forked from maboss-bkmc/MaBoSS
-
Notifications
You must be signed in to change notification settings - Fork 2
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Improved, updated actions, splitted maboss and cmaboss
- Loading branch information
1 parent
8293837
commit 6a0a831
Showing
8 changed files
with
1,828 additions
and
2,639 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,303 @@ | ||
| name: cMaBoSS MacOS Workflow | ||
|
|
||
| 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/ | ||
| LIBXML_INCLUDEDIR: /usr/local/opt/libxml2/include/libxml2/ | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Install dependencies | ||
| run: | | ||
| brew install flex bison python3 libxml2 cmake | ||
| pip3 install numpy wheel delocate | ||
| - name: Cache compiled libSBML | ||
| id: cache-libsbml-clang | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: /tmp/libSBML-5.19.0-Source | ||
| key: ${{ runner.os }}-libSBML-5.19-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 | ||
| needs: cmaboss_macos | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: '3.10' | ||
|
|
||
| - name: Install cibuildwheel | ||
| run: python -m pip install cibuildwheel==2.11.3 numpy twine | ||
|
|
||
| - name: Build wheels | ||
| 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@v3 | ||
| with: | ||
| path: wheelhouse/*.whl | ||
|
|
||
| - name: Upload cMaBoSS to test Pypi | ||
| if: github.repository == 'vincent-noel/MaBoSS-env-2.0' && 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-env-2.0' && 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-11 | ||
| needs: cmaboss_macos | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: s-weigand/setup-conda@v1 | ||
|
|
||
| - name: Install conda-build | ||
| run: | | ||
| conda update conda | ||
| conda update --all | ||
| conda install conda-build conda-verify | ||
| - name: Downgrading XCode to 11.7 | ||
| run: | | ||
| sudo xcode-select -s /Applications/Xcode_11.7.app/Contents/Developer | ||
| brew reinstall llvm | ||
| - name: Build cMaBoSS Anaconda package | ||
| run: | | ||
| conda build -c colomoto --variants "{\"python\": [\"3.6\", \"3.7\", \"3.8\", \"3.9\"], \"numpy\": \"1.19\"}" conda/cmaboss; | ||
| conda build -c colomoto --variants "{\"python\": [\"3.7\", \"3.8\", \"3.9\"], \"numpy\": \"1.20\"}" conda/cmaboss; | ||
| conda build -c colomoto --variants "{\"python\": [\"3.7\", \"3.8\", \"3.9\", \"3.10\"], \"numpy\": \"1.21\"}" conda/cmaboss; | ||
| conda build -c colomoto --variants "{\"python\": [\"3.8\", \"3.9\", \"3.10\"], \"numpy\": \"1.22\"}" conda/cmaboss; | ||
| conda build -c colomoto --variants "{\"python\": [\"3.8\", \"3.9\", \"3.10\"], \"numpy\": \"1.23\"}" conda/cmaboss; | ||
| - name: Caching produced conda package | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: | | ||
| /usr/local/miniconda/conda-bld/osx-64/* | ||
| key: ${{ runner.os }}-cmaboss-conda-${{ github.run_id }} | ||
|
|
||
| conda_cmaboss_conda_forge_macosx: | ||
| name: cMaBoSS Conda package (conda-forge) | ||
| runs-on: macos-11 | ||
| needs: cmaboss_macos | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: s-weigand/setup-conda@v1 | ||
|
|
||
| - name: Install conda-build | ||
| run: | | ||
| conda update conda | ||
| conda config --add channels conda-forge | ||
| conda config --set channel_priority strict | ||
| conda update --all | ||
| conda install conda-build conda-verify | ||
| - name: Build cMaBoSS Anaconda package | ||
| run: | | ||
| CUSTOM_BUILD_NUMBER=1 conda build -c colomoto --variants "{\"python\": [\"3.6\", \"3.7\", \"3.8\", \"3.9\"], \"numpy\": \"1.19\"}" conda/cmaboss; | ||
| CUSTOM_BUILD_NUMBER=1 conda build -c colomoto --variants "{\"python\": [\"3.7\", \"3.8\", \"3.9\"], \"numpy\": \"1.20\"}" conda/cmaboss; | ||
| CUSTOM_BUILD_NUMBER=1 conda build -c colomoto --variants "{\"python\": [\"3.7\", \"3.8\", \"3.9\", \"3.10\"], \"numpy\": \"1.21\"}" conda/cmaboss; | ||
| CUSTOM_BUILD_NUMBER=1 conda build -c colomoto --variants "{\"python\": [\"3.8\", \"3.9\", \"3.10\"], \"numpy\": \"1.22\"}" conda/cmaboss; | ||
| CUSTOM_BUILD_NUMBER=1 conda build -c colomoto --variants "{\"python\": [\"3.8\", \"3.9\", \"3.10\"], \"numpy\": \"1.23\"}" conda/cmaboss; | ||
| - name: Caching produced conda package | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: | | ||
| /usr/local/miniconda/conda-bld/osx-64/* | ||
| key: ${{ runner.os }}-cmaboss-conda-forge-${{ github.run_id }} | ||
|
|
||
|
|
||
| cmaboss_conda_test_macosx: | ||
| name: cMaBoSS Anaconda package test | ||
| runs-on: macos-11 | ||
| needs: conda_cmaboss_macosx | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: s-weigand/setup-conda@v1 | ||
|
|
||
| - name: Install conda-build | ||
| run: | | ||
| conda update conda | ||
| conda update conda --all | ||
| conda install conda-build anaconda-client | ||
| - name: Caching produced conda package | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: | | ||
| /usr/local/miniconda/conda-bld/osx-64/* | ||
| key: ${{ runner.os }}-cmaboss-conda-${{ github.run_id }} | ||
|
|
||
| - name: Install package | ||
| run: | | ||
| conda index /usr/local/miniconda/conda-bld | ||
| conda install -c colomoto cmaboss --use-local | ||
| - 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-11 | ||
| needs: conda_cmaboss_conda_forge_macosx | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: s-weigand/setup-conda@v1 | ||
|
|
||
| - name: Install conda-build | ||
| run: | | ||
| conda update conda | ||
| conda config --add channels conda-forge | ||
| conda config --set channel_priority strict | ||
| conda update conda --all | ||
| conda install conda-build anaconda-client | ||
| - name: Caching produced conda package | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: | | ||
| /usr/local/miniconda/conda-bld/osx-64/* | ||
| key: ${{ runner.os }}-cmaboss-conda-forge-${{ github.run_id }} | ||
|
|
||
| - name: Install package | ||
| run: | | ||
| conda index /usr/local/miniconda/conda-bld | ||
| conda install -c colomoto cmaboss --use-local | ||
| - 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-11 | ||
| needs: cmaboss_conda_test_macosx | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: s-weigand/setup-conda@v1 | ||
|
|
||
| - name: Install conda-build | ||
| run: | | ||
| conda update conda | ||
| conda update conda --all | ||
| conda install conda-build anaconda-client | ||
| - name: Caching produced conda package | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: | | ||
| /usr/local/miniconda/conda-bld/osx-64/* | ||
| key: ${{ runner.os }}-cmaboss-conda-${{ github.run_id }} | ||
|
|
||
| - name: Upload MaBoSS to Anaconda cloud on vincent-noel | ||
| if: github.repository == 'vincent-noel/MaBoSS-env-2.0' && github.ref == 'refs/heads/master' | ||
| run: | | ||
| anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u vincent-noel /usr/local/miniconda/conda-bld/osx-64/*.tar.bz2 --force; | ||
|
|
||
| - name: Upload MaBoSS to Anaconda cloud on colomoto | ||
| if: github.repository == 'sysbio-curie/MaBoSS-env-2.0' && github.event_name == 'release' | ||
| run: | | ||
| anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u colomoto /usr/local/miniconda/conda-bld/osx-64/*.tar.bz2 --force; | ||
| cmaboss_conda_publish_conda_forge_macosx: | ||
| name: cMaBoSS Anaconda package publication (conda-forge) | ||
| runs-on: macos-11 | ||
| needs: cmaboss_conda_test_conda_forge_macosx | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: s-weigand/setup-conda@v1 | ||
|
|
||
| - name: Install conda-build | ||
| run: | | ||
| conda update conda | ||
| conda config --add channels conda-forge | ||
| conda config --set channel_priority strict | ||
| conda update conda --all | ||
| conda install conda-build anaconda-client | ||
| - name: Caching produced conda package | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: | | ||
| /usr/local/miniconda/conda-bld/osx-64/* | ||
| key: ${{ runner.os }}-cmaboss-conda-forge-${{ github.run_id }} | ||
|
|
||
| - name: Upload MaBoSS to Anaconda cloud on vincent-noel | ||
| if: github.repository == 'vincent-noel/MaBoSS-env-2.0' && github.ref == 'refs/heads/master' | ||
| run: | | ||
| anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u vincent-noel /usr/local/miniconda/conda-bld/osx-64/*.tar.bz2 --force; | ||
|
|
||
| - name: Upload MaBoSS to Anaconda cloud on colomoto | ||
| if: github.repository == 'sysbio-curie/MaBoSS-env-2.0' && github.event_name == 'release' | ||
| run: | | ||
| anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u colomoto /usr/local/miniconda/conda-bld/osx-64/*.tar.bz2 --force; | ||
Oops, something went wrong.