/
azure-pipeline.yml
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/
azure-pipeline.yml
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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/{common,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 | configure-conda.sh | common.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/{common,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 | configure-conda.sh | common.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/{common,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 | configure-conda.sh | common.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