README.md

Summary of the Documentation Generation Workflow

The GitHub Actions workflow for our documentation repository automates the process of generating and updating both the Python and R documentation. Here's how it works:

1. Clones the Repositories:

   • Documentation Repo: It starts by checking out the current documentation repository (where this workflow runs).
   • Stochtree Repo: It then clones the stochtree repository into a subfolder (stochtree-repo). This allows the workflow to access the source code needed to build the documentation.

2. Sets Up the Python Environment:

   • Python Version: The workflow sets up Python 3.10 using the actions/setup-python@v5 action.
   • Dependencies: It installs all necessary Python packages and dependencies required to build the documentation.

3. Builds the Python Documentation:

   • Sphinx: Using Sphinx, a tool for creating documentation, the workflow generates the HTML files from the source code in the stochtree repository. This converts the docstrings and comments in the code into readable documentation.
   • Copies Documentation: The newly generated Python documentation files are copied into the docs/python-documentation directory of the documentation repository. Any old files in this directory are removed beforehand to ensure only the latest documentation is present.

4. Sets Up the R Environment:

   • Pandoc: The workflow sets up Pandoc using the r-lib/actions/setup-pandoc@v2 action, which is required for building R documentation.
   • R Version: It sets up R using the r-lib/actions/setup-r@v2 action with use-public-rspm: true to utilize the public R package repository.
   • Dependencies: The workflow installs all necessary R packages, including remotes, pkgdown, ggplot2, latex2exp, and decor, to build the R documentation.

5. Prepares the R Documentation Build Environment:

   • Directory Setup: It creates a stochtree_cran/src directory and copies the Makevars file from stochtree-repo/src/Makevars to stochtree_cran/src/Makevars.
   • Copies Essential Files: Copies DESCRIPTION, cran-bootstrap.R, _pkgdown.yml, and R_README.md into the stochtree_cran/ directory.

6. Builds the R Documentation:

   • Run Bootstrap Script: Executes cran-bootstrap.R to prepare the R package for documentation.
   • Install Dependencies: Installs all R package dependencies listed in the DESCRIPTION file.
   • Generate Documentation: Uses pkgdown to build the R documentation site, outputting it to docs/r-documentation.

7. Copies R Documentation to Docs Directory:

   • The built R documentation is copied from stochtree-repo/docs/r-documentation/ to docs/r-documentation/ in the root of the documentation repository. This ensures that both Python and R documentation are located within the docs/ directory.

8. Commits and Pushes the Updated Documentation:

   • Branch Creation: The workflow checks if there are any changes to the documentation. If there are, it creates a new temporary branch (e.g., docs-temp-11060215628).
   • Commit Changes: It commits the updated Python and R documentation to this temporary branch.
   • Push Branch: The temporary branch is pushed to the repository.
   • Merge Changes: The workflow then merges the temporary branch back into the main branch, effectively updating the documentation in the repository.
   • Clean Up: After merging, the temporary branch is deleted to keep the repository clean.

9. Automates Documentation Updates:

   • By running this workflow whenever changes are pushed to the main branch, it ensures that both Python and R documentation are always up-to-date with the latest code changes without any manual effort.