Package 'ReleaseLaunch'

Description

The function add_bioc_remote adds an 'upstream' remote that points to [email protected]. If an upstream remote already exists, it will be validated against the SSH URL. By design, the Bioconductor remote location is called the 'upstream' remote. The 'origin' is set to the GitHub location.

Usage

add_bioc_remote(repo = ".")

set_bioc_remotes(repo = ".", org = "Bioconductor")

Arguments

Details

The set_bioc_remotes function will update a repository's remotes by setting origin to the GitHub location and upstream to the Bioconductor git server. If the origin remote is not set to the GitHub location, the function will overwrite the URL. If the upstream remote is not set, the function will add it. If the upstream remote is set, the function will overwrite the URL with the Bioconductor SSH URL. Note that the remotes will follow this template:

origin [email protected]:{org}/{package}
upstream [email protected]:packages/{package}

Value

• add_bioc_remote: adds an 'upstream' remote with the Bioconductor git address for a given package.

• set_bioc_remotes: updates the remotes for a given package, setting the 'origin' remote to the GitHub location and the 'upstream' remote to the Bioconductor git server.

Description

This function assumes that you have admin push access to the GitHub organization indicated by org.

Usage

add_gh_release_branch(
  package_name,
  release = bioc_release_yaml(),
  gh_branch = .BIOC_DEFAULT_BRANCH,
  bioc_branch = .BIOC_DEFAULT_BRANCH,
  org = "Bioconductor"
)

add_gh_release_branches(
  packages = character(0L),
  release = bioc_release_yaml(),
  bioc_branch = .BIOC_DEFAULT_BRANCH,
  org = "Bioconductor"
)

bioc_version_yaml(config = .BIOC_CONFIG_FILE)

bioc_release_yaml(config = .BIOC_CONFIG_FILE)

Arguments

See Also

packages_without_release_branch

Examples

if (interactive()) {
    bioc_release_yaml()
    add_gh_release_branch(
      package_name = "BiocParallel",
      release = "RELEASE_3_19"
    )

    add_gh_release_branches(
        release = bioc_release_yaml(),
        org = "Bioconductor"
    )
}

Description

Extracts NEWS files from source tarballs of packages.

Usage

extractNEWS(
  reposRoot,
  srcContrib,
  destDir = file.path(reposRoot, "news"),
  unpackDir = tempdir()
)

Arguments

Description

To ensure that a GitHub repository is a software package, its name is checked against a list of Bioconductor packages. This list is called the manifest. This function obtains the manifest using git.

Usage

get_bioc_software_manifest()

Description

get_user_github_repos and get_org_github_repos use the GitHub API, to obtain the repositories hosted on GitHub via the 'username' or the organization ('org') names, respectively.

Usage

get_org_github_repos(
  per_page = 100,
  pages = 10,
  org = "Bioconductor",
  archived = FALSE
)

get_user_github_repos(per_page = 100, pages = 10, username, archived = FALSE)

Arguments

Value

A vector of default branches whose names correspond to the organization or user GitHub repositories

Examples

if (interactive()) {
  get_user_github_repos(username = "github-username")
}

Description

The function uses previous and current versions of Bioconductor to generate a single package's NEWS file.

Usage

getPackagesNEWS(
  prevRepos = "3.15",
  currRepos = "3.16",
  repo = c("bioc", "data/experiment", "workflows"),
  srcdir = NULL
)

printNEWS(
  dbs,
  destfile,
  overwrite = FALSE,
  width = 68,
  output = c("md", "text"),
  relativeLink = FALSE,
  ...
)

Arguments

Value

A list of NEWS

Description

These functions obtain all the repositories from the designated organization and filters them to only valid R packages and repositories that do not have a RELEASE_X_Y branch or that do, depending on the function called.

Usage

packages_without_release_branch(
  version = bioc_version_yaml(),
  release = bioc_release_yaml(),
  org = "Bioconductor",
  type = c("BioCsoft", "BioCexp")
)

packages_with_release_branch(
  version = bioc_version_yaml(),
  release = bioc_release_yaml(),
  org = "Bioconductor",
  type = c("BioCsoft", "BioCexp")
)

Arguments

Value

A named scalar string of the default branch whose name corresponds to a Bioconductor GitHub repository

Examples

if (interactive()) {
    packages_without_release_branch(version = "3.19")
}

Description

These functions should be used after a Bioconductor Release. They ensure that the local repositories are in sync with Bioconductor. For convenience, the singular update_local_repo function will update a single local repository on the user's system. The function checks repositories against the available.packages() in the Bioconductor owned BiocManager::repositories().

Usage

update_local_repos(
  repos_dir,
  release = bioc_release_yaml(),
  username,
  org = username,
  set_upstream = "origin/devel",
  restart_from = character(0L),
  BPPARAM = NULL
)

update_local_repo(
  repo_dir,
  release,
  set_upstream = "origin/devel",
  org = "Bioconductor"
)

Arguments

Details

The update_local_repos function will update all local repositories in the repos_dir directory that are found in either the users or organization's GitHub repository. The function syncs the devel and current release branches from both the origin (GH) and upstream (Bioconductor) remotes. If a upstream remote is not set, the function will set it to the Bioconductor git server. Finally, the function sets origin/devel as the remote branch to track with the set_upstream argument.

Examples

if (interactive()) {
    ## add PAT credentials
    gitcreds::gitcreds_set()
    ## update multiple packages at a time
    update_local_repos(
        repos_dir = "~/bioc/",
        org = "Bioconductor",
        release = "RELEASE_3_20"
    )

    ## update a single package
    update_local_repo(
        "~/bioc/AnnotationHub",
        release = bioc_release_yaml(),
        org = "Bioconductor"
    )
    setwd("~/bioc/AnnotationHub")
    update_local_repo(
        ".",
        release = bioc_release_yaml(),
        org = "Bioconductor"
    )
}