azure-pipeline.yml

pr:
  autoCancel: true
trigger:
  branches:
    exclude:
      - master
      - '*'

stages:
- stage: 'lint'
  jobs:
  - job: 'lint'
    pool:
      vmImage: 'ubuntu-latest'
    strategy:
      maxParallel: 8

    steps:
    - bash: echo "##vso[task.prependpath]/opt/mambaforge/bin"
      displayName: Add conda to PATH

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

    - bash: |
        sudo mkdir -p /opt
        sudo chown -R $USER /opt
      displayName: Ensure cache has path to restore to

    - task: Cache@2
      inputs:
        path: "/opt/mambaforge"
        key: '"$(Agent.OS)" | **/install-and-set-up-conda.sh'
        cacheHitVar: CACHE_RESTORED
      displayName: Restore cache

    - script: bash install-and-set-up-conda.sh
      condition: ne(variables.CACHE_RESTORED, 'true')
      displayName: Install bioconda-utils

    # We 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 by --system).
    - script: bash configure-conda.sh
      displayName: Configure conda

    - bash: |
        set -e
        eval "$(conda shell.bash hook)"
        conda activate bioconda
        source=`echo $(Build.SourceBranch) | sed -e "s#^refs/pull/#pull/#"`
        bioconda-utils lint --loglevel debug --full-report --git-range origin/"$SYSTEM_PULLREQUEST_TARGETBRANCH" "$source"
      displayName: Lint

- stage: 'test_linux'
  jobs:
  - job: 'test_linux'
    pool:
      vmImage: 'ubuntu-latest'
    strategy:
      maxParallel: 8
    timeoutInMinutes: 360

    steps:
    - bash: echo "##vso[task.prependpath]/opt/mambaforge/bin"
      displayName: Add conda to PATH

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

    - bash: |
        sudo mkdir -p /opt
        sudo chown -R $USER /opt
      displayName: Ensure cache has path to restore to

    - task: Cache@2
      inputs:
        path: "/opt/mambaforge"
        key: '"$(Agent.OS)" | **/install-and-set-up-conda.sh'
        cacheHitVar: CACHE_RESTORED
      displayName: Restore cache

    - script: bash install-and-set-up-conda.sh
      condition: ne(variables.CACHE_RESTORED, 'true')
      displayName: Install bioconda-utils

    # We 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 by --system).
    - script: bash configure-conda.sh
      displayName: Configure conda

    - bash: |
        set -e
        eval "$(conda shell.bash hook)"
        conda activate bioconda
        docker pull quay.io/dpryan79/mulled_container:latest
        export OSTYPE="linux-gnu"
        export CI="true"
        bioconda-utils build recipes config.yml \
            --docker --mulled-test \
            --git-range origin/"$SYSTEM_PULLREQUEST_TARGETBRANCH" HEAD
        docker rmi quay.io/dpryan79/mulled_container:latest
      displayName: Test

    - bash: |
        (
        mkdir -p /tmp/artifacts/packages
        cd /opt/mambaforge/envs/bioconda/conda-bld || exit 0
        find -name .cache | xargs rm -rf || true
        for n in index.html channeldata.json linux-64 osx-64 noarch; do
          cp -rv $n /tmp/artifacts/packages || true
        done
        if command -V docker >/dev/null; then
          mkdir -p /tmp/artifacts/images
          cd /tmp/artifacts/images
          docker image ls --format='{{.Repository}}:{{.Tag}}' | \
            { grep biocontainers || true ; } | \
            xargs -n1 -P4 bash -c '
              test -n "${1+x}" || exit 0
              echo "Start compressing docker image ${1} ..."
              docker save "${1}" | gzip -c > "${1##*/}.tar.gz"
              echo "Finished compressing docker image ${1} ."
              ' --
        fi
        ) || true
      displayName: Prepare artifacts

    - publish: /tmp/artifacts
      artifact: LinuxArtifacts

- stage: 'test_osx'
  jobs:
  - job: 'test_osx'
    pool:
      vmImage: 'macOS-latest'
    strategy:
      maxParallel: 4
    timeoutInMinutes: 360

    steps:
    - bash: echo "##vso[task.prependpath]/opt/mambaforge/bin"
      displayName: Add conda to PATH

    - bash: |
        wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda}.sh
      displayName: Fetch setup scripts

    - bash: |
        sudo mkdir -p /opt
        sudo chown -R $USER /opt
      displayName: Ensure cache has path to restore to

    - task: Cache@2
      inputs:
        path: "/opt/mambaforge"
        key: '"$(Agent.OS)" | **/install-and-set-up-conda.sh'
        cacheHitVar: CACHE_RESTORED
      displayName: Restore cache

    - script: bash install-and-set-up-conda.sh
      condition: ne(variables.CACHE_RESTORED, 'true')
      displayName: Install bioconda-utils

    # We 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 by --system).
    - script: bash configure-conda.sh
      displayName: Configure conda

    - bash: |
        set -e
        eval "$(conda shell.bash hook)"
        conda activate bioconda
        export OSTYPE="darwin"
        export CI="true"
        bioconda-utils build recipes config.yml \
            --git-range origin/"$SYSTEM_PULLREQUEST_TARGETBRANCH" HEAD
      displayName: Test

    - bash: |
        (
        mkdir -p /tmp/artifacts/packages
        cd /opt/mambaforge/envs/bioconda/conda-bld || exit 0
        find -name .cache | xargs rm -rf || true
        for n in index.html channeldata.json linux-64 osx-64 noarch; do
          cp -rv $n /tmp/artifacts/packages || true
        done
        ) || true
      displayName: Prepare artifacts

    - publish: /tmp/artifacts
      artifact: OSXArtifacts