Use rdkit for SSSR and RCs (bug fix + Python upgrade)
#2798
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| 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 "github-actions@github.com" | |
| - name: Clone RMG-Py | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Setup Miniforge Python 3.9 | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: environment.yml | |
| miniforge-variant: Miniforge3 | |
| miniforge-version: latest | |
| python-version: "3.9" | |
| activate-environment: rmg_env | |
| auto-update-conda: true | |
| show-channel-urls: true | |
| conda-remove-defaults: "true" | |
| - name: Make libtiff Symlink to Avoid Runner Bug | |
| run: | # This action may need to be removed/adjusted in future runs. | |
| if [ ! -f /usr/lib/x86_64-linux-gnu/libtiff.so.5 ] && [ -f /usr/lib/x86_64-linux-gnu/libtiff.so.6 ]; then sudo ln -s /usr/lib/x86_64-linux-gnu/libtiff.so.6 /usr/lib/x86_64-linux-gnu/libtiff.so.5; fi | |
| find /usr/lib -name libtiff* | |
| - name: Install sphinx | |
| run: conda install -y sphinx~=5.0 | |
| - name: conda info | |
| run: | | |
| conda info | |
| conda 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: 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 |