.gitlab-ci.yml

@@ -69,18 +69,19 @@ variables:
 .check_code:
   artifacts:
     reports:
-      cobertura: cov.xml
+      cobertura: coverage.xml
       junit: junit.xml
   before_script:
     # install dependencies
-    - pipenv --site-packages install --dev --pre --skip-lock
-    - pipenv run which python
+    - pipenv install --dev --pre --system
+    - which python
   image: ${DEVOPS_REGISTRY}usgs/obspy:latest
   script:
     # run checks
-    - pipenv run black --check .
-    - pipenv run pytest --cov=geomagio --cov-report xml:cov.xml --junitxml junit.xml
-    - pipenv run safety check
+    - black --check .
+    - pytest --cov=geomagio --junitxml junit.xml
+    - coverage xml
+    - safety check
   stage: test
   tags:
     - development
@@ -150,10 +151,11 @@ variables:
 # Test Stage
 ## --------------------------------------------------
 
-Check Python 3.6:
-  extends:
-    - .check_code
-  image: ${DEVOPS_REGISTRY}usgs/obspy:3
+# Numpy 1.20 requires python 3.7 or newer
+# Check Python 3.6:
+#   extends:
+#     - .check_code
+#   image: ${DEVOPS_REGISTRY}usgs/obspy:3
 
 Check Python 3.8:
   extends:

Dockerfile

@@ -13,24 +13,22 @@ ENV GIT_BRANCH_NAME=${GIT_BRANCH_NAME} \
     WEBSERVICE=${WEBSERVICE}
 
 
-RUN useradd \
-    -c 'Docker image user' \
-    -m \
-    -r \
-    -s /sbin/nologin \
-    geomag_user \
-    && mkdir -p /data \
-    && chown -R geomag_user:geomag_user /data
+# install packages into system python, when Pipfile changes
+COPY Pipfile Pipfile.lock /geomag-algorithms/
+RUN cd /geomag-algorithms \
+    && pipenv install --dev --pre --system
 
-USER geomag_user
+# install rest of library as editable
+COPY . /geomag-algorithms
+RUN cd /geomag-algorithms \
+    && pip install -e . \
+    # add data directory owned by usgs-user
+    && mkdir -p /data \
+    && chown -R usgs-user:usgs-user /data
 
-# install dependencies via pipenv
+USER usgs-user
 WORKDIR /data
-COPY Pipfile /data/
-RUN pipenv --site-packages install --dev --skip-lock
 
-# copy library (ignores set in .dockerignore)
-COPY . /geomag-algorithms
 
 # entrypoint needs double quotes
 ENTRYPOINT [ "/geomag-algorithms/docker-entrypoint.sh" ]

Pipfile

@@ -6,7 +6,6 @@ verify_ssl = true
 [dev-packages]
 bandit = "*"
 black = "==20.8b1"
-jupyter = "*"
 pre-commit = "*"
 pytest = "*"
 pytest-cov = "*"
@@ -30,6 +29,7 @@ openpyxl = "*"
 pydantic = "*"
 sqlalchemy = "*"
 sqlalchemy-utc = "*"
+typer = "*"
 typing = "*"
 typing-extensions = "*"
 uvicorn = {extras=["standard"], version="*"}

README.md

-Geomag Algorithms
-=================
-[![Build Status](https://travis-ci.org/usgs/geomag-algorithms.svg?branch=master)](https://travis-ci.org/usgs/geomag-algorithms)
+# Geomag Algorithms
 
+[![pipeline status](https://code.usgs.gov/ghsc/geomag/geomag-algorithms/badges/master/pipeline.svg)](https://code.usgs.gov/ghsc/geomag/geomag-algorithms/-/commits/master)
+[![coverage report](https://code.usgs.gov/ghsc/geomag/geomag-algorithms/badges/master/coverage.svg)](https://code.usgs.gov/ghsc/geomag/geomag-algorithms/-/commits/master)
 
 Geomag Algorithms is an open source library for processing
-Geomagnetic timeseries data.  It includes algorithms and input/output factories
+Geomagnetic timeseries data. It includes algorithms and input/output factories
 used by the [USGS Geomagnetism Program](http://geomag.usgs.gov) to
-  translate between data formats,
-  generate derived data and indices in near-realtime,
-  and research and develop new algorithms.
-
+translate between data formats,
+generate derived data and indices in near-realtime,
+and research and develop new algorithms.
 
 - Accesses USGS data services.
 - Built using established open source python libraries
-    [NumPy](http://www.numpy.org/),
-    [SciPy](http://www.scipy.org/), and
-    [ObsPy](http://www.obspy.org/).
+  [NumPy](http://www.numpy.org/),
+  [SciPy](http://www.scipy.org/), and
+  [ObsPy](http://www.obspy.org/).
 - Common geomagnetic formats including
-    IAGA2002,
-    IMFV122,
-    IMFV283 (read only), and
-    PCDCP.
+  IAGA2002,
+  IMFV122,
+  IMFV283 (read only), and
+  PCDCP.
 - Defines command line interface, `geomag.py`.
 - Embeddable Python API, `import geomagio`.
 
-
 ## Examples
+
 > [More Examples in docs/example/](./docs/example/)
 
 The following examples request data from USGS for
-  `BOU` observatory,
-  `H`, `E`, `Z`, and `F` component,
-  `minute` interval,
-  and `variation` type data
-  for the day `2016-07-04`,
+`BOU` observatory,
+`H`, `E`, `Z`, and `F` component,
+`minute` interval,
+and `variation` type data
+for the day `2016-07-04`,
 then write `IAGA2002` formatted output to the console.
 
 ### Command Line Interface Example
+
 ```
 geomag.py \
     --input edge \
@@ -49,9 +49,11 @@ geomag.py \
     --starttime 2016-07-04T00:00:00Z \
     --endtime 2016-07-04T23:59:00Z
 ```
+
 [Command Line Interface documentation](./docs/cli.md)
 
 ### Python API Example
+
 ```
 import sys
 import geomagio
@@ -72,66 +74,55 @@ output_factory.write_file(
     fh = sys.stdout,
     timeseries = timeseries)
 ```
-[Python API documentation](./docs/api.md)
 
+[Python API documentation](./docs/api.md)
 
 ## Install
+
 > [More Install options in docs/install.md](./docs/install.md).
 
 ### Docker
+
 Docker is the simplest install option.
 
 1. Create and start a new container
 
-    named `geomagio`,
-    listening on local port `8000`,
-    from the image `usgs/geomag-algorithms` on docker hub
-
-    ```
-    docker run -d --name geomagio -p 8000:8000 usgs/geomag-algorithms
-    ```
+   named `geomagio`,
+   listening on local port `8000`,
+   from the image `usgs/geomag-algorithms` on docker hub
 
-2. Find the token, (the token improves security)
+   ```
+   docker run -d --name geomagio -p 8000:8000 usgs/geomag-algorithms
+   ```
 
-    ```
-    docker logs geomagio
-    ```
+2. Use the running container
 
-    This outputs a URL to copy/paste into your browser address bar:
-    ```
-    Copy/paste this URL into your browser when you connect for the first time,
-    to login with a token:
-        http://localhost:8000/?token=TOKEN
-    ```
+- Run the `geomag.py` command line interface:
 
-3. Use the running container
+  > To work with files outside the container,
+  > use a volume mount when starting the container
 
-  - Run the `geomag.py` command line interface:
+  ```
+  docker exec -it geomagio geomag.py
+  ```
 
-    ```
-    docker exec -it geomagio geomag.py
-    ```
-
-  - Run python interactively in a web browser (using the token found in step 2):
-
-    ```
-    http://localhost:8000/?token=TOKEN
-    ```
-
-    > In the top right corner, choose "New" then "Python 2"
+- Or, to run an interactive python prompt:
 
+  ```
+  docker exec -it geomagio python
+  ```
 
 ## Algorithms
-[Algorithms described in docs/algorithms/](./docs/algorithms)
 
+[Algorithms described in docs/algorithms/](./docs/algorithms)
 
 ## Developing
-[Developing described in docs/develop.md](./docs/develop.md).
 
+[Developing described in docs/develop.md](./docs/develop.md).
 
 ## License
-[License described in LICENSE.md](./LICENSE.md)
 
+[License described in LICENSE.md](./LICENSE.md)
 
 ## Problems or Questions?
 
@@ -139,7 +130,6 @@ Docker is the simplest install option.
 - [Join the USGS geomag-data mailing list](https://geohazards.usgs.gov/mailman/listinfo/geomag-data)
 - [Email jmfee at usgs.gov](mailto:jmfee@usgs.gov)
 
-
 ## Additional Links
 
 - [USGS Geomagnetism Program Home Page](http://geomag.usgs.gov/)

docker-entrypoint.sh

 #! /bin/bash
 
+
 # Environment variable to determine whether to start webservice
 export WEBSERVICE=${WEBSERVICE:-false}
 
-# add geomagio to notebook path
-export PYTHONPATH=/geomag-algorithms
-
 
 if [ "${WEBSERVICE}" = "false" ]; then
-  # run jupyter notebook server
-  exec pipenv run jupyter \
-      notebook \
-      --ip='*' \
-      --notebook-dir=/data \
-      --no-browser \
-      --port=8000
+  # run arguments as command, or bash prompt if no arguments
+  exec "${@:-/bin/bash}"
 else
   # run gunicorn server for web service
-  exec pipenv run gunicorn \
+  exec gunicorn \
       --access-logfile - \
       --bind 0.0.0.0:8000 \
       --threads 2 \

docs/install_docker.md

@@ -25,13 +25,8 @@ The following command creates and starts a container in the background.
 
 - Run an interactive python prompt
 
-
       docker exec -it geomagio python
 
-- Use the Jupyter Notebook server
-
-  Check the output for a URL like this, that can be opened in a web browser: `http://127.0.0.1:8000/?token=...`
-
 - Use the `geomag.py` command line interface
 
       docker exec -it geomagio geomag.py \

geomagio/Controller.py

@@ -203,8 +203,8 @@ class Controller(object):
             output_observatory=options.output_observatory,
             starttime=options.starttime,
             endtime=options.endtime,
-            input_channels=options.input_channels,
-            output_channels=options.output_channels,
+            input_channels=options.inchannels,
+            output_channels=options.outchannels,
             no_trim=options.no_trim,
             realtime=options.realtime,
             rename_input_channel=options.rename_input_channel,

geomagio/algorithm/SqDistAlgorithm.py

@@ -465,7 +465,7 @@ class SqDistAlgorithm(Algorithm):
         ts = np.linspace(
             np.max((-m, -3 * np.round(sig))),
             np.min((m, 3 * np.round(sig))),
-            np.int(np.round(np.min((2 * m, 6 * np.round(sig))) + 1)),
+            int(np.round(np.min((2 * m, 6 * np.round(sig))) + 1)),
         )
         nts = ts.size
         weights = np.exp(-0.5 * (ts / sig) ** 2)

geomagio/pcdcp/PCDCPParser.py

@@ -4,9 +4,9 @@
 import numpy
 
 # values that represent missing data points in PCDCP
-NINES = numpy.int("9999999")
-NINES_RAW = numpy.int("99999990")
-NINES_DEG = numpy.int("9999")
+NINES = int("9999999")
+NINES_RAW = int("99999990")
+NINES_DEG = int("9999")
 
 
 class PCDCPParser(object):

geomagio/temperature/TEMPWriter.py

@@ -11,7 +11,7 @@ from obspy.core import Stream
 class TEMPWriter(object):
     """TEMP writer."""
 
-    def __init__(self, empty_value=numpy.int("9999")):
+    def __init__(self, empty_value=int("9999")):
         self.empty_value = empty_value
 
     def write(self, out, timeseries, channels):

geomagio/vbf/VBFWriter.py

@@ -11,7 +11,7 @@ from obspy.core import Stream
 class VBFWriter(object):
     """VBF writer."""
 
-    def __init__(self, empty_value=numpy.int("9999999")):
+    def __init__(self, empty_value=int("9999999")):
         self.empty_value = empty_value
 
     def write(self, out, timeseries, channels):