Support single z-stack tif file for input #280
Workflow file for this run
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: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # Run tests on ubuntu across all supported versions | |
| python-version: ["3.9", "3.10"] | |
| os: [ubuntu-latest] | |
| # Include a Windows test and old/new Mac runs | |
| include: | |
| - os: macos-13 | |
| python-version: "3.10" | |
| - os: macos-latest | |
| python-version: "3.10" | |
| - os: windows-latest | |
| python-version: "3.10" | |
| steps: | |
| # Cache the tensorflow model so we don't have to remake it every time | |
| - name: Cache tensorflow model | |
| uses: actions/cache@v3 | |
| with: | |
| path: "~/.cellfinder" | |
| key: models-${{ hashFiles('~/.cellfinder/**') }} | |
| # Cache atlases | |
| - name: Cache atlases | |
| uses: actions/cache@v3 | |
| with: | |
| path: "~/.brainglobe" | |
| key: atlases | |
| 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 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| - name: Install dependencies | |
| shell: bash | |
| run: | | |
| python -mpip install --upgrade pip | |
| python -mpip install .[asv_version] | |
| - name: Run asv check | |
| shell: bash | |
| run: asv check -v -E existing | |
| 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 }} |