DEVELOPING.md

BPCells Development guide

BPCells has switched to a multi-language repository setup, meaning that R and Python packages are saved in the same repository. For the most part, single-language changes just go in their respective repositories, though adding C++ files requires a few updates (described below)

Helper scripts included for building docs and running tests. Within r, python, or cpp run bash scripts/run_tests.sh or bash scripts/build_docs.sh. Run from the root directory to run tests/docs for all languages in one command.

Building docs

Warning: Docs setup may change as python and C++ docs get created

1. Docs site is built into the root folder of the docs-html branch
2. Run git worktree add r/docs docs-html to put a copy of the docs-html branch in the r/docs folder
3. In r folder, run pkgdown::build_site()
4. In r/docs folder, run git commit

R

Dev requirements: install.packages(c("pkgdown", "devtools", "testthat"))

• Documentation uses pkgdown
• Tests use testthat

Installation: remotes::install_github("bnprks/BPCells/r")

Python

Dev requirements: tox

• Documentation uses Sphinx with PyData theme
• Tests use pytest
• Includes a helper file with the overal project home page, linking to C++, R, and Python docs.
• tox handles virtualenv setup for tests + documentation

Installation: pip install "git+https://github.com/bnprks/BPCells#subdirectory=python"

C++

Dev requirements: cmake, doxygen

• Documentation uses Doxygen with the Doxygen Awesome theme
• Tests use googletest + cmake + ctest

Adding files:

• If C++ tests are added: Update cpp/CMakeLists.txt
• If a new .cpp file is added: Update r/src/Makevars.in

VS Code editing extensions

• Python: autoDocstring
• C++: Doxygen Documentation Generator

To avoid multiple copies of results for C++ files and searches, add to .vscode/settings.json:

"search.exclude": {
    "r/src/bpcells-cpp/**": true,
    "python/src/bpcells-cpp/**": true,
    "r/src/vendor/**": true,
    "python/src/vendor/**": true
}