remove upsert for targetphot stage. Too slow. #289
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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: ['3.10'] # , '3.11'] The 3.11 tests take a long time, so skip for now. | |
| numpy-version: ['<1.23'] # , '<2.0'] Need to find a scipy version that works for 3.11 and pre-2.0 numpy | |
| astropy-version: ['<6.1', '<7.0'] | |
| env: | |
| # Versions correspond to desimodules/24.6 | |
| DESIUTIL_VERSION: '3.4.2' | |
| DESISPEC_VERSION: '0.63.7' | |
| DESITARGET_VERSION: '2.7.0' | |
| DESIMODEL_VERSION: '0.19.1' | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| 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 | |
| python -m pip install git+https://github.com/desihub/desispec.git@${DESISPEC_VERSION}#egg=desispec | |
| python -m pip install git+https://github.com/desihub/desitarget.git@${DESITARGET_VERSION}#egg=desitarget | |
| python -m pip install git+https://github.com/desihub/desimodel.git@${DESIMODEL_VERSION}#egg=desimodel | |
| python -m pip install --upgrade "numpy${{ matrix.numpy-version }}" | |
| python -m pip install --upgrade "astropy${{ matrix.astropy-version }}" 'scipy<1.13' fitsio numba | |
| python -m pip install --editable .[test] | |
| - name: Run the test | |
| run: pytest | |
| coverage: | |
| name: Test coverage | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ['3.10'] | |
| numpy-version: ['<1.23'] | |
| astropy-version: ['<6.1'] | |
| env: | |
| DESIUTIL_VERSION: '3.4.2' | |
| DESISPEC_VERSION: '0.63.7' | |
| DESITARGET_VERSION: '2.7.0' | |
| DESIMODEL_VERSION: '0.19.1' | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| 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 | |
| python -m pip install git+https://github.com/desihub/desispec.git@${DESISPEC_VERSION}#egg=desispec | |
| python -m pip install git+https://github.com/desihub/desitarget.git@${DESITARGET_VERSION}#egg=desitarget | |
| python -m pip install git+https://github.com/desihub/desimodel.git@${DESIMODEL_VERSION}#egg=desimodel | |
| python -m pip install --upgrade "numpy${{ matrix.numpy-version }}" | |
| python -m pip install --upgrade "astropy${{ matrix.astropy-version }}" 'scipy<1.13' fitsio numba | |
| python -m pip install --editable .[coverage] | |
| - name: Run the test with coverage | |
| run: pytest --cov | |
| - name: Coveralls | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }} | |
| run: coveralls | |
| docs: | |
| name: Doc test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ['3.10'] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip setuptools wheel Sphinx sphinx-rtd-theme | |
| - 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: ['3.10'] | |
| env: | |
| DESIUTIL_VERSION: '3.4.2' | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| 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 specprodDB | |
| - 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: ['3.10'] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip setuptools wheel pycodestyle | |
| - name: Test the style | |
| # Uncomment continue-on-error to allow failures. | |
| # continue-on-error: true | |
| run: pycodestyle --count py/specprodDB |