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build.yml
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name: build
on:
workflow_dispatch:
push:
pull_request:
release:
types: [created]
jobs:
pymaboss_test:
name: Testing pyMaBoSS (Linux)
runs-on: ubuntu-22.04
strategy:
matrix:
python:
- "3.8"
- "3.9"
- "3.10"
- "3.11"
- "3.12"
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.python }}
miniforge-variant: Mambaforge
use-mamba: true
- name: Install MaBoSS
run: |
conda install -c colomoto maboss
- name: Test MaBoSS
run: |
MaBoSS --version
- name: Install dependencies
run: |
pip3 install pip coveralls --upgrade
- name: Launch MaBoSS Server docker
run: |
docker run -p 7777:7777 --network host -d sysbiocurie/maboss
- name: Install pyMaBoSS
run: |
pip3 install .
- name: Test pyMaBoSS
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: |
coverage run -m unittest discover -v
coveralls --service=github
pymaboss_scripts:
name: Testing pyMaBoSS scripts (Linux)
runs-on: ubuntu-22.04
strategy:
matrix:
python:
- "3.8"
- "3.9"
- "3.10"
- "3.11"
- "3.12"
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.python }}
miniforge-variant: Mambaforge
use-mamba: true
- name: Install MaBoSS
run: |
conda install -c colomoto maboss
- name: Test MaBoSS
run: |
MaBoSS --version
- name: Install dependencies
run: |
pip3 install pip coveralls --upgrade
- name: Launch MaBoSS Server docker
run: |
docker run -p 7777:7777 --network host -d sysbiocurie/maboss
- name: Install pyMaBoSS
run: |
pip3 install .
- name: Test pyMaBoSS
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: |
coverage run -a scripts/MBSS_FormatTable.py test/p53_Mdm2.bnd test/p53_Mdm2_runcfg.cfg
coverage run -a scripts/UpPMaBoSS.py test/CellFateModel.bnd test/CellFateModel_1h.cfg test/CellFate_1h.upp
coveralls --service=github
pymaboss_test_macos:
name: Testing pyMaBoSS (MacOS)
runs-on: macos-13
strategy:
matrix:
python:
- "3.8"
- "3.9"
- "3.10"
- "3.11"
- "3.12"
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.python }}
miniforge-variant: Mambaforge
use-mamba: true
- name: Install MaBoSS
run: |
conda install -c colomoto maboss
- name: Test MaBoSS
run: |
MaBoSS --version
- name: Install dependencies
run: |
pip3 install pip coveralls --upgrade
- name: Install pyMaBoSS
run: |
pip3 install .
- name: Test pyMaBoSS
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: |
coverage run -m unittest test.test_conversion
coverage run -m unittest test.test_ensemble
coverage run -m unittest test.test_loadmodels
coverage run -m unittest test.test_probtrajs
coverage run -m unittest test.test_statdist
coverage run -m unittest test.test_types
coverage run -m unittest test.test_uppmaboss
coverage run -m unittest test.test_pipelines
coveralls --service=github
pymaboss_scripts_macos:
name: Testing pyMaBoSS scripts (MacOS)
runs-on: macos-13
strategy:
matrix:
python:
- "3.8"
- "3.9"
- "3.10"
- "3.11"
- "3.12"
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.python }}
miniforge-variant: Mambaforge
use-mamba: true
- name: Install MaBoSS
run: |
conda install -c colomoto maboss
- name: Test MaBoSS
run: |
MaBoSS --version
- name: Install dependencies
run: |
pip3 install pip coveralls --upgrade
- name: Install pyMaBoSS
run: |
pip3 install .
- name: Test pyMaBoSS
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: |
coverage run -a scripts/MBSS_FormatTable.py test/p53_Mdm2.bnd test/p53_Mdm2_runcfg.cfg
coverage run -a scripts/UpPMaBoSS.py test/CellFateModel.bnd test/CellFateModel_1h.cfg test/CellFate_1h.upp
coveralls --service=github
pymaboss_test_macos_m1:
name: Testing pyMaBoSS (MacOS M1)
runs-on: macos-14
strategy:
matrix:
python:
- "3.8"
- "3.9"
- "3.10"
- "3.11"
- "3.12"
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.python }}
miniforge-variant: Mambaforge
use-mamba: true
- name: Install MaBoSS
run: |
conda install -c colomoto maboss
- name: Test MaBoSS
run: |
MaBoSS --version
- name: Install dependencies
run: |
pip3 install pip coveralls --upgrade
- name: Install pyMaBoSS
run: |
pip3 install .
- name: Test pyMaBoSS
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: |
coverage run -m unittest test.test_conversion
coverage run -m unittest test.test_ensemble
coverage run -m unittest test.test_loadmodels
coverage run -m unittest test.test_probtrajs
coverage run -m unittest test.test_statdist
coverage run -m unittest test.test_types
coverage run -m unittest test.test_uppmaboss
coverage run -m unittest test.test_pipelines
coveralls --service=github
pymaboss_scripts_macos_m1:
name: Testing pyMaBoSS scripts (MacOS M1)
runs-on: macos-14
strategy:
matrix:
python:
- "3.8"
- "3.9"
- "3.10"
- "3.11"
- "3.12"
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.python }}
miniforge-variant: Mambaforge
use-mamba: true
- name: Install MaBoSS
run: |
conda install -c colomoto maboss
- name: Test MaBoSS
run: |
MaBoSS --version
- name: Install dependencies
run: |
pip3 install pip coveralls --upgrade
- name: Install pyMaBoSS
run: |
pip3 install .
- name: Test pyMaBoSS
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: |
coverage run -a scripts/MBSS_FormatTable.py test/p53_Mdm2.bnd test/p53_Mdm2_runcfg.cfg
coverage run -a scripts/UpPMaBoSS.py test/CellFateModel.bnd test/CellFateModel_1h.cfg test/CellFate_1h.upp
coveralls --service=github
conda_pymaboss:
name: pyMaBoSS Conda package
runs-on: ubuntu-20.04
needs: [pymaboss_test, pymaboss_scripts, pymaboss_test_macos, pymaboss_scripts_macos, pymaboss_test_macos_m1, pymaboss_scripts_macos_m1]
steps:
- uses: actions/checkout@v4
- uses: s-weigand/setup-conda@v1
- name: Install conda-build and anaconda-client
run: conda install conda-build anaconda-client
- name: Build pyMaBoSS Anaconda package
run: |
conda build conda -c colomoto
- name: Upload Anaconda package to colomoto's repo
if: github.event_name == 'release' && github.event.action == 'created' && github.repository == 'colomoto/pyMaBoSS'
run: |
anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u colomoto /usr/share/miniconda/conda-bld/noarch/*.tar.bz2 --force;
- name: Upload Anaconda package to vincent-noel's repo
if: github.repository == 'vincent-noel/pyMaBoSS' && github.ref == 'refs/heads/master'
run: |
anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u vincent-noel /usr/share/miniconda/conda-bld/noarch/*.tar.bz2 --force;
pypi_pymaboss:
name: pyMaBoSS PyPi package
runs-on: ubuntu-20.04
needs: [pymaboss_test, pymaboss_scripts, pymaboss_test_macos, pymaboss_scripts_macos, pymaboss_test_macos_m1, pymaboss_scripts_macos_m1]
if: github.event_name == 'release' && github.event.action == 'created' && github.repository == 'colomoto/pyMaBoSS'
steps:
- uses: actions/checkout@v4
- name: Install twine
run: pip3 install twine
- name: Build pyMaBoSS PyPi package
env:
TWINE_USERNAME: __token__
TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
run: |
python3 setup.py sdist bdist_wheel
python3 -m twine upload --skip-existing dist/*