Update get_fastq.smk (#1025) #2744
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| 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. |