Define two asv configurations for pip and latest-github dependencies … #352
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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: ["3.9", "3.10"] | |
| os: [ubuntu-latest] | |
| # Include a Windows test and old/new Mac runs | |
| include: | |
| - os: macos-13 | |
| python-version: "3.10" | |
| - os: macos-latest | |
| python-version: "3.10" | |
| - os: windows-latest | |
| python-version: "3.10" | |
| 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: ["3.10"] | |
| 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 }} |