azure-pipeline.yml

# Disable Azure checks in favor of GitHub Actions due to memory issues
# pr:
#   autoCancel: true
pr: none
trigger: none
# 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/{common,install-and-set-up-conda,configure-conda}.sh
            displayName: Fetch bioconda install script

          - script: bash install-and-set-up-conda.sh
            displayName: Install bioconda-utils

          # We reconfigure conda to use the right channel setup.
          - 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"
        ##timeoutInMinutes: 90 # how long to run the job before automatically cancelling
        ##cancelTimeoutInMinutes: 40 # how much time to give 'run always even if cancelled tasks' before stopping them
        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/{common,install-and-set-up-conda,configure-conda}.sh
            displayName: Fetch bioconda install script

          - script: bash install-and-set-up-conda.sh
            displayName: Install bioconda-utils

          # We reconfigure conda to use the right channel setup.
          - script: bash configure-conda.sh
            displayName: Configure conda

          - bash: |
              set -e
              eval "$(conda shell.bash hook)"
              conda activate bioconda
              export OSTYPE="linux-gnu"
              export CI="true"
              bioconda-utils build recipes config.yml \
                  --docker --mulled-test \
                  --git-range origin/"$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 $n /tmp/artifacts/packages || true
              done
              if command -V docker >/dev/null; then
                mkdir -p /tmp/artifacts/images
                cd /tmp/artifacts/images
                docker image ls --format='{{.Repository}}:{{.Tag}}' | \
                  { grep biocontainers || true ; } | \
                  xargs -n1 -P4 bash -c '
                    test -n "${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/{common,install-and-set-up-conda,configure-conda}.sh
            displayName: Fetch setup scripts

          - script: bash install-and-set-up-conda.sh
            displayName: Install bioconda-utils

          # We reconfigure conda to use the right channel setup.
          - 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"

              # Get MACOSX vars
              source common.sh

              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