Merge pull request #359 from bioimage-io/fix-tiling #753
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| name: Test and Deploy bioimageio.core | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ "**" ] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| black: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Check files using the black formatter | |
| uses: rickstaa/action-black@v1 | |
| id: action_black | |
| with: | |
| black_args: "." | |
| - name: Annotate diff changes using reviewdog | |
| if: steps.action_black.outputs.is_formatted == 'true' | |
| uses: reviewdog/action-suggester@v1 | |
| with: | |
| tool_name: blackfmt | |
| test-spec-conda: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.7, 3.8, 3.9] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Conda environment with Micromamba | |
| uses: mamba-org/provision-with-micromamba@main | |
| with: | |
| cache-downloads: true | |
| cache-env: true | |
| environment-file: dev/environment-torch.yaml | |
| extra-specs: | | |
| python=${{ matrix.python-version }} | |
| - name: additional setup | |
| run: pip install --no-deps -e . | |
| - name: pytest-spec-conda | |
| run: pytest --disable-pytest-warnings | |
| test-spec-main: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.7, 3.8, 3.9] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Conda environment with Micromamba | |
| uses: mamba-org/provision-with-micromamba@main | |
| with: | |
| cache-downloads: true | |
| cache-env: true | |
| environment-file: dev/environment-torch.yaml | |
| extra-specs: | | |
| python=${{ matrix.python-version }} | |
| - name: additional setup | |
| run: | | |
| conda remove --yes --force bioimageio.spec || true # allow failure for cached env | |
| pip install --no-deps git+https://github.com/bioimage-io/spec-bioimage-io | |
| pip install --no-deps -e . | |
| - name: pytest-spec-main | |
| run: pytest --disable-pytest-warnings | |
| test-spec-tf: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.7, 3.8, 3.9] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Conda environment with Micromamba | |
| uses: mamba-org/provision-with-micromamba@main | |
| with: | |
| cache-downloads: true | |
| cache-env: true | |
| environment-file: dev/environment-tf.yaml | |
| channel-priority: flexible | |
| extra-specs: | | |
| python=${{ matrix.python-version }} | |
| - name: additional setup | |
| run: | | |
| conda remove --yes --force bioimageio.spec || true # allow failure for cached env | |
| pip install --no-deps git+https://github.com/bioimage-io/spec-bioimage-io | |
| pip install --no-deps -e . | |
| - name: pytest-spec-tf | |
| run: pytest --disable-pytest-warnings | |
| test-spec-tf-legacy: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.7] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Conda environment with Micromamba | |
| uses: mamba-org/provision-with-micromamba@main | |
| with: | |
| cache-downloads: true | |
| cache-env: true | |
| environment-file: dev/environment-tf-legacy.yaml | |
| channel-priority: flexible | |
| extra-specs: | | |
| python=${{ matrix.python-version }} | |
| - name: additional setup | |
| run: | | |
| conda remove --yes --force bioimageio.spec || true # allow failure for cached env | |
| pip install --no-deps git+https://github.com/bioimage-io/spec-bioimage-io | |
| pip install --no-deps -e . | |
| - name: pytest-spec-tf-legacy | |
| run: pytest --disable-pytest-warnings | |
| conda-build: | |
| runs-on: ubuntu-latest | |
| needs: test-spec-conda | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Install Conda environment with Micromamba | |
| uses: mamba-org/provision-with-micromamba@main | |
| with: | |
| cache-downloads: true | |
| cache-env: true | |
| environment-file: false | |
| environment-name: build-env | |
| channels: conda-forge | |
| extra-specs: | | |
| boa | |
| - name: linux conda build | |
| run: | | |
| conda mambabuild -c conda-forge conda-recipe |