fix old serialized S4 instances

git-utils

R Documentation

Convenience Git-related utility functions used by updateBiocPackageRepoObjects()

Description

prepare_git_repo_for_work() and git_commit() are used internally by updateBiocPackageRepoObjects() to perform Git operations.

Usage

prepare_git_repo_for_work(repopath=".", branch=NULL, git=NULL,
                          use.https=FALSE)

git_commit(repopath=".", commit_msg, push=FALSE,
           git=NULL, user_name=NULL, user_email=NULL)

Arguments

`repopath`	The path (as a single string) to the local Git repository of a Bioconductor package. If the specified path exists, `prepare_git_repo_for_work()` will check that it's a workable Git repo (i.e. contains no uncommitted changes). If that's the case then it will call `git pull` on it, otherwise it will return an error. If the specified path does not exist, `prepare_git_repo_for_work()` will try to infer the package name from `repopath` and clone it from git.bioconductor.org.
`branch`	The branch (as a single string) of the Git repository to work on. If `NULL`, then the current branch is used (if `repopath` already exists) or the default branch is used (if `repopath` does not exist and needs to be cloned).
`git`	The path (as a single string) to the git command if it's not in the PATH.
`use.https`	By default, `git clone git@git.bioconductor.org:packages/MyPackage` is used to clone a package repo from the Bioconductor Git server. Note that this works only for authorized maintainers of package MyPackage. By setting `use.https` to `TRUE`, the package will be cloned instead from `https://git.bioconductor.org:packages/MyPackage`, which should work for anybody, but then pushing back the changes to the package won't be possible.
`commit_msg`	The Git commit message.
`push`	Whether to push the changes or not. Changes are committed but not pushed by default. You need push access to the package Git repository at git.bioconductor.org in order to use `push=TRUE`.
`user_name`, `user_email`	Set the Git user name and/or email to use for the commit. This overrides the Git user name and/or email that the git command would otherwise use. See the COMMIT INFORMATION section in `system2("git", c("commit", "--help"))` for the details about where the git command normally takes this information from.

Value

prepare_git_repo_for_work() returns FALSE if the supplied path already exists, and TRUE if it didn't exist and needed to be cloned.

git_commit() returns an invisible NULL.

Examples

repopath <- file.path(tempdir(), "IdeoViz")

## We must use HTTPS access to clone the package because we are
## not maintainers of the IdeoViz package. A more realistic situation
## would be to use prepare_git_repo_for_work() on a package that we
## maintain, in which case 'use.https=TRUE' would not be needed:
prepare_git_repo_for_work(repopath, use.https=TRUE)

bump_pkg_version(repopath, update.Date=TRUE)

git_commit(repopath, commit_msg="version bump", push=FALSE)

unlink(repopath, recursive=TRUE)

Bioconductor/updateObject documentation built on May 1, 2024, 9:29 p.m.