Add xlrd #269
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| paths-ignore: | |
| - README.md | |
| pull_request: | |
| paths-ignore: | |
| - README.md | |
| workflow_dispatch: | |
| defaults: | |
| run: | |
| # This is the same as GitHub Action's `bash` keyword as of 14 May 2024: | |
| # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsshell | |
| # | |
| # Completely spelling it out here so that GitHub can't change it out from under us | |
| # and we don't have to refer to the docs to know the expected behavior. | |
| shell: bash --noprofile --norc -eo pipefail {0} | |
| jobs: | |
| generate-version: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - id: set | |
| run: | | |
| echo "version=$(./devel/generate-version)" | tee -a "$GITHUB_OUTPUT" | |
| echo "label=$(./devel/label-for-ref "$GITHUB_REF")" | tee -a "$GITHUB_OUTPUT" | |
| outputs: | |
| version: ${{ steps.set.outputs.version }} | |
| label: ${{ steps.set.outputs.label }} | |
| build-and-test: | |
| needs: generate-version | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: | |
| - ubuntu-22.04 | |
| - macos-12 | |
| name: build and test (os=${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Install Micromamba | |
| run: | | |
| curl -fsSL --proto 'https=' https://micro.mamba.pm/install.sh | bash | |
| echo ~/.local/bin >> "$GITHUB_PATH" | |
| - uses: actions/checkout@v4 | |
| - run: ./devel/setup | |
| - run: ./devel/build | |
| env: | |
| VERSION: ${{ needs.generate-version.outputs.version }} | |
| - if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: build-outputs-${{ matrix.os }} | |
| path: | | |
| build/ | |
| locked/ | |
| - if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: packages-${{ matrix.os }} | |
| path: build/locked/*/nextstrain-base-*.conda | |
| - name: Test install of nextstrain-base | |
| run: | | |
| micromamba create \ | |
| --yes \ | |
| --prefix ./test-env \ | |
| --strict-channel-priority \ | |
| --override-channels \ | |
| --channel ./build/locked \ | |
| --channel conda-forge \ | |
| --channel bioconda \ | |
| nextstrain-base | |
| - name: Generate summary | |
| run: | | |
| ./devel/download-latest | |
| ./devel/diff-pkgs nextstrain-base-*.conda build/locked/*/nextstrain-base-*.conda \ | |
| > "$GITHUB_STEP_SUMMARY" | |
| release: | |
| needs: | |
| - generate-version | |
| - build-and-test | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Install Micromamba | |
| run: | | |
| curl -fsSL --proto 'https=' https://micro.mamba.pm/install.sh | bash | |
| echo ~/.local/bin >> "$GITHUB_PATH" | |
| - uses: actions/checkout@v4 | |
| - uses: actions/upload-artifact/merge@v4 | |
| with: | |
| name: packages | |
| pattern: packages-* | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: packages | |
| path: build/locked/ | |
| - run: ./devel/setup | |
| - run: ./devel/upload | |
| env: | |
| ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} | |
| LABEL: ${{ needs.generate-version.outputs.label }} | |
| - name: Generate summary | |
| run: | | |
| # Replace ${x} in Markdown with value of environment variable "x". | |
| perl -pe 's/\$\{(.+?)\}/$ENV{$1}/ge' \ | |
| < .github/workflows/ci.release.md \ | |
| > "$GITHUB_STEP_SUMMARY" | |
| env: | |
| VERSION: ${{ needs.generate-version.outputs.version }} | |
| LABEL: ${{ needs.generate-version.outputs.label }} | |
| # Run pathogen repo CI builds with the final packages | |
| # This is running pathogen-repo-ci@v0 for pathogen repos that do not conform | |
| # to the standard pathogen repo structure and is not expected to be updated. | |
| # Any new pathogen repos should be added to the job using the latest version | |
| # of the pathogen-repo-ci below. | |
| test-pathogen-repo-ci-v0: | |
| needs: | |
| - generate-version | |
| - release | |
| strategy: | |
| matrix: | |
| include: | |
| - { pathogen: avian-flu, build-args: --configfile config/gisaid.yaml -pf test_target } | |
| - { pathogen: ebola } | |
| - { pathogen: mumps } | |
| - { pathogen: ncov, build-args: all_regions -j 2 --profile nextstrain_profiles/nextstrain-ci } | |
| - { pathogen: rsv } | |
| - { pathogen: seasonal-flu, build-args: --configfile profiles/ci/builds.yaml -p } | |
| name: test-pathogen-repo-ci@v0 (${{ matrix.pathogen }}) | |
| uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@v0 | |
| with: | |
| repo: nextstrain/${{ matrix.pathogen }} | |
| build-args: ${{ matrix.build-args }} | |
| runtimes: | | |
| - conda | |
| env: | | |
| NEXTSTRAIN_CONDA_CHANNEL: nextstrain/label/${{ needs.generate-version.outputs.label }} | |
| NEXTSTRAIN_CONDA_BASE_PACKAGE: nextstrain-base ==${{ needs.generate-version.outputs.version }} | |
| artifact-name: ${{ matrix.pathogen }}-outputs | |
| continue-on-error: true | |
| # Run pathogen repo CI builds with the final packages | |
| # This is running pathogen-repo-ci@master for pathogen repos that _do_ follow | |
| # standard pathogen repo structure and new pathogens should be added here | |
| # to be supported for future updates such as testing on multiple platforms. | |
| test-pathogen-repo-ci: | |
| needs: | |
| - generate-version | |
| - release | |
| strategy: | |
| # XXX TODO: Test on multiple platforms (os, maybe arch) via the matrix too | |
| matrix: | |
| pathogen: | |
| - dengue | |
| - lassa | |
| - measles | |
| - mpox | |
| - seasonal-cov | |
| - zika | |
| name: test-pathogen-repo-ci (${{ matrix.pathogen }}) | |
| uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master | |
| with: | |
| repo: nextstrain/${{ matrix.pathogen }} | |
| runtimes: | | |
| - conda | |
| env: | | |
| NEXTSTRAIN_CONDA_CHANNEL: nextstrain/label/${{ needs.generate-version.outputs.label }} | |
| NEXTSTRAIN_CONDA_BASE_PACKAGE: nextstrain-base ==${{ needs.generate-version.outputs.version }} | |
| artifact-name: ${{ matrix.pathogen }}-outputs | |
| continue-on-error: true |