Merge branch 'python-safety' into 'master'

Python safety

See merge request !169

Dockerfile

 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

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

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()

geomagio/geomag_types.py

-from typing_extensions import Literal
+from typing import Literal
 
 DataInterval = Literal["tenhertz", "second", "minute", "hour", "day", "month"]
 DataType = Literal[

geomagio/residual/Calculation.py

-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:

geomagio/residual/Reading.py

-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)
 
 

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"