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@@ -2,78 +2,53 @@ name: JWQL CI | |
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| on: [push, pull_request] | ||
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| jobs: | ||
| concurrency: | ||
| group: ${{ github.workflow }}-${{ github.ref }} | ||
| cancel-in-progress: true | ||
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| JWQL-CI: | ||
| defaults: | ||
| run: | ||
| shell: bash -l {0} | ||
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| name: Python - ${{ matrix.python-version }} | ||
| jobs: | ||
| check: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: "3.x" | ||
| - run: pip install bandit | ||
| - run: bandit ./jwql/ -c .bandit | ||
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| test: | ||
| name: test (Python ${{ matrix.python-version }}, ${{ matrix.os }}) | ||
| runs-on: ${{ matrix.os }} | ||
| strategy: | ||
| max-parallel: 5 | ||
| fail-fast: false | ||
| matrix: | ||
| os: [ubuntu-latest, macos-latest] | ||
| python-version: [3.8, 3.9] | ||
| python-version: [3.9, "3.10"] | ||
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| steps: | ||
| - uses: actions/checkout@v3 | ||
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| - uses: conda-incubator/setup-miniconda@v2 | ||
| - uses: mamba-org/provision-with-micromamba@v15 | ||
| with: | ||
| activate-environment: jwql-${{ matrix.python-version }} | ||
| environment-file: ./environment_python_${{ matrix.python-version }}.yml | ||
| cache-env: true | ||
| cache-downloads: true | ||
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| - name: Bandit Check | ||
| uses: jpetrucciani/bandit-check@master | ||
| with: | ||
| path: "./jwql/" | ||
| bandit_flags: "-c .bandit" | ||
| continue-on-error: false | ||
| if: runner.os == 'Linux' | ||
| - run: pip install -e .[test] | ||
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| - name: Start Redis | ||
| uses: supercharge/[email protected] | ||
| - run: conda env export | ||
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| - uses: supercharge/[email protected] | ||
| with: | ||
| redis-version: 5.0 | ||
| if: runner.os == 'Linux' | ||
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| - name: Build jwql conda environment and run tests | ||
| shell: bash -l {0} | ||
| run: | | ||
| echo "Setting useful environment variables:" | ||
| echo " " | ||
| export PYTHONVERSION=${{ 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 | ||
| 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])" | ||
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| echo " " | ||
| echo "Running pytests" | ||
| echo " " | ||
| pytest jwql/tests/ | ||
| - run: pytest jwql/tests/ | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,73 @@ | ||
| # This file describes a conda environment that can be to install jwql | ||
| # | ||
| # Run the following command to set up this environment: | ||
| # $ conda env create -f environment_python_3.10.yml | ||
| # | ||
| # The environment name can be overridden with the following command: | ||
| # $ conda env create -n <custom name> -f environment_python_3.10.yml | ||
| # | ||
| # Run the following command to activate the environment: | ||
| # $ source activate jwql-3.10 | ||
| # | ||
| # To deactivate the environment run the following command: | ||
| # $ source deactivate | ||
| # | ||
| # To remove the environment entirely, run the following command: | ||
| # $ conda env remove -n jwql-3.10 | ||
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| name: jwql-3.10 | ||
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| channels: | ||
| - conda-forge | ||
| - defaults | ||
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| dependencies: | ||
| - astropy=5.3.4 | ||
| - beautifulsoup4=4.12.2 | ||
| - bokeh=2.4.3 | ||
| - celery=5.3.4 | ||
| - cryptography=41.0.4 | ||
| - django=4.2.6 | ||
| - inflection=0.5.1 | ||
| - ipython=8.16.1 | ||
| - jinja2=3.1.2 | ||
| - jsonschema=4.19.1 | ||
| - matplotlib=3.8.0 | ||
| - nodejs=20.8.0 | ||
| - numpy=1.25.2 | ||
| - numpydoc=1.5.0 | ||
| - pandas=2.1.1 | ||
| - pip=23.2.1 | ||
| - postgresql=15.4 | ||
| - psycopg2=2.9.7 | ||
| - pytest=7.4.2 | ||
| - pytest-cov=4.1.0 | ||
| - pytest-mock=3.11.1 | ||
| - python=3.10.12 | ||
| - pyyaml=6.0.1 | ||
| - redis=5.0.0 | ||
| - ruff=0.0.292 | ||
| - scipy=1.9.3 | ||
| - setuptools=68.2.2 | ||
| - sphinx=7.2.6 | ||
| - sphinx_rtd_theme=1.3.0 | ||
| - sqlalchemy=2.0.21 | ||
| - twine=4.0.2 | ||
| - wtforms=3.0.1 | ||
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| - pip: | ||
| - astroquery==0.4.6 | ||
| - bandit==1.7.5 | ||
| - jwst==1.12.3 | ||
| - pysiaf==0.20.0 | ||
| - pysqlite3==0.5.2 | ||
| - pyvo==1.4.2 | ||
| - redis==5.0.0 | ||
| - selenium==4.13.0 | ||
| - stdatamodels==1.8.3 | ||
| - stsci_rtd_theme==1.0.0 | ||
| - vine==5.0.0 | ||
| - git+https://github.com/spacetelescope/jwst_reffiles | ||
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| # Current package | ||
| - -e . |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,73 @@ | ||
| # This file describes a conda environment that can be to install jwql | ||
| # | ||
| # Run the following command to set up this environment: | ||
| # $ conda env create -f environment_python_3.9.yml | ||
| # | ||
| # The environment name can be overridden with the following command: | ||
| # $ conda env create -n <custom name> -f environment_python_3.9.yml | ||
| # | ||
| # Run the following command to activate the environment: | ||
| # $ source activate jwql-3.9 | ||
| # | ||
| # To deactivate the environment run the following command: | ||
| # $ source deactivate | ||
| # | ||
| # To remove the environment entirely, run the following command: | ||
| # $ conda env remove -n jwql-3.9 | ||
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| name: jwql-3.9 | ||
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| channels: | ||
| - conda-forge | ||
| - defaults | ||
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| dependencies: | ||
| - astropy=5.3.3 | ||
| - beautifulsoup4=4.12.2 | ||
| - bokeh=2.4.3 | ||
| - celery=5.3.4 | ||
| - cryptography=41.0.4 | ||
| - django=4.2.5 | ||
| - inflection=0.5.1 | ||
| - ipython=8.16.1 | ||
| - jinja2=3.1.2 | ||
| - jsonschema=4.19.1 | ||
| - matplotlib=3.8.0 | ||
| - nodejs=20.8.0 | ||
| - numpy=1.25.2 | ||
| - numpydoc=1.5.0 | ||
| - pandas=2.1.1 | ||
| - pip=23.2.1 | ||
| - postgresql=15.4 | ||
| - psycopg2=2.9.7 | ||
| - pytest=7.4.2 | ||
| - pytest-cov=4.1.0 | ||
| - pytest-mock=3.11.1 | ||
| - python=3.9.17 | ||
| - pyyaml=6.0.1 | ||
| - redis=5.0.0 | ||
| - ruff=0.0.292 | ||
| - scipy=1.9.3 | ||
| - setuptools=68.2.2 | ||
| - sphinx=7.2.6 | ||
| - sphinx_rtd_theme=1.3.0 | ||
| - sqlalchemy=2.0.21 | ||
| - twine=4.0.2 | ||
| - wtforms=3.0.1 | ||
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| - pip: | ||
| - astroquery==0.4.6 | ||
| - bandit==1.7.5 | ||
| - jwst==1.12.3 | ||
| - pysiaf==0.20.0 | ||
| - pysqlite3==0.5.2 | ||
| - pyvo==1.4.2 | ||
| - redis==5.0.0 | ||
| - selenium==4.13.0 | ||
| - stdatamodels==1.8.3 | ||
| - stsci_rtd_theme==1.0.0 | ||
| - vine==5.0.0 | ||
| - git+https://github.com/spacetelescope/jwst_reffiles | ||
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| # Current package | ||
| - -e . |
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