ci.yaml

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:
  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
          - '1.76' # first to support Python 3.8
          - '1.79' # first to support Python 3.9
          - '1.80' # first to support Python 3.10 and 3.11
          - ''     # latest
        exclude:
          # some older Biopython versions are incompatible with later Python versions
          - { biopython-version: '1.76', python-version: '3.9' }
          - { biopython-version: '1.76', python-version: '3.10' }
          - { biopython-version: '1.76', python-version: '3.11' }
          - { biopython-version: '1.79', python-version: '3.10' }
          - { biopython-version: '1.79', python-version: '3.11' }
    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@v3
    - uses: conda-incubator/setup-miniconda@v2
      with:
        python-version: ${{ matrix.python-version }}
        miniforge-variant: Mambaforge
        channels: conda-forge,bioconda
    - run: |
        mamba install \
          mafft \
          raxml \
          fasttree \
          iqtree \
          vcftools \
          biopython=${{ matrix.biopython-version }}
    - run: pip install .[dev]
    - run: conda info
    - run: conda list
    - run: pytest -c pytest.python3.ini --cov=augur
    - run: cram tests/
      env:
        AUGUR: coverage run -a ${{ github.workspace }}/bin/augur
    - run: bash tests/builds/runner.sh
    - uses: actions/upload-artifact@v3
      with:
        name: coverage
        path: "${{ env.COVERAGE_FILE }}"

  # TODO: Use the central pathogen-repo-ci workflow¹. Currently, this is not
  # possible because it only supports "stock" docker and conda runtimes.
  # ¹ https://github.com/nextstrain/.github/blob/-/.github/workflows/pathogen-repo-ci.yaml
  pathogen-repo-ci:
    runs-on: ubuntu-latest
    continue-on-error: true
    env:
      repodata_use_zst: true
    strategy:
      matrix:
        include:
          - { pathogen: avian-flu, build-args: auspice/flu_avian_h5n1_ha.json }
          - { pathogen: ebola }
          - { pathogen: lassa }
          - { pathogen: monkeypox }
          - { 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: zika }
    name: pathogen-repo-ci (${{ matrix.pathogen }})
    defaults:
      run:
        shell: bash -l {0}
    steps:
      - uses: actions/checkout@v3
        with:
          path: ./augur

      - uses: mamba-org/setup-micromamba@v1
        with:
          create-args: nextstrain-base
          condarc: |
            channels:
              - nextstrain
              - conda-forge
              - bioconda
            channel_priority: strict
          cache-environment: true
          environment-name: augur

      - run: pip install ./augur

      - uses: actions/checkout@v3
        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@v3
        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@v3
      - uses: actions/setup-python@v4
      - run: pip install coverage

      - uses: actions/download-artifact@v3
        with:
          name: coverage

      - run: coverage combine .coverage@*
      - run: coverage xml

      - uses: codecov/codecov-action@v3
        with:
          fail_ci_if_error: false

  build-docs:
    uses: nextstrain/.github/.github/workflows/docs-ci.yaml@master
    with:
      docs-directory: docs/
      pip-install-target: .[dev]