update manuscript #235
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| name: Github Action | |
| on: [push, pull_request] | |
| jobs: | |
| clean: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Black formatting | |
| uses: lgeiger/black-action@v1.0.1 | |
| with: | |
| args: "./" | |
| - name: Check for modified files | |
| id: git-check | |
| run: echo ::set-output name=modified::$(if git diff-index --quiet HEAD --; then echo "false"; else echo "true"; fi) | |
| - name: Push changes | |
| if: steps.git-check.outputs.modified == 'true' | |
| run: | | |
| git config --global user.name "romainsacchi" | |
| git config --global user.email "r_s@me.com" | |
| git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY | |
| git checkout $GITHUB_HEAD_REF | |
| git commit -am "Black reformating" | |
| git push | |
| build: | |
| runs-on: ${{matrix.os}} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| needs: clean | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install system dependencies for pyenv | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install build-essential zlib1g-dev libffi-dev libssl-dev \ | |
| libbz2-dev libreadline-dev libsqlite3-dev liblzma-dev \ | |
| libncurses-dev tk-dev | |
| - name: Install python version | |
| uses: gabrielfalcao/pyenv-action@v13 | |
| with: | |
| default: 3.10.6 | |
| command: pip install -U pip | |
| - name: create environment | |
| run: pyenv local 3.10.6 && python -mvenv .venv390 | |
| - name: Install dependencies | |
| run: | | |
| pip install -r requirements.txt --upgrade pip | |
| pip install . | |
| pip install pytest | |
| - name: Run tests | |
| run: | | |
| pip list | |
| pytest | |
| Pypi: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ "ubuntu-latest" ] | |
| python-version: [ "3.11" ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install pypa/build | |
| run: >- | |
| python -m | |
| pip install | |
| build | |
| - name: Build a binary wheel and a source tarball | |
| run: >- | |
| python -m | |
| build | |
| --sdist | |
| --wheel | |
| --outdir dist/ | |
| . | |
| - name: Publish distribution 📦 to PyPI if Release | |
| if: startsWith(github.ref, 'refs/tags') | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| skip-existing: true | |
| - name: Publish distribution 📦 to Test PyPI if Push | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| password: ${{ secrets.TEST_PYPI_API_TOKEN }} | |
| repository-url: https://test.pypi.org/legacy/ | |
| skip-existing: true | |
| conda: | |
| name: (${{ matrix.python-version }}, ubuntu-latest) | |
| runs-on: ubuntu-latest | |
| needs: build | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: [ "3.11" ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| channels: conda-forge,cmutel,konstantinstadler,haasad,romainsacchi | |
| allow-softlinks: true | |
| auto-update-conda: true | |
| activate-environment: test | |
| - name: Conda info | |
| shell: bash -l {0} | |
| run: conda info | |
| - name: Git checkout | |
| uses: actions/checkout@v4 | |
| - name: Branch name | |
| run: echo running on branch ${GITHUB_REF##*/} | |
| - name: Publish distribution 📦 to Anaconda if Push from non-master branch | |
| if: github.ref != 'refs/heads/master' | |
| shell: bash -l {0} | |
| run: | | |
| conda clean --all | |
| PKG_NAME=pathways | |
| USER=romainsacchi | |
| conda install anaconda-client | |
| conda install conda-build | |
| mkdir ~/conda-bld | |
| conda config --set anaconda_upload no | |
| export CONDA_BLD_PATH=~/conda-bld | |
| export VERSION=`date +%Y.%m.%d` | |
| conda build "conda/" --old-build-string | |
| ls $CONDA_BLD_PATH/noarch/ | |
| anaconda -t ${{ secrets.ANACONDA_CLOUD }} upload -u $USER $CONDA_BLD_PATH/noarch/$PKG_NAME-$VERSION-py_0.tar.bz2 --force | |
| testconda: | |
| name: (${{ matrix.python-version }}, ${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| needs: conda | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: [ "3.11" ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| channels: conda-forge,cmutel,konstantinstadler,haasad,pascallesage,romainsacchi | |
| allow-softlinks: true | |
| channel-priority: strict | |
| auto-update-conda: true | |
| activate-environment: test | |
| - name: Pull distribution 📦 from Anaconda and test it if master branch | |
| if: github.ref == 'refs/heads/master' | |
| shell: bash -l {0} | |
| run: | | |
| conda install -c romainsacchi pathways | |
| conda update pathways | |
| conda install pytest | |
| pytest | |
| - name: Pull distribution 📦 from Anaconda and test it if non-master branch | |
| if: github.ref != 'refs/heads/master' | |
| shell: bash -l {0} | |
| run: | | |
| conda install -c romainsacchi pathways | |
| conda update pathways | |
| conda install pytest | |
| pytest |