Cython perf simplification (#861) #1492
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| --- | |
| name: Coverage test | |
| defaults: | |
| run: | |
| shell: bash | |
| env: | |
| CFLAGS: -Og | |
| on: | |
| push: | |
| branches: [main] | |
| paths: | |
| - '**.py' | |
| - '**.ipynb' | |
| pull_request: | |
| paths: | |
| - '**.py' | |
| - '**.ipynb' | |
| schedule: | |
| # only once every 4 days | |
| # We can always force run this. | |
| - cron: '37 10 */4 * *' | |
| workflow_dispatch: | |
| inputs: | |
| branch: | |
| description: 'Which branch to test' | |
| required: false | |
| default: 'main' | |
| marks: | |
| description: 'Which marks to test' | |
| required: false | |
| default: '' | |
| verbose: | |
| description: 'Run pytest with -vvv' | |
| required: false | |
| type: boolean | |
| jobs: | |
| # Define a few jobs that can be runned | |
| lint: | |
| uses: ./.github/workflows/linter.yml | |
| runnable: | |
| if: | | |
| github.event_name == 'schedule' | |
| && github.actor != 'dependabot[bot]' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: '${{ github.event.inputs.branch }}' | |
| - run: test -n $(git rev-list --after="1 week" --max-count=1 ${{ github.sha }}) | |
| test: | |
| needs: [lint, runnable] | |
| if: | | |
| always() && | |
| contains(needs.lint.result, 'success') && | |
| (contains(needs.runnable.result, 'success') || contains(needs.runnable.result, 'skipped')) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| python-version: ['3.9', '3.13'] | |
| full-test: [true, false] | |
| minimal-dep: [true, false] | |
| os: [ubuntu-latest, macos-13, macos-latest] | |
| exclude: | |
| # only full test suite on 3.13 | |
| - python-version: '3.13' | |
| full-test: false | |
| # no minimal dependency on 3.13 | |
| - python-version: '3.13' | |
| minimal-dep: true | |
| # minimal dependency on ARM does not make sense (wheels not present) | |
| - os: macos-latest | |
| minimal-dep: true | |
| # only run full test suite for minimal-dependency checks | |
| - full-test: false | |
| minimal-dep: true | |
| steps: | |
| - name: Checkout sisl | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: '${{ github.event.inputs.branch }}' | |
| # The files submodule is required for tests purposes | |
| submodules: ${{ matrix.full-test }} | |
| # the 'files' submodule uses lfs | |
| lfs: ${{ matrix.full-test }} | |
| - name: Ensure fortran | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: gcc | |
| version: 11 | |
| - name: Print-out commit information | |
| id: info | |
| run: | | |
| echo "branch: ${{ github.event.inputs.branch }}" | |
| echo "hash: ${{ github.sha }}" | |
| echo "python-version: ${{ matrix.python-version }}" | |
| # Put stuff in the environment | |
| # | |
| # Test everything including LSF files submodule? | |
| if [[ "${{ matrix.full-test }}" == "true" ]]; then | |
| echo "sisl_extras=test,viz" >> $GITHUB_OUTPUT | |
| else | |
| echo "sisl_extras=test" >> $GITHUB_OUTPUT | |
| fi | |
| # Test minimal versioning? | |
| if [[ "${{ matrix.minimal-dep }}" == "true" ]]; then | |
| echo "sisl_install_packages='numpy==1.21.*' 'scipy==1.6.*' 'xarray==0.21.*'" >> $GITHUB_OUTPUT | |
| else | |
| echo "sisl_install_packages=" >> $GITHUB_OUTPUT | |
| fi | |
| - name: Python installation | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Upgrade pip | |
| run: | | |
| python -m pip install --progress-bar=off --upgrade pip | |
| - name: Python minimal versions | |
| if: ${{ matrix.minimal-dep }} | |
| run: | | |
| python -m pip install --progress-bar=off -v ${{ steps.info.outputs.sisl_install_packages }} | |
| - name: Install sisl + dependencies | |
| env: | |
| SKBUILD_CMAKE_ARGS: -DWITH_COVERAGE:bool=true;-DWITH_LINE_DIRECTIVES:bool=true | |
| CC: gcc | |
| FC: gfortran | |
| run: | | |
| python -m pip install --progress-bar=off -v .[${{ steps.info.outputs.sisl_extras }}] \ | |
| ${{ steps.info.outputs.sisl_install_packages }} | |
| - name: sisl debug info | |
| run: | | |
| python -c 'from sisl._debug_info import * ; print_debug_info()' | |
| - name: sisl import test | |
| run: | | |
| sgeom --help | |
| stoolbox atom-plot --help | |
| - name: sisl tests | |
| env: | |
| SISL_NUM_PROCS: 1 | |
| OMP_NUM_THREADS: 1 | |
| SISL_FILES_TESTS: ${{ github.workspace }}/files/tests | |
| run: | | |
| ls -al | |
| if [[ "${{ github.event.inputs.marks }}" == "" ]]; then | |
| ADD_FLAGS="" | |
| else | |
| ADD_FLAGS="-m ${{ github.event.inputs.marks }}" | |
| fi | |
| if [[ "${{ github.event.inputs.verbose }}" == "true" ]]; then | |
| ADD_FLAGS="$ADD_FLAGS -vvv" | |
| fi | |
| ADD_TOOLS="" | |
| for tool in btd models ; do | |
| ADD_TOOLS="$ADD_TOOLS sisl_toolbox.$tool" | |
| done | |
| for tool in atom minimizer ; do | |
| ADD_TOOLS="$ADD_TOOLS sisl_toolbox.siesta.$tool" | |
| done | |
| for tool in poisson ; do | |
| ADD_TOOLS="$ADD_TOOLS sisl_toolbox.transiesta.$tool" | |
| done | |
| # Try to enable code-coverage in the tests | |
| coverage run -m pytest --pyargs sisl $ADD_FLAGS $ADD_TOOLS | |
| ls -al | |
| - name: Upload code-coverage | |
| if: ${{ github.event.inputs.marks == '' }} | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| verbose: true | |
| token: ${{ secrets.CODECOV_TOKEN }} |