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Development notes

R package dev

Command Comment
devtools::check() build and check the pkg
devtools::load_all() load the pkg
R CMD INSTALL --no-multiarch --with-keep.source pcgr.git/pcgrr install the pkg into the first library of .libPaths()
options(lifecycle_verbosity = "warning") ensure lifecycle deprecated messages are shown

Python package dev

Command Comment
pip install -e . install Python pkg in editable mode (think of it like loading the dev version)

conda

Command Comment
mamba install foo -c bar install pkg foo from channel bar
mamba create --file env.yml --prefix ./pcgr install conda pkgs listed in env.yml into the ./pcgr directory
conda info -e list conda environments installed on this machine
conda-lock --mamba -f env.yml -p osx-64 -p linux-64 build conda lock files from given env.yml for both osx and linux
conda mambabuild recipe_folder/ -c conda-forge -c bioconda build conda pkg from given recipe (folder with meta.yaml, build.sh)

pkgdown

Command Comment
pkgdown::build_site() builds entire site
pkgdown::build_articles() builds vignettes only