Drop support for xopen v1 #3067
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 | |
| # Routinely check that tests pass with new versions of dependencies. | |
| schedule: | |
| # Every day at 17:42 UTC / 9:42 Seattle (winter) / 10:42 Seattle (summer) | |
| - cron: "42 17 * * *" | |
| pull_request: | |
| workflow_dispatch: | |
| workflow_call: | |
| inputs: | |
| version: | |
| required: true | |
| type: string | |
| jobs: | |
| mypy: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/setup-python@v5 | |
| - uses: actions/checkout@v4 | |
| - run: pip install .[dev] | |
| - run: mypy | |
| pyright: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/setup-python@v5 | |
| - uses: actions/checkout@v4 | |
| - run: npx pyright --stats | |
| pytest-cram: | |
| name: test (python=${{ matrix.python-version }} biopython=${{ matrix.biopython-version || 'latest' }}) | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: | |
| - '3.8' | |
| - '3.9' | |
| - '3.10' | |
| - '3.11' | |
| - '3.12' | |
| biopython-version: | |
| # list of Biopython versions with support for a new Python version | |
| # from https://github.com/biopython/biopython/blob/master/NEWS.rst | |
| - '1.80' # first to support Python 3.10 and 3.11 | |
| - '1.82' # first to support Python 3.12 | |
| - '' # latest | |
| exclude: | |
| # some older Biopython versions are incompatible with later Python versions | |
| - { biopython-version: '1.80', python-version: '3.12' } | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| COVERAGE_FILE: ${{ github.workspace }}/.coverage@python=${{ matrix.python-version }},biopython=${{ matrix.biopython-version || 'latest' }} | |
| COVERAGE_RCFILE: ${{ github.workspace }}/.coveragerc | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set cache key | |
| run: echo "DATE=$(date +'%Y-%m-%d')" >> "$GITHUB_ENV" | |
| # While it may be tempting to install Augur using Conda to avoid hardcoding | |
| # the list of dependencies here, installing just the dependencies not | |
| # available on PyPI allows us to test against dependencies installed by pip, | |
| # which may have slightly different versions compared to Conda counterparts. | |
| - name: Install dependencies from Conda | |
| uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| create-args: mafft raxml fasttree iqtree vcftools sqlite tsv-utils biopython=${{ matrix.biopython-version }} python=${{ matrix.python-version }} | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| channel_priority: strict | |
| cache-environment: true | |
| cache-environment-key: ${{ env.DATE }} | |
| environment-name: augur | |
| # Replace the Conda Augur installation with the local version. | |
| - run: pip install .[dev] | |
| - run: conda info | |
| - run: conda list | |
| - run: pytest --cov=augur | |
| - run: cram tests/ | |
| env: | |
| AUGUR: coverage run -a ${{ github.workspace }}/bin/augur | |
| # Only upload coverage for one job | |
| - if: matrix.python-version == '3.11' && matrix.biopython-version == '' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage | |
| include-hidden-files: true | |
| path: "${{ env.COVERAGE_FILE }}" | |
| # Replicating pathogen-repo-ci workflow because we decided not to support | |
| # local versions of Augur in the centralized workflow | |
| # <https://github.com/nextstrain/.github/issues/66> | |
| # This job is for pathogen repos _do_ follow standard pathogen repo structure | |
| # and new pathogens should be added here. | |
| pathogen-repo-ci: | |
| runs-on: ubuntu-latest | |
| continue-on-error: true | |
| strategy: | |
| matrix: | |
| pathogen: | |
| - dengue | |
| - lassa | |
| - measles | |
| - mpox | |
| - seasonal-cov | |
| - zika | |
| name: pathogen-repo-ci (${{ matrix.pathogen }}) | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| path: ./augur | |
| - name: Set cache key | |
| run: echo "DATE=$(date +'%Y-%m-%d')" >> "$GITHUB_ENV" | |
| # Set up a Conda environment that replicates Nextstrain's Conda runtime. | |
| - name: Install nextstrain-base from Conda | |
| uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| create-args: nextstrain-base | |
| condarc: | | |
| channels: | |
| - nextstrain | |
| - conda-forge | |
| - bioconda | |
| channel_priority: strict | |
| cache-environment: true | |
| cache-environment-key: ${{ env.DATE }} | |
| environment-name: augur | |
| # Replace the Conda Augur installation with the local version. | |
| - run: pip install ./augur | |
| - uses: actions/checkout@v4 | |
| with: | |
| repository: nextstrain/${{ matrix.pathogen }} | |
| path: ./pathogen-repo | |
| - name: Verify nextstrain-pathogen.yaml file | |
| run: > | |
| if [[ ! -f './pathogen-repo/nextstrain-pathogen.yaml' ]]; then | |
| echo "To use this workflow, there must be a 'nextstrain-pathogen.yaml' file present in the repository root"; | |
| exit 1; | |
| fi | |
| - name: Run ingest | |
| if: hashFiles('./pathogen-repo/ingest/Snakefile') && hashFiles('./pathogen-repo/ingest/build-configs/ci/config.yaml') | |
| id: ingest | |
| run: nextstrain build --ambient ./pathogen-repo/ingest --configfile build-configs/ci/config.yaml | |
| - name: Run phylogenetic | |
| if: hashFiles('./pathogen-repo/phylogenetic/Snakefile') && hashFiles('./pathogen-repo/phylogenetic/build-configs/ci/config.yaml') && !cancelled() | |
| id: phylogenetic | |
| run: nextstrain build --ambient ./pathogen-repo/phylogenetic --configfile build-configs/ci/config.yaml | |
| - name: Run nextclade | |
| if: hashFiles('./pathogen-repo/nextclade/Snakefile') && hashFiles('./pathogen-repo/nextclade/build-configs/ci/config.yaml') && !cancelled() | |
| id: nextclade | |
| run: nextstrain build --ambient ./pathogen-repo/nextclade --configfile build-configs/ci/config.yaml | |
| - if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: output-${{ matrix.pathogen }} | |
| if-no-files-found: ignore | |
| path: | | |
| ./pathogen-repo/ingest/.snakemake/log/ | |
| ./pathogen-repo/ingest/auspice/ | |
| ./pathogen-repo/ingest/benchmarks/ | |
| ./pathogen-repo/ingest/logs/ | |
| ./pathogen-repo/ingest/results/ | |
| ./pathogen-repo/phylogenetic/.snakemake/log/ | |
| ./pathogen-repo/phylogenetic/auspice/ | |
| ./pathogen-repo/phylogenetic/benchmarks/ | |
| ./pathogen-repo/phylogenetic/logs/ | |
| ./pathogen-repo/phylogenetic/results/ | |
| ./pathogen-repo/nextclade/.snakemake/log/ | |
| ./pathogen-repo/nextclade/auspice/ | |
| ./pathogen-repo/nextclade/benchmarks/ | |
| ./pathogen-repo/nextclade/logs/ | |
| ./pathogen-repo/nextclade/results/ | |
| - if: always() | |
| name: Verify a workflow ran | |
| env: | |
| # "outcome" is success/failure/cancelled/skipped _before_ | |
| # "continue-on-error" is applied to calculate "conclusion"; we no | |
| # longer use continue-on-error for these steps, but even so, | |
| # conceptually here what we want is outcome not conclusion. | |
| ingest: ${{ steps.ingest.outcome }} | |
| phylogenetic: ${{ steps.phylogenetic.outcome }} | |
| nextclade: ${{ steps.nextclade.outcome }} | |
| run: | | |
| # Show step outcomes in job logs… | |
| echo "ingest $ingest" | tee -a "$GITHUB_STEP_SUMMARY" | |
| echo "phylogenetic $phylogenetic" | tee -a "$GITHUB_STEP_SUMMARY" | |
| echo "nextclade $nextclade"| tee -a "$GITHUB_STEP_SUMMARY" | |
| # Assert status; we're good if we see at least one success and the | |
| # rest are success or skipped. | |
| [[ | |
| ($ingest == success || $phylogenetic == success || $nextclade == success) | |
| && ($ingest == success || $ingest == skipped) | |
| && ($phylogenetic == success || $phylogenetic == skipped) | |
| && ($nextclade == success || $nextclade == skipped) | |
| ]] | |
| # Replicating pathogen-repo-ci-v0 workflow because we decided not to support | |
| # local versions of Augur in the centralized workflow | |
| # <https://github.com/nextstrain/.github/issues/66> | |
| # This particular jobs is for pathogen repos that do not follow the standard | |
| # pathogen repo structure and is not expected to be updated. | |
| # Any new pathogen repos should be added to the job replicating the latest version | |
| # of the pathogen-repo-ci above. | |
| pathogen-repo-ci-v0: | |
| runs-on: ubuntu-latest | |
| continue-on-error: true | |
| env: | |
| repodata_use_zst: true | |
| strategy: | |
| matrix: | |
| include: | |
| - { pathogen: avian-flu, build-args: --configfile config/gisaid.yaml -pf test_target } | |
| - { pathogen: ebola } | |
| - { pathogen: mumps } | |
| - { | |
| pathogen: ncov, | |
| build-args: all_regions -j 2 --profile nextstrain_profiles/nextstrain-ci, | |
| } | |
| - { pathogen: rsv } | |
| - { | |
| pathogen: seasonal-flu, | |
| build-args: --configfile profiles/ci/builds.yaml -p, | |
| } | |
| - { pathogen: tb } | |
| name: pathogen-repo-ci-v0 (${{ matrix.pathogen }}) | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| path: ./augur | |
| - name: Set cache key | |
| run: echo "DATE=$(date +'%Y-%m-%d')" >> "$GITHUB_ENV" | |
| # Set up a Conda environment that replicates Nextstrain's Conda runtime. | |
| - name: Install nextstrain-base from Conda | |
| uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| create-args: nextstrain-base | |
| condarc: | | |
| channels: | |
| - nextstrain | |
| - conda-forge | |
| - bioconda | |
| channel_priority: strict | |
| cache-environment: true | |
| cache-environment-key: ${{ env.DATE }} | |
| environment-name: augur | |
| # Replace the Conda Augur installation with the local version. | |
| - run: pip install ./augur | |
| - uses: actions/checkout@v4 | |
| with: | |
| repository: nextstrain/${{ matrix.pathogen }} | |
| path: ./pathogen-repo | |
| - name: Copy example data | |
| working-directory: ./pathogen-repo | |
| run: | | |
| if [[ -d example_data ]]; then | |
| mkdir -p data/ | |
| cp -r -v example_data/* data/ | |
| else | |
| echo No example data to copy. | |
| fi | |
| - run: nextstrain build --ambient ./pathogen-repo ${{ matrix.build-args }} | |
| - if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: output-${{ matrix.pathogen }} | |
| path: | | |
| ./pathogen-repo/auspice/ | |
| ./pathogen-repo/results/ | |
| ./pathogen-repo/benchmarks/ | |
| ./pathogen-repo/logs/ | |
| ./pathogen-repo/.snakemake/log/ | |
| codecov: | |
| if: github.repository == 'nextstrain/augur' | |
| needs: [pytest-cram] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| - run: pip install coverage | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: coverage | |
| - run: coverage combine .coverage@* | |
| - run: coverage xml | |
| - uses: codecov/codecov-action@v5 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| fail_ci_if_error: false | |
| build-docs: | |
| uses: nextstrain/.github/.github/workflows/docs-ci.yaml@master | |
| with: | |
| docs-directory: docs/ | |
| pip-install-target: .[dev] | |
| check-docs: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/setup-python@v5 | |
| - uses: actions/checkout@v4 | |
| - run: pip install .[dev] | |
| - run: ./devel/regenerate-developer-api-docs | |
| - name: Check for changes | |
| run: | | |
| if [[ -n $(git status --porcelain) ]]; then | |
| git add . | |
| git diff --staged >&2 | |
| echo "There are changes that affect the developer API docs. Please update: <https://github.com/nextstrain/augur/blob/-/docs/contribute/DEV_DOCS.md#regenerating-developer-api-docs>" >&2 | |
| echo "If there are changes to the Augur CLI, please manually adjust files under 'docs/usage/cli/'." >&2 | |
| exit 1 | |
| fi | |
| release: | |
| # Only run when called by the release workflow on the default branch | |
| if: github.workflow_ref == format('{0}/.github/workflows/release.yaml@refs/heads/{1}', github.repository, github.event.repository.default_branch) | |
| needs: [pytest-cram] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| # Fetch all branches and tags. | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10' | |
| - name: Set Nextstrain bot as git user | |
| run: | | |
| git config --global user.email "hello@nextstrain.org" | |
| git config --global user.name "Nextstrain bot" | |
| - run: python3 -m pip install --upgrade build twine | |
| - run: devel/release ${{ github.event.inputs.version }} | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: dist | |
| path: dist/ | |
| - run: git push origin master tag ${{ github.event.inputs.version }} | |
| - name: Publish to PyPI | |
| run: twine upload dist/* | |
| env: | |
| TWINE_USERNAME: __token__ | |
| TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} | |
| TWINE_REPOSITORY_URL: https://upload.pypi.org/legacy/ | |
| - name: Create GitHub Release | |
| run: ./devel/create-github-release "${{github.event.inputs.version }}" dist/* | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| rebuild-docker-image: | |
| needs: [release] | |
| runs-on: ubuntu-latest | |
| steps: | |
| # Delay for 10 minutes to allow the PyPI package to be available. | |
| # See https://github.com/nextstrain/docker-base/issues/128 | |
| - name: Sleep for 10 minutes | |
| run: sleep 600 | |
| shell: bash | |
| - run: gh workflow run ci.yml --repo nextstrain/docker-base | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_WORKFLOW_DISPATCH }} |