Merge branch 'develop' into patch_chipseeker #2745
Workflow file for this run
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: docs | |
| on: | |
| push: | |
| jobs: | |
| docs: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| persist-credentials: false | |
| - uses: actions/setup-python@v3 | |
| with: | |
| python-version: 3.8 | |
| - name: Install dependencies 🔨 & Build 🔧 | |
| run: | | |
| # setup mambaforge | |
| wget -q -O Mambaforge.sh "https://github.com/conda-forge/miniforge/releases/download/4.11.0-1/Mambaforge-$(uname)-$(uname -m).sh" | |
| bash Mambaforge.sh -b -p "${HOME}/conda" > /dev/null | |
| source "${HOME}/conda/etc/profile.d/conda.sh" | |
| source "${HOME}/conda/etc/profile.d/mamba.sh" | |
| mamba activate | |
| # load channels | |
| $CONDA/bin/conda config --add channels bioconda | |
| $CONDA/bin/conda config --add channels conda-forge | |
| # install seq2science with added docs requirements | |
| declare -a requirements=( | |
| "graphviz>=7" | |
| "importlib_metadata=4.11.4" | |
| "m2r2>=0.3.3" | |
| "networkx>=3" | |
| "sphinx>=6" | |
| "sphinx_rtd_theme>=1.2" | |
| "sphinx-argparse>=0.4" | |
| ) | |
| cp requirements.yaml doc_reqs.yaml | |
| for pkg in "${requirements[@]}"; do | |
| echo " - conda-forge::${pkg}" >> doc_reqs.yaml | |
| done | |
| mamba env create --name seq2science --file doc_reqs.yaml | |
| rm doc_reqs.yaml | |
| mamba activate seq2science | |
| pip3 install . | |
| # make the docs | |
| python docs/scripts/schemas.py | |
| python docs/scripts/rule_description.py | |
| python docs/scripts/gen_dags.py | |
| cp CHANGELOG.md docs/content | |
| sphinx-build docs/ build -W | |
| touch build/.nojekyll | |
| # only deploy | |
| - name: Deploy 📬 | |
| uses: JamesIves/github-pages-deploy-action@releases/v3 | |
| if: github.ref == 'refs/heads/master' | |
| with: | |
| ACCESS_TOKEN: ${{ secrets.AccessToken }} | |
| BRANCH: gh-pages # The branch the action should deploy to. | |
| FOLDER: build # The folder the action should deploy. |