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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-ubuntu.yml at e79d62f
name: cMaBoSS Linux
on:
push:
pull_request:
release:
types: [created]
jobs:
cmaboss:
name: cMaBoSS
runs-on: ubuntu-22.04
env:
GCC: gcc
CXX: g++
INSTALL_PATH: /usr/
BUILD_PATH: /tmp/
LIBXML_LIBDIR: /usr/lib/x86_64-linux-gnu/libxml2.so
LIBXML_INCLUDEDIR: /usr/include/libxml2
steps:
- uses: actions/checkout@v4
- name: Install dependencies
run: |
sudo apt-get update
sudo apt-get install -yq python3-pip python3-setuptools
sudo pip3 install numpy pandas
- name: Cache compiled libSBML
id: cache-libsbml-gcc
uses: actions/cache@v4
with:
path: /tmp/libsbml-5.20.2
key: ${{ runner.os }}-libSBML-5.20.2-gcc-namespace
- name: Compiling libSBML
if: steps.cache-libsbml-gcc.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
pip3 install .
cd ../..
- name: Test cMaBoSS
run: bash scripts/run_cmaboss_tests.sh
build_wheels_linux:
name: Build linux wheels
runs-on: ubuntu-22.04
strategy:
matrix:
build: ["cp*-manylinux_x86_64", "pp*-manylinux_x86_64"]
needs: cmaboss
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_BUILD: ${{ matrix.build }}
CIBW_BEFORE_ALL: >
yum install wget libxml2-devel -y &&
GCC=gcc CXX=g++ INSTALL_PATH=/usr/ BUILD_PATH=/tmp/ \
LIBXML_LIBDIR=/usr/lib64/libxml2.so \
LIBXML_INCLUDEDIR=/usr/include/libxml2 bash scripts/build_libsbml.sh &&
BUILD_PATH=/tmp/ bash scripts/install_libsbml.sh
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
if: matrix.build == 'cp*-manylinux_x86_64'
with:
name: wheels-cpython
path: wheelhouse/*.whl
- uses: actions/upload-artifact@v4
if: matrix.build == 'pp*-manylinux_x86_64'
with:
name: wheels-pypy
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: ${{ secrets.PYPI_TOKEN }}
run: |
python -m twine upload --skip-existing wheelhouse/cmaboss*
cmaboss_conda_defaults:
name: Build cMaBoSS Anaconda package
runs-on: ubuntu-22.04
needs: cmaboss
strategy:
matrix:
version: [{python: "3.8", numpy: "1.22"}, {python: "3.9", numpy: "1.22"}, {python: "3.10", numpy: "1.22"}, {python: "3.11", numpy: "1.23"}, {python: "3.12", numpy: "1.26"}]
defaults:
run:
shell: bash -el {0}
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
channels: defaults
python-version: 3.12
miniforge-variant: Mambaforge
use-mamba: true
- name: Install conda-build
run: |
conda install conda-build anaconda-client conda-verify
- name: Build cMaBoSS Anaconda package
run: |
conda build -c colomoto --variants "{\"python\": [\"${{ matrix.version.python }}\"], \"numpy\": [\"${{ matrix.version.numpy }}\"]}" conda/cmaboss;
- name: Caching produced conda package
uses: actions/cache@v4
with:
path: |
/home/runner/miniconda3/envs/test/conda-bld/*
key: ${{ runner.os }}-cmaboss-conda-defaults-${{ github.run_id }}-${{ matrix.version.python }}
cmaboss_conda:
name: Build cMaBoSS Anaconda package (conda-forge)
runs-on: ubuntu-22.04
needs: cmaboss
strategy:
matrix:
version: [{python: "3.8", numpy: "1.22"}, {python: "3.9", numpy: "1.22"}, {python: "3.10", numpy: "1.22"}, {python: "3.11", numpy: "1.23"}, {python: "3.12", numpy: "1.26"}]
defaults:
run:
shell: bash -el {0}
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
channels: conda-forge
python-version: 3.12
miniforge-variant: Mambaforge
use-mamba: true
- name: Install conda-build
run: |
conda install conda-build anaconda-client conda-verify
- name: Build cMaBoSS Anaconda package
run: |
CUSTOM_BUILD_NUMBER=1 conda build -c conda-forge -c colomoto --variants "{\"python\": [\"${{ matrix.version.python }}\"], \"numpy\": [\"${{ matrix.version.numpy }}\"]}" conda/cmaboss;
- name: Caching produced conda package
uses: actions/cache@v4
with:
path: |
/home/runner/miniconda3/envs/test/conda-bld/*
key: ${{ runner.os }}-cmaboss-conda-${{ github.run_id }}-${{ matrix.version.python }}
cmaboss_conda_defaults_test:
name: Test cMaBoSS Anaconda package
runs-on: ubuntu-22.04
needs: cmaboss_conda_defaults
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: bash -el {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: Caching produced conda package
uses: actions/cache@v4
with:
path: |
/home/runner/miniconda3/envs/test/conda-bld/*
key: ${{ runner.os }}-cmaboss-conda-defaults-${{ github.run_id }}-${{ matrix.version.python }}
- name: Install conda-build
run: |
conda install conda-build conda-index
- name: Install package
run: |
python -m conda_index /home/runner/miniconda3/envs/test/conda-bld/
conda install -c file:///home/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:
name: Test cMaBoSS Anaconda package (conda-forge)
runs-on: ubuntu-22.04
needs: cmaboss_conda
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: bash -el {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: Caching produced conda package
uses: actions/cache@v4
with:
path: |
/home/runner/miniconda3/envs/test/conda-bld/*
key: ${{ runner.os }}-cmaboss-conda-${{ github.run_id }}-${{ matrix.version.python }}
- name: Install conda-build
run: |
conda install conda-build conda-index
- name: Install package
run: |
python -m conda_index /home/runner/miniconda3/envs/test/conda-bld/
conda install -c file:///home/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_defaults:
name: Publish cMaBoSS Anaconda package
runs-on: ubuntu-22.04
needs: cmaboss_conda_defaults_test
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: bash -el {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: Caching produced conda package
uses: actions/cache@v4
with:
path: |
/home/runner/miniconda3/envs/test/conda-bld/*
key: ${{ runner.os }}-cmaboss-conda-defaults-${{ github.run_id }}-${{ matrix.version.python }}
- name: Install anaconda-client
run: |
conda install anaconda-client
- name: Upload cMaBoSS Ananconda package on vincent-noel
run: |
anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u vincent-noel /home/runner/miniconda3/envs/test/conda-bld/linux-64/*.tar.bz2 --force;
- name: Upload cMaBoSS Ananconda package on colomoto
if: github.repository == 'sysbio-curie/MaBoSS' && github.event_name == 'release'
run: |
anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u colomoto /home/runner/miniconda3/envs/test/conda-bld/linux-64/*.tar.bz2 --force;
cmaboss_conda_publish:
name: Publish cMaBoSS Anaconda package (conda-forge)
runs-on: ubuntu-22.04
needs: cmaboss_conda_test
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: bash -el {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: Caching produced conda package
uses: actions/cache@v4
with:
path: |
/home/runner/miniconda3/envs/test/conda-bld/*
key: ${{ runner.os }}-cmaboss-conda-${{ github.run_id }}-${{ matrix.version.python }}
- name: Install anaconda-client
run: |
conda install anaconda-client
- name: Upload cMaBoSS Ananconda package on vincent-noel
run: |
anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u vincent-noel /home/runner/miniconda3/envs/test/conda-bld/linux-64/*.tar.bz2 --force;
- name: Upload cMaBoSS Ananconda package on colomoto
if: github.repository == 'sysbio-curie/MaBoSS' && github.event_name == 'release'
run: |
anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u colomoto /home/runner/miniconda3/envs/test/conda-bld/linux-64/*.tar.bz2 --force;