Merge pull request #549 from bioimage-io/change-ilastik-default-weights #1122
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| name: Test and Deploy bioimageio.spec | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ "**" ] | |
| 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: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.7, 3.8, 3.9] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| - name: Install dependencies | |
| run: | | |
| pip install --upgrade pip | |
| pip install -e .[test] | |
| - name: Test with pytest | |
| run: pytest tests | |
| - name: Check passthrough models | |
| run: python scripts/generate_passthrough_modules.py check | |
| # todo: add mypy checks for python 3.10 when we can add KW_ONLY to dataclasses | |
| # allowing dataclass inheritance w/o the 'missing' default value | |
| # - name: MyPy | |
| # if: ${{ matrix.python-version == '3.10' }} | |
| # run: | | |
| # mkdir -p .mypy-cache | |
| # mypy . --install-types --non-interactive --cache-dir .mypy-cache --explicit-package-bases --check-untyped-defs | |
| conda-build: | |
| runs-on: ubuntu-latest | |
| needs: test | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Install Conda environment with Micromamba | |
| uses: mamba-org/provision-with-micromamba@main | |
| with: | |
| environment-file: false | |
| environment-name: build-env | |
| channels: conda-forge | |
| extra-specs: | | |
| boa | |
| - name: linux conda build | |
| shell: bash -l {0} | |
| run: | | |
| conda mambabuild -c conda-forge conda-recipe | |
| deploy: | |
| runs-on: ubuntu-latest | |
| needs: test | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9 | |
| - name: Install dependencies | |
| run: | | |
| pip install . | |
| - name: Generate Docs | |
| run: python scripts/generate_rdf_docs.py | |
| - name: Generate pre-/postprocessing docs | |
| run: python scripts/generate_processing_docs.py | |
| - name: Generate weight formats docs | |
| run: python scripts/generate_weight_formats_docs.py | |
| - name: Generate JSON Schema | |
| run: python scripts/generate_json_specs.py | |
| - name: Generate weight formats overview | |
| run: python scripts/generate_weight_formats_overview.py generate | |
| - name: Get branch name to deploy to | |
| id: get_branch | |
| shell: bash | |
| run: | | |
| if [[ -n '${{ github.event.pull_request.head.ref }}' ]]; then branch=gh-pages-${{ github.event.pull_request.head.ref }}; else branch=gh-pages; fi | |
| echo "::set-output name=branch::$branch" | |
| - name: Deploy to ${{ steps.get_branch.outputs.branch }} 🚀 | |
| uses: JamesIves/github-pages-deploy-action@v4 | |
| with: | |
| branch: ${{ steps.get_branch.outputs.branch }} | |
| folder: dist |