[pre-commit.ci] pre-commit autoupdate #2327
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Run tests | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| tags-ignore: # exclude tags created by "ci_addons publish_github_release" | |
| - 'latest' | |
| - 'latest-tmp' | |
| pull_request: | |
| jobs: | |
| run-tests: | |
| name: ${{ matrix.name }} | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.name }} | |
| cancel-in-progress: true | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| # NOTE config below with "upload-wheels: true" specifies that wheels should be uploaded as an artifact | |
| - { name: linux-python3.8-minimum , test-tox-env: pytest-py38-minimum , python-ver: "3.8" , os: ubuntu-latest } | |
| - { name: linux-python3.12 , test-tox-env: pytest-py312-pinned , python-ver: "3.12", os: ubuntu-latest } | |
| - { name: linux-python3.12-upgraded , test-tox-env: pytest-py312-upgraded , python-ver: "3.12", os: ubuntu-latest , upload-wheels: true } | |
| - { name: windows-python3.8-minimum , test-tox-env: pytest-py38-minimum , python-ver: "3.8" , os: windows-latest } | |
| - { name: windows-python3.12-upgraded , test-tox-env: pytest-py312-upgraded , python-ver: "3.12", os: windows-latest } | |
| - { name: macos-python3.8-minimum , test-tox-env: pytest-py38-minimum , python-ver: "3.8" , os: macos-13 } | |
| - { name: macos-python3.12-upgraded , test-tox-env: pytest-py312-upgraded , python-ver: "3.12", os: macos-latest } | |
| steps: | |
| - name: Checkout repo with submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: 'recursive' | |
| fetch-depth: 0 # tags are required to determine the version | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-ver }} | |
| - name: Install build dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install tox | |
| python -m pip list | |
| - name: Run tox tests | |
| run: | | |
| tox -e ${{ matrix.test-tox-env }} | |
| - name: Build wheel and source distribution | |
| run: | | |
| tox -e build | |
| ls -1 dist | |
| - name: Test installation from a wheel | |
| run: | | |
| tox -e wheelinstall --installpkg dist/*-none-any.whl | |
| - name: Test installation from a source distribution | |
| run: | | |
| tox -e wheelinstall --installpkg dist/*.tar.gz | |
| - name: Upload distribution as a workspace artifact | |
| if: ${{ matrix.upload-wheels }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: distributions | |
| path: dist | |
| run-gallery-tests: | |
| name: ${{ matrix.name }} | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.name }} | |
| cancel-in-progress: true | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - { name: linux-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: ubuntu-latest } | |
| - { name: linux-gallery-python3.12-upgraded , test-tox-env: gallery-py312-upgraded , python-ver: "3.12", os: ubuntu-latest } | |
| - { name: windows-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: windows-latest } | |
| - { name: windows-gallery-python3.12-upgraded , test-tox-env: gallery-py312-upgraded , python-ver: "3.12", os: windows-latest } | |
| steps: | |
| - name: Checkout repo with submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: 'recursive' | |
| fetch-depth: 0 # tags are required to determine the version | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-ver }} | |
| - name: Install build dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install tox | |
| python -m pip list | |
| - name: Run tox tests | |
| run: | | |
| tox -e ${{ matrix.test-tox-env }} | |
| run-tests-on-conda: | |
| name: ${{ matrix.name }} | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.name }} | |
| cancel-in-progress: true | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - { name: conda-linux-python3.8-minimum , test-tox-env: pytest-py38-minimum , python-ver: "3.8" , os: ubuntu-latest } | |
| - { name: conda-linux-python3.12-upgraded , test-tox-env: pytest-py312-upgraded , python-ver: "3.12", os: ubuntu-latest } | |
| steps: | |
| - name: Checkout repo with submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: 'recursive' | |
| fetch-depth: 0 # tags are required to determine the version | |
| - name: Set up Conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-ver }} | |
| channels: conda-forge | |
| - name: Install build dependencies | |
| run: | | |
| conda config --set always_yes yes --set changeps1 no | |
| conda info | |
| conda install -c conda-forge "tox>=4" | |
| - name: Conda reporting | |
| run: | | |
| conda info | |
| conda config --show-sources | |
| conda list --show-channel-urls | |
| # NOTE tox installs packages from PyPI not conda-forge... | |
| - name: Run tox tests | |
| run: | | |
| tox -e ${{ matrix.test-tox-env }} | |
| - name: Build wheel and source distribution | |
| run: | | |
| tox -e build | |
| ls -1 dist | |
| - name: Test installation from a wheel | |
| run: | | |
| tox -e wheelinstall --installpkg dist/*-none-any.whl | |
| - name: Test installation from a source distribution | |
| run: | | |
| tox -e wheelinstall --installpkg dist/*.tar.gz | |
| deploy-dev: | |
| name: Deploy pre-release from dev | |
| needs: [run-tests, run-gallery-tests, run-tests-on-conda] | |
| if: ${{ github.event_name == 'push' }} | |
| runs-on: ubuntu-latest | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| steps: | |
| - name: Checkout repo with submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: 'recursive' | |
| fetch-depth: 0 # tags are required to determine the version | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Download wheel and source distributions from artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: distributions | |
| path: dist | |
| - name: Publish wheel and source distributions as a GitHub release | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install scikit-ci-addons | |
| ci_addons publish_github_release hdmf-dev/hdmf \ | |
| --prerelease-packages "dist/*" \ | |
| --prerelease-sha $GITHUB_SHA \ | |
| --prerelease-packages-clear-pattern "*" \ | |
| --prerelease-packages-keep-pattern "*dev<COMMIT_DISTANCE>*" \ | |
| --token ${{ secrets.BOT_GITHUB_TOKEN }} \ | |
| --re-upload | |
| run-ros3-tests: | |
| name: ${{ matrix.name }} | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} # necessary for conda | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.name }} | |
| cancel-in-progress: true | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - { name: linux-python3.12-ros3 , python-ver: "3.12", os: ubuntu-latest } | |
| steps: | |
| - name: Checkout repo with submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: 'recursive' | |
| fetch-depth: 0 # tags are required to determine the version | |
| - name: Set up Conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| activate-environment: ros3 | |
| environment-file: environment-ros3.yml | |
| python-version: ${{ matrix.python-ver }} | |
| channels: conda-forge | |
| auto-activate-base: false | |
| - name: Install run dependencies | |
| run: | | |
| pip install . | |
| pip list | |
| - name: Conda reporting | |
| run: | | |
| conda info | |
| conda config --show-sources | |
| conda list --show-channel-urls | |
| - name: Run ros3 tests # TODO include gallery tests after they are written | |
| run: | | |
| pytest tests/unit/test_io_hdf5_streaming.py |