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azure-pipelines.yml
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stages:
- stage: 'Building'
jobs:
- job: 'Debug'
strategy:
matrix:
ubuntu2204:
imageName: 'ubuntu-22.04'
artifactName: 'ubuntu2204'
binDir: 'bin'
# macos1200:
# imageName: 'macos-12'
# artifactName: 'macos1200'
# binDir: 'bin'
# macos1100:
# imageName: 'macos-11'
# artifactName: 'macos1100'
# binDir: 'bin'
windows2022:
imageName: 'windows-2022'
artifactName: 'windows2022'
binDir: 'bin/Debug'
windows2019:
imageName: 'windows-2019'
artifactName: 'windows2019'
binDir: 'bin/Debug'
pool:
vmImage: $(imageName)
steps:
- bash: |
export PATH="$HOME/.local/bin:$PATH"
pip3 install --upgrade pip
sudo pip3 install cpplint
sudo apt-get update
sudo apt-get install cppcheck
sudo apt-get install doxygen
displayName: 'Install prerequisites (Ubuntu 22.04)'
condition: eq( variables['artifactName'], 'ubuntu2204')
- bash: brew install libomp
displayName: 'Openmp installation (OSX)'
condition: eq( variables['Agent.OS'], 'Darwin' )
- bash: |
git clone https://github.com/samtools/htslib.git
cd htslib
git checkout tags/1.12
git submodule update --init --recursive
autoreconf -i
./configure
make -j
sudo make install
displayName: 'Install HTSLib (Unix)'
condition: ne( variables['Agent.OS'], 'Windows_NT' )
- bash: ./ci/src_test.sh
displayName: 'Check source code (Ubuntu 22.04)'
condition: eq( variables['artifactName'], 'ubuntu2204')
- bash: ./ci/build.sh doc
displayName: 'Build documentation (Ubuntu 22.04)'
condition: eq( variables['artifactName'], 'ubuntu2204')
- bash: ./ci/build.sh debug
displayName: 'Genie build'
- task: VSBuild@1
inputs:
solution: 'cmake-build-debug\genie.sln'
msbuildArgs: '-m'
displayName: 'Genie build (MSVC)'
condition: eq( variables['Agent.OS'], 'Windows_NT' )
- publish: cmake-build-debug/$(binDir)
artifact: 'genie-debug-$(artifactName)-$(Build.SourceVersion)'
displayName: 'Publish binaries'
- publish: cmake-build-debug/documentation/html
artifact: 'genie-documentation-$(Build.SourceVersion)'
displayName: 'Publish documentation (ubuntu2204)'
condition: eq( variables['artifactName'], 'ubuntu2204')
- job: 'Release'
strategy:
matrix:
ubuntu2204:
imageName: 'ubuntu-22.04'
artifactName: 'ubuntu2204'
architecture: ''
binDir: 'bin'
# macos1200:
# imageName: 'macos-12'
# artifactName: 'macos1200'
# architecture: ''
# binDir: 'bin'
# macos1100:
# imageName: 'macos-11'
# artifactName: 'macos1100'
# architecture: ''
# binDir: 'bin'
windows2022:
imageName: 'windows-2022'
artifactName: 'windows2022'
architecture: '-A x64'
binDir: 'bin/Release'
windows2019:
imageName: 'windows-2019'
artifactName: 'windows2019'
architecture: '-A x64'
binDir: 'bin/Release'
pool:
vmImage: $(imageName)
steps:
- bash: brew install libomp
displayName: 'Openmp installation (OSX)'
condition: eq( variables['Agent.OS'], 'Darwin' )
- bash: |
git clone https://github.com/samtools/htslib.git
cd htslib
git checkout tags/1.12
git submodule update --init --recursive
autoreconf -i
./configure
make -j
sudo make install
displayName: 'Install HTSLib (Unix)'
condition: ne( variables['Agent.OS'], 'Windows_NT' )
- bash: ./ci/build.sh release
displayName: 'Genie build'
- task: VSBuild@1
inputs:
solution: 'cmake-build-release\genie.sln'
msbuildArgs: '-m'
configuration: 'Release'
displayName: 'Genie build (MSVC)'
condition: eq( variables['Agent.OS'], 'Windows_NT' )
- publish: cmake-build-release/$(binDir)
artifact: 'genie-release-$(artifactName)-$(Build.SourceVersion)'
displayName: 'Publish binaries'
- stage: 'Testing'
jobs:
- job: 'Unit'
strategy:
matrix:
ubuntu2204:
imageName: 'ubuntu-22.04'
artifactName: 'ubuntu2204'
fileExt: ''
# macos1200:
# imageName: 'macos-12'
# artifactName: 'macos1200'
# fileExt: ''
# macos1100:
# imageName: 'macos-11'
# artifactName: 'macos1100'
# fileExt: ''
windows2022:
imageName: 'windows-2022'
artifactName: 'windows2022'
fileExt: '.exe'
windows2019:
imageName: 'windows-2019'
artifactName: 'windows2019'
fileExt: '.exe'
pool:
vmImage: $(imageName)
steps:
- bash: brew install libomp
displayName: 'Openmp installation (OSX)'
condition: eq( variables['Agent.OS'], 'Darwin' )
- bash: |
git clone https://github.com/samtools/htslib.git
cd htslib
git checkout tags/1.12
git submodule update --init --recursive
autoreconf -i
./configure
make -j
sudo make install
displayName: 'Install HTSLib (Unix)'
condition: ne( variables['Agent.OS'], 'Windows_NT' )
- download: current
artifact: 'genie-debug-$(artifactName)-$(Build.SourceVersion)'
displayName: 'Download binaries'
- bash: |
mkdir cmake-build-debug
mv ../genie-debug-$(artifactName)-$(Build.SourceVersion) cmake-build-debug/bin
chmod +x cmake-build-debug/bin/*
displayName: 'Copy binaries'
- bash: ci/unit_test.sh
displayName: 'Genie run unit tests'
- task: PublishTestResults@2
displayName: Publish utils test Results
inputs:
testResultsFiles: 'cmake-build-debug/bin/utils_test.xml'
testRunTitle: 'utils-$(artifactName)-$(Build.SourceVersion)'
- task: PublishTestResults@2
displayName: Publish coding test Results
inputs:
testResultsFiles: 'cmake-build-debug/bin/coding_test.xml'
testRunTitle: 'coding-$(artifactName)-$(Build.SourceVersion)'
- task: PublishTestResults@2
displayName: Publish gabac test Results
inputs:
testResultsFiles: 'cmake-build-debug/bin/gabac_test.xml'
testRunTitle: 'gabac-$(artifactName)-$(Build.SourceVersion)'
# - job: 'Memory'
# strategy:
# matrix:
# ubuntu2204:
# imageName: 'ubuntu-22.04'
# artifactName: 'ubuntu2204'
# fileExt: ''
# pool:
# vmImage: $(imageName)
# steps:
# - bash: |
# sudo apt-get install valgrind
# displayName: 'Installation prerequisites (Linux)'
# condition: eq( variables['Agent.OS'], 'Linux' )
# - bash: |
# git clone https://github.com/samtools/htslib.git
# cd htslib
# git checkout tags/1.12
# git submodule update --init --recursive
# autoreconf -i
# ./configure
# make -j
# sudo make install
# displayName: 'Install HTSLib (Unix)'
# condition: ne( variables['Agent.OS'], 'Windows_NT' )
# - download: current
# artifact: 'genie-release-$(artifactName)-$(Build.SourceVersion)'
# displayName: 'Download binaries'
# - bash: |
# mkdir cmake-build-release
# mv ../genie-release-$(artifactName)-$(Build.SourceVersion) cmake-build-release/bin
# chmod +x cmake-build-release/bin/*
# displayName: 'Copy binaries'
# - bash: ci/memory_test.sh
# displayName: 'Genie run memory tests'
- job: 'Conformance_Roundtrip'
strategy:
matrix:
ubuntu2204:
imageName: 'ubuntu-22.04'
artifactName: 'ubuntu2204'
fileExt: ''
# macos1200:
# imageName: 'macos-12'
# artifactName: 'macos1200'
# fileExt: ''
# macos1100:
# imageName: 'macos-11'
# artifactName: 'macos1100'
# fileExt: ''
windows2022:
imageName: 'windows-2022'
artifactName: 'windows2022'
binDir: 'bin/Debug'
windows2019:
imageName: 'windows-2019'
artifactName: 'windows2019'
binDir: 'bin/Debug'
pool:
vmImage: $(imageName)
steps:
- bash: |
brew install libomp
brew install gnu-time
displayName: 'Openmp installation (OSX)'
condition: eq( variables['Agent.OS'], 'Darwin' )
- bash: |
git clone https://github.com/samtools/htslib.git
cd htslib
git checkout tags/1.12
git submodule update --init --recursive
autoreconf -i
./configure
make -j
sudo make install
displayName: 'Install HTSLib (Unix)'
condition: ne( variables['Agent.OS'], 'Windows_NT' )
- bash: |
mkdir ref-decoder
cd ref-decoder
git config --global init.defaultBranch master
git config --global pull.ff only
git init
git config user.email "mitogen-group@gmail.com"
git config user.name "Azure test script"
git pull http://${USERNAME}:${PASSWORD}@mpegx.int-evry.fr/software/MPEG/Genomic_Information_Representation/mpegg-reference-sw.git Fix_LA
displayName: 'Reference decoder checkout'
env:
USERNAME: $(EPFL_SCI-STI-MM_GITLAB_USERNAME)
PASSWORD: $(EPFL_SCI-STI-MM_GITLAB_PASSWORD)
- bash: |
cd ref-decoder
cmake .
displayName: 'Reference decoder cmake'
- bash: |
cd ref-decoder
make --jobs
displayName: 'Reference decoder build (make)'
condition: ne( variables['Agent.OS'], 'Windows_NT' )
- download: current
artifact: 'genie-release-$(artifactName)-$(Build.SourceVersion)'
displayName: 'Download binaries'
- bash: |
mkdir cmake-build-release
mv ../genie-release-$(artifactName)-$(Build.SourceVersion) cmake-build-release/bin
chmod +x cmake-build-release/bin/*
displayName: 'Copy binaries'
- bash: MPEGG_REF_DECODER=$PWD/ref-decoder/bin/decoder/mpegg-decoder-p2 ci/conformance_test.sh
displayName: 'Genie run conformance tests'
- stage: 'Deployment'
jobs:
- job: 'Debian'
strategy:
matrix:
ubuntu2204:
imageName: 'ubuntu-22.04'
artifactName: 'ubuntu2204'
fileExt: ''
pool:
vmImage: $(imageName)
steps:
- checkout: none
- download: current
artifact: 'genie-release-$(artifactName)-$(Build.SourceVersion)'
displayName: 'Download binaries'
- bash: echo "Not yet implemented"
displayName: 'Build debian package'
# - job: 'OSX'
# strategy:
# matrix:
# macos1200:
# imageName: 'macos-12'
# artifactName: 'macos1200'
# fileExt: ''
# macos1100:
# imageName: 'macos-11'
# artifactName: 'macos1100'
# fileExt: ''
# pool:
# vmImage: $(imageName)
# steps:
# - checkout: none
# - download: current
# artifact: 'genie-release-$(artifactName)-$(Build.SourceVersion)'
# displayName: 'Download binaries'
# - bash: echo "Not yet implemented"
# displayName: 'Build OSX dmg'