Merge branch 'master' into macos14-for-silicon #1271
Workflow file for this run
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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 |