Fix conversion of Zarr string dataset to HDF5 #2227
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| 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 | |
| mamba-version: "*" | |
| - name: Install build dependencies | |
| run: | | |
| conda config --set always_yes yes --set changeps1 no | |
| conda info | |
| mamba 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 | |
| mamba-version: "*" | |
| - 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 |