Bump bioimageio spec/0.5.3.3 core/0.6.10 #110
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| pre_commit_check: | |
| name: Pre-Commit Check | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| activate-environment: tiktorch-server-env | |
| environment-file: environment.yml | |
| channel-priority: flexible | |
| miniforge-variant: Miniforge3 | |
| - name: Get the latest commit hash and target ref | |
| run: | | |
| echo "COMMIT_HASH=$(git log -1 --format='%H')" >> $GITHUB_ENV | |
| echo "REF=${{ github.event.pull_request.base.ref || github.ref_name }}" >> $GITHUB_ENV | |
| - name: Run Pre-Commit | |
| run: | | |
| echo $REF | |
| echo $COMMIT_HASH | |
| git fetch origin | |
| pre-commit run --from-ref origin/$REF --to-ref $COMMIT_HASH | |
| test-dev: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| activate-environment: tiktorch-server-env | |
| environment-file: environment.yml | |
| channel-priority: flexible | |
| miniforge-variant: Miniforge3 | |
| - name: conda diagnostics | |
| run: | | |
| conda list | |
| conda info | |
| - name: install submodules | |
| run: | | |
| git submodule init | |
| git submodule update | |
| make install_submodules | |
| - name: Run tests | |
| run: | | |
| pytest -v -s --cov=tiktorch --cov-report=xml | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| file: ./coverage.xml | |
| fail_ci_if_error: true | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| conda-noarch-build: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| version: ${{ steps.version.outputs.version }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| auto-activate-base: true | |
| channel-priority: flexible | |
| miniforge-variant: Miniforge3 | |
| - name: install common conda dependencies | |
| run: conda install -n base -c conda-forge conda-build setuptools_scm -y | |
| - name: Cache Conda Packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| pkgs/noarch | |
| pkgs/channeldata.json | |
| key: ${{ github.sha }}-packages | |
| - id: version | |
| run: | | |
| vers=$( python setup.py --version ) | |
| echo "version=${vers}" >> $GITHUB_OUTPUT | |
| - name: Linux Conda Build | |
| run: | | |
| mkdir -p ./pkgs/noarch | |
| conda build -c ilastik-forge -c pytorch -c conda-forge \ | |
| conda-recipe --no-test --output-folder ./pkgs | |
| test-build-conda-packages: | |
| needs: [conda-noarch-build] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [macos-latest, windows-latest, ubuntu-latest] | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| TIKTORCH_PACKAGE_NAME: tiktorch-${{ needs.conda-noarch-build.outputs.version }}-py_0.tar.bz2 | |
| steps: | |
| # Use GNU tar instead of BSD tar on Windows | |
| - name: "Use GNU tar instead of BSD tar" | |
| if: matrix.os == 'windows-latest' | |
| shell: cmd | |
| run: echo C:\Program Files\Git\usr\bin>>"%GITHUB_PATH%" | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| auto-activate-base: true | |
| channel-priority: flexible | |
| miniforge-variant: Miniforge3 | |
| - name: install common conda dependencies | |
| run: conda install -n base -c conda-forge conda-build setuptools_scm -y | |
| - name: Cache Conda Packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| pkgs/noarch | |
| pkgs/channeldata.json | |
| key: ${{ github.sha }}-packages | |
| enableCrossOsArchive: true | |
| - name: Linux Test | |
| if: matrix.os == 'ubuntu-latest' | |
| shell: bash -l {0} | |
| run: | | |
| conda build --test --override-channels \ | |
| -c ./pkgs -c ilastik-forge -c pytorch -c conda-forge \ | |
| ./pkgs/noarch/${TIKTORCH_PACKAGE_NAME} | |
| - name: macOS Test | |
| if: matrix.os == 'macos-latest' | |
| shell: bash -l {0} | |
| run: | | |
| conda build --test --override-channels \ | |
| -c ./pkgs -c ilastik-forge -c pytorch -c conda-forge \ | |
| ./pkgs/noarch/${TIKTORCH_PACKAGE_NAME} | |
| - name: Windows Test | |
| if: matrix.os == 'windows-latest' | |
| # HACK: due to a bug in conda-build need to point to | |
| # libarchive explicitly. | |
| # https://github.com/conda/conda/issues/12563#issuecomment-1494264704 | |
| env: | |
| LIBARCHIVE: C:\Miniconda\Library\bin\archive.dll | |
| shell: cmd /C CALL {0} | |
| run: | | |
| conda build --test --override-channels ^ | |
| -c %CD%\pkgs -c ilastik-forge -c pytorch -c conda-forge ^ | |
| .\pkgs\noarch\%TIKTORCH_PACKAGE_NAME% |