[Python 3.9] Clar SciPy Re-implementation, pythoncall Debugging, Optional RMS
#2315
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
| name: Build Documentation | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| schedule: | |
| # * is a special character in YAML so you have to quote this string | |
| - cron: "0 8 * * 1" | |
| jobs: | |
| build-documentation: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Sign into GitHub Actions Bot | |
| run: | | |
| git config --global user.name "github-actions" | |
| git config --global user.email "[email protected]" | |
| - name: Clone RMG-Py | |
| uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Setup Mambaforge Python 3.9 | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| environment-file: environment.yml | |
| miniforge-variant: Miniforge3 | |
| miniforge-version: latest | |
| python-version: 3.9 | |
| activate-environment: rmg_env | |
| use-mamba: true | |
| # installs the extra RMS conda dependencies | |
| - name: Add RMS dependencies | |
| run: | | |
| mamba install -c conda-forge julia=1.9.1 pyjulia>=0.6 | |
| mamba install -c rmg pyrms diffeqpy | |
| - name: Install sphinx | |
| run: mamba install -y sphinx | |
| - name: Mamba info | |
| run: | | |
| mamba info | |
| mamba list | |
| - name: Clone RMG-database | |
| run: | | |
| cd .. | |
| git clone https://github.com/ReactionMechanismGenerator/RMG-database.git | |
| - name: Set Environment Variables | |
| run: | | |
| RUNNER_CWD=$(pwd) | |
| echo "PYTHONPATH=$RUNNER_CWD/RMG-Py:$PYTHONPATH" >> $GITHUB_ENV | |
| echo "$RUNNER_CWD/RMG-Py" >> $GITHUB_PATH | |
| - name: make RMG | |
| run: | | |
| make clean | |
| make | |
| - name: Install and link Julia dependencies | |
| timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours). | |
| run: | | |
| which julia | |
| export JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba | |
| julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator' | |
| - name: Checkout gh-pages Branch | |
| uses: actions/checkout@v2 | |
| with: | |
| ref: gh-pages | |
| fetch-depth: 0 | |
| path: documentation/build/html | |
| clean: false | |
| - name: Build Documentation | |
| run: | | |
| cd documentation | |
| make html | |
| cd build/html | |
| touch .nojekyll | |
| git add -A --force . | |
| git diff --staged --exit-code --quiet || git commit -m "Automated documentation rebuild" # only commit if changes were made | |
| - name: Check documentation links | |
| continue-on-error: true | |
| run: | | |
| cd documentation | |
| sphinx-build -b linkcheck -d build/doctrees/ source/ build/linkcheck | grep -e broken -e redirect | grep -v -e 'redirect https://doi.org/' -e 'broken https://doi.org/.* 403 Client Error: Forbidden' | |
| - name: Publish Updated Documentation | |
| if: ${{ github.event_name == 'push' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }} | |
| run: | | |
| cd documentation/build/html | |
| git push origin gh-pages |