Replace imio with brainglobe-utils (#128)
#381
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| name: tests | |
| on: | |
| push: | |
| branches: | |
| - "main" | |
| tags: | |
| - "*" | |
| pull_request: | |
| workflow_dispatch: | |
| env: | |
| REGISTRY: ghcr.io | |
| IMAGE_NAME: ${{ github.repository }} | |
| jobs: | |
| linting: | |
| name: Linting | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: neuroinformatics-unit/actions/lint@v2 | |
| manifest: | |
| name: Check manifest | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: neuroinformatics-unit/actions/check_manifest@v2 | |
| test: | |
| needs: [linting, manifest] | |
| name: ${{ matrix.os }} py${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| KERAS_BACKEND: torch | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # Run tests on ubuntu across all supported versions | |
| python-version: ["3.10", "3.11", "3.12"] | |
| os: [ubuntu-latest] | |
| # Include a Windows test and new Mac runs | |
| include: | |
| - os: macos-latest | |
| python-version: "3.12" | |
| - os: windows-latest | |
| python-version: "3.12" | |
| steps: | |
| # Cache atlases | |
| - name: Cache brainglobe directory | |
| uses: actions/cache@v3 | |
| with: | |
| path: | # ensure we don't cache any interrupted atlas download and extraction, if e.g. we cancel the workflow manually | |
| ~/.brainglobe | |
| !~/.brainglobe/atlas.tar.gz | |
| key: atlases-models | |
| fail-on-cache-miss: true | |
| enableCrossOsArchive: true | |
| # install additional Macos dependencies | |
| - name: install HDF5 libraries (needed on M1 Macs only) | |
| if: matrix.os == 'macos-latest' | |
| run: | | |
| brew install hdf5 | |
| # Cache cellfinder workflow data | |
| - name: Cache data for cellfinder workflow tests | |
| uses: actions/cache@v3 | |
| with: | |
| path: "~/.brainglobe-tests" | |
| key: cellfinder-test-data | |
| fail-on-cache-miss: true | |
| enableCrossOsArchive: true | |
| # Run tests | |
| - uses: neuroinformatics-unit/actions/test@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| secret-codecov-token: ${{ secrets.CODECOV_TOKEN }} | |
| benchmarks: | |
| name: Check benchmarks | |
| runs-on: ubuntu-latest | |
| # Set shell in login mode as global setting for the job | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| matrix: | |
| python-version: ["3.12"] | |
| steps: | |
| - name: Checkout brainglobe-workflows repository | |
| uses: actions/checkout@v4 | |
| - name: Create and activate conda environment # we need conda for asv management of environments | |
| uses: conda-incubator/[email protected] # see https://github.com/conda-incubator/setup-miniconda/issues/261 | |
| with: | |
| miniconda-version: py310_24.1.2-0 # we need conda<24.3, see https://github.com/airspeed-velocity/asv/pull/1397 | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: asv-only | |
| - name: Install asv | |
| run: | | |
| pip install --upgrade pip | |
| pip install asv | |
| - name: Run asv check with pip dependencies | |
| working-directory: ${{ github.workspace }}/benchmarks | |
| run: | | |
| # check benchmarks with pip dependencies | |
| asv check -v --config $GITHUB_WORKSPACE/benchmarks/asv.pip.conf.json | |
| - name: Run asv check with latest-github dependencies | |
| working-directory: ${{ github.workspace }}/benchmarks | |
| run: | | |
| # check benchmarks with latest-github dependencies | |
| asv check -v --config $GITHUB_WORKSPACE/benchmarks/asv.latest-github.conf.json | |
| build_sdist_wheels: | |
| name: Build source distribution | |
| needs: [test] | |
| if: github.event_name == 'push' && github.ref_type == 'tag' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: neuroinformatics-unit/actions/build_sdist_wheels@v2 | |
| upload_all: | |
| name: Publish build distributions | |
| needs: [build_sdist_wheels] | |
| runs-on: ubuntu-latest | |
| if: github.event_name == 'push' && github.ref_type == 'tag' | |
| steps: | |
| - uses: neuroinformatics-unit/actions/upload_pypi@v2 | |
| with: | |
| secret-pypi-key: ${{ secrets.TWINE_API_KEY }} |