Merge pull request #26 from bioio-devs/feature/public-s3-prefix-witho… #124
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| tags: | |
| - "v*" | |
| pull_request: | |
| branches: | |
| - main | |
| schedule: | |
| # <minute [0,59]> <hour [0,23]> <day of the month [1,31]> | |
| # <month of the year [1,12]> <day of the week [0,6]> | |
| # https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07 | |
| # Run every Monday at 10:24:00 PST | |
| # (Since these CRONs are used by a lot of people - | |
| # let's be nice to the servers and schedule it _not_ on the hour) | |
| - cron: "24 18 * * 1" | |
| workflow_dispatch: | |
| jobs: | |
| # Check that all files listed in manifest make it into build | |
| check-manifest: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.x" | |
| - run: pip install check-manifest && check-manifest | |
| # Check tests pass on multiple Python and OS combinations | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [3.9, "3.10", 3.11] | |
| os: [ubuntu-latest, macOS-latest, windows-latest] | |
| env: | |
| BUCKET_NAME : "bioio-dev-test-resources" | |
| AWS_REGION : "us-west-2" | |
| permissions: | |
| id-token: write # This is required for requesting the JWT | |
| contents: read # This is required for actions/checkout | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: arn:aws:iam::978220035532:role/bioio_github | |
| role-session-name: bioio-lif-${{ github.sha }} | |
| aws-region: ${{ env.AWS_REGION }} | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: extractions/setup-just@v2 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Install Dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install .[test] | |
| - uses: actions/cache@v4 | |
| id: cache | |
| with: | |
| path: bioio_ome_zarr/tests/resources | |
| key: ${{ hashFiles('scripts/TEST_RESOURCES_HASH.txt') }} | |
| - name: Download Test Resources | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: | | |
| python scripts/download_test_resources.py --debug | |
| - name: Run Tests | |
| run: just test | |
| - name: Upload Codecov | |
| uses: codecov/codecov-action@v4 | |
| # Check linting, formating, types, etc. | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - uses: extractions/setup-just@v2 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Install Dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install .[lint] | |
| - name: Lint | |
| run: just lint | |
| # Publish to PyPI if test, lint, and manifest checks passed | |
| publish: | |
| if: "success() && startsWith(github.ref, 'refs/tags/')" | |
| needs: [check-manifest, test, lint] | |
| runs-on: ubuntu-latest | |
| environment: release | |
| permissions: | |
| id-token: write # IMPORTANT: this permission is mandatory for trusted publishing | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install Dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install build wheel | |
| - name: Build Package | |
| run: | | |
| python -m build | |
| - name: Publish to PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| # GitHub does not provide a "all status checks must pass" option | |
| # in branch protection settings. Instead, you have to specify exactly | |
| # what status checks want to require to pass before merging. However, | |
| # naming each individual check would be effectively impossible. | |
| # Therefore, by creating this stage in every repo in the org we can | |
| # require "Report Result" to pass before merging and this stage can | |
| # represent the result of the other checks where it only passes if | |
| # all the other checks pass. | |
| results: | |
| if: ${{ always() && github.event_name == 'pull_request' }} | |
| needs: [check-manifest, test, lint] | |
| runs-on: ubuntu-latest | |
| name: Report Result | |
| steps: | |
| - run: exit 1 | |
| # see https://stackoverflow.com/a/67532120/4907315 | |
| if: >- | |
| ${{ | |
| contains(needs.*.result, 'failure') | |
| || contains(needs.*.result, 'cancelled') | |
| }} | |