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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]$CONDA/bin"
displayName: Add conda to PATH
- bash: |
wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/common.sh
displayName: Fetch common.sh
- task: Cache@2
inputs:
path: "/usr/share/miniconda/envs/bioconda"
key: '"$(Agent.OS)" | **/common.sh'
cacheHitVar: CACHE_RESTORED
displayName: Restore cache
- script: .azure-pipelines/createEnv.py
condition: ne(variables.CACHE_RESTORED, 'true')
displayName: Install bioconda-utils
- bash: |
source activate bioconda
set -e
source=`echo $(Build.SourceBranch) | sed -e "s#^refs/pull/#pull/#"`
bioconda-utils lint --loglevel debug --full-report --git-range origin/"$SYSTEM_PULLREQUEST_TARGETBRANCH" "$source"
displayName: Lint
- stage: 'test_linux'
jobs:
- job: 'test_linux'
pool:
vmImage: 'ubuntu-latest'
strategy:
maxParallel: 8
timeoutInMinutes: 360
steps:
- bash: echo "##vso[task.prependpath]$CONDA/bin"
displayName: Add conda to PATH
- bash: |
wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/common.sh
displayName: Fetch common.sh
- task: Cache@2
inputs:
path: "/usr/share/miniconda/envs/bioconda"
key: '"$(Agent.OS)" | **/common.sh'
cacheHitVar: CACHE_RESTORED
displayName: Restore cache
- script: .azure-pipelines/createEnv.py
condition: ne(variables.CACHE_RESTORED, 'true')
displayName: Install bioconda-utils
- bash: |
set -e
rm -f "${HOME}/.condarc"
# Activate our Conda installation as "base".
. /usr/share/miniconda/envs/bioconda/etc/profile.d/conda.sh
conda activate base
conda config --system --add channels defaults
conda config --system --add channels bioconda
conda config --system --add channels conda-forge
docker pull quay.io/dpryan79/mulled_container:latest
mkdir -p ${CONDA_PREFIX}/conda-bld
export OSTYPE="linux-gnu"
export CI="true"
bioconda-utils build recipes config.yml \
--docker --mulled-test \
--git-range origin/"$SYSTEM_PULLREQUEST_TARGETBRANCH" HEAD
docker rmi quay.io/dpryan79/mulled_container:latest
displayName: Test
- bash: |
(
mkdir -p /tmp/artifacts/packages
cd /usr/share/miniconda/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 ${1} ."
' --
fi
) || true
displayName: Prepare artifacts
- publish: /tmp/artifacts
artifact: LinuxArtifacts
- stage: 'test_osx'
jobs:
- job: 'test_osx'
pool:
vmImage: 'macOS-latest'
strategy:
maxParallel: 4
timeoutInMinutes: 360
steps:
- bash: echo "##vso[task.prependpath]$CONDA/bin"
displayName: Add conda to PATH
- bash: sudo chown -R $USER $CONDA
displayName: Take ownership of conda installation
- bash: |
wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/common.sh
displayName: Fetch common.sh
- task: Cache@2
inputs:
path: "/usr/local/miniconda/envs/bioconda"
key: '"$(Agent.OS)" | **/common.sh'
cacheHitVar: CACHE_RESTORED
displayName: Restore cache
- script: .azure-pipelines/createEnv.py
condition: ne(variables.CACHE_RESTORED, 'true')
displayName: Install bioconda-utils
- script: |
# download SDK and setup sysroot on macOS
# primarily, run_conda_forge_build_setup does the following:
# - download/setup SDK:
# https://github.com/conda-forge/conda-forge-ci-setup-feedstock/blob/a1026adb523b6562c16329170e7e304a25ed4033/recipe/run_conda_forge_build_setup_osx#L21-L26
# - add activation script to set MACOSX_DEPLOYMENT_TARGET and CONDA_BUILD_SYSROOT:
# https://github.com/conda-forge/conda-forge-ci-setup-feedstock/blob/a1026adb523b6562c16329170e7e304a25ed4033/recipe/run_conda_forge_build_setup_osx#L60-L63
# use "CONFIG=" to avoid writing ./.ci_support/${CONFIG}.yaml which we don't need/use.
. /usr/local/miniconda/envs/bioconda/etc/profile.d/conda.sh
conda activate base
CONFIG= OSX_FORCE_SDK_DOWNLOAD=1 MACOSX_DEPLOYMENT_TARGET=10.13 run_conda_forge_build_setup
conda_forge_ci_setup_activate_sh="${CONDA_PREFIX}/etc/conda/activate.d/conda-forge-ci-setup-activate.sh"
sed -Ei.bak "s/^(export MACOSX_DEPLOYMENT_TARGET)=.*$/\\1='10.9'/" "${conda_forge_ci_setup_activate_sh}"
rm "${conda_forge_ci_setup_activate_sh}".bak
cat "${conda_forge_ci_setup_activate_sh}"
grep -qFx "export MACOSX_DEPLOYMENT_TARGET='10.9'" "${conda_forge_ci_setup_activate_sh}"
conda list
displayName: OSX setup
- bash: |
set -e
. /usr/local/miniconda/envs/bioconda/etc/profile.d/conda.sh
conda activate base
conda config --system --add channels defaults
conda config --system --add channels bioconda
conda config --system --add channels conda-forge
mkdir -p ${CONDA_PREFIX}/conda-bld
export OSTYPE="darwin"
export CI="true"
export HOME=`pwd`
bioconda-utils build recipes config.yml \
--git-range origin/"$SYSTEM_PULLREQUEST_TARGETBRANCH" HEAD
displayName: Test
- bash: |
(
mkdir -p /tmp/artifacts/packages
cd /usr/local/miniconda/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