First, you will need the stochtree repo on your local machine.
Navigate to the documentation repo in your terminal (replace ~/path/to/documentation with the path to the documentation repo on your local system).
cd ~/path/to/documentation
Now, recursively clone the main stochtree repo into a stochtree_repo subfolder of the documentation repo
git clone --recursive git@github.com:StochasticTree/stochtree.git stochtree_repo
The docs are largely built using mkdocs, pkgdown and doxygen,
with everything tied together using the "Material for MkDocs" theme.
We first create a virtual environment and install the dependencies for stochtree as well as the doc site (several python packages: mkdocs-material, mkdocstrings-python, and mkdocs-jupyter).
python -m venv venv
source venv/bin/activate
pip install --upgrade pip
pip install -r requirements.txt
Now, we build the stochtree python library locally in the virtual environment activated above
cd stochtree_repo
pip install .
cd ..
To use pkgdown, you need to install R.
One R is installed, make sure the dependendencies of the pkgdown build are installed
Rscript -e 'install.packages(c("remotes", "devtools", "roxygen2", "ggplot2", "latex2exp", "decor", "pkgdown", "cpp11", "BH", "doParallel", "foreach", "knitr", "Matrix", "MASS", "mvtnorm", "rmarkdown", "testthat", "tgp"), repos="https://cloud.r-project.org/")'
To build the R docs, first run a script that lays out the package as needed
cd stochtree_repo
Rscript cran-bootstrap.R 1 1 1
cd ..
Then run the pkgdown build workflow to put the R docs in the correct folder
mkdir -p docs/R_docs/pkgdown
Rscript -e 'pkgdown::build_site_github_pages("stochtree_repo/stochtree_cran", dest_dir = "../../docs/R_docs/pkgdown", install = TRUE)'
rm -rf stochtree_repo/stochtree_cran
First, ensure that you have doxygen installed.
On MacOS, this can be done via homebrew (i.e. brew install doxygen).
Then, modify the Doxyfile to build the C++ documentation as desired and build the doxygen site
sed -i '' 's|^OUTPUT_DIRECTORY *=.*|OUTPUT_DIRECTORY = ../docs/cpp_docs/|' stochtree_repo/Doxyfile
sed -i '' 's|^GENERATE_XML *=.*|GENERATE_XML = NO|' stochtree_repo/Doxyfile
sed -i '' 's|^GENERATE_HTML *=.*|GENERATE_HTML = YES|' stochtree_repo/Doxyfile
mkdir -p docs/cpp_docs/
cd stochtree_repo
doxygen Doxyfile
cd ..
cp stochtree_repo/demo/notebooks/supervised_learning.ipynb docs/python_docs/demo/supervised_learning.ipynb
cp stochtree_repo/demo/notebooks/causal_inference.ipynb docs/python_docs/demo/causal_inference.ipynb
cp stochtree_repo/demo/notebooks/heteroskedastic_supervised_learning.ipynb docs/python_docs/demo/heteroskedastic_supervised_learning.ipynb
cp stochtree_repo/demo/notebooks/multivariate_treatment_causal_inference.ipynb docs/python_docs/demo/multivariate_treatment_causal_inference.ipynb
cp stochtree_repo/demo/notebooks/serialization.ipynb docs/python_docs/demo/serialization.ipynb
cp stochtree_repo/demo/notebooks/tree_inspection.ipynb docs/python_docs/demo/tree_inspection.ipynb
cp stochtree_repo/demo/notebooks/prototype_interface.ipynb docs/python_docs/demo/prototype_interface.ipynb
cp vignettes/Python/RDD/rdd.html docs/vignettes/Python/rdd.html
cp vignettes/Python/RDD/RDD_DAG.png docs/vignettes/Python/RDD_DAG.png
cp vignettes/Python/RDD/trees1.png docs/vignettes/Python/trees1.png
cp vignettes/Python/RDD/trees2.png docs/vignettes/Python/trees2.png
cp vignettes/Python/RDD/trees3.png docs/vignettes/Python/trees3.png
cp vignettes/R/RDD/rdd.html docs/vignettes/R/rdd.html
cp vignettes/Python/IV/iv.html docs/vignettes/Python/iv.html
cp vignettes/Python/IV/IV_CDAG.png docs/vignettes/Python/IV_CDAG.png
cp vignettes/R/IV/iv.html docs/vignettes/R/iv.html
To build and preview the site locally, run
mkdocs serve
To build the files underlying the static site, run
mkdocs build