Merge branch 'master' into add-py312-ci #1276
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| name: Sphinx documentation | |
| on: [push] | |
| env: | |
| R-VERSION: "release" | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ env.R-VERSION }} | |
| - name: Cache R packages | |
| uses: actions/cache@v2 | |
| env: | |
| cache-name: cache-R-packages | |
| with: | |
| path: /opt/R/**/lib/R/library | |
| key: ${{ runner.os }}-R${{ env.R-VERSION }}-build-${{ env.cache-name }} | |
| restore-keys: | | |
| ${{ runner.os }}-${{ env.R_VERSION }}-build- | |
| - name: Set RSPM | |
| if: startsWith(matrix.os, 'ubuntu') | |
| run: | | |
| echo "RSPM=\"https://packagemanager.rstudio.com/cran/__linux__/$(lsb_release -sc)/latest\"" >> $GITHUB_ENV | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install pandoc graphviz libgraphviz-dev | |
| python -m pip install --upgrade pip | |
| pip uninstall -y rpy2 | |
| pip install -r doc/requirements.txt | |
| pip install . | |
| sudo Rscript ./install_r_packages.r BiocManager dbplyr dplyr ggplot2 hexbin lazyeval RSQLite tidyr viridis | |
| sudo Rscript -e 'BiocManager::install("Biobase")' | |
| - name: Build HTML doc | |
| run: | | |
| export LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):${LD_LIBRARY_PATH} | |
| python -m rpy2.situation | |
| cd doc | |
| make notebooks | |
| make html | |
| - name: Archive documentation | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: html-doc | |
| path: doc/_build/html |