parse: Prefer strain over name as sequence ID field
#2840
Workflow file for this run
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| 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: | |
| 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' | |
| 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 | |
| - '' # latest | |
| 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')" >> "$GITHUB_ENV" | |
| # While it may be tempting to install Augur using Conda to avoid hardcoding | |
| # the list of dependencies here, installing just the dependencies not | |
| # available on PyPI allows us to test against dependencies installed by pip, | |
| # which may have slightly different versions compared to Conda counterparts. | |
| - name: Install dependencies from Conda | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| create-args: mafft raxml fasttree iqtree vcftools sqlite tsv-utils biopython=${{ 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@v1 | |
| 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@v1 | |
| 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@v4 | |
| 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 |