setup-nextstrain-cli: Use a standalone installation instead of Pip/PyPI #393
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: 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-pathogen-repo-ci-failure: | |
| uses: ./.github/workflows/pathogen-repo-ci.yaml | |
| with: | |
| repo: nextstrain/zika-tutorial | |
| artifact-name: outputs-test-pathogen-repo-ci-failure | |
| build-args: __BOGUS_BUILD_TARGET__ | |
| continue-on-error: true | |
| 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 |