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 |