master.yml

name: Upload
on:
  push:
    branches:
      - master
jobs:
  build-linux:
    name: Linux Upload
    if: github.repository == 'bioconda/bioconda-recipes'
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      max-parallel: 13
    steps:
      - uses: actions/checkout@v3
        with:
          fetch-depth: 0

      - name: set path
        run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH

      - name: Fetch conda install script
        run: |
          wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh

      - name: Restore cache
        id: cache
        uses: actions/cache@v3
        with:
          path: /opt/mambaforge
          key: ${{ runner.os }}--bulk--${{ hashFiles('**/install-and-set-up-conda.sh') }}

      - name: Set up bioconda-utils
        if: steps.cache.outputs.cache-hit != 'true'
        run: bash install-and-set-up-conda.sh

      # This script can be used to reconfigure conda to use the right channel setup.
      # This has to be done after the cache is restored, because
      # the channel setup is not cached as it resides in the home directory.
      # We could use a system-wide (and therefore cached) channel setup,
      # but mamba does not support that at the time of implementation
      # (it ignores settings made with --system).
      - name: Configure conda
        run: bash configure-conda.sh

      - name: Build and upload
        env:
          QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }}
          QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
          ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
          INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }}
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          # Mimic circleci
          OSTYPE: "linux-gnu"
          CI: "true"
        run: |
          set -ex
          eval "$(conda shell.bash hook)"
          conda activate bioconda
          docker pull quay.io/dpryan79/mulled_container:latest
          # bioconda-utils handle-merged-pr recipes config.yml \
          #   --repo bioconda/bioconda-recipes \
          #   --git-range ${BUILD_SOURCEVERSION}~1 ${BUILD_SOURCEVERSION} \
          #   --quay-upload-target biocontainers \
          #   --fallback build
          bioconda-utils build recipes config.yml \
            --git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} \
            --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers
          docker rmi quay.io/dpryan79/mulled_container:latest

  build-osx:
    name: OSX Upload
    if: github.repository == 'bioconda/bioconda-recipes'
    runs-on: macos-13
    strategy:
      fail-fast: false
      max-parallel: 4
    steps:
      - uses: actions/checkout@v3
        with:
          fetch-depth: 0

      - name: set path
        run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH

      - name: Fetch conda install script
        run: |
          wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh

      - name: Restore cache
        id: cache
        uses: actions/cache@v3
        with:
          path: /opt/mambaforge
          key: ${{ runner.os }}--bulk--${{ hashFiles('**/install-and-set-up-conda.sh') }}

      - name: Set up bioconda-utils
        if: steps.cache.outputs.cache-hit != 'true'
        run: bash install-and-set-up-conda.sh

      # This script can be used to reconfigure conda to use the right channel setup.
      # This has to be done after the cache is restored, because
      # the channel setup is not cached as it resides in the home directory.
      # We could use a system-wide (and therefore cached) channel setup,
      # but mamba does not support that at the time of implementation
      # (it ignores settings made with --system).
      - name: Configure conda
        run: bash configure-conda.sh

      - name: Build and Test
        env:
          QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }}
          QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
          ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
          INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }}
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          # Mimic circleci
          OSTYPE: "darwin"
          CI: "true"
        run: |
          set -e
          eval "$(conda shell.bash hook)"
          conda activate bioconda

          # The SDK isn't actually cached, so reinstall it
          run_conda_forge_build_setup

          # bioconda-utils handle-merged-pr recipes config.yml \
          #   --repo bioconda/bioconda-recipes \
          #   --git-range ${BUILD_SOURCEVERSION}~1 ${BUILD_SOURCEVERSION} \
          #   --fallback build
          bioconda-utils build recipes config.yml \
            --anaconda-upload --git-range ${GITHUB_SHA}~1 ${GITHUB_SHA}