Keep yellow-fever workflows enabled too. #560
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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: | |
| repo: nextstrain/zika | |
| artifact-name: outputs-test-pathogen-repo-ci | |
| secrets: inherit | |
| 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] | |
| 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 | |
| # This job has to be separate from the matrix above because we want | |
| # to check the aws-batch-job-id output from the workflow but matrix outputs | |
| # currently will overwrite each other. | |
| # See <https://github.com/orgs/community/discussions/26639> | |
| test-pathogen-repo-build-aws-batch: | |
| permissions: | |
| id-token: write | |
| uses: ./.github/workflows/pathogen-repo-build.yaml | |
| with: | |
| repo: nextstrain/zika-tutorial | |
| runtime: aws-batch | |
| run: nextstrain build --env BOGUS_ENVVAR . | |
| artifact-name: build-output-aws-batch | |
| env: | | |
| BOGUS_ENVVAR: BOGUS_ENVVAR | |
| secrets: inherit | |
| test-pathogen-repo-build-aws-batch-id-output: | |
| needs: [test-pathogen-repo-build-aws-batch] | |
| permissions: | |
| id-token: write | |
| uses: ./.github/workflows/pathogen-repo-build.yaml | |
| with: | |
| repo: nextstrain/zika-tutorial | |
| runtime: aws-batch | |
| run: nextstrain build --attach "$AWS_BATCH_JOB_ID" . | |
| artifact-name: build-output-aws-batch-reattached | |
| env: | | |
| AWS_BATCH_JOB_ID: ${{ needs.test-pathogen-repo-build-aws-batch.outputs.aws-batch-job-id }} | |
| secrets: inherit | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - run: make check | |
| - run: ./devel/check-readme | |
| - uses: ./actions/shellcheck |