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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@v4
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\"" >> $GITHUB_ENV
- name: Install dependencies
run: |
sudo apt-get update
sudo apt-get install pandoc graphviz libgraphviz-dev
python -m pip install --upgrade pip
pip install 'rpy2-rinterface/[doc]'
pip install 'rpy2-robjects/[doc]'
sudo Rscript ./install_r_packages.r BiocManager dbplyr dplyr ggplot2 hexbin lazyeval RSQLite tidyr viridis
sudo Rscript -e 'BiocManager::install("Biobase")'
- name: Build HTML doc
run: |
export LD_LIBRARY_PATH=$(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@v4
with:
name: html-doc
path: doc/_build/html
|
