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refactor: split init in separate R file
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@js2264
js2264 committed Oct 5, 2023
1 parent 178da43 commit 37dfd42
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1 change: 1 addition & 0 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -58,6 +58,7 @@ License: MIT + file LICENSE
Collate:
'doc.R'
'imports.R'
'init.R'
'BiocBook.R'
'BiocBook-methods.R'
'check.R'
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316 changes: 1 addition & 315 deletions R/BiocBook.R
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@@ -1,6 +1,7 @@
#' @rdname BiocBook
#' @include imports.R
#' @include doc.R
#' @include init.R
#' @export

methods::setClass("BiocBook",
Expand All @@ -11,321 +12,6 @@ methods::setClass("BiocBook",
)
)

#' @rdname BiocBook
#' @include imports.R
#' @include doc.R
#' @export

init <- function(
new_package,
push = NA,
skip_availability = FALSE,
.local = FALSE
) {

cli::cat_rule("Running preflight checklist", col = "cyan", line = 2)
cli::cli_progress_message(cli::col_grey("{cli::pb_spin} Checking that no folder named `{new_package}` already exists"))
Sys.sleep(1)

## Check that a folder named `new_package` can be created
if (file.exists(new_package)) {
cli::cli_abort("A folder named {new_package} already exists.")
}

if (!.local) {

## Check that git is configured
cli::cli_progress_message(cli::col_grey("{cli::pb_spin} Checking git configuration"))
Sys.sleep(1)
gitconf <- gert::git_config_global()
if (!"user.name" %in% gitconf$name)
cli::cli_abort("Missing `user.name` in the git global configuration.\
Set it with `gert::git_config_global_set('user.name', value = '...')`.")
if (!"user.email" %in% gitconf$name)
cli::cli_abort("Missing `user.email` in the git global configuration.\
Set it with `gert::git_config_global_set('user.email', value = '...')`.")
gituser <- gitconf$value[gitconf$name == "user.name"]
gitmail <- gitconf$value[gitconf$name == "user.email"]
gitsig <- gert::git_signature(name = gituser, email = gitmail)
cli::cli_alert_success(cli::col_grey("Git successfully configured"))
cli::cli_ul(c(
cli::col_grey("git user: `{gituser}`"),
cli::col_grey("git email: `{gitmail}`")
))
Sys.sleep(1)

## Check that user is logged in Github
cli::cli_progress_message(cli::col_grey("{cli::pb_spin} Checking Github credentials"))
Sys.sleep(1)
GH_api <- "https://api.github.com"
PAT <- tryCatch(
{gitcreds::gitcreds_get()$password},
error = function(e) {
cli::cli_abort("Could not find any stored Github credentials. Consider adding a Github token (a.k.a. `PAT`) to your `.Renviron`.\n")
}
)
user <- gh::gh_whoami(.token = PAT)$login
cli::cli_alert_success(cli::col_grey("Successfully logged in Github"))
cli::cli_ul(c(
cli::col_grey("user: `{user}`"),
cli::col_grey("token: `{stringr::str_trunc(PAT, width = 18, side = 'center')}`")
))
Sys.sleep(1)

## Get all repos for one user
req <- gh::gh("/users/{user}/repos", user = user, per_page = 30)
gh_repos <- purrr::map_chr(req, 'name')
while({length(gh_repos) %% 30} == 0) {
req <- gh::gh_next(req)
gh_repos <- c(gh_repos, purrr::map_chr(req, 'name'))
}

## Check that new_package does not already exist
if (new_package %in% gh_repos) {
cli::cli_abort("A Github repo named `{new_package}` already exists for user `{user}`.")
}

}
else {
gituser <- "dummy"
gitmail <- "[email protected]"
gitsig <- gert::git_signature(name = gituser, email = gitmail)
cli::cli_alert_warning(cli::col_grey("Dummy git configured"))
cli::cli_ul(c(
cli::col_grey("git user: `{gituser}`"),
cli::col_grey("git email: `{gitmail}`")
))
cli::cli_alert_warning(cli::col_grey("No GitHub configured"))
user <- gituser
PAT <- NULL
Sys.sleep(1)
}

## Check that package name is valid
if (!skip_availability) {
cli::cli_progress_message(cli::col_grey("{cli::pb_spin} Checking package name availability"))
Sys.sleep(1)
tryCatch(
expr = {
x <- available::available(name = new_package, browse = FALSE)
if (any(!unlist(x[c(1, 2, 3)]))) {
print(x)
cli::cli_abort("Package name is not available. Please pick another name for this BiocBook.")
}
cli::cli_alert_success(cli::col_grey("Package name `{new_package}` is available"))
}
)
Sys.sleep(1)
}

## Create new local repo copied from BiocBook.template archive, in a temp folder
cli::cli_text("")
cli::cat_rule("Initiating a new `BiocBook`", col = "cyan", line = 2)
Sys.sleep(1)
cli::cli_progress_message(cli::col_grey("{cli::pb_spin} Creating new repository from template provided in BiocBook `inst/` directory`"))

## Extract template archive in a temp folder
tmpdir <- tempfile()
dir.create(tmpdir)
template <- system.file("template", "archive.tar.gz", package = "BiocBook")
utils::untar(template, exdir = tmpdir)

## Move files from temp folder to `new_package` folder
repo <- new_package
dir.create(repo)
d <- list.dirs(tmpdir, full.names = TRUE, recursive = TRUE)
d <- d[dirname(d) != '.']
pattern <- file.path(tmpdir, basename(d)[dirname(dirname(d)) == '.'])
d <- d[dirname(dirname(d)) != '.']
f <- list.files(
tmpdir,
all.files = TRUE, full.names = TRUE, recursive = TRUE
)
f <- f[!grepl("archive.zip$", f)]
for (.d in d) dir.create(gsub(pattern, repo, .d))
for (.f in f) file.copy(from = .f, to = gsub(pattern, repo, .f))
unlink(tmpdir, recursive = TRUE)
cli::cli_alert_success(cli::col_grey(
"New local book `{repo}` successfully created"
))
Sys.sleep(1)

## Fix placeholders
# ---- in `_book.yml`
path <- file.path("inst", "assets", "_book.yml")
.fix_placeholders(file.path(repo, path), pkg = repo, usr = user)
cli::cli_alert_success(cli::col_grey("Filled out `{cli::col_cyan(path)}` fields"))
Sys.sleep(1)

# ---- in `README.md`
path <- "README.md"
.fix_placeholders(file.path(repo, path), pkg = repo, usr = user)
cli::cli_alert_success(cli::col_grey("Filled out `{cli::col_cyan(path)}` fields"))
Sys.sleep(1)

# ---- in `DESCRIPTION`
path <- "DESCRIPTION"
.fix_placeholders(file.path(repo, path), pkg = repo, usr = user)
cli::cli_alert_success(cli::col_grey("Filled out `{cli::col_cyan(path)}` fields"))
cli::cli_alert_info(cli::col_grey("Please finish editing the `{cli::col_cyan(path)}` fields, including:"))
d <- cli::cli_div(theme = list(ul = list(`margin-left` = 2, before = "")))
cli::cli_ul(c(" Title", " Description", " Authors@R"))
cli::cli_end(d)
Sys.sleep(1)

# ---- in `index.qmd`
path <- file.path("inst", "index.qmd")
.fix_placeholders(file.path(repo, path), pkg = repo, usr = user)
cli::cli_alert_success(cli::col_grey("Filled out `{cli::col_cyan(path)}` fields"))
cli::cli_alert_info(cli::col_grey("Please finish editing the `{cli::col_cyan(path)}` fields, including the `Welcome` section"))
Sys.sleep(1)

## Init local git repo in the `new_package` folder
gert::git_init(path = repo)
cli::cli_alert_info(cli::col_grey("The following files need to be committed: "))
d <- cli::cli_div(theme = list(ul = list(`margin-left` = 2, before = "")))
f <- gert::git_status(repo = repo)
cli::cli_ul(f$file)
cli::cli_end(d)
Sys.sleep(1)

## Commit all changes to local git repo
staged <- gert::git_add(files = f$file, repo = repo)
commit_sha <- gert::git_commit(
repo = repo,
message = paste0("Init BiocBook from template version ", version),
author = gitsig
)

## Make sure default `git` branch is named `devel`
b <- gert::git_branch_list(repo = repo)
if (b$name != 'devel') {
gert::git_branch_move(repo = repo, b$name, 'devel')
}
cli::cli_alert_success(cli::col_grey("The new files have been commited to the `devel` branch."))
Sys.sleep(1)

## Syncing Github: create new repo, configure Pages, add remote, push
if (!is.null(PAT)) {

## Create a new Github repo
remote <- gh::gh("POST /user/repos", name = repo, description = "BiocBook")
cli::cli_alert_success(cli::col_grey("New Github repository `{user}/{repo}` successfully created"))
Sys.sleep(1)

## Connect local git to remote
cli::cli_progress_message(cli::col_grey("{cli::pb_spin} Adding remote Github branch to local repo"))
Sys.sleep(1)
gert::git_remote_add(url = remote$html_url, name = 'origin', repo = repo)

## Pushing first commit to Github
prompt_msg <- glue::glue("Is it ok to push the first commit to Github?")
success_msg <- cli::col_grey("Commits pushed to origin {cli::col_cyan(gert::git_remote_list(repo = repo)$url[1])}")
abort_msg <- cli::col_grey("Don't forget to push the latest commit to the remote `origin`.")
if (!is.na(push)) {
if (push) {
gert::git_push(repo = repo)
cli::cli_alert_success(success_msg)
}
else {
cli::cli_alert_info(abort_msg)
}
}
else if (rlang::is_interactive()) {
if (usethis::ui_yeah(prompt_msg)) {
gert::git_push(repo = repo)
cli::cli_alert_success(success_msg)
}
else {
cli::cli_alert_info(abort_msg)
}
}
else {
cli::cli_alert_info(abort_msg)
}

## Create remote empty `gh-pages` branch [ripped from usethis]
cli::cli_progress_message(cli::col_grey("{cli::pb_spin} Creating an empty local `gh-pages` branch"))
tree <- gh(
"POST /repos/{user}/{repo}/git/trees",
tree = list(list(
path = "_temp",
mode = "100644",
type = "blob",
content = ""
)),
user = user, repo = repo
)
commit <- gh(
"POST /repos/{user}/{repo}/git/commits",
message = "Init orphan branch",
tree = tree$sha,
user = user, repo = repo
)
ref <- gh(
"POST /repos/{user}/{repo}/git/refs",
ref = glue("refs/heads/gh-pages"),
sha = commit$sha,
user = user, repo = repo
)
del <- gh(
"DELETE /repos/{user}/{repo}/contents/_temp",
message = "\U1F9F9 Purging `gh-pages` branch",
sha = purrr::pluck(tree, "tree", 1, "sha"),
branch = 'gh-pages', user = user, repo = repo
)
cli::cli_alert_success(cli::col_grey("New empty `gh-pages` branch created on remote."))
Sys.sleep(1)

## Enable Pages service
cli::cli_progress_message(cli::col_grey("{cli::pb_spin} Configuring Pages service"))
Sys.sleep(1)
gh::gh(
"PUT /repos/{user}/{repo}/pages",
user = user, repo = repo,
charToRaw('{ "source": { "branch": "gh-pages", "path": "/docs" } }'),
.token = PAT
)
res <- gh::gh(
"/repos/{user}/{repo}/pages",
user = user, repo = repo,
.token = PAT
)
cli::cli_alert_success(cli::col_grey(
"Github Pages are now serving the `docs/` directory from `gh-pages` branch."
))
cli::cli_alert_success(cli::col_grey(
"Book versions will be deployed to {cli::col_cyan(res$html_url)}."
))
Sys.sleep(1)

}

## Remaining placeholders
cli::cli_text("")
cli::cat_rule("NOTES", col = "grey", line = 1)
cli::cli_alert_info(cli::col_grey("If you wish to change the cover picture, please replace the following file:"))
cli::cli_ul(c(
file.path("inst", "assets", "cover.png")
))
Sys.sleep(1)

## Wrapping up
cli::cli_text("")
cli::cat_rule("Results", col = "cyan", line = 2)
cli::cli_alert_success("Local `BiocBook` directory successfully created : {cli::col_cyan(repo)}")
if (!.local) cli::cli_alert_success("Remote `BiocBook` repository successfully created: {cli::col_cyan(gert::git_remote_list(repo = repo)$url[1])}")
if (.local) cli::cli_alert_warning(cli::col_white(cli::style_bold(
"This book will be only available in local until a Github remote is set."
)))
cli::cli_text("")
cli::cli_text(cli::col_grey('# You can connect to the local directory as follows: \n') )
cli::cli_code(glue::glue(" biocbook <- BiocBook('{repo}')"))
cli::cli_text("")
invisible(BiocBook(repo))

}

#' @rdname BiocBook
#' @include imports.R
#' @include doc.R
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