Title:	Install the 'Natverse' Packages from Scratch
Version:	0.5.1
URL:	https://github.com/natverse/natmanager, http://natverse.org/natmanager/
BugReports:	https://github.com/natverse/natmanager/issues
Description:	Provides streamlined installation for packages from the 'natverse', a suite of R packages for computational neuroanatomy built on top of the 'nat' 'NeuroAnatomy Toolbox' package. Installation of the complete 'natverse' suite requires a 'GitHub' user account and personal access token 'GITHUB_PAT'. 'natmanager' will help the end user set this up if necessary.
License:	GPL-3
Imports:	gh (≥ 1.2.1), utils, remotes, pak, usethis (≥ 2.0.0), curl, withr
Suggests:	testthat (≥ 2.1.0), knitr, mockery, rstudioapi, covr, spelling, rappdirs
Encoding:	UTF-8
Language:	en-GB
RoxygenNote:	7.2.3
NeedsCompilation:	no
Packaged:	2023-09-11 11:02:44 UTC; jefferis
Author:	Sridhar Jagannathan [aut], Gregory Jefferis [aut, cre]
Maintainer:	Gregory Jefferis <jefferis@gmail.com>
Repository:	CRAN
Date/Publication:	2023-09-11 11:40:02 UTC

natmanager: Install the 'Natverse' Packages from Scratch

Description

Provides streamlined installation for packages from the 'natverse', a suite of R packages for computational neuroanatomy built on top of the 'nat' 'NeuroAnatomy Toolbox' package. Installation of the complete 'natverse' suite requires a 'GitHub' user account and personal access token 'GITHUB_PAT'. 'natmanager' will help the end user set this up if necessary.

Author(s)

Maintainer: Gregory Jefferis jefferis@gmail.com (ORCID)

Authors:

• Sridhar Jagannathan j.sridharrajan@gmail.com (ORCID)

See Also

install

Examples

## Not run: 
# install core packages to try out the core natverse
if(is.interactive()) {
natmanager::install('core')
}
# Full "batteries included" installation with all packages
# You need a GitHub account and personal access token (PAT) for this
if(is.interactive()) {
natmanager::install('natverse')
}

## End(Not run)

Install natverse packages from GitHub

Description

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

Value

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

Examples

## Not run: 
# 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'))
}

## End(Not run)
## Not run: 
# 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)

## End(Not run)

List all the repos inside a particular GitHub organisation

Description

by default this will list all the repositories inside the 'natverse' organization.

Usage

list_repo(orgname = "natverse")

Arguments

Value

Character vector of repository names

Examples

## Not run: 
natmanager::list_repo()

## End(Not run)

Update the 'natmanager' package itself.

Description

Update the 'natmanager' package itself.

Usage

selfupdate(
  source = c("GITHUB", "CRAN"),
  upgrade.dependencies = TRUE,
  force = FALSE,
  method = c("pak", "remotes"),
  ...
)

Arguments

Value

Logical indicating whether an update was required (invisibly).

See Also

install

Examples

## Not run: 
natmanager::selfupdate()

## End(Not run)