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Update M1 working directory #3

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Update M1 working directory

Update M1 working directory #3

Workflow file for this run

.github/workflows/cmaboss-macos.yml at e79d62f
name: cMaBoSS MacOS
on:
push:
pull_request:
release:
types: [created]
jobs:
cmaboss_macos:
name: cMaBoSS
runs-on: macos-11
env:
GCC: clang
CXX: clang++
INSTALL_PATH: /usr/local/
BUILD_PATH: /tmp/
LIBXML_LIBDIR: /usr/local/opt/libxml2/lib/libxml2.dylib
LIBXML_INCLUDEDIR: /usr/local/opt/libxml2/include/libxml2/
steps:
- uses: actions/checkout@v4
- name: Install dependencies
run: |
brew install flex bison python3 cmake
pip3 install numpy wheel delocate pandas
- name: Manually install libxml2 2.11
run: |
wget https://github.com/Homebrew/homebrew-core/raw/38ba35404e3cdb398694419850179e0023158887/Formula/lib/libxml2.rb
brew install -s libxml2.rb
- name: Cache compiled libSBML
id: cache-libsbml-clang
uses: actions/cache@v4
with:
path: /tmp/libsbml-5.20.2
key: ${{ runner.os }}-libSBML-5.20.2-clang++-namespace
- name: Compiling libSBML
if: steps.cache-libsbml-clang.outputs.cache-hit != 'true'
run: bash scripts/build_libsbml.sh
- name: Install libSBML
run: sudo bash scripts/install_libsbml.sh
- name: Build cMaBoSS
run: |
cd engine/src
make
cd ../python
cp -r ../src cmaboss
python3 -m pip wheel -w wheelhouse .
cp /usr/local/lib/libsbml*.dylib .
delocate-wheel -w fixed_wheels -v `ls wheelhouse/cmaboss*.whl`
pip3 install `ls fixed_wheels/cmaboss*.whl`
- name: Test cMaBoSS
run: bash scripts/run_cmaboss_tests.sh
build_wheels_macos:
name: Build MacOS wheels
runs-on: macOS-11
strategy:
matrix:
arch: ["x86_64", "arm64"]
needs: cmaboss_macos
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: '3.10'
- name: Install cibuildwheel
run: python -m pip install cibuildwheel numpy twine
- name: Build wheels
env:
CIBW_ARCHS: ${{ matrix.arch }}
CIBW_TEST_SKIP: "*-macosx_arm64"
CIBW_BEFORE_ALL: >
wget https://github.com/Homebrew/homebrew-core/raw/38ba35404e3cdb398694419850179e0023158887/Formula/lib/libxml2.rb &&
brew install -s libxml2.rb &&
GCC=clang CXX=clang++ INSTALL_PATH=/usr/local/ BUILD_PATH=/tmp/ \
LIBXML_LIBDIR=/usr/local/opt/libxml2/lib/libxml2.dylib \
LIBXML_INCLUDEDIR=/usr/local/opt/libxml2/include/libxml2/ \
bash scripts/build_libsbml.sh &&
BUILD_PATH=/tmp/ bash scripts/install_libsbml.sh
CIBW_REPAIR_WHEEL_COMMAND_MACOS: >
DYLD_LIBRARY_PATH=/usr/local/lib/ delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}
run: |
cd engine/src
make grammars
cd ../../
cp -r engine/src engine/python/cmaboss/
python -m cibuildwheel --output-dir wheelhouse engine/python
- uses: actions/upload-artifact@v4
with:
name: wheels-${{ matrix.arch }}
path: wheelhouse/*.whl
- name: Upload cMaBoSS to test Pypi
if: github.repository == 'vincent-noel/MaBoSS' && github.ref == 'refs/heads/master'
env:
TWINE_USERNAME: __token__
TWINE_PASSWORD: ${{ secrets.PYPI_TEST_TOKEN }}
run: |
python -m twine upload --repository testpypi --skip-existing wheelhouse/cmaboss*
- name: Upload cMaBoSS to Pypi
if: github.repository == 'sysbio-curie/MaBoSS' && github.event_name == 'release'
env:
TWINE_USERNAME: __token__
TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
run: |
python -m twine upload --skip-existing wheelhouse/cmaboss*
conda_cmaboss_macosx:
name: cMaBoSS Conda package
runs-on: macos-12
needs: cmaboss_macos
strategy:
matrix:
version: [{python: "3.8", numpy: "1.22"}, {python: "3.9", numpy: "1.22"}, {python: "3.10", numpy: "1.22"}, {python: "3.11", numpy: "1.23"}, {python: "3.12", numpy: "1.26"}]
defaults:
run:
shell: sh -l {0}
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
channels: defaults
python-version: 3.12
miniforge-variant: Mambaforge
use-mamba: true
- name: Install conda-build
run: |
conda install conda-build conda-verify
- name: Installing MacOSX10.10 SDK
run: |
wget https://github.com/phracker/MacOSX-SDKs/releases/download/11.3/MacOSX10.10.sdk.tar.xz
sudo tar xf MacOSX10.10.sdk.tar.xz -C /opt
echo "conda_build:" > ~/.condarc
echo " config_file: ~/.conda/conda_build_config.yaml" >> ~/.condarc
echo "CONDA_BUILD_SYSROOT:" > ~/.conda/conda_build_config.yaml
echo " - /opt/MacOSX10.10.sdk # [osx]" >> ~/.conda/conda_build_config.yaml
- name: Build cMaBoSS Anaconda package
run: |
conda build -c colomoto --variants "{\"python\": [\"${{ matrix.version.python }}\"], \"numpy\": [\"${{ matrix.version.numpy }}\"]}" conda/cmaboss;
- name: Caching produced conda package
uses: actions/cache@v4
with:
path: |
/Users/runner/miniconda3/envs/test/conda-bld/*
key: ${{ runner.os }}-cmaboss-conda-${{ github.run_id }}-${{ matrix.version.python }}
conda_cmaboss_conda_forge_macosx:
name: cMaBoSS Conda package (conda-forge)
runs-on: macos-12
needs: cmaboss_macos
strategy:
matrix:
version: [{python: "3.8", numpy: "1.22"}, {python: "3.9", numpy: "1.22"}, {python: "3.10", numpy: "1.22"}, {python: "3.11", numpy: "1.23"}, {python: "3.12", numpy: "1.26"}]
defaults:
run:
shell: sh -l {0}
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
channels: conda-forge
python-version: 3.12
miniforge-variant: Mambaforge
use-mamba: true
- name: Install conda-build
run: |
conda install conda-build conda-verify
- name: Installing MacOSX10.10 SDK
run: |
wget https://github.com/phracker/MacOSX-SDKs/releases/download/11.3/MacOSX10.10.sdk.tar.xz
sudo tar xf MacOSX10.10.sdk.tar.xz -C /opt
echo "conda_build:" > ~/.condarc
echo " config_file: ~/.conda/conda_build_config.yaml" >> ~/.condarc
echo "CONDA_BUILD_SYSROOT:" > ~/.conda/conda_build_config.yaml
echo " - /opt/MacOSX10.10.sdk # [osx]" >> ~/.conda/conda_build_config.yaml
- name: Build cMaBoSS Anaconda package
run: |
CUSTOM_BUILD_NUMBER=1 conda build -c conda-forge -c colomoto --variants "{\"python\": [\"${{ matrix.version.python }}\"], \"numpy\": [\"${{ matrix.version.numpy }}\"]}" conda/cmaboss;
- name: Caching produced conda package
uses: actions/cache@v4
with:
path: |
/Users/runner/miniconda3/envs/test/conda-bld/*
key: ${{ runner.os }}-cmaboss-conda-forge-${{ github.run_id }}-${{ matrix.version.python }}
cmaboss_conda_test_macosx:
name: cMaBoSS Anaconda package test
runs-on: macos-12
needs: conda_cmaboss_macosx
strategy:
matrix:
version: [{python: "3.8", numpy: "1.22"}, {python: "3.9", numpy: "1.22"}, {python: "3.10", numpy: "1.22"}, {python: "3.11", numpy: "1.23"}, {python: "3.12", numpy: "1.26"}]
defaults:
run:
shell: sh -l {0}
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
channels: defaults
python-version: ${{ matrix.version.python }}
miniforge-variant: Mambaforge
use-mamba: true
- name: Install conda-build
run: |
conda install conda-build conda-index
- name: Caching produced conda package
uses: actions/cache@v4
with:
path: |
/Users/runner/miniconda3/envs/test/conda-bld/*
key: ${{ runner.os }}-cmaboss-conda-${{ github.run_id }}-${{ matrix.version.python }}
- name: Install package
run: |
python -m conda_index /Users/runner/miniconda3/envs/test/conda-bld/
conda install -c file:///Users/runner/miniconda3/envs/test/conda-bld/ -c colomoto cmaboss
- name: Install test dependencies
run: |
pip install pandas
- name: Test package
run: |
cd engine/tests
python -m unittest test
python -m unittest test_128n
cmaboss_conda_test_conda_forge_macosx:
name: cMaBoSS Anaconda package test (conda-forge)
runs-on: macos-12
needs: conda_cmaboss_conda_forge_macosx
strategy:
matrix:
version: [{python: "3.8", numpy: "1.22"}, {python: "3.9", numpy: "1.22"}, {python: "3.10", numpy: "1.22"}, {python: "3.11", numpy: "1.23"}, {python: "3.12", numpy: "1.26"}]
defaults:
run:
shell: sh -l {0}
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
channels: conda-forge
python-version: ${{ matrix.version.python }}
miniforge-variant: Mambaforge
use-mamba: true
- name: Install conda-build
run: |
conda install conda-build conda-index
- name: Caching produced conda package
uses: actions/cache@v4
with:
path: |
/Users/runner/miniconda3/envs/test/conda-bld/*
key: ${{ runner.os }}-cmaboss-conda-forge-${{ github.run_id }}-${{ matrix.version.python }}
- name: Install package
run: |
python -m conda_index /Users/runner/miniconda3/envs/test/conda-bld/
conda install -c file:///Users/runner/miniconda3/envs/test/conda-bld/ -c colomoto cmaboss
- name: Install test dependencies
run: |
pip install pandas
- name: Test package
run: |
cd engine/tests
python -m unittest test
python -m unittest test_128n
cmaboss_conda_publish_macosx:
name: cMaBoSS Anaconda package publication
runs-on: macos-12
needs: cmaboss_conda_test_macosx
strategy:
matrix:
version: [{python: "3.8", numpy: "1.22"}, {python: "3.9", numpy: "1.22"}, {python: "3.10", numpy: "1.22"}, {python: "3.11", numpy: "1.23"}, {python: "3.12", numpy: "1.26"}]
defaults:
run:
shell: sh -l {0}
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
channels: conda-forge
python-version: 3.12
miniforge-variant: Mambaforge
use-mamba: true
- name: Install conda-build
run: |
conda install conda-build anaconda-client
- name: Caching produced conda package
uses: actions/cache@v4
with:
path: |
/Users/runner/miniconda3/envs/test/conda-bld/*
key: ${{ runner.os }}-cmaboss-conda-${{ github.run_id }}-${{ matrix.version.python }}
- name: Upload MaBoSS to Anaconda cloud on vincent-noel
run: |
anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u vincent-noel /Users/runner/miniconda3/envs/test/conda-bld/osx-64/*.tar.bz2 --force;
- name: Upload MaBoSS to Anaconda cloud on colomoto
if: github.repository == 'sysbio-curie/MaBoSS' && github.event_name == 'release'
run: |
anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u colomoto /Users/runner/miniconda3/envs/test/conda-bld/osx-64/*.tar.bz2 --force;
cmaboss_conda_publish_conda_forge_macosx:
name: cMaBoSS Anaconda package publication (conda-forge)
runs-on: macos-12
needs: cmaboss_conda_test_conda_forge_macosx
strategy:
matrix:
version: [{python: "3.8", numpy: "1.22"}, {python: "3.9", numpy: "1.22"}, {python: "3.10", numpy: "1.22"}, {python: "3.11", numpy: "1.23"}, {python: "3.12", numpy: "1.26"}]
defaults:
run:
shell: sh -l {0}
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
channels: conda-forge
python-version: 3.12
miniforge-variant: Mambaforge
use-mamba: true
- name: Install conda-build
run: |
conda install conda-build anaconda-client
- name: Caching produced conda package
uses: actions/cache@v4
with:
path: |
/Users/runner/miniconda3/envs/test/conda-bld/*
key: ${{ runner.os }}-cmaboss-conda-forge-${{ github.run_id }}-${{ matrix.version.python }}
- name: Upload MaBoSS to Anaconda cloud on vincent-noel
run: |
anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u vincent-noel /Users/runner/miniconda3/envs/test/conda-bld/osx-64/*.tar.bz2 --force;
- name: Upload MaBoSS to Anaconda cloud on colomoto
if: github.repository == 'sysbio-curie/MaBoSS' && github.event_name == 'release'
run: |
anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u colomoto /Users/runner/miniconda3/envs/test/conda-bld/osx-64/*.tar.bz2 --force;