ci.yaml

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