional = false
@@ -1066,7 +1063,7 @@ types-urllib3 = "<1.27"
[[package]]
name = "types-urllib3"
-version = "1.26.25.1"
+version = "1.26.25.4"
description = "Typing stubs for urllib3"
category = "dev"
optional = false
@@ -1082,11 +1079,11 @@ python-versions = ">=3.7"
[[package]]
name = "urllib3"
-version = "1.26.12"
+version = "1.26.13"
description = "HTTP library with thread-safe connection pooling, file post, and more."
category = "main"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, <4"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
[package.extras]
brotli = ["brotlicffi (>=0.8.0)", "brotli (>=1.0.9)", "brotlipy (>=0.6.0)"]
@@ -1130,14 +1127,14 @@ test = ["flake8 (>=3.9.2,<3.10.0)", "psutil", "pycodestyle (>=2.7.0,<2.8.0)", "p
[[package]]
name = "watchfiles"
-version = "0.18.0"
+version = "0.18.1"
description = "Simple, modern and high performance file watching and code reload in python."
category = "main"
optional = false
python-versions = ">=3.7"
[package.dependencies]
-anyio = ">=3.0.0,<4"
+anyio = ">=3.0.0"
[[package]]
name = "websockets"
@@ -1149,7 +1146,7 @@ python-versions = ">=3.7"
[[package]]
name = "zipp"
-version = "3.10.0"
+version = "3.11.0"
description = "Backport of pathlib-compatible object wrapper for zip files"
category = "main"
optional = false
@@ -1157,7 +1154,7 @@ python-versions = ">=3.7"
[package.extras]
docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "jaraco.itertools", "func-timeout", "jaraco.functools", "more-itertools", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
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-zipp = [
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-]
+typer = []
+types-python-dateutil = []
+types-requests = []
+types-urllib3 = []
+typing-extensions = []
+urllib3 = []
+uvicorn = []
+uvloop = []
+watchfiles = []
+websockets = []
+zipp = []
--
GitLab
From a1410be8c24b445af06d2494c9c7ab3df7711ca5 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Thu, 8 Dec 2022 12:10:11 -0700
Subject: [PATCH 123/142] Force pip to do eager install of wheels
---
Dockerfile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Dockerfile b/Dockerfile
index 4e4219ff..dfa7f2f3 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -33,7 +33,7 @@ COPY --from=build /app/dist/*.whl /app/docker-entrypoint.sh /app/
USER root
RUN apt update \
&& apt upgrade -y \
- && pip install /app/*.whl \
+ && pip install --upgrade-strategy eager /app/*.whl \
&& pip cache purge
USER usgs-user
--
GitLab
From 93f491127d5498aeda5c3382f6890f8fb14e45d9 Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Thu, 8 Dec 2022 12:22:56 -0700
Subject: [PATCH 124/142] add --upgrade option to pip
---
Dockerfile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Dockerfile b/Dockerfile
index dfa7f2f3..fa21605f 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -33,7 +33,7 @@ COPY --from=build /app/dist/*.whl /app/docker-entrypoint.sh /app/
USER root
RUN apt update \
&& apt upgrade -y \
- && pip install --upgrade-strategy eager /app/*.whl \
+ && pip install --upgrade --upgrade-strategy eager /app/*.whl \
&& pip cache purge
USER usgs-user
--
GitLab
From 54dc0f88d146a83e403b3467bc9c07ac7b06452d Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Fri, 13 Jan 2023 13:30:48 -0700
Subject: [PATCH 125/142] Changed Controller's default update-limit to 1
---
geomagio/Controller.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/geomagio/Controller.py b/geomagio/Controller.py
index 8018b9f9..4469066a 100644
--- a/geomagio/Controller.py
+++ b/geomagio/Controller.py
@@ -1112,7 +1112,7 @@ def parse_args(args):
processing_group.add_argument(
"--update-limit",
type=int,
- default=0,
+ default=1,
help="""
Update mode checks for gaps and will step backwards
to gap fill, if the start of the current interval is a gap,
--
GitLab
From 8dfc9f036dff12c74648c4629d663bedc03566ab Mon Sep 17 00:00:00 2001
From: Alex Wernle <awernle@usgs.gov>
Date: Wed, 25 Jan 2023 10:55:29 -0700
Subject: [PATCH 126/142] Change pyproject.toml to ignore sqlalchemy
vulnerability
---
pyproject.toml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/pyproject.toml b/pyproject.toml
index 1e83497e..a681634a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -81,7 +81,7 @@ copy-absolutes = "geomagio.processing.copy_absolutes:main"
[tool.poe.tasks]
# e.g. "poetry run poe lint"
audit = [
- { shell = "safety check"}
+ { shell = "safety check --ignore 51668"}
]
lint = [
{ shell = "black --check ." },
--
GitLab
From f98c9294443e7ceb199c40b694ddc8a0b7d545d3 Mon Sep 17 00:00:00 2001
From: Wilbur <swilbur@igskci164lm017.gs.doi.net>
Date: Thu, 2 Feb 2023 11:21:59 -0700
Subject: [PATCH 127/142] Changed the web address used in pip install command
for code.usgs.gov
---
docs/install.md | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/docs/install.md b/docs/install.md
index 2217fb73..df1b3037 100644
--- a/docs/install.md
+++ b/docs/install.md
@@ -34,7 +34,7 @@
2. Install **geomagio**
- pip install git+https://github.com/usgs/geomag-algorithms.git
+ pip install git+https://code.usgs.gov/ghsc/geomag/geomag-algorithms.git
3. Use **geomagio**
--
GitLab
From 8d27f2ae6d0e97953f9a6d2116929e4dc73d5af2 Mon Sep 17 00:00:00 2001
From: Wilbur <swilbur@igskci164lm017.gs.doi.net>
Date: Thu, 2 Feb 2023 12:28:29 -0700
Subject: [PATCH 128/142] changed the web address in develop.md to reflect teh
new gitlab repository
---
docs/develop.md | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/docs/develop.md b/docs/develop.md
index d7f5ba63..ec98f89b 100644
--- a/docs/develop.md
+++ b/docs/develop.md
@@ -14,9 +14,9 @@ https://guides.github.com/activities/forking/
2. Clone your fork
- git clone https://github.com/{YOUR_GITHUB_ACCOUNT}/geomag-algorithms.git
+ git clone https://code.usgs.gov/ghsc/{YOUR_GITHUB_ACCOUNT}/geomag-algorithms.git
cd geomag-algorithms
- git remote add upstream https://github.com/usgs/geomag-algorithms.git
+ git remote add upstream https://code.usgs.gov/ghsc/geomag/geomag-algorithms.git
3. Use branches to develop new features and submit pull requests.
--
GitLab
From a42025de0d32b83e8d190ddba0e5877c1e2a5529 Mon Sep 17 00:00:00 2001
From: Wilbur <swilbur@igskci164lm017.gs.doi.net>
Date: Thu, 2 Feb 2023 13:18:16 -0700
Subject: [PATCH 129/142] changed the directory used to set the container to
geomag/geomag-algorithms
---
docs/install_docker.md | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/docs/install_docker.md b/docs/install_docker.md
index f87b9193..43e06dd3 100644
--- a/docs/install_docker.md
+++ b/docs/install_docker.md
@@ -11,7 +11,7 @@ The container includes a Jupyter Notebook server for interactive development.
The following command creates and starts a container in the background.
- docker run --rm -it --name geomagio -p 8000:8000 -v $(pwd)/data:/data usgs/geomag-algorithms
+ docker run --rm -it --name geomagio -p 8000:8000 -v $(pwd)/data:/data geomag/geomag-algorithms
- `--rm` runs a temporary container
- `-it` makes the container interactive (so you can stop it with `ctrl+c`)
--
GitLab
From 2d7b7e02a2a907b79b1f34ff3b4db140c7a7dcd7 Mon Sep 17 00:00:00 2001
From: Wilbur <swilbur@igskci164lm017.gs.doi.net>
Date: Tue, 7 Feb 2023 11:51:07 -0700
Subject: [PATCH 130/142] changed the directory back to usgs/geomag-algorithms
---
docs/install_docker.md | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/docs/install_docker.md b/docs/install_docker.md
index 43e06dd3..f87b9193 100644
--- a/docs/install_docker.md
+++ b/docs/install_docker.md
@@ -11,7 +11,7 @@ The container includes a Jupyter Notebook server for interactive development.
The following command creates and starts a container in the background.
- docker run --rm -it --name geomagio -p 8000:8000 -v $(pwd)/data:/data geomag/geomag-algorithms
+ docker run --rm -it --name geomagio -p 8000:8000 -v $(pwd)/data:/data usgs/geomag-algorithms
- `--rm` runs a temporary container
- `-it` makes the container interactive (so you can stop it with `ctrl+c`)
--
GitLab
From 0af76a754219e9bcb9d7c94daa410b148ef1f38e Mon Sep 17 00:00:00 2001
From: Wilbur <swilbur@igskci164lm017.gs.doi.net>
Date: Tue, 7 Feb 2023 13:47:51 -0700
Subject: [PATCH 131/142] added lines so that the eleventh and following gaps
are shown in collapsible list. Added line 186 to create break and new line
after all gaps or no gaps are printed
---
geomagio/processing/monitor.py | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/geomagio/processing/monitor.py b/geomagio/processing/monitor.py
index 0bede2a5..d1aa4cae 100755
--- a/geomagio/processing/monitor.py
+++ b/geomagio/processing/monitor.py
@@ -66,6 +66,10 @@ def get_gaps(gaps):
gap_string += "<details>\n"
gap_string += f"<summary>+ {len(gaps) - 10}</summary>\n"
gap_string += "<span>\n"
+ gap_string += " %s to %s <br>\n" % (
+ format_time(gaps[i][0]),
+ format_time(gaps[i][1]),
+ )
else:
gap_string += " %s to %s <br>\n" % (
format_time(gaps[i][0]),
@@ -74,6 +78,7 @@ def get_gaps(gaps):
if i == len(gaps) - 1:
gap_string += "</span>\n"
gap_string += "</details>\n"
+
else:
gap_string = " None<br>"
return gap_string
@@ -178,6 +183,7 @@ def print_html_header(starttime, endtime, title):
+ "<title> %s \n to %s \n</title>"
% (format_time(starttime), format_time(endtime))
+ "</head>\n"
+ + "<br>\n"
+ "<body>\n"
+ '<style type="text/css">\n'
+ "table {border-collapse: collapse;}\n"
--
GitLab
From 9dafdcd5aa62871e24d4db6f3bfa28cace47d31a Mon Sep 17 00:00:00 2001
From: Wilbur <swilbur@igskci164lm017.gs.doi.net>
Date: Thu, 9 Feb 2023 08:31:30 -0700
Subject: [PATCH 132/142] Updated the script to create a new line following the
last line of any information pertianing to body summary. Should prevent other
files from being concatonated to the end of a previous line.
---
geomagio/processing/monitor.py | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/geomagio/processing/monitor.py b/geomagio/processing/monitor.py
index d1aa4cae..ab2e540d 100755
--- a/geomagio/processing/monitor.py
+++ b/geomagio/processing/monitor.py
@@ -78,7 +78,7 @@ def get_gaps(gaps):
if i == len(gaps) - 1:
gap_string += "</span>\n"
gap_string += "</details>\n"
-
+
else:
gap_string = " None<br>"
return gap_string
@@ -183,7 +183,6 @@ def print_html_header(starttime, endtime, title):
+ "<title> %s \n to %s \n</title>"
% (format_time(starttime), format_time(endtime))
+ "</head>\n"
- + "<br>\n"
+ "<body>\n"
+ '<style type="text/css">\n'
+ "table {border-collapse: collapse;}\n"
@@ -323,7 +322,7 @@ def generate_report(
location_code=location_code,
warning_threshold=warning_threshold,
)
- print("</body>\n" + "</html>\n")
+ print("<br>\n" + "<br>\n" + "</body>\n" + "</html>\n")
sys.exit(warning_issued)
--
GitLab
From 00644dd2fe48af90f3664287056a1d411245f289 Mon Sep 17 00:00:00 2001
From: spencer <swilbur@usgs.gov>
Date: Mon, 13 Feb 2023 08:40:33 -0700
Subject: [PATCH 133/142] updated the cryptography package to 39.0.1
---
pyproject.toml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/pyproject.toml b/pyproject.toml
index a681634a..4ad2a33e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -34,7 +34,7 @@ typer = "^0.6.1"
# webservice
alembic = "^1.8.1"
Authlib = "^1.1.0"
-cryptography = "^38.0.1"
+cryptography = "^39.0.1"
databases = {extras = ["mysql", "sqlite"], version = "^0.6.1"}
fastapi = "^0.85.1"
gunicorn = "^20.1.0"
--
GitLab
From 5a55dedbcc1dce98f4c4088af36ae592d8b225c6 Mon Sep 17 00:00:00 2001
From: spencer <swilbur@usgs.gov>
Date: Mon, 13 Feb 2023 09:57:54 -0700
Subject: [PATCH 134/142] Updated the poety.lock file
---
poetry.lock | 1897 ++++++++++++++++++++++++++++++++++++++++-----------
1 file changed, 1515 insertions(+), 382 deletions(-)
diff --git a/poetry.lock b/poetry.lock
index d29f2a27..8f27ad50 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,3 +1,5 @@
+# This file is automatically @generated by Poetry and should not be changed by hand.
+
[[package]]
name = "aiomysql"
version = "0.1.1"
@@ -5,6 +7,10 @@ description = "MySQL driver for asyncio."
category = "main"
optional = false
python-versions = ">=3.7"
+files = [
+ {file = "aiomysql-0.1.1-py3-none-any.whl", hash = "sha256:b66fa1481ca71c5ee0d933ec3abf51f6136543a3710ba80b134eb33da7ed6f13"},
+ {file = "aiomysql-0.1.1.tar.gz", hash = "sha256:0d686c4fdae6b67d1825d8be60fa3b0e644fca2c84d3c936d850fc259c8e107e"},
+]
[package.dependencies]
PyMySQL = ">=1.0"
@@ -15,22 +21,27 @@ sa = ["sqlalchemy (>=1.0,<1.4)"]
[[package]]
name = "aiosqlite"
-version = "0.17.0"
+version = "0.18.0"
description = "asyncio bridge to the standard sqlite3 module"
category = "main"
optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-typing_extensions = ">=3.7.2"
+python-versions = ">=3.7"
+files = [
+ {file = "aiosqlite-0.18.0-py3-none-any.whl", hash = "sha256:c3511b841e3a2c5614900ba1d179f366826857586f78abd75e7cbeb88e75a557"},
+ {file = "aiosqlite-0.18.0.tar.gz", hash = "sha256:faa843ef5fb08bafe9a9b3859012d3d9d6f77ce3637899de20606b7fc39aa213"},
+]
[[package]]
name = "alembic"
-version = "1.8.1"
+version = "1.9.3"
description = "A database migration tool for SQLAlchemy."
category = "main"
optional = false
python-versions = ">=3.7"
+files = [
+ {file = "alembic-1.9.3-py3-none-any.whl", hash = "sha256:ed2f73ea9c986f43af8ad7502c5f60d6bb1400bcd6d29f230e760e08884cb476"},
+ {file = "alembic-1.9.3.tar.gz", hash = "sha256:8fd6aaea56f5a703a190d25a705dfa91d7c313bb71de2f9c68f5abdcaf5df164"},
+]
[package.dependencies]
importlib-metadata = {version = "*", markers = "python_version < \"3.9\""}
@@ -48,29 +59,38 @@ description = "High level compatibility layer for multiple asynchronous event lo
category = "main"
optional = false
python-versions = ">=3.6.2"
+files = [
+ {file = "anyio-3.6.2-py3-none-any.whl", hash = "sha256:fbbe32bd270d2a2ef3ed1c5d45041250284e31fc0a4df4a5a6071842051a51e3"},
+ {file = "anyio-3.6.2.tar.gz", hash = "sha256:25ea0d673ae30af41a0c442f81cf3b38c7e79fdc7b60335a4c14e05eb0947421"},
+]
[package.dependencies]
idna = ">=2.8"
sniffio = ">=1.1"
[package.extras]
-doc = ["packaging", "sphinx-rtd-theme", "sphinx-autodoc-typehints (>=1.2.0)"]
-test = ["coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "contextlib2", "uvloop (<0.15)", "mock (>=4)", "uvloop (>=0.15)"]
+doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
+test = ["contextlib2", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (<0.15)", "uvloop (>=0.15)"]
trio = ["trio (>=0.16,<0.22)"]
[[package]]
name = "attrs"
-version = "22.1.0"
+version = "22.2.0"
description = "Classes Without Boilerplate"
category = "dev"
optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
+files = [
+ {file = "attrs-22.2.0-py3-none-any.whl", hash = "sha256:29e95c7f6778868dbd49170f98f8818f78f3dc5e0e37c0b1f474e3561b240836"},
+ {file = "attrs-22.2.0.tar.gz", hash = "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"},
+]
[package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
-docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "cloudpickle"]
+cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"]
+dev = ["attrs[docs,tests]"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"]
+tests = ["attrs[tests-no-zope]", "zope.interface"]
+tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy (>=0.971,<0.990)", "mypy (>=0.971,<0.990)", "pympler", "pympler", "pytest (>=4.3.0)", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-mypy-plugins", "pytest-xdist[psutil]", "pytest-xdist[psutil]"]
[[package]]
name = "authlib"
@@ -79,17 +99,35 @@ description = "The ultimate Python library in building OAuth and OpenID Connect
category = "main"
optional = false
python-versions = "*"
+files = [
+ {file = "Authlib-1.2.0-py2.py3-none-any.whl", hash = "sha256:4ddf4fd6cfa75c9a460b361d4bd9dac71ffda0be879dbe4292a02e92349ad55a"},
+ {file = "Authlib-1.2.0.tar.gz", hash = "sha256:4fa3e80883a5915ef9f5bc28630564bc4ed5b5af39812a3ff130ec76bd631e9d"},
+]
[package.dependencies]
cryptography = ">=3.2"
[[package]]
name = "black"
-version = "22.10.0"
+version = "22.12.0"
description = "The uncompromising code formatter."
category = "dev"
optional = false
python-versions = ">=3.7"
+files = [
+ {file = "black-22.12.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9eedd20838bd5d75b80c9f5487dbcb06836a43833a37846cf1d8c1cc01cef59d"},
+ {file = "black-22.12.0-cp310-cp310-win_amd64.whl", hash = "sha256:159a46a4947f73387b4d83e87ea006dbb2337eab6c879620a3ba52699b1f4351"},
+ {file = "black-22.12.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d30b212bffeb1e252b31dd269dfae69dd17e06d92b87ad26e23890f3efea366f"},
+ {file = "black-22.12.0-cp311-cp311-win_amd64.whl", hash = "sha256:7412e75863aa5c5411886804678b7d083c7c28421210180d67dfd8cf1221e1f4"},
+ {file = "black-22.12.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c116eed0efb9ff870ded8b62fe9f28dd61ef6e9ddd28d83d7d264a38417dcee2"},
+ {file = "black-22.12.0-cp37-cp37m-win_amd64.whl", hash = "sha256:1f58cbe16dfe8c12b7434e50ff889fa479072096d79f0a7f25e4ab8e94cd8350"},
+ {file = "black-22.12.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:77d86c9f3db9b1bf6761244bc0b3572a546f5fe37917a044e02f3166d5aafa7d"},
+ {file = "black-22.12.0-cp38-cp38-win_amd64.whl", hash = "sha256:82d9fe8fee3401e02e79767016b4907820a7dc28d70d137eb397b92ef3cc5bfc"},
+ {file = "black-22.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:101c69b23df9b44247bd88e1d7e90154336ac4992502d4197bdac35dd7ee3320"},
+ {file = "black-22.12.0-cp39-cp39-win_amd64.whl", hash = "sha256:559c7a1ba9a006226f09e4916060982fd27334ae1998e7a38b3f33a37f7a2148"},
+ {file = "black-22.12.0-py3-none-any.whl", hash = "sha256:436cc9167dd28040ad90d3b404aec22cedf24a6e4d7de221bec2730ec0c97bcf"},
+ {file = "black-22.12.0.tar.gz", hash = "sha256:229351e5a18ca30f447bf724d007f890f97e13af070bb6ad4c0a441cd7596a2f"},
+]
[package.dependencies]
click = ">=8.0.0"
@@ -112,6 +150,10 @@ description = "Python package for providing Mozilla's CA Bundle."
category = "main"
optional = false
python-versions = ">=3.6"
+files = [
+ {file = "certifi-2022.12.7-py3-none-any.whl", hash = "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18"},
+ {file = "certifi-2022.12.7.tar.gz", hash = "sha256:35824b4c3a97115964b408844d64aa14db1cc518f6562e8d7261699d1350a9e3"},
+]
[[package]]
name = "cffi"
@@ -120,20 +162,173 @@ description = "Foreign Function Interface for Python calling C code."
category = "main"
optional = false
python-versions = "*"
+files = [
+ {file = "cffi-1.15.1-cp27-cp27m-macosx_10_9_x86_64.whl", hash = "sha256:a66d3508133af6e8548451b25058d5812812ec3798c886bf38ed24a98216fab2"},
+ {file = "cffi-1.15.1-cp27-cp27m-manylinux1_i686.whl", hash = "sha256:470c103ae716238bbe698d67ad020e1db9d9dba34fa5a899b5e21577e6d52ed2"},
+ {file = "cffi-1.15.1-cp27-cp27m-manylinux1_x86_64.whl", hash = "sha256:9ad5db27f9cabae298d151c85cf2bad1d359a1b9c686a275df03385758e2f914"},
+ {file = "cffi-1.15.1-cp27-cp27m-win32.whl", hash = "sha256:b3bbeb01c2b273cca1e1e0c5df57f12dce9a4dd331b4fa1635b8bec26350bde3"},
+ {file = "cffi-1.15.1-cp27-cp27m-win_amd64.whl", hash = "sha256:e00b098126fd45523dd056d2efba6c5a63b71ffe9f2bbe1a4fe1716e1d0c331e"},
+ {file = "cffi-1.15.1-cp27-cp27mu-manylinux1_i686.whl", hash = "sha256:d61f4695e6c866a23a21acab0509af1cdfd2c013cf256bbf5b6b5e2695827162"},
+ {file = "cffi-1.15.1-cp27-cp27mu-manylinux1_x86_64.whl", hash = "sha256:ed9cb427ba5504c1dc15ede7d516b84757c3e3d7868ccc85121d9310d27eed0b"},
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optional = false
python-versions = ">=3.7"
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optional = false
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name = "cycler"
@@ -212,6 +552,10 @@ description = "Composable style cycles"
category = "main"
optional = false
python-versions = ">=3.6"
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name = "data-science-types"
@@ -220,6 +564,10 @@ description = "Type stubs for Python machine learning libraries"
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optional = false
python-versions = ">=3.6"
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@@ -231,6 +579,10 @@ description = "Async database support for Python."
category = "main"
optional = false
python-versions = ">=3.7"
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aiomysql = {version = "*", optional = true, markers = "extra == \"mysql\""}
@@ -254,6 +606,10 @@ description = "Decorators for Humans"
category = "main"
optional = false
python-versions = ">=3.5"
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name = "dparse"
@@ -262,6 +618,10 @@ description = "A parser for Python dependency files"
category = "dev"
optional = false
python-versions = ">=3.5"
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packaging = "*"
@@ -278,14 +638,22 @@ description = "An implementation of lxml.xmlfile for the standard library"
category = "main"
optional = false
python-versions = ">=3.6"
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description = "Backport of PEP 654 (exception groups)"
category = "dev"
optional = false
python-versions = ">=3.7"
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@@ -297,6 +665,10 @@ description = "FastAPI framework, high performance, easy to learn, fast to code,
category = "main"
optional = false
python-versions = ">=3.7"
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optional = false
python-versions = "*"
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-types-requests = []
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-typing-extensions = []
-urllib3 = []
-uvicorn = []
-uvloop = []
-watchfiles = []
-websockets = []
-zipp = []
+content-hash = "2883f577e02e870b17d909247e71c203a5c3ea21ff8873232621b1b4e6e9b9e4"
--
GitLab
From c4a56f3fddc3206ab1c86b61acc580629c01a0d2 Mon Sep 17 00:00:00 2001
From: "Erin (Josh) Rigler" <erigler@usgs.gov>
Date: Wed, 15 Feb 2023 17:33:48 +0000
Subject: [PATCH 135/142] Update pyproject.toml version info
---
pyproject.toml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/pyproject.toml b/pyproject.toml
index 4ad2a33e..cd2f4047 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ packages = [
{include = "geomagio" }
]
repository="https://code.usgs.gov/ghsc/geomag/geomag-algorithms"
-version = "1.6.2"
+version = "1.6.3"
[tool.poetry.dependencies]
--
GitLab
From e20bf09d6fa6ade82c320877159a25ab50ed2e93 Mon Sep 17 00:00:00 2001
From: "Erin (Josh) Rigler" <erigler@usgs.gov>
Date: Wed, 15 Feb 2023 17:34:32 +0000
Subject: [PATCH 136/142] Update code.json version info
---
code.json | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/code.json b/code.json
index 5056bd55..4bdbf3c1 100644
--- a/code.json
+++ b/code.json
@@ -3,7 +3,7 @@
"name": "geomag-algorithms",
"organization": "U.S. Geological Survey",
"description": "Library for processing Geomagnetic timeseries data.",
- "version": "1.6.2",
+ "version": "1.6.3",
"status": "Development",
"permissions": {
"usageType": "openSource",
@@ -35,7 +35,7 @@
"email": "gs-haz_dev_team_group@usgs.gov"
},
"date": {
- "metadataLastUpdated": "2022-12-07"
+ "metadataLastUpdated": "2023-02-15"
}
}
-]
\ No newline at end of file
+]
--
GitLab
From df1aa0a30b8ca90071633507f69b3c446a2529ac Mon Sep 17 00:00:00 2001
From: "E. Joshua Rigler" <erigler@usgs.gov>
Date: Wed, 15 Feb 2023 19:09:19 -0700
Subject: [PATCH 137/142] Bump fastapi in pyproject.toml; update poetry.lock
A vulnerability in the fastapi dependency starlette required a bump
to [fastapi v0.92.0](https://github.com/tiangolo/fastapi/releases/tag/0.92.0)
and update to the poetry.lock file.
---
poetry.lock | 219 +++++++++++++++++++++++++------------------------
pyproject.toml | 2 +-
2 files changed, 111 insertions(+), 110 deletions(-)
diff --git a/poetry.lock b/poetry.lock
index 8f27ad50..3040904d 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -660,25 +660,25 @@ test = ["pytest (>=6)"]
[[package]]
name = "fastapi"
-version = "0.85.2"
+version = "0.92.0"
description = "FastAPI framework, high performance, easy to learn, fast to code, ready for production"
category = "main"
optional = false
python-versions = ">=3.7"
files = [
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- {file = "fastapi-0.85.2.tar.gz", hash = "sha256:3e10ea0992c700e0b17b6de8c2092d7b9cd763ce92c49ee8d4be10fee3b2f367"},
+ {file = "fastapi-0.92.0-py3-none-any.whl", hash = "sha256:ae7b97c778e2f2ec3fb3cb4fb14162129411d99907fb71920f6d69a524340ebf"},
+ {file = "fastapi-0.92.0.tar.gz", hash = "sha256:023a0f5bd2c8b2609014d3bba1e14a1d7df96c6abea0a73070621c9862b9a4de"},
]
[package.dependencies]
pydantic = ">=1.6.2,<1.7 || >1.7,<1.7.1 || >1.7.1,<1.7.2 || >1.7.2,<1.7.3 || >1.7.3,<1.8 || >1.8,<1.8.1 || >1.8.1,<2.0.0"
-starlette = "0.20.4"
+starlette = ">=0.25.0,<0.26.0"
[package.extras]
-all = ["email-validator (>=1.1.1,<2.0.0)", "itsdangerous (>=1.1.0,<3.0.0)", "jinja2 (>=2.11.2,<4.0.0)", "orjson (>=3.2.1,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "pyyaml (>=5.3.1,<7.0.0)", "requests (>=2.24.0,<3.0.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)", "uvicorn[standard] (>=0.12.0,<0.19.0)"]
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python-versions = "*"
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]
[[package]]
name = "types-requests"
-version = "2.28.11.12"
+version = "2.28.11.13"
description = "Typing stubs for requests"
category = "dev"
optional = false
python-versions = "*"
files = [
- {file = "types-requests-2.28.11.12.tar.gz", hash = "sha256:fd530aab3fc4f05ee36406af168f0836e6f00f1ee51a0b96b7311f82cb675230"},
- {file = "types_requests-2.28.11.12-py3-none-any.whl", hash = "sha256:dbc2933635860e553ffc59f5e264264981358baffe6342b925e3eb8261f866ee"},
+ {file = "types-requests-2.28.11.13.tar.gz", hash = "sha256:3fd332842e8759ea5f7eb7789df8aa772ba155216ccf10ef4aa3b0e5b42e1b46"},
+ {file = "types_requests-2.28.11.13-py3-none-any.whl", hash = "sha256:94896f6f8e9f3db11e422c6e3e4abbc5d7ccace853eac74b23bdd65eeee3cdee"},
]
[package.dependencies]
@@ -2290,26 +2291,26 @@ types-urllib3 = "<1.27"
[[package]]
name = "types-urllib3"
-version = "1.26.25.5"
+version = "1.26.25.6"
description = "Typing stubs for urllib3"
category = "dev"
optional = false
python-versions = "*"
files = [
- {file = "types-urllib3-1.26.25.5.tar.gz", hash = "sha256:5630e578246d170d91ebe3901788cd28d53c4e044dc2e2488e3b0d55fb6895d8"},
- {file = "types_urllib3-1.26.25.5-py3-none-any.whl", hash = "sha256:e8f25c8bb85cde658c72ee931e56e7abd28803c26032441eea9ff4a4df2b0c31"},
+ {file = "types-urllib3-1.26.25.6.tar.gz", hash = "sha256:35586727cbd7751acccf2c0f34a88baffc092f435ab62458f10776466590f2d5"},
+ {file = "types_urllib3-1.26.25.6-py3-none-any.whl", hash = "sha256:a6c23c41bd03e542eaee5423a018f833077b51c4bf9ceb5aa544e12b812d5604"},
]
[[package]]
name = "typing-extensions"
-version = "4.4.0"
+version = "4.5.0"
description = "Backported and Experimental Type Hints for Python 3.7+"
category = "main"
optional = false
python-versions = ">=3.7"
files = [
- {file = "typing_extensions-4.4.0-py3-none-any.whl", hash = "sha256:16fa4864408f655d35ec496218b85f79b3437c829e93320c7c9215ccfd92489e"},
- {file = "typing_extensions-4.4.0.tar.gz", hash = "sha256:1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa"},
+ {file = "typing_extensions-4.5.0-py3-none-any.whl", hash = "sha256:fb33085c39dd998ac16d1431ebc293a8b3eedd00fd4a32de0ff79002c19511b4"},
+ {file = "typing_extensions-4.5.0.tar.gz", hash = "sha256:5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb"},
]
[[package]]
@@ -2532,4 +2533,4 @@ pycurl = ["pycurl"]
[metadata]
lock-version = "2.0"
python-versions = "^3.8,<3.11"
-content-hash = "2883f577e02e870b17d909247e71c203a5c3ea21ff8873232621b1b4e6e9b9e4"
+content-hash = "f26dd987ec9faf3186872977ec4ea9e38a5ebbee7b3c9600b7ca1a1cb0644ec3"
diff --git a/pyproject.toml b/pyproject.toml
index cd2f4047..910d159f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -36,7 +36,7 @@ alembic = "^1.8.1"
Authlib = "^1.1.0"
cryptography = "^39.0.1"
databases = {extras = ["mysql", "sqlite"], version = "^0.6.1"}
-fastapi = "^0.85.1"
+fastapi = "^0.92.0"
gunicorn = "^20.1.0"
httpx = "0.23.0"
# 2022-10-24 pin sqlalchemy to 1.4.41 for now
--
GitLab
From 4e7ccd83ac3ad3ff393325b8d05c6c366b654e98 Mon Sep 17 00:00:00 2001
From: spencer <swilbur@usgs.gov>
Date: Thu, 23 Feb 2023 13:29:34 -0700
Subject: [PATCH 138/142] updated pyproject.toml to allow python versions
3.8.12 to 3.11.*
---
poetry.lock | 194 ++++++++++++++++++++++++-------------------------
pyproject.toml | 2 +-
2 files changed, 98 insertions(+), 98 deletions(-)
diff --git a/poetry.lock b/poetry.lock
index 3040904d..155e9f7f 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -33,14 +33,14 @@ files = [
[[package]]
name = "alembic"
-version = "1.9.3"
+version = "1.9.4"
description = "A database migration tool for SQLAlchemy."
category = "main"
optional = false
python-versions = ">=3.7"
files = [
- {file = "alembic-1.9.3-py3-none-any.whl", hash = "sha256:ed2f73ea9c986f43af8ad7502c5f60d6bb1400bcd6d29f230e760e08884cb476"},
- {file = "alembic-1.9.3.tar.gz", hash = "sha256:8fd6aaea56f5a703a190d25a705dfa91d7c313bb71de2f9c68f5abdcaf5df164"},
+ {file = "alembic-1.9.4-py3-none-any.whl", hash = "sha256:6f1c2207369bf4f49f952057a33bb017fbe5c148c2a773b46906b806ea6e825f"},
+ {file = "alembic-1.9.4.tar.gz", hash = "sha256:4d3bd32ecdbb7bbfb48a9fe9e6d6fd6a831a1b59d03e26e292210237373e7db5"},
]
[package.dependencies]
@@ -434,63 +434,63 @@ test-no-images = ["pytest"]
[[package]]
name = "coverage"
-version = "7.1.0"
+version = "7.2.0"
description = "Code coverage measurement for Python"
category = "dev"
optional = false
python-versions = ">=3.7"
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python-versions = "*"
files = [
- {file = "types-python-dateutil-2.8.19.7.tar.gz", hash = "sha256:7af5a5d1b80ab1dfa0ba4d879facb382e836a62c2d408c2a509be4680fd8b1c8"},
- {file = "types_python_dateutil-2.8.19.7-py3-none-any.whl", hash = "sha256:669751e1e6d4f3dbbff471231740e7ecdae2135b604383e477fe31fd56223967"},
+ {file = "types-python-dateutil-2.8.19.8.tar.gz", hash = "sha256:316c6b107d055bbd06324b71362e6104102220e6988aa4a388550aa3a8ad5d06"},
+ {file = "types_python_dateutil-2.8.19.8-py3-none-any.whl", hash = "sha256:6b44741d3e79b2f2ba595f6bfa96f1a5091a00703848547efb3bc5b71df3cf9d"},
]
[[package]]
name = "types-requests"
-version = "2.28.11.13"
+version = "2.28.11.14"
description = "Typing stubs for requests"
category = "dev"
optional = false
python-versions = "*"
files = [
- {file = "types-requests-2.28.11.13.tar.gz", hash = "sha256:3fd332842e8759ea5f7eb7789df8aa772ba155216ccf10ef4aa3b0e5b42e1b46"},
- {file = "types_requests-2.28.11.13-py3-none-any.whl", hash = "sha256:94896f6f8e9f3db11e422c6e3e4abbc5d7ccace853eac74b23bdd65eeee3cdee"},
+ {file = "types-requests-2.28.11.14.tar.gz", hash = "sha256:232792870b60adb07d23175451ab4e6190021b0c584edf052d92d9b993118f06"},
+ {file = "types_requests-2.28.11.14-py3-none-any.whl", hash = "sha256:f84613b0d4c5d0eeb7879dfa05e14a3702b9c1f7a4ee81dfe9b4321b13fe93a1"},
]
[package.dependencies]
@@ -2291,14 +2291,14 @@ types-urllib3 = "<1.27"
[[package]]
name = "types-urllib3"
-version = "1.26.25.6"
+version = "1.26.25.7"
description = "Typing stubs for urllib3"
category = "dev"
optional = false
python-versions = "*"
files = [
- {file = "types-urllib3-1.26.25.6.tar.gz", hash = "sha256:35586727cbd7751acccf2c0f34a88baffc092f435ab62458f10776466590f2d5"},
- {file = "types_urllib3-1.26.25.6-py3-none-any.whl", hash = "sha256:a6c23c41bd03e542eaee5423a018f833077b51c4bf9ceb5aa544e12b812d5604"},
+ {file = "types-urllib3-1.26.25.7.tar.gz", hash = "sha256:df4d3e5472bf8830bd74eac12d56e659f88662ba040c7d106bf3a5bee26fff28"},
+ {file = "types_urllib3-1.26.25.7-py3-none-any.whl", hash = "sha256:28d2d7f5c31ff8ed4d9d2e396ce906c49d37523c3ec207d03d3b1695755a7199"},
]
[[package]]
@@ -2513,14 +2513,14 @@ files = [
[[package]]
name = "zipp"
-version = "3.13.0"
+version = "3.14.0"
description = "Backport of pathlib-compatible object wrapper for zip files"
category = "main"
optional = false
python-versions = ">=3.7"
files = [
- {file = "zipp-3.13.0-py3-none-any.whl", hash = "sha256:e8b2a36ea17df80ffe9e2c4fda3f693c3dad6df1697d3cd3af232db680950b0b"},
- {file = "zipp-3.13.0.tar.gz", hash = "sha256:23f70e964bc11a34cef175bc90ba2914e1e4545ea1e3e2f67c079671883f9cb6"},
+ {file = "zipp-3.14.0-py3-none-any.whl", hash = "sha256:188834565033387710d046e3fe96acfc9b5e86cbca7f39ff69cf21a4128198b7"},
+ {file = "zipp-3.14.0.tar.gz", hash = "sha256:9e5421e176ef5ab4c0ad896624e87a7b2f07aca746c9b2aa305952800cb8eecb"},
]
[package.extras]
@@ -2532,5 +2532,5 @@ pycurl = ["pycurl"]
[metadata]
lock-version = "2.0"
-python-versions = "^3.8,<3.11"
-content-hash = "f26dd987ec9faf3186872977ec4ea9e38a5ebbee7b3c9600b7ca1a1cb0644ec3"
+python-versions = ">=3.8,<=3.11.*"
+content-hash = "5614e41f7479fbe3909c79979eaa80ae4fa6cb9ab59c29249424afd890d9cd21"
diff --git a/pyproject.toml b/pyproject.toml
index 910d159f..9eb586ce 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,7 +21,7 @@ version = "1.6.3"
[tool.poetry.dependencies]
-python = "^3.8,<3.11"
+python = ">=3.8,<=3.11.*"
# core
numpy = "^1.23.4"
obspy = "^1.3.1"
--
GitLab
From c79e7ca31e67fba6a14e4849aab140d34b249be5 Mon Sep 17 00:00:00 2001
From: spencer <swilbur@usgs.gov>
Date: Fri, 17 Mar 2023 11:44:27 -0600
Subject: [PATCH 139/142] committing IRISSNCL_test.py after running lint
---
test/edge_test/IRISSNCL_test.py | 34 ++++++++++++++-------------------
1 file changed, 14 insertions(+), 20 deletions(-)
diff --git a/test/edge_test/IRISSNCL_test.py b/test/edge_test/IRISSNCL_test.py
index b67cc640..b1bfec0c 100644
--- a/test/edge_test/IRISSNCL_test.py
+++ b/test/edge_test/IRISSNCL_test.py
@@ -107,17 +107,14 @@ def test_get_iris_channel():
def test_get_sncl():
"""edge_test.IRISSNCL_test.test_get_sncl()"""
- assert (
- IRISSNCL.get_sncl(
- data_type="variation",
- element="H",
- interval="second",
- station="ANMO",
- network="IU",
- location="40",
- )
- == IRISSNCL(station="ANMO", network="IU", channel="LF1", location="40")
- )
+ assert IRISSNCL.get_sncl(
+ data_type="variation",
+ element="H",
+ interval="second",
+ station="ANMO",
+ network="IU",
+ location="40",
+ ) == IRISSNCL(station="ANMO", network="IU", channel="LF1", location="40")
with pytest.raises(ValueError) as error:
IRISSNCL.get_sncl(
data_type="adjusted",
@@ -128,15 +125,12 @@ def test_get_sncl():
location="40",
)
assert error.value == "Unsupported data type: adjusted"
- assert (
- IRISSNCL.get_sncl(
- data_type="adjusted",
- element="H",
- interval="second",
- station="BOU",
- )
- == IRISSNCL(station="BOU", network="NT", channel="LFH", location="A0")
- )
+ assert IRISSNCL.get_sncl(
+ data_type="adjusted",
+ element="H",
+ interval="second",
+ station="BOU",
+ ) == IRISSNCL(station="BOU", network="NT", channel="LFH", location="A0")
def test_interval():
--
GitLab
From 973d5d8ccecb5fea2d11970e299caa0046bdbfb1 Mon Sep 17 00:00:00 2001
From: spencer <swilbur@usgs.gov>
Date: Wed, 29 Mar 2023 14:39:02 -0600
Subject: [PATCH 140/142] Updated the pyproject.toml, Metadata.py, and
Code.json files to reflect most current versions and code found in the Master
branch. This was done to resolve a merge conflict.
---
code.json | 4 +--
geomagio/Metadata.py | 67 ++++++++++++++++++++++----------------------
pyproject.toml | 2 +-
3 files changed, 37 insertions(+), 36 deletions(-)
diff --git a/code.json b/code.json
index 4bdbf3c1..f995592b 100644
--- a/code.json
+++ b/code.json
@@ -3,7 +3,7 @@
"name": "geomag-algorithms",
"organization": "U.S. Geological Survey",
"description": "Library for processing Geomagnetic timeseries data.",
- "version": "1.6.3",
+ "version": "1.6.5",
"status": "Development",
"permissions": {
"usageType": "openSource",
@@ -35,7 +35,7 @@
"email": "gs-haz_dev_team_group@usgs.gov"
},
"date": {
- "metadataLastUpdated": "2023-02-15"
+ "metadataLastUpdated": "2023-03-29"
}
}
]
diff --git a/geomagio/Metadata.py b/geomagio/Metadata.py
index 9c2ad7ca..24c58b1d 100644
--- a/geomagio/Metadata.py
+++ b/geomagio/Metadata.py
@@ -41,26 +41,26 @@ _INSTRUMENT_METADATA = [
# Temporary values until actuals are obtained.
# TODO: calculate these lists based on "FGE" type
# TODO: Adjust offset for new FGE sensor & electronics? (installed 3/20/22)
- "U": [{"channel": "U_Volt", "offset": 20613, "scale": 980}],
- "V": [{"channel": "V_Volt", "offset": 0, "scale": 980}],
- "W": [{"channel": "W_Volt", "offset": 47450, "scale": 980}],
+ "U": [{"channel": "U_Volt", "offset": 20613, "scale": 966.7624}],
+ "V": [{"channel": "V_Volt", "offset": 0, "scale": 944.1253}],
+ "W": [{"channel": "W_Volt", "offset": 47450, "scale": 975.5875}],
},
"electronics": {
- "serial": "TBD",
- # these scale values are used to convert voltage
- # Temporary values until actuals are obtained.
- "x-scale": 980, # nT/V
- "y-scale": 980, # nT/V
- "z-scale": 980, # nT/V
+ "serial": "E574",
+ # these scale values are calculated manually.
+ "x-scale": 966.7624, # nT/V
+ "y-scale": 944.1253, # nT/V
+ "z-scale": 975.5875, # nT/V
"temperature-scale": 0.01, # V/K
},
"sensor": {
- "serial": "TBD",
+ "serial": "S0449",
# these constants combine with instrument setting for offset
# Temporary values until actuals are obtained.
- "x-constant": 1, # nT/mA
- "y-constant": 1, # nT/mA
- "z-constant": 1, # nT/mA
+ "x-constant": 37027, # nT/mA
+ "y-constant": 36160, # nT/mA
+ "z-constant": 37365, # nT/mA
+
},
},
},
@@ -561,26 +561,27 @@ _INSTRUMENT_METADATA = [
"channels": {
# each channel maps to a list of components to calculate nT
# TODO: calculate these lists based on "FGE" type
- "U": [{"channel": "U_Volt", "offset": 0, "scale": 320.0}],
- "V": [{"channel": "V_Volt", "offset": 0, "scale": 320.0}],
- "W": [{"channel": "W_Volt", "offset": 0, "scale": 320.0}],
- },
- ## this info should get updated when available
- # "electronics": {
- # "serial": "E0542",
- # # these scale values are used to convert voltage
- # "x-scale": 313.2, # nT/V
- # "y-scale": 312.3, # nT/V
- # "z-scale": 312.0, # nT/V
- # "temperature-scale": 0.01, # V/K
- # },
- # "sensor": {
- # "serial": "S0419",
- # # these constants combine with instrument setting for offset
- # "x-constant": 36958, # nT/mA
- # "y-constant": 36849, # nT/mA
- # "z-constant": 36811, # nT/mA
- # },
+ "U": [{"channel": "U_Volt", "offset": 0, "scale": 313.2034}],
+ "V": [{"channel": "V_Volt", "offset": 0, "scale": 312.2797}],
+ "W": [{"channel": "W_Volt", "offset": 0, "scale": 311.9576}],
+ },
+ # this info should get updated when available
+ "electronics": {
+ "serial": "E0543",
+ # these scale values are calculated manually
+ "x-scale": 313.2034, # nT/V
+ "y-scale": 312.2797, # nT/V
+ "z-scale": 311.9576, # nT/V
+ "temperature-scale": 0.01, # V/K
+ },
+ "sensor": {
+ "serial": "S0419",
+ # these constants combine with instrument setting for offset
+ "x-constant": 36958, # nT/mA
+ "y-constant": 36849, # nT/mA
+ "z-constant": 36811, # nT/mA
+ },
+
},
},
{
diff --git a/pyproject.toml b/pyproject.toml
index 9eb586ce..1f9f2922 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ packages = [
{include = "geomagio" }
]
repository="https://code.usgs.gov/ghsc/geomag/geomag-algorithms"
-version = "1.6.3"
+version = "1.6.5"
[tool.poetry.dependencies]
--
GitLab
From c1ab3fcff7af741269641eb8e5e0c331791e6ad3 Mon Sep 17 00:00:00 2001
From: spencer <swilbur@usgs.gov>
Date: Wed, 29 Mar 2023 14:46:55 -0600
Subject: [PATCH 141/142] Reformatted Metadata.py to pass lint test.
---
geomagio/Metadata.py | 2 --
1 file changed, 2 deletions(-)
diff --git a/geomagio/Metadata.py b/geomagio/Metadata.py
index 24c58b1d..99486667 100644
--- a/geomagio/Metadata.py
+++ b/geomagio/Metadata.py
@@ -60,7 +60,6 @@ _INSTRUMENT_METADATA = [
"x-constant": 37027, # nT/mA
"y-constant": 36160, # nT/mA
"z-constant": 37365, # nT/mA
-
},
},
},
@@ -581,7 +580,6 @@ _INSTRUMENT_METADATA = [
"y-constant": 36849, # nT/mA
"z-constant": 36811, # nT/mA
},
-
},
},
{
--
GitLab
From b07d7bb1abb7f519820f8f323e2055d9d02c69fa Mon Sep 17 00:00:00 2001
From: spencer <swilbur@usgs.gov>
Date: Tue, 18 Apr 2023 09:56:55 -0600
Subject: [PATCH 142/142] updated the host server to edgecwb
---
geomagio/edge/EdgeFactory.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/geomagio/edge/EdgeFactory.py b/geomagio/edge/EdgeFactory.py
index d07f3fa5..7b18ac56 100644
--- a/geomagio/edge/EdgeFactory.py
+++ b/geomagio/edge/EdgeFactory.py
@@ -79,7 +79,7 @@ class EdgeFactory(TimeseriesFactory):
def __init__(
self,
- host: str = "cwbpub.cr.usgs.gov",
+ host: str = "edgecwb.usgs.gov",
port: int = 2060,
write_port: int = 7981,
cwbport: int = 0,
--
GitLab