spacetelescope · mfixstsci · Nov 15, 2023 · Apr 17, 2023 · Apr 17, 2023 · Apr 17, 2023
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,7 @@
+
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "monthly"
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -2,72 +2,53 @@ name: JWQL CI
 
 on: [push, pull_request]
 
-jobs:
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
-  JWQL-CI:
+defaults:
+  run:
+    shell: bash -l {0}
 
-    name: Python - ${{ matrix.python-version }}
+jobs:
+  check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+      - run: pip install bandit
+      - run: bandit ./jwql/ -c .bandit
+
+  test:
+    name: test (Python ${{ matrix.python-version }}, ${{ matrix.os }})
     runs-on: ${{ matrix.os }}
     strategy:
       max-parallel: 5
+      fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [3.8, 3.9]
+        python-version: [3.9, "3.10"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: mamba-org/provision-with-micromamba@v15
         with:
-          activate-environment: jwql-${{ matrix.python-version }}
+          environment-file: ./environment_python_${{ matrix.python-version }}.yml
+          cache-env: true
+          cache-downloads: true
 
-      - name: Bandit Check
-        uses: jpetrucciani/bandit-check@master
-        with:
-          path: "./jwql/"
-          bandit_flags: "-c .bandit"
-        continue-on-error: false
-        if: runner.os == 'Linux'
+      - run: pip install -e .[test]
 
-      - name: Build jwql conda environment and run tests
-        shell: bash -l {0}
-        run: |
+      - run: conda env export
 
-          echo "Setting useful environment variables:"
-          echo " "
-          export PYTHONVERSION=${{ matrix.python-version }}
-          export MAJOR="$(echo $PYTHONVERSION | head -c 1)"
-          export MINOR="$(echo $PYTHONVERSION | tail -c 2)"
-          echo "PYTHONVERSION: $PYTHONVERSION"
-
-          echo " "
-          echo "Installing jwql conda environment"
-          echo " "
-          cd $RUNNER_WORKSPACE/
-          cd jwql/
-          $CONDA/bin/conda env update -f environment_python_${MAJOR}_${MINOR}.yml -n jwql-${{ matrix.python-version }}
-
-          echo " "
-          echo "Installing jwql package"
-          echo " "
-          python setup.py develop
-
-          echo " "
-          echo "Testing package installation"
-          echo " "
-          python -c "import jwql; print('Version: ' + jwql.__version__); print('Path: ' + jwql.__path__[0])"
-
-          # echo " "
-          # echo "Reinstall numpy to fix numpy.core.multiarray error"
-          # echo " "
-          pip install -U numpy
+      - uses: supercharge/[email protected]
+        with:
+          redis-version: 5.0
+        if: runner.os == 'Linux'
 
-          echo " "
-          echo "The conda environment being used:"
-          echo " "
-          $CONDA/bin/conda env export
+      - run: python -c "import jwql; print('Version ' + jwql.__version__); print('Path ' + jwql.__path__[0])"
 
-          echo " "
-          echo "Running pytests"
-          echo " "
-          pytest jwql/tests/
+      - run: pytest jwql/tests/
diff --git a/.gitignore b/.gitignore
@@ -3,6 +3,8 @@
 *.ipynb_checkpoints/
 config.json
 .DS_Store
+.idea
+.coverage*
 build/
 dist/
 jwql.egg-info/

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -4,17 +4,29 @@
 # Required
 version: 2
 # Set the version of Python and other tools you might need
+# Explicit sqlalchemy install using post_install in order to get around the RTD
+# command pip install --upgrade --upgrade-strategy eager
+# This command upgrades all packages listed in rtd_reuirements.txt. This was causing
+# a problem when upgrading to sqlalchemy >=2.0, which has large changes from versions
+# <2.0, and was causing jwql to crash.
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
     python: "3.9"
+  jobs:
+    post_install:
+      - pip install sqlalchemy==1.4.46
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: docs/source/conf.py
+   fail_on_warning: false
 # If using Sphinx, optionally build your docs in additional formats such as PDF
 # formats:
 #    - pdf
 # Optionally declare the Python requirements required to build your docs
 python:
    install:
-   - requirements: rtd_requirements.txt
+      - requirements: rtd_requirements.txt
+      - method: pip
+        path: .
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,3 +1,12 @@
+Unreleased
+==========
+
+Web Application
+~~~~~~~~~~~~~~~
+
+- Dark and Bad Pixel Monitors delete unnecessary outputs to save disk space (#933)
+
+
 1.1.1 (2022-04-05)
 ==================
 

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -4,7 +4,7 @@ include LICENSE
 include CHANGES.rst
 include environment_python_3_7.yml
 include environment_python_3_8.yml
-include setup.py
+include pyproject.toml
 include requirements.txt
 include rtd_requirements.txt
 include jwql/example_config.json

diff --git a/README.md b/README.md
@@ -44,12 +44,12 @@ Getting `jwql` up and running on your own computer requires four steps, detailed
 
 ### Prerequisites
 
-It is highly suggested that contributors have a working installation of `anaconda` or `miniconda` for Python 3.8.  Downloads and installation instructions are  available here:
+It is highly suggested that contributors have a working installation of `anaconda` or `miniconda` for Python 3.9+.  Downloads and installation instructions are  available here:
 
 - [Miniconda](https://conda.io/miniconda.html)
 - [Anaconda](https://www.continuum.io/downloads)
 
-Requirements for contributing to the `jwql` package will be included in the `jwql` `conda` environment, which is included in our installation instructions below. Further package requirements will be provided for `jwql` by a `setup.py` script included in the repository.
+Requirements for contributing to the `jwql` package will be included in the `jwql` `conda` environment, which is included in our installation instructions below. Further package requirements will be provided for `jwql` by a `pyproject.toml` file included in the repository.
 
 ### Clone the `jwql` repo
 
@@ -83,16 +83,16 @@ source activate base/root
 
 **Note:** If you have added a step activating conda to your default terminal/shell (e.g. the `.bashrc`, `.zshrc`, or `.profile` file) then you don't need to do the above step.
 
-Lastly, create the `jwql` environment via one of the `environment.yml` files (currently `environment_python_3_8.yml`, for python 3.8, and `environment_python_3.9.yml`, for python 3.9, are supported by `jwql`):
+Lastly, create the `jwql` environment via one of the `environment.yml` files (currently `environment_python_3.9.yml`, for python 3.9, and `environment_python_3.10.yml`, for python 3.10, are supported by `jwql`):
 
 ```
-conda env create -f environment_python_3_8.yml
+conda env create -f environment_python_3.9.yml
 ```
 
 or
 
 ```
-conda env create -f environment_python_3.9.yml
+conda env create -f environment_python_3.10.yml
 ```
 
 ### Configuration File
@@ -154,10 +154,11 @@ Any questions about the `jwql` project or its software can be directed to `jwql@
 - Mees Fix (Technical Lead, INS) [@mfixstsci](https://github.com/mfixstsci)
 - Misty Cracraft (INS) [@cracraft](https://github.com/cracraft)
 - Mike Engesser (INS) [@mengesser](https://github.com/mengesser)
-- Shannon Osborne (INS) [@shanosborne](https://github.com/shanosborne)
 - Maria Pena-Guerrero [@penaguerrero](https://github.com/penaguerrero)
 - Ben Sunnquist (INS) [@bsunnquist](https://github.com/bsunnquist)
 - Brian York (INS) [@york-stsci](https://github.com/york-stsci)
+- Bradley Sappington (INS) [@bradleysappington](https://github.com/bradleysappington)
+- Melanie Clarke (INS) [@melanieclarke](https://github.com/melanieclarke)
 
 ## Past Development Team Members
 - Matthew Bourque (INS) [@bourque](https://github.com/bourque)
@@ -168,7 +169,7 @@ Any questions about the `jwql` project or its software can be directed to `jwql@
 - Sara Ogaz (DMD) [@SaOgaz](https://github.com/SaOgaz)
 - Catherine Martlin (INS) [@catherine-martlin](https://github.com/catherine-martlin)
 - Johannes Sahlmann (INS) [@Johannes-Sahlmann](https://github.com/johannes-sahlmann)
-
+- Shannon Osborne (INS) [@shanosborne](https://github.com/shanosborne)
 
 ## Acknowledgments:
 - Faith Abney (DMD)

diff --git a/docs/source/common_monitors.rst b/docs/source/common_monitors.rst
@@ -20,6 +20,12 @@ dark_monitor.py
     :members:
     :undoc-members:
 
+edb_telemetry_monitor.py
+------------------------
+.. automodule:: jwql.instrument_monitors.common_monitors.edb_telemetry_monitor
+    :members:
+    :undoc-members:
+
 readnoise_monitor.py
 --------------------
 .. automodule:: jwql.instrument_monitors.common_monitors.readnoise_monitor

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -82,7 +82,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # This is a fix for warnings because of sphinx-autodoc interaction for classes,
 # however it removes method table from the docs.

diff --git a/docs/source/jwql_monitors.rst b/docs/source/jwql_monitors.rst
@@ -25,9 +25,3 @@ monitor_filesystem.py
 .. automodule:: jwql.jwql_monitors.monitor_filesystem
     :members:
     :undoc-members:
-
-monitor_mast.py
----------------
-.. automodule:: jwql.jwql_monitors.monitor_mast
-    :members:
-    :undoc-members:
diff --git a/docs/source/tests.rst b/docs/source/tests.rst
@@ -50,6 +50,12 @@ test_edb.py
     :members:
     :undoc-members:
 
+test_edb_telemetry_monitor.py
+-----------------------------
+.. automodule:: jwql.tests.test_edb_telemetry_monitor
+    :members:
+    :undoc-members:
+
 test_instrument_properties.py
 -----------------------------
 .. automodule:: jwql.tests.test_instrument_properties
@@ -68,9 +74,9 @@ test_logging_functions.py
     :members:
     :undoc-members:
 
-test_monitor_mast.py
+test_mast_utils.py
 --------------------
-.. automodule:: jwql.tests.test_monitor_mast
+.. automodule:: jwql.tests.test_mast_utils
     :members:
     :undoc-members:
 

diff --git a/docs/source/utils.rst b/docs/source/utils.rst
@@ -2,12 +2,6 @@
 utils
 *****
 
-anomaly_query_config.py
------------------------
-.. automodule:: jwql.utils.anomaly_query_config
-    :members:
-    :undoc-members:
-
 calculations.py
 ---------------
 .. automodule:: jwql.utils.calculations
@@ -90,4 +84,4 @@ utils.py
 --------
 .. automodule:: jwql.utils.utils
     :members:
-    :undoc-members:
+    :undoc-members:
diff --git a/docs/source/website.rst b/docs/source/website.rst
@@ -26,12 +26,6 @@ data_containers.py
     :members:
     :undoc-members:
 
-db.py
------
-.. automodule:: jwql.website.apps.jwql.db
-    :members:
-    :undoc-members:
-
 forms.py
 --------
 .. automodule:: jwql.website.apps.jwql.forms