Update pathogen-repo-ci #478
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| workflow_dispatch: | |
| jobs: | |
| test-setup-nextstrain-cli: | |
| name: test-setup-nextstrain-cli (os=${{ matrix.os }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: | |
| - ubuntu-latest | |
| - macos-latest | |
| - windows-latest | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: ./actions/setup-nextstrain-cli | |
| - run: nextstrain version --verbose | |
| test-pathogen-repo-ci: | |
| uses: ./.github/workflows/pathogen-repo-ci.yaml | |
| with: | |
| # XXX TODO: Revert back to nextstrain/zika (for consistency with | |
| # elsewhere) once pathogen-repo-ci has support for running workflows in | |
| # subdirs (i.e. for our new repo layout). | |
| # -trs, 30 Jan 2024 | |
| repo: nextstrain/ebola | |
| artifact-name: outputs-test-pathogen-repo-ci | |
| secrets: inherit | |
| test-pathogen-repo-ci-no-example-data: | |
| uses: ./.github/workflows/pathogen-repo-ci.yaml | |
| with: | |
| repo: nextstrain/zika-tutorial | |
| artifact-name: outputs-test-pathogen-repo-ci-no-example-data | |
| test-docs-ci-conda: | |
| uses: ./.github/workflows/docs-ci.yaml | |
| with: | |
| repo: nextstrain/docs.nextstrain.org | |
| docs-directory: . | |
| environment-file: conda.yml | |
| test-docs-ci-pip: | |
| uses: ./.github/workflows/docs-ci.yaml | |
| with: | |
| repo: nextstrain/augur | |
| docs-directory: docs/ | |
| pip-install-target: .[dev] | |
| test-pathogen-repo-build: | |
| permissions: | |
| id-token: write | |
| strategy: | |
| matrix: | |
| runtime: [docker, conda, aws-batch] | |
| uses: ./.github/workflows/pathogen-repo-build.yaml | |
| with: | |
| repo: nextstrain/zika-tutorial | |
| runtime: ${{ matrix.runtime }} | |
| run: nextstrain build --env BOGUS_ENVVAR . | |
| artifact-name: build-output-${{ matrix.runtime }} | |
| env: | | |
| BOGUS_ENVVAR: BOGUS_ENVVAR | |
| secrets: inherit | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - run: make check | |
| - run: ./devel/check-readme | |
| - uses: ./actions/shellcheck |