Install natverse packages from GitHub — install • natmanager

install allows you to install one of two collections of nat packages

core a minimal install that can help users to get started with nat and already solve many problems (the default)
natverse a powerful "batteries included" distribution with all mature packages in the natverse.

Since the natverse option will install many packages from GitHub, you need to have a GitHub account and personal access token (GITHUB_PAT). Install will check to see if you have a GITHUB_PAT already and, if not, walk you through the steps of setting one up. A fall-back PAT is built into the package but we strongly recommend that you sign up to GitHub and get your own if you start using the natverse regularly.

check_pat can be used to check if you have a GITHUB_PAT set and will advise on how to do this if necessary.

Usage

install(
  collection = c("core", "natverse"),
  pkgs = NULL,
  dependencies = TRUE,
  upgrade.dependencies = FALSE,
  method = c("pak", "remotes"),
  ...
)

check_pat(create = TRUE)

Arguments

collection: The collection of natverse packages that you would like to install. The current options are core, the default, or natverse. See Description for more information.
pkgs: A character vector of package names specifying natverse packages to install. When present overrides the collection argument.
dependencies: Which dependencies you want to install. The default value (TRUE) will install all dependencies, NA will install only hard (essential) dependencies, while F will not install any dependencies (not recommended). See pak::pkg_install or install_github for further details.
upgrade.dependencies: Whether to upgrade dependencies of requested packages See the upgrade argument of pak::pkg_install or install_github for details. The default value (FALSE) will do the minimum amount to enable you to install the package(s) you have requested. In contrast TRUE will go ahead and upgrade all dependencies to the latest version; pak will potentially install source packages to do this.
method: Whether to use the pak (now the default) or install_github package for installation.
...: extra arguments to pass to pak::pkg_install or remotes::install_github.
create: Whether to help you create a personal GITHUB_PAT if you do not have one set. When create=FALSE a default PAT will be used if you have not set your own. This could cause trouble if other people are using the same PAT.

Value

check_pat returns the PAT invisibly or errors out if create=TRUE and none can be set.

Examples

if (FALSE) { # \dontrun{
# install core packages to try out the core natverse
if(is.interactive()) {
natmanager::install('core')
}
# Full "batteries included" installation with all packages
if(is.interactive()) {
natmanager::install('natverse')
# same but upgrading all dependencies to latest version
natmanager::install('natverse', upgrade.dependencies = T)
}
# Install natverse, non-natverse package
# for natverse packages no need to specify the repo
if(is.interactive()) {
natmanager::install(pkgs=c('nat.jrcbrains','flyconnectome/hemibrainr'))
}
} # }
if (FALSE) { # \dontrun{
# Check status of GitHub PAT and create one if required
natmanager::check_pat(create=TRUE)
# Check status of GitHub PAT and use default if no personal one available
natmanager::check_pat(create=FALSE)
} # }