Fix spectra coaddition and cosmic masking #5621
Workflow file for this run
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| # Workflow is based on the Astropy GitHub actions workflow, ci_workflows.yml | |
| name: CI | |
| on: | |
| push: | |
| branches: | |
| - '*' | |
| tags: | |
| - '*' | |
| pull_request: | |
| jobs: | |
| tests: | |
| name: Unit tests | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ['3.9', '3.10'] # fuji+guadalupe, not ready for 3.11 yet? | |
| astropy-version: ['==5.0', '<6'] # fuji+guadalupe, latest | |
| fitsio-version: ['==1.1.6', '<2'] # fuji+guadalupe, latest | |
| numpy-version: ['<1.23'] # to keep asscalar, used by astropy | |
| env: | |
| DESIUTIL_VERSION: 3.4.2 | |
| DESIMODEL_DATA: branches/test-0.18 | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel | |
| python -m pip install pytest | |
| python -m pip install git+https://github.com/desihub/desiutil.git@${DESIUTIL_VERSION}#egg=desiutil | |
| python -m pip install -r requirements.txt | |
| python -m pip install -U 'numpy${{ matrix.numpy-version }}' | |
| python -m pip install -U 'astropy${{ matrix.astropy-version }}' | |
| python -m pip cache remove fitsio | |
| python -m pip install --no-deps --force-reinstall --ignore-installed 'fitsio${{ matrix.fitsio-version }}' | |
| svn export https://desi.lbl.gov/svn/code/desimodel/${DESIMODEL_DATA}/data | |
| - name: Run the test | |
| run: DESIMODEL=$(pwd) pytest | |
| coverage: | |
| name: Test coverage | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ['3.10'] # latest | |
| astropy-version: ['<6'] # latest | |
| fitsio-version: ['<2'] # latest | |
| numpy-version: ['<1.23'] # to keep asscalar, used by astropy | |
| env: | |
| DESIUTIL_VERSION: 3.4.2 | |
| DESIMODEL_DATA: branches/test-0.18 | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel | |
| python -m pip install pytest pytest-cov coveralls | |
| python -m pip install git+https://github.com/desihub/desiutil.git@${DESIUTIL_VERSION}#egg=desiutil | |
| python -m pip install -r requirements.txt | |
| python -m pip install specutils | |
| python -m pip install -U 'numpy${{ matrix.numpy-version }}' | |
| python -m pip install -U 'astropy${{ matrix.astropy-version }}' | |
| python -m pip cache remove fitsio | |
| python -m pip install --no-deps --force-reinstall --ignore-installed 'fitsio${{ matrix.fitsio-version }}' | |
| svn export https://desi.lbl.gov/svn/code/desimodel/${DESIMODEL_DATA}/data | |
| - name: Run the test with coverage | |
| run: DESIMODEL=$(pwd) pytest --cov | |
| - name: Coveralls | |
| env: | |
| COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: coveralls | |
| desilite: | |
| name: Test minimal env | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ['3.10'] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel | |
| python -m pip install astropy scipy numba "numpy<2.0" | |
| python -m pip install pytest | |
| python -m pip cache remove fitsio | |
| python -m pip install --no-deps --force-reinstall --ignore-installed fitsio | |
| python -m pip install git+https://github.com/desihub/desiutil.git | |
| python -m pip install git+https://github.com/desihub/desitarget.git | |
| - name: Run just the lite env test | |
| run: pytest py/desispec/test/test_lite.py | |
| docs: | |
| name: Doc test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ['3.9'] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip setuptools wheel Sphinx | |
| # run: python -m pip install --upgrade pip wheel docutils\<0.18 Sphinx==3.1.2 | |
| - name: Test the documentation | |
| run: sphinx-build -W --keep-going -b html doc doc/_build/html | |
| api: | |
| name: API doc completeness test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ['3.9'] | |
| env: | |
| DESIUTIL_VERSION: 3.3.0 | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel | |
| python -m pip install git+https://github.com/desihub/desiutil.git@${DESIUTIL_VERSION}#egg=desiutil | |
| - name: Generate api.rst | |
| run: desi_api_file --api ./api.rst desispec | |
| - name: Compare generated api.rst to checked-in version | |
| run: diff --ignore-space-change --ignore-blank-lines ./api.rst ./doc/api.rst | |
| style: | |
| name: Style check | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ['3.9'] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip setuptools wheel pycodestyle | |
| - name: Test the style; failures are allowed | |
| # This is equivalent to an allowed falure. | |
| continue-on-error: true | |
| run: pycodestyle --count py/desispec | |
| # SAVE |