container.yml

name: Container

on:
  workflow_dispatch:
    inputs:
      publish_version:
        description: Existing package version to rebuild, for example 0.2.2
        required: false
        type: string
  push:
    tags:
      - "v*"
  pull_request:
    paths:
      - Dockerfile
      - packaging/container/environment.yml
      - pyproject.toml
      - setup.py
      - src/**
      - .github/workflows/container.yml

permissions:
  contents: write

jobs:
  image:
    name: ${{ matrix.label }}
    runs-on: ${{ matrix.runner }}
    timeout-minutes: 120
    strategy:
      fail-fast: false
      matrix:
        include:
          - label: linux-amd64
            runner: ubuntu-latest
            platform: linux/amd64
            arch: amd64
          - label: linux-arm64
            runner: ubuntu-24.04-arm
            platform: linux/arm64
            arch: arm64
    steps:
      - uses: actions/checkout@v7
      - uses: docker/setup-buildx-action@v4
      - name: Build native smoke image
        uses: docker/build-push-action@v7
        with:
          context: .
          platforms: ${{ matrix.platform }}
          load: true
          tags: fp-tools:smoke
          cache-from: type=gha,scope=container-${{ matrix.arch }}
          cache-to: type=gha,mode=max,scope=container-${{ matrix.arch }}
      - name: Test packaged commands, dependencies, regression, and GUI health
        shell: bash
        run: |
          docker run --rm fp-tools:smoke python -c "import fp_tools.utils.sequences, fp_tools.utils.ngs, fp_tools.utils.signals"
          docker run --rm fp-tools:smoke atac-correct --help >/dev/null
          docker run --rm fp-tools:smoke prepare-atac --doctor --profile modern | tee /tmp/fp-tools-doctor.txt
          grep -q $'bedtools\tyes\t' /tmp/fp-tools-doctor.txt
          docker run --rm fp-tools:smoke python -c 'from fp_tools.utils.regions import OneRegion, RegionList; x=RegionList([OneRegion(["chr1",0,10,"outer"]),OneRegion(["chr1",2,8,"inner"])]); x.merge(); assert [(r.chrom,r.start,r.end) for r in x] == [("chr1",0,10)]'
          docker run --rm -d --name fp-tools-gui-smoke -p 8891:8891 fp-tools:smoke
          trap 'docker rm -f fp-tools-gui-smoke >/dev/null 2>&1 || true' EXIT
          for attempt in {1..60}; do
            if curl --fail --silent http://127.0.0.1:8891/_stcore/health >/dev/null; then
              exit 0
            fi
            sleep 2
          done
          docker logs fp-tools-gui-smoke
          exit 1
      - name: Pack architecture image
        if: startsWith(github.ref, 'refs/tags/') || inputs.publish_version != ''
        shell: bash
        env:
          ARCH: ${{ matrix.arch }}
          PUBLISH_VERSION: ${{ inputs.publish_version }}
        run: |
          release_tag="${GITHUB_REF_NAME}"
          if [[ "${GITHUB_REF}" != refs/tags/* ]]; then release_tag="v${PUBLISH_VERSION#v}"; fi
          version="${release_tag#v}"
          mkdir -p release
          docker tag fp-tools:smoke "fp-tools:${release_tag}"
          docker tag fp-tools:smoke fp-tools:latest
          docker save "fp-tools:${release_tag}" fp-tools:latest | gzip -1 \
            > "release/fp-tools-container-${version}-linux-${ARCH}.tar.gz"
      - uses: actions/upload-artifact@v7
        if: startsWith(github.ref, 'refs/tags/') || inputs.publish_version != ''
        with:
          name: fp-tools-container-${{ matrix.arch }}
          path: release/fp-tools-container-*.tar.gz
          if-no-files-found: error

  release:
    name: container release archives
    if: startsWith(github.ref, 'refs/tags/') || inputs.publish_version != ''
    needs: image
    runs-on: ubuntu-latest
    steps:
      - uses: actions/download-artifact@v8
        with:
          pattern: fp-tools-container-*
          merge-multiple: true
          path: release
      - name: Upload container archives to the GitHub release
        shell: bash
        env:
          GH_TOKEN: ${{ github.token }}
          PUBLISH_VERSION: ${{ inputs.publish_version }}
        run: |
          release_tag="${GITHUB_REF_NAME}"
          if [[ "${GITHUB_REF}" != refs/tags/* ]]; then release_tag="v${PUBLISH_VERSION#v}"; fi
          (cd release && sha256sum fp-tools-container-*.tar.gz > CONTAINER_SHA256SUMS.txt)
          if ! gh release view "${release_tag}" --repo "${GITHUB_REPOSITORY}" >/dev/null 2>&1; then
            release_flags=()
            if [[ "${release_tag}" == *rc* ]]; then release_flags+=(--prerelease); fi
            gh release create "${release_tag}" \
              --repo "${GITHUB_REPOSITORY}" \
              --title "fp-tools ${release_tag}" \
              --generate-notes \
              "${release_flags[@]}"
          fi
          gh release upload "${release_tag}" release/* --repo "${GITHUB_REPOSITORY}" --clobber