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azure-pipelines.yml
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azure-pipelines.yml
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#=============================================================================
# Azure Pipeline NMODL settings
#=============================================================================
variables:
# defined in UI
#- ReleaseWheelBuild: False
#- UploadWheel: False
buildWheel: ${{ or(in(variables['Build.Reason'], 'Schedule'), in(variables['Build.Reason'], 'Manual')) }}
MACOSX_DEPLOYMENT_TARGET: 10.15
# Nightly build master for pypi upload
schedules:
- cron: "5 0 * * *"
branches:
include:
- master
always: True
# Auto cancel old PR builds
pr: none
# Trigger build for certain branches only
trigger:
- master
- llvm
- releases/*
stages:
- stage: fetch_config
jobs:
- job: github
pool:
vmImage: ubuntu-latest
steps:
- checkout: none
- script: |
if [[ -z ${SYSTEM_PULLREQUEST_PULLREQUESTNUMBER+x} ]]; then
echo "Not running on a PR."
exit 0
fi
cat > parse_description.py << END_SCRIPT
import os
import re
import requests
pr_info = requests.get("https://api.github.com/repos/{}/pulls/{}".format(
os.environ['BUILD_REPOSITORY_NAME'],
os.environ['SYSTEM_PULLREQUEST_PULLREQUESTNUMBER']),
headers={'Accept': 'application/vnd.github.v3+json'})
pr_body = pr_info.json()["body"]
# match something like NEURON_BRANCH=foo/bar
pat = re.compile('^([A-Z0-9_]+)_([A-Z]+)=([A-Z0-9\-\_\/\+]+)$', re.IGNORECASE)
def parse_term(m):
ref_type = m.group(2).lower()
if ref_type not in {'branch', 'tag', 'ref'}: return
variable = m.group(1).upper() + '_' + ref_type.upper()
value = m.group(3)
print('{}={}'.format(variable, value))
print('#{}[task.setvariable variable={};isOutput=true]{}'.format('#vso', variable, value))
if pr_body is not None:
for pr_body_line in pr_body.splitlines():
if not pr_body_line.startswith('CI_BRANCHES:'): continue
for config_term in pr_body_line[12:].split(','):
pat.sub(parse_term, config_term)
END_SCRIPT
echo '----'
cat parse_description.py
echo '----'
python parse_description.py
name: prdesc
- stage: build
dependsOn: fetch_config
variables:
NEURON_BRANCH: $[stageDependencies.fetch_config.github.outputs['prdesc.NEURON_BRANCH']]
jobs:
- job: 'ubuntu2004'
pool:
vmImage: 'ubuntu-20.04'
displayName: 'Ubuntu (20.04), GCC 9.4'
steps:
- checkout: self
submodules: False
- script: |
sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
sudo apt-add-repository -y ppa:deadsnakes/ppa
sudo apt-get update
sudo apt-get install -y g++-9 flex bison libfl-dev cython libx11-dev libxcomposite-dev libncurses-dev mpich
sudo apt-get install -y python3.8 python3.8-dev python3.8-venv ninja-build
sudo apt-get remove -y python3-importlib-metadata
python3.8 -m pip install --upgrade pip setuptools
python3.8 -m pip install --user -r requirements.txt
# we manually get version 3.15.0 to make sure that changes in the cmake
# files do not require unsupported versions of cmake in our package.
wget --quiet --output-document=- "https://github.com/Kitware/CMake/releases/download/$CMAKE_VER/$CMAKE_PKG.tar.gz" | tar xzpf -
env:
CMAKE_VER: 'v3.15.0'
CMAKE_PKG: 'cmake-3.15.0-Linux-x86_64'
displayName: 'Install Dependencies'
- script: |
export PATH=$(pwd)/$CMAKE_PKG/bin:/home/vsts/.local/bin:$PATH
export CXX='g++-9'
mkdir -p $(Build.Repository.LocalPath)/build
cd $(Build.Repository.LocalPath)/build
cmake --version
cmake .. -DPYTHON_EXECUTABLE=$(which python3.8) -DCMAKE_INSTALL_PREFIX=$HOME/nmodl -DCMAKE_BUILD_TYPE=Release
make -j 2
if [ $? -ne 0 ]
then
make VERBOSE=1
exit 1
fi
make install #this is needed for the integration tests
env CTEST_OUTPUT_ON_FAILURE=1 make test
env:
CMAKE_PKG: 'cmake-3.15.0-Linux-x86_64'
displayName: 'Build and Run Unit Tests'
- script: |
export PATH=$(pwd)/$CMAKE_PKG/bin:/home/vsts/.local/bin:$PATH
export CC='gcc-9'
export CXX='g++-9'
git clone${NEURON_BRANCH:+ --branch }${NEURON_BRANCH} --single-branch https://github.com/neuronsimulator/nrn.git
mkdir nrn/build
cd nrn/build
cmake --version
cmake .. -DNRN_ENABLE_CORENEURON=ON -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_RX3D=OFF -DNRN_ENABLE_MPI=ON -DNRN_ENABLE_TESTS=ON -DCORENRN_ENABLE_NMODL=ON -DCORENRN_NMODL_DIR=$HOME/nmodl -DPYTHON_EXECUTABLE=$(which python3.8) -DCORENRN_NMODL_FLAGS="sympy --analytic"
make -j 2
if [ $? -ne 0 ]
then
make VERBOSE=1
exit 1
fi
ctest --output-on-failure
if [ $? -ne 0 ]
then
exit 1
fi
./bin/nrnivmodl-core $(Build.Repository.LocalPath)/test/integration/mod
env:
CMAKE_PKG: 'cmake-3.15.0-Linux-x86_64'
SHELL: 'bash'
displayName: 'Build Neuron and Run Integration Tests'
- job: 'osx11'
pool:
vmImage: 'macOS-12'
displayName: 'MacOS (12), AppleClang 14.0'
steps:
- checkout: self
submodules: True
- script: |
brew install flex bison cmake python@3
python3 -m pip install --upgrade pip "setuptools<=70.3.0"
python3 -m pip install --user -r requirements.txt
displayName: 'Install Dependencies'
- script: |
export PATH=/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH;
mkdir -p $(Build.Repository.LocalPath)/build
cd $(Build.Repository.LocalPath)/build
cmake .. -DPYTHON_EXECUTABLE=$(which python3) -DCMAKE_INSTALL_PREFIX=$HOME/nmodl -DCMAKE_BUILD_TYPE=RelWithDebInfo -DNMODL_ENABLE_PYTHON_BINDINGS=OFF
make -j 2
if [ $? -ne 0 ]
then
make VERBOSE=1
exit 1
fi
ctest --output-on-failure
if [ $? -ne 0 ]
then
exit 1
fi
make install
displayName: 'Build and Run Tests'
- script: |
export PATH=$(pwd)/$CMAKE_PKG/bin:/home/vsts/.local/bin:$PATH
export PATH=/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH;
export CC='gcc'
export CXX='g++'
git clone${NEURON_BRANCH:+ --branch }${NEURON_BRANCH} --single-branch https://github.com/neuronsimulator/nrn.git
mkdir nrn/build
cd nrn/build
cmake --version
cmake .. -DNRN_ENABLE_CORENEURON=ON -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_RX3D=OFF -DNRN_ENABLE_MPI=OFF -DNRN_ENABLE_TESTS=ON -DCORENRN_ENABLE_MPI=OFF -DCORENRN_ENABLE_NMODL=ON -DCORENRN_NMODL_DIR=$HOME/nmodl -Dnmodl_PYTHONPATH=$HOME/nmodl/lib -DPYTHON_EXECUTABLE=$(which python3) -DCORENRN_NMODL_FLAGS="sympy --analytic"
make -j 2
if [ $? -ne 0 ]
then
make VERBOSE=1
exit 1
fi
ctest --output-on-failure
if [ $? -ne 0 ]
then
exit 1
fi
./bin/nrnivmodl-core $(Build.Repository.LocalPath)/test/integration/mod
env:
SHELL: 'bash'
displayName: 'Build Neuron and Run Integration Tests'
- job: 'manylinux_wheels'
timeoutInMinutes: 90
pool:
vmImage: 'ubuntu-20.04'
steps:
- task: UsePythonVersion@0
- checkout: self
submodules: True
condition: succeeded()
- script: |
if [[ "$(RELEASEWHEELBUILD)" != "True" ]]; then
echo "##vso[task.setvariable variable=TAG;]-nightly"
else
echo "##vso[task.setvariable variable=TAG;]"
fi
echo "Wheel tag: $TAG"
displayName: "Set wheel tag"
- script: |
echo "##vso[task.setvariable variable=CIBW_BUILD;]cp38* cp312*"
echo "Build identifiers: $CIBW_BUILD"
condition: and(succeeded(), eq(variables['Build.Reason'], 'PullRequest'))
displayName: "Set build identifiers"
- script: |
python3 -m pip install --upgrade pip
python3 -m pip install cibuildwheel==2.16.5 tomli tomli-w
# change the name accordingly
python3 packaging/change_name.py pyproject.toml "NMODL${TAG}"
export SETUPTOOLS_SCM_PRETEND_VERSION="$(git describe --tags | cut -d '-' -f 1,2 | tr - .)"
CIBW_BUILD="$(CIBW_BUILD)" CIBW_ENVIRONMENT_PASS_LINUX='SETUPTOOLS_SCM_PRETEND_VERSION' python3 -m cibuildwheel --output-dir wheelhouse
condition: succeeded()
displayName: 'Building ManyLinux Wheels'
- task: PublishBuildArtifacts@1
inputs:
pathToPublish: '$(Build.SourcesDirectory)/wheelhouse'
condition: succeeded()
displayName: 'Publish wheel as build artifact'
- template: ci/upload-wheels.yml
- job: 'macos_wheels_x86_64'
timeoutInMinutes: 45
pool:
vmImage: 'macOS-12'
steps:
- checkout: self
submodules: True
condition: succeeded()
- script: |
brew install flex bison cmake ninja
condition: succeeded()
displayName: 'Install Dependencies'
- script: |
if [[ "$(RELEASEWHEELBUILD)" != "True" ]]; then
echo "##vso[task.setvariable variable=TAG;]-nightly"
else
echo "##vso[task.setvariable variable=TAG;]"
fi
echo "Wheel tag: $TAG"
displayName: "Set wheel tag"
- script: |
echo "##vso[task.setvariable variable=CIBW_BUILD;]cp38* cp312*"
echo "Build identifiers: $CIBW_BUILD"
condition: and(succeeded(), eq(variables['Build.Reason'], 'PullRequest'))
displayName: "Set build identifiers"
- task: UsePythonVersion@0
- script: |
python3 -m pip install --upgrade pip
python3 -m pip install cibuildwheel==2.16.5 tomli tomli-w
# change the name accordingly
python3 packaging/change_name.py pyproject.toml "NMODL${TAG}"
CIBW_BUILD="$(CIBW_BUILD)" SETUPTOOLS_SCM_PRETEND_VERSION="$(git describe --tags | cut -d '-' -f 1,2 | tr - .)" python3 -m cibuildwheel --output-dir wheelhouse
condition: succeeded()
displayName: 'Build macos Wheel (x86_64)'
- task: PublishBuildArtifacts@1
inputs:
pathToPublish: '$(Build.SourcesDirectory)/wheelhouse'
condition: succeeded()
displayName: 'Publish wheel as build artifact'
- template: ci/upload-wheels.yml
- job: 'test_manylinux_wheels'
dependsOn: 'manylinux_wheels'
timeoutInMinutes: 45
pool:
vmImage: 'ubuntu-20.04'
strategy:
matrix:
${{ if eq(variables.buildWheel, True) }}:
Python38:
python.version: '3.8'
Python39:
python.version: '3.9'
Python310:
python.version: '3.10'
Python311:
python.version: '3.11'
Python312:
python.version: '3.12'
${{ if eq(variables.buildWheel, False) }}:
Python311:
python.version: '3.11'
steps:
- download: current
patterns: 'drop/*.whl'
displayName: "Make manylinux wheels available"
- script: |
set -eux
sudo apt-add-repository -y ppa:deadsnakes/ppa
sudo apt-get update
sudo apt-get install -y python$(python.version) python$(python.version)-dev python$(python.version)-venv
dotless_version="$(echo "$(python.version)" | tr -d '.')"
find $(Pipeline.Workspace) -name "*cp${dotless_version}-manylinux*.whl" -exec bash packaging/test_wheel.bash python$(python.version) {} \;
condition: succeeded()
displayName: 'Test manylinux Wheel with Python $(python.version)'