Fix XRayTransform boundary conditions #548
Workflow file for this run
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| # Install scico requirements and run pytest | |
| name: unit tests (ubuntu) | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| workflow_dispatch: | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| group: [1, 2, 3, 4, 5] | |
| name: pytest split ${{ matrix.group }} (ubuntu) | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| # Check-out the repository under $GITHUB_WORKSPACE | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| # Set up conda environment | |
| - name: Set up miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| activate-environment: test-env | |
| python-version: "3.12" | |
| # Configure conda environment cache | |
| - name: Set up conda environment cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: conda-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('requirements.txt') }}-${{ hashFiles('dev_requirements.txt') }}-${{ env.CACHE_NUMBER }} | |
| env: | |
| CACHE_NUMBER: 1 # Increase this value to force cache reset | |
| id: cache | |
| # Display environment details | |
| - name: Display environment details | |
| run: | | |
| conda info | |
| printenv | sort | |
| # Install required system package | |
| - name: Install required system package | |
| run: sudo apt-get install -y libopenblas-dev | |
| # Install dependencies in conda environment | |
| - name: Install dependencies | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: | | |
| conda install -c conda-forge pytest pytest-cov | |
| python -m pip install --upgrade pip | |
| pip install pytest-split | |
| pip install -r requirements.txt | |
| pip install -r dev_requirements.txt | |
| # svmbir install temporarily disabled due to import errors | |
| #conda install -c conda-forge svmbir>=0.3.3 | |
| conda install -c conda-forge astra-toolbox | |
| conda install -c conda-forge pyyaml | |
| pip install --upgrade --force-reinstall scipy>=1.6.0 # Temporary fix for GLIBCXX_3.4.30 not found in conda forge version | |
| pip install bm3d>=4.0.0 | |
| pip install bm4d>=4.2.2 | |
| pip install "ray[tune]>=2.5.0" | |
| pip install hyperopt | |
| # Install package to be tested | |
| - name: Install package to be tested | |
| run: pip install -e . | |
| # Run unit tests | |
| - name: Run main unit tests | |
| run: | | |
| DURATIONS_FILE=$(mktemp) | |
| bzcat data/pytest/durations_ubuntu.bz2 > $DURATIONS_FILE | |
| pytest -x --cov --level=2 --durations-path=$DURATIONS_FILE --splits=5 --group=${{ matrix.group }} --pyargs scico | |
| # Upload coverage data | |
| - name: Upload coverage | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| include-hidden-files: true | |
| name: coverage${{ matrix.group }} | |
| path: ${{ github.workspace }}/.coverage | |
| # Run doc tests | |
| - name: Run doc tests | |
| if: matrix.group == 1 | |
| run: | | |
| pytest --ignore-glob="*test_*.py" --ignore=scico/linop/xray --doctest-modules scico | |
| pytest --doctest-glob="*.rst" docs | |
| coverage: | |
| needs: test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.12 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Install deps | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install coverage | |
| - name: Download all artifacts | |
| # Downloads coverage1, coverage2, etc. | |
| uses: actions/download-artifact@v4 | |
| - name: Run coverage | |
| run: | | |
| coverage combine coverage?/.coverage | |
| coverage report | |
| coverage xml | |
| - uses: codecov/codecov-action@v3 | |
| with: | |
| env_vars: OS,PYTHON | |
| fail_ci_if_error: false | |
| files: coverage.xml | |
| flags: unittests | |
| name: codecov-umbrella | |
| verbose: true |