35 | #' }
36 |
37 | add_citation <- function(given = NULL, family = NULL, organisation = NULL,
38 | open = TRUE, overwrite = FALSE, quiet = FALSE) {
39 |
40 |
41 | stop_if_not_logical(open, overwrite, quiet)
42 |
43 | path <- file.path(path_proj(), "inst", "CITATION")
44 |
45 |
46 | ## Do not replace current file but open it if required ----
47 |
48 | if (file.exists(path) && !overwrite) {
49 |
50 | if (!open) {
51 |
52 | stop("An 'inst/CITATION' file is already present. If you want to ",
53 | "replace it, please use `overwrite = TRUE`.")
54 |
55 | } else {
56 |
57 | edit_file(path)
58 | return(invisible(NULL))
59 | }
60 | }
61 |
62 |
63 | ## Get fields values ----
64 |
65 | if (is.null(given)) given <- getOption("given")
66 | if (is.null(family)) family <- getOption("family")
67 |
68 | if (!is.null(organisation)) {
69 |
70 | github <- organisation
71 |
72 | } else {
73 |
74 | github <- gh::gh_whoami()$"login"
75 |
76 | if (is.null(github)) {
77 | stop("Unable to find GitHub username. Please run ",
78 | "`?gert::git_config_global` for more information.")
79 | }
80 | }
81 |
82 | stop_if_not_string(given, family, github)
83 |
84 |
85 | project_name <- get_package_name()
86 | pkg_version <- get_package_version()
87 | year <- format(Sys.Date(), "%Y")
88 |
89 |
90 | ## Copy Template ----
91 |
92 | if (!dir.exists(file.path(path_proj(), "inst")))
93 | dir.create(file.path(path_proj(), "inst"), showWarnings = FALSE)
94 |
95 | invisible(
96 | file.copy(system.file(file.path("templates", "citation"),
97 | package = "rcompendium"), path, overwrite = TRUE))
98 |
99 |
100 | ## Change defaults values ----
101 |
102 | xfun::gsub_file(path, "{{project_name}}", project_name, fixed = TRUE)
103 | xfun::gsub_file(path, "{{pkg_version}}", pkg_version, fixed = TRUE)
104 | xfun::gsub_file(path, "{{year}}", year, fixed = TRUE)
105 | xfun::gsub_file(path, "{{given}}", given, fixed = TRUE)
106 | xfun::gsub_file(path, "{{family}}", family, fixed = TRUE)
107 | xfun::gsub_file(path, "{{github}}", github, fixed = TRUE)
108 |
109 |
110 | ## Messages ----
111 |
112 | if (!quiet) ui_done("Writing {ui_value('inst/CITATION')} file")
113 |
114 | if (open) edit_file(path)
115 |
116 | invisible(NULL)
117 | }
118 |
--------------------------------------------------------------------------------
/R/add_code_of_conduct.R:
--------------------------------------------------------------------------------
1 | #' Add code of conduct
2 | #'
3 | #' @description
4 | #' This function creates a `CODE_OF_CONDUCT.md` file adapted from the
5 | #' Contributor Covenant, version 2.1 available at
6 | #' \url{https://www.contributor-covenant.org/version/2/1/code_of_conduct.html}.
7 | #'
8 | #' @param open A logical value. If `TRUE` (default) the `CONTRIBUTING.md` file
9 | #' is opened in the editor.
10 | #'
11 | #' @param overwrite A logical value. If files are already present and
12 | #' `overwrite = TRUE`, they will be erased and replaced. Default is `FALSE`.
13 | #'
14 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
15 | #' `FALSE`.
16 | #'
17 | #' @inheritParams set_credentials
18 | #'
19 | #' @return No return value.
20 | #'
21 | #' @export
22 | #'
23 | #' @family create files
24 | #'
25 | #' @examples
26 | #' \dontrun{
27 | #' add_code_of_conduct()
28 | #' }
29 |
30 | add_code_of_conduct <- function(email = NULL,
31 | open = TRUE, overwrite = FALSE, quiet = FALSE) {
32 |
33 |
34 | stop_if_not_logical(open, overwrite, quiet)
35 |
36 | path <- file.path(path_proj(), "CODE_OF_CONDUCT.md")
37 |
38 |
39 | ## Do not replace current file but open it if required ----
40 |
41 | if (file.exists(path) && !overwrite) {
42 |
43 | if (!open) {
44 |
45 | stop("A 'CODE_OF_CONDUCT.md' file is already present. If you want to ",
46 | "replace it, please use `overwrite = TRUE`.")
47 |
48 | } else {
49 |
50 | edit_file(path)
51 | return(invisible(NULL))
52 | }
53 | }
54 |
55 |
56 | ## Get fields values ----
57 |
58 | if (is.null(email)) email <- getOption("email")
59 |
60 |
61 | stop_if_not_string(email)
62 |
63 |
64 | ## Copy Template ----
65 |
66 | invisible(
67 | file.copy(system.file(file.path("templates", "CODE_OF_CONDUCT.md"),
68 | package = "rcompendium"), path, overwrite = TRUE))
69 |
70 |
71 | ## Change defaults values ----
72 |
73 | xfun::gsub_file(path, "{{email}}", email, fixed = TRUE)
74 |
75 |
76 | ## Messages ----
77 |
78 | if (!quiet) {
79 | ui_done("Writing {ui_value('CODE_OF_CONDUCT.md')} file")
80 | }
81 |
82 | add_to_buildignore("CODE_OF_CONDUCT.md", quiet = quiet)
83 |
84 |
85 | if (open) edit_file(path)
86 |
87 | invisible(NULL)
88 | }
89 |
--------------------------------------------------------------------------------
/R/add_codecov_badge.R:
--------------------------------------------------------------------------------
1 | #' Add a Codecov badge
2 | #'
3 | #' @description
4 | #' This function adds a **Code coverage** badge to the `README.Rmd`, i.e. the
5 | #' percentage of code cover by units tests. This percentage is computed by
6 | #' the codecov.io service.
7 | #'
8 | #' **Note:** this service must be manually activated for the package by visiting
9 | #' \url{https://about.codecov.io/}.
10 | #'
11 | #' Make sure that 1) a `README.Rmd` file exists at the project root and 2) it
12 | #' contains a block starting with the line `` and ending
13 | #' with the line ``.
14 | #'
15 | #' Don't forget to re-render the `README.md`.
16 | #'
17 | #' @param organisation A character of length 1. The name of the GitHub
18 | #' organisation to host the package. If `NULL` (default) the GitHub account
19 | #' will be used.
20 | #'
21 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
22 | #' `FALSE`.
23 | #'
24 | #' @return A badge as a markdown expression.
25 | #'
26 | #' @export
27 | #'
28 | #' @family adding badges
29 | #'
30 | #' @examples
31 | #' \dontrun{
32 | #' add_codecov_badge()
33 | #' }
34 |
35 | add_codecov_badge <- function(organisation = NULL, quiet = FALSE) {
36 |
37 |
38 | stop_if_not_logical(quiet)
39 |
40 | ## Check if GH Actions are set ----
41 |
42 | if (!file.exists(file.path(path_proj(), ".github", "workflows",
43 | "test-coverage.yaml"))) {
44 | stop("Please run `add_github_actions_codecov()` to setup GitHub Actions.")
45 | }
46 |
47 |
48 | ## Retrieve GitHub pseudo/organization ----
49 |
50 | if (!is.null(organisation)) {
51 |
52 | github <- organisation
53 |
54 | } else {
55 |
56 | github <- gh::gh_whoami()$"login"
57 |
58 | if (is.null(github)) {
59 | stop("Unable to find GitHub username. Please run ",
60 | "`?gert::git_config_global` for more information.")
61 | }
62 | }
63 |
64 |
65 | stop_if_not_string(github)
66 |
67 |
68 | ## Check URL ----
69 |
70 | is_gh_user()
71 |
72 | project_name <- get_package_name()
73 |
74 |
75 | ## Create Badge Markdown Expression ----
76 |
77 | alt <- "codecov"
78 | href <- paste0("https://codecov.io/gh/", github,"/", project_name)
79 | img <- paste0("https://codecov.io/gh/", github,"/", project_name,
80 | "/branch/", gert::git_branch(), "/graph/badge.svg")
81 |
82 | badge <- paste0("[![", alt, "](", img, ")](", href, ")")
83 |
84 |
85 | ## Add Badge ----
86 |
87 | add_badge(badge, pattern = alt)
88 |
89 |
90 | if (!quiet) {
91 | ui_done(paste0("Adding {ui_field('codecov')} badge to ",
92 | "{ui_value('README.Rmd')}"))
93 | }
94 |
95 | invisible(badge)
96 | }
97 |
--------------------------------------------------------------------------------
/R/add_compendium.R:
--------------------------------------------------------------------------------
1 | #' Create additional folders
2 | #'
3 | #' @description
4 | #' This function creates a compendium, i.e. additional folders to a package
5 | #' structure. By default, the following directories are created:
6 | #' `data`, `analyses/`, `outputs/`, and `figures/`. A `README.md` is added to
7 | #' each folder and must be edited. The argument `compendium` allows user to
8 | #' hoose its own compendium structure. All theses folders are added to the
9 | #' `.Rbuildignore` file.
10 | #'
11 | #' @param compendium A character vector specifying the folders to be created.
12 | #'
13 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
14 | #' `FALSE`.
15 | #'
16 | #' @return No return value.
17 | #'
18 | #' @export
19 | #'
20 | #' @family create files
21 | #'
22 | #' @examples
23 | #' \dontrun{
24 | #' add_compendium()
25 | #' add_compendium(compendium = "paper")
26 | #' add_compendium(compendium = c("data", "outputs", "code", "manuscript"))
27 | #' }
28 |
29 | add_compendium <- function(compendium = NULL, quiet = FALSE) {
30 |
31 | stop_if_not_logical(quiet)
32 |
33 | if (is.null(compendium)) {
34 | compendium <- c("data", "outputs", "figures", "analyses")
35 | }
36 |
37 | if (!is.character(compendium)) {
38 | stop("Argument 'compendium' must be a character.")
39 | }
40 |
41 | path <- path_proj()
42 |
43 | for (i in 1:length(compendium)) {
44 |
45 | if (!dir.exists(file.path(path, compendium[i]))) {
46 |
47 | dir.create(file.path(path, compendium[i]), recursive = TRUE)
48 |
49 | if (!quiet) {
50 | ui_done("Creating {ui_value(paste0(compendium[i], '/'))} directory")
51 | }
52 | }
53 |
54 | add_to_buildignore(compendium, quiet = quiet)
55 |
56 |
57 | if (!file.exists(file.path(path, compendium[i], "README.md"))) {
58 |
59 | readme <- c("# README",
60 | "",
61 | "**{{ PLEASE DESCRIBE THE CONTENT OF THIS FOLDER}}**")
62 |
63 | writeLines(readme, con = file.path(path, compendium[i], "README.md"))
64 |
65 | if (!quiet) {
66 |
67 | ui_done(paste0("Adding a {ui_value('README.md')} to ",
68 | "{ui_value(paste0(compendium[i], '/'))} directory"))
69 | cli::cat_line()
70 | }
71 | }
72 | }
73 |
74 | invisible(NULL)
75 | }
76 |
--------------------------------------------------------------------------------
/R/add_cran_badge.R:
--------------------------------------------------------------------------------
1 | #' Add a CRAN Status badge
2 | #'
3 | #' @description
4 | #' This function adds a **CRAN Status** badge to the `README.Rmd`. If the
5 | #' package is not hosted on the CRAN the badge will indicate
6 | #' _not published on the CRAN_.
7 | #'
8 | #' Make sure that 1) a `README.Rmd` file exists at the project root and 2) it
9 | #' contains a block starting with the line `` and ending
10 | #' with the line ``.
11 | #'
12 | #' Don't forget to re-render the `README.md`.
13 | #'
14 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
15 | #' `FALSE`.
16 | #'
17 | #' @return A badge as a markdown expression.
18 | #'
19 | #' @export
20 | #'
21 | #' @family adding badges
22 | #'
23 | #' @examples
24 | #' \dontrun{
25 | #' add_cran_badge()
26 | #' }
27 |
28 | add_cran_badge <- function(quiet = FALSE) {
29 |
30 |
31 | stop_if_not_logical(quiet)
32 |
33 | ## Create Badge Markdown Expression ----
34 |
35 | project_name <- get_package_name()
36 |
37 | alt <- "CRAN status"
38 | href <- paste0("https://CRAN.R-project.org/package=", project_name)
39 | img <- paste0("https://www.r-pkg.org/badges/version/", project_name)
40 |
41 | badge <- paste0("[![", alt, "](", img, ")](", href, ")")
42 |
43 |
44 | ## Add Badge ----
45 |
46 | add_badge(badge, pattern = "CRAN status")
47 |
48 |
49 | if (!quiet) {
50 | ui_done(paste0("Adding {ui_field('CRAN status')} badge to ",
51 | "{ui_value('README.Rmd')}"))
52 | }
53 |
54 | invisible(badge)
55 | }
56 |
--------------------------------------------------------------------------------
/R/add_dependencies_badge.R:
--------------------------------------------------------------------------------
1 | #' Add a Dependencies badge
2 | #'
3 | #' @description
4 | #' This function adds or updates the **Dependencies** badge to the `README.Rmd`.
5 | #' The first number corresponds to the direct dependencies and the second to the
6 | #' recursive dependencies.
7 | #'
8 | #' **Note:** this function can work with packages not published on the CRAN
9 | #' and is based on the function [gtools::getDependencies()]. See also the
10 | #' function [get_all_dependencies()].
11 | #'
12 | #' Make sure that 1) a `README.Rmd` file exists at the project root and 2) it
13 | #' contains a block starting with the line `` and ending
14 | #' with the line ``.
15 | #'
16 | #' Don't forget to re-render the `README.md`.
17 | #'
18 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
19 | #' `FALSE`.
20 | #'
21 | #' @return A badge as a markdown expression.
22 | #'
23 | #' @export
24 | #'
25 | #' @family adding badges
26 | #'
27 | #' @examples
28 | #' \dontrun{
29 | #' add_dependencies_badge()
30 | #' }
31 |
32 | add_dependencies_badge <- function(quiet = FALSE) {
33 |
34 |
35 | stop_if_not_logical(quiet)
36 |
37 | deps <- get_all_dependencies()
38 | deps <- unlist(lapply(deps, length))
39 |
40 |
41 | ## Create Badge Markdown Expression ----
42 |
43 | if (deps["direct_deps"] == 0)
44 | color <- "brightgreen"
45 | if (deps["direct_deps"] > 0 &&
46 | deps["direct_deps"] < 5)
47 | color <- "green"
48 | if (deps["direct_deps"] > 4 &&
49 | deps["direct_deps"] < 10)
50 | color <- "orange"
51 | if (deps["direct_deps"] > 9)
52 | color <- "red"
53 |
54 | url <- "https://img.shields.io/badge/dependencies"
55 |
56 | img <- paste0(url, "-", deps["direct_deps"], "/", deps["all_deps"], "-")
57 | img <- paste0(img, color, "?style=flat")
58 |
59 | badge <- paste0("[![Dependencies](", img, ")](#)")
60 |
61 |
62 | ## Add Badge ----
63 |
64 | add_badge(badge, pattern = "Dependencies")
65 |
66 |
67 | if (!quiet) {
68 | ui_done(paste0("Adding {ui_field('Dependencies')} badge to ",
69 | "{ui_value('README.Rmd')}"))
70 | }
71 |
72 | invisible(badge)
73 | }
74 |
--------------------------------------------------------------------------------
/R/add_description.R:
--------------------------------------------------------------------------------
1 | #' Create a DESCRIPTION file
2 | #'
3 | #' @description
4 | #' This function creates a `DESCRIPTION` file at the root of the project. This
5 | #' file contains metadata of the project. Some information (title, description,
6 | #' version, etc.) must be edited by hand. For more information:
7 | #' \url{https://r-pkgs.org/description.html}.
8 | #' User credentials can be passed as arguments but it is recommended to store
9 | #' them in the `.Rprofile` file with [set_credentials()].
10 | #'
11 | #' @param organisation A character of length 1. The name of the GitHub
12 | #' organisation to host the package. If `NULL` (default) the GitHub account
13 | #' will be used.
14 | #'
15 | #' @param open A logical value. If `TRUE` (default) the file is opened in the
16 | #' editor.
17 | #'
18 | #' @param overwrite A logical value. If a `DESCRIPTION` is already present and
19 | #' `overwrite = TRUE`, this file will be erased and replaced. Default is
20 | #' `FALSE`.
21 | #'
22 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
23 | #' `FALSE`.
24 | #'
25 | #' @inheritParams set_credentials
26 | #'
27 | #' @return No return value.
28 | #'
29 | #' @export
30 | #'
31 | #' @family create files
32 | #'
33 | #' @examples
34 | #' \dontrun{
35 | #' add_description(organisation = "MySociety")
36 | #' }
37 |
38 | add_description <- function(given = NULL, family = NULL, email = NULL,
39 | orcid = NULL, organisation = NULL, open = TRUE,
40 | overwrite = FALSE, quiet = FALSE) {
41 |
42 |
43 | stop_if_not_logical(open, overwrite, quiet)
44 |
45 |
46 | path <- file.path(path_proj(), "DESCRIPTION")
47 |
48 |
49 | ## Do not replace current file but open it if required ----
50 |
51 | if (file.exists(path) && !overwrite) {
52 |
53 | if (!open) {
54 |
55 | stop("A 'DESCRIPTION' file is already present. If you want to ",
56 | "replace it, please use `overwrite = TRUE`.")
57 |
58 | } else {
59 |
60 | edit_file(path)
61 | return(invisible(NULL))
62 | }
63 | }
64 |
65 |
66 | ## Get fields values ----
67 |
68 | if (is.null(given)) given <- getOption("given")
69 | if (is.null(family)) family <- getOption("family")
70 | if (is.null(email)) email <- getOption("email")
71 | if (is.null(orcid)) orcid <- getOption("orcid")
72 |
73 | if (!is.null(organisation)) {
74 |
75 | github <- organisation
76 |
77 | } else {
78 |
79 | github <- gh::gh_whoami()$"login"
80 |
81 | if (is.null(github)) {
82 | stop("Unable to find GitHub username. Please run ",
83 | "`?gert::git_config_global` for more information.")
84 | }
85 | }
86 |
87 |
88 | stop_if_not_string(given, family, email, github)
89 |
90 | if (!is.null(orcid)) stop_if_not_string(orcid)
91 |
92 |
93 | project_name <- get_package_name()
94 | roxygen2_version <- get_roxygen2_version()
95 |
96 |
97 | ## Copy Template ----
98 |
99 | invisible(
100 | file.copy(system.file(file.path("templates", "DESCRIPTION"),
101 | package = "rcompendium"), path, overwrite = TRUE))
102 |
103 |
104 | ## Change default values (in file) ----
105 |
106 | xfun::gsub_file(path, "{{project_name}}", project_name, fixed = TRUE)
107 | xfun::gsub_file(path, "{{roxygen2_version}}", roxygen2_version, fixed = TRUE)
108 | xfun::gsub_file(path, "{{given}}", given, fixed = TRUE)
109 | xfun::gsub_file(path, "{{family}}", family, fixed = TRUE)
110 | xfun::gsub_file(path, "{{email}}", email, fixed = TRUE)
111 | xfun::gsub_file(path, "{{github}}", github, fixed = TRUE)
112 |
113 | if (!is.null(orcid)) xfun::gsub_file(path, "{{orcid}}", orcid, fixed = TRUE)
114 |
115 |
116 | ## Message ----
117 |
118 | if (!quiet) ui_done("Writing {ui_value('DESCRIPTION')} file")
119 |
120 | if (open) edit_file(path)
121 |
122 | invisible(NULL)
123 | }
124 |
--------------------------------------------------------------------------------
/R/add_github_actions_check.R:
--------------------------------------------------------------------------------
1 | #' Setup GitHub Actions to check package
2 | #'
3 | #' @description
4 | #' This function creates a configuration file (`.yaml`) to setup GitHub Actions
5 | #' to check the package.
6 | #' This workflow is derived
7 | #' from \url{https://github.com/r-lib/actions/tree/v2-branch/examples}.
8 | #' This file will be written as `.github/workflows/R-CMD-check.yaml`.
9 | #'
10 | #' @param open A logical value. If `TRUE` (default) the file is opened in the
11 | #' editor.
12 | #'
13 | #' @param overwrite A logical value. If this file is already present and
14 | #' `overwrite = TRUE`, it will be erased and replaced. Default is `FALSE`.
15 | #'
16 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
17 | #' `FALSE`.
18 | #'
19 | #' @details
20 | #' This workflow runs `R CMD check` on the three major operating systems
21 | #' (Ubuntu, macOS, and Windows) using the latest release of R. The package is
22 | #' also checked on Ubuntu (latest version) using the development and previous
23 | #' versions of R.
24 | #'
25 | #' @return No return value.
26 | #'
27 | #' @export
28 | #'
29 | #' @family development functions
30 | #'
31 | #' @examples
32 | #' \dontrun{
33 | #' add_github_actions_check()
34 | #' }
35 |
36 | add_github_actions_check <- function(open = FALSE, overwrite = FALSE,
37 | quiet = FALSE) {
38 |
39 |
40 | stop_if_not_logical(open, overwrite, quiet)
41 |
42 | if (!dir.exists(file.path(path_proj(), ".git"))) {
43 | stop("The project is not versioning with git.")
44 | }
45 |
46 |
47 | path <- file.path(path_proj(), ".github", "workflows", "R-CMD-check.yaml")
48 |
49 |
50 | ## Do not replace current file but open it if required ----
51 |
52 | if (file.exists(path) && !overwrite) {
53 |
54 | if (!open) {
55 |
56 | stop("An '.github/workflows/R-CMD-check.yaml' file is already present. ",
57 | "If you want to replace it, please use `overwrite = TRUE`.")
58 |
59 | } else {
60 |
61 | edit_file(path)
62 | return(invisible(NULL))
63 | }
64 | }
65 |
66 |
67 | ## Copy Template ----
68 |
69 | dir.create(file.path(path_proj(), ".github", "workflows"),
70 | showWarnings = FALSE, recursive = TRUE)
71 |
72 | add_to_buildignore(".github", quiet = FALSE)
73 |
74 | invisible(
75 | file.copy(system.file(file.path("templates", "R-CMD-check.yaml"),
76 | package = "rcompendium"), path))
77 |
78 |
79 | if (!quiet)
80 | ui_done("Writing {ui_value('.github/workflows/R-CMD-check.yaml')} file")
81 |
82 | if (open) edit_file(path)
83 |
84 | invisible(NULL)
85 | }
86 |
--------------------------------------------------------------------------------
/R/add_github_actions_check_badge.R:
--------------------------------------------------------------------------------
1 | #' Add a R CMD Check badge
2 | #'
3 | #' @description
4 | #' This function adds a **R CMD Check** badge to the `README.Rmd`. This function
5 | #' must be run after [add_github_actions_check()] which will setup GitHub
6 | #' Actions to check and test the package.
7 | #'
8 | #' Make sure that 1) a `README.Rmd` file exists at the project root and 2) it
9 | #' contains a block starting with the line `` and ending
10 | #' with the line ``.
11 | #'
12 | #' Don't forget to re-render the `README.md`.
13 | #'
14 | #' @param organisation A character of length 1. The name of the GitHub
15 | #' organisation to host the package. If `NULL` (default) the GitHub account
16 | #' will be used.
17 | #'
18 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
19 | #' `FALSE`.
20 | #'
21 | #' @return A badge as a markdown expression.
22 | #'
23 | #' @export
24 | #'
25 | #' @family adding badges
26 | #'
27 | #' @examples
28 | #' \dontrun{
29 | #' add_github_actions_check_badge()
30 | #' }
31 |
32 | add_github_actions_check_badge <- function(organisation = NULL,
33 | quiet = FALSE) {
34 |
35 |
36 | stop_if_not_logical(quiet)
37 |
38 | ## Check if GH Actions are set ----
39 |
40 | if (!file.exists(file.path(path_proj(), ".github", "workflows",
41 | "R-CMD-check.yaml"))) {
42 | stop("Please run `add_github_actions_check()` to setup GitHub Actions.")
43 | }
44 |
45 |
46 | ## Retrieve GitHub pseudo/organization ----
47 |
48 | if (!is.null(organisation)) {
49 |
50 | github <- organisation
51 |
52 | } else {
53 |
54 | github <- gh::gh_whoami()$"login"
55 |
56 | if (is.null(github)) {
57 | stop("Unable to find GitHub username. Please run ",
58 | "`?gert::git_config_global` for more information.")
59 | }
60 | }
61 |
62 |
63 | stop_if_not_string(github)
64 |
65 |
66 | ## Check URL ----
67 |
68 | is_gh_user()
69 |
70 | project_name <- get_package_name()
71 |
72 |
73 | ## Create Badge Markdown Expression ----
74 |
75 | alt <- "R CMD Check"
76 | href <- paste("https://github.com", github, project_name,
77 | "actions/workflows/R-CMD-check.yaml", sep = "/")
78 | img <- paste("https://github.com", github, project_name,
79 | "actions/workflows/R-CMD-check.yaml/badge.svg", sep = "/")
80 |
81 | badge <- paste0("[![", alt, "](", img, ")](", href, ")")
82 |
83 |
84 | ## Add Badge ----
85 |
86 | add_badge(badge, pattern = alt)
87 |
88 | if (!quiet) {
89 | ui_done(paste0("Adding {ui_field('R CMD Check')} badge to ",
90 | "{ui_value('README.Rmd')}"))
91 | }
92 |
93 |
94 | invisible(badge)
95 | }
96 |
--------------------------------------------------------------------------------
/R/add_github_actions_citation.R:
--------------------------------------------------------------------------------
1 | #' Setup GitHub Actions to update CITATION.cff
2 | #'
3 | #' @description
4 | #' This function creates a configuration file (`.yaml`) to setup GitHub Actions
5 | #' to update the `CITATION.cff`.
6 | #' This workflow is derived
7 | #' from \url{https://github.com/r-lib/actions/tree/v2-branch/examples}.
8 | #' This file will be written as `.github/workflows/update-citation-cff.yaml`.
9 | #'
10 | #' This function also create the `CITATION.cff` using the package [cffr].
11 | #'
12 | #' @param open A logical value. If `TRUE` (default) the file is opened in the
13 | #' editor.
14 | #'
15 | #' @param overwrite A logical value. If this file is already present and
16 | #' `overwrite = TRUE`, it will be erased and replaced. Default is `FALSE`.
17 | #'
18 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
19 | #' `FALSE`.
20 | #'
21 | #' @return No return value.
22 | #'
23 | #' @export
24 | #'
25 | #' @family development functions
26 | #'
27 | #' @examples
28 | #' \dontrun{
29 | #' add_github_actions_citation()
30 | #' }
31 |
32 | add_github_actions_citation <- function(open = FALSE, overwrite = FALSE,
33 | quiet = FALSE) {
34 |
35 |
36 | stop_if_not_logical(open, overwrite, quiet)
37 |
38 | if (!dir.exists(file.path(path_proj(), ".git"))) {
39 | stop("The project is not versioning with git.")
40 | }
41 |
42 |
43 | path <- file.path(path_proj(), ".github", "workflows",
44 | "update-citation-cff.yaml")
45 |
46 |
47 | ## Do not replace current file but open it if required ----
48 |
49 | if (file.exists(path) && !overwrite) {
50 |
51 | if (!open) {
52 |
53 | stop("An '.github/workflows/update-citation-cff.yaml' file is already ",
54 | "present. If you want to replace it, please use `overwrite = TRUE`.")
55 |
56 | } else {
57 |
58 | edit_file(path)
59 | return(invisible(NULL))
60 | }
61 | }
62 |
63 |
64 | ## Copy Template ----
65 |
66 | dir.create(file.path(path_proj(), ".github", "workflows"),
67 | showWarnings = FALSE, recursive = TRUE)
68 |
69 | add_to_buildignore(".github", quiet = FALSE)
70 |
71 | invisible(
72 | file.copy(system.file(file.path("templates", "update-citation-cff.yaml"),
73 | package = "rcompendium"), path))
74 |
75 |
76 | if (!quiet)
77 | ui_done(paste0("Writing {ui_value('.github/workflows/",
78 | "update-citation-cff.yaml')} file"))
79 |
80 |
81 | ## Add CITATION.cff file ----
82 |
83 | cffr::cff_write(verbose = FALSE)
84 |
85 |
86 | ## Messages ----
87 |
88 | if (!quiet) ui_done("Writing {ui_value('CITATION.cff')} file")
89 |
90 | if (open) edit_file(path)
91 |
92 | invisible(NULL)
93 | }
94 |
--------------------------------------------------------------------------------
/R/add_github_actions_codecov.R:
--------------------------------------------------------------------------------
1 | #' Setup GitHub Actions to report code coverage
2 | #'
3 | #' @description
4 | #' This function creates a configuration file (`.yaml`) to setup GitHub Actions
5 | #' to report code coverage when testing the package.
6 | #' This workflow is derived
7 | #' from \url{https://github.com/r-lib/actions/tree/v2-branch/examples}.
8 | #' This file will be written as `.github/workflows/test-coverage.yaml`.
9 | #'
10 | #' @param open A logical value. If `TRUE` (default) the file is opened in the
11 | #' editor.
12 | #'
13 | #' @param overwrite A logical value. If this file is already present and
14 | #' `overwrite = TRUE`, it will be erased and replaced. Default is `FALSE`.
15 | #'
16 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
17 | #' `FALSE`.
18 | #'
19 | #' @return No return value.
20 | #'
21 | #' @export
22 | #'
23 | #' @family development functions
24 | #'
25 | #' @examples
26 | #' \dontrun{
27 | #' add_github_actions_codecov()
28 | #' }
29 |
30 | add_github_actions_codecov <- function(open = FALSE, overwrite = FALSE,
31 | quiet = FALSE) {
32 |
33 |
34 | stop_if_not_logical(open, overwrite, quiet)
35 |
36 | if (!dir.exists(file.path(path_proj(), ".git"))) {
37 | stop("The project is not versioning with git.")
38 | }
39 |
40 |
41 | path <- file.path(path_proj(), ".github", "workflows", "test-coverage.yaml")
42 |
43 |
44 | ## Do not replace current file but open it if required ----
45 |
46 | if (file.exists(path) && !overwrite) {
47 |
48 | if (!open) {
49 |
50 | stop("An '.github/workflows/test-coverage.yaml' file is already ",
51 | "present. If you want to replace it, please use `overwrite = TRUE`")
52 |
53 | } else {
54 |
55 | edit_file(path)
56 | return(invisible(NULL))
57 | }
58 | }
59 |
60 |
61 | ## Copy Template ----
62 |
63 | dir.create(file.path(path_proj(), ".github", "workflows"),
64 | showWarnings = FALSE, recursive = TRUE)
65 |
66 | add_to_buildignore(".github", quiet = FALSE)
67 |
68 | invisible(
69 | file.copy(system.file(file.path("templates", "test-coverage.yaml"),
70 | package = "rcompendium"), path))
71 |
72 |
73 | if (!quiet)
74 | ui_done("Writing {ui_value('.github/workflows/test-coverage.yaml')} file")
75 |
76 | if (open) edit_file(path)
77 |
78 | invisible(NULL)
79 | }
80 |
--------------------------------------------------------------------------------
/R/add_github_actions_codecov_badge.R:
--------------------------------------------------------------------------------
1 | #' Add a Test coverage badge
2 | #'
3 | #' @description
4 | #' This function adds a **Test coverage** badge to the `README.Rmd`. This
5 | #' function must be run after [add_github_actions_codecov()] which will setup
6 | #' GitHub Actions to report the percentage of code cover by units tests.
7 | #'
8 | #' Make sure that 1) a `README.Rmd` file exists at the project root and 2) it
9 | #' contains a block starting with the line `` and ending
10 | #' with the line ``.
11 | #'
12 | #' Don't forget to re-render the `README.md`.
13 | #'
14 | #' @param organisation A character of length 1. The name of the GitHub
15 | #' organisation to host the package. If `NULL` (default) the GitHub account
16 | #' will be used.
17 | #'
18 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
19 | #' `FALSE`.
20 | #'
21 | #' @return A badge as a markdown expression.
22 | #'
23 | #' @export
24 | #'
25 | #' @family adding badges
26 | #'
27 | #' @examples
28 | #' \dontrun{
29 | #' add_github_actions_codecov_badge()
30 | #' }
31 |
32 | add_github_actions_codecov_badge <- function(organisation = NULL,
33 | quiet = FALSE) {
34 |
35 |
36 | stop_if_not_logical(quiet)
37 |
38 | ## Check if GH Actions are set ----
39 |
40 | if (!file.exists(file.path(path_proj(), ".github", "workflows",
41 | "test-coverage.yaml"))) {
42 | stop("Please run `add_github_actions_codecov()` to setup GitHub Actions.")
43 | }
44 |
45 |
46 | ## Retrieve GitHub pseudo/organization ----
47 |
48 | if (!is.null(organisation)) {
49 |
50 | github <- organisation
51 |
52 | } else {
53 |
54 | github <- gh::gh_whoami()$"login"
55 |
56 | if (is.null(github)) {
57 | stop("Unable to find GitHub username. Please run ",
58 | "`?gert::git_config_global` for more information.")
59 | }
60 | }
61 |
62 |
63 | stop_if_not_string(github)
64 |
65 |
66 | ## Check URL ----
67 |
68 | is_gh_user()
69 |
70 | project_name <- get_package_name()
71 |
72 |
73 | ## Create Badge Markdown Expression ----
74 |
75 | alt <- "Test coverage"
76 | href <- paste("https://github.com", github, project_name,
77 | "actions/workflows/test-coverage.yaml", sep = "/")
78 | img <- paste("https://github.com", github, project_name,
79 | "actions/workflows/test-coverage.yaml/badge.svg", sep = "/")
80 |
81 | badge <- paste0("[![", alt, "](", img, ")](", href, ")")
82 |
83 |
84 | ## Add Badge ----
85 |
86 | add_badge(badge, pattern = alt)
87 |
88 | if (!quiet) {
89 | ui_done(paste0("Adding {ui_field('Test coverage')} badge to ",
90 | "{ui_value('README.Rmd')}"))
91 | }
92 |
93 |
94 | invisible(badge)
95 | }
96 |
--------------------------------------------------------------------------------
/R/add_github_actions_codemeta.R:
--------------------------------------------------------------------------------
1 | #' Setup GitHub Actions to update codemeta.json
2 | #'
3 | #' @description
4 | #' This function creates a configuration file (`.yaml`) to setup GitHub Actions
5 | #' to update the `codemeta.json`.
6 | #' This workflow is derived
7 | #' from \url{https://github.com/r-lib/actions/tree/v2-branch/examples}.
8 | #' This file will be written as `.github/workflows/update-citation-cff.yaml`.
9 | #'
10 | #' This function also create the `codemeta.json` using the package [codemetar].
11 | #'
12 | #' @param open A logical value. If `TRUE` (default) the file is opened in the
13 | #' editor.
14 | #'
15 | #' @param overwrite A logical value. If this file is already present and
16 | #' `overwrite = TRUE`, it will be erased and replaced. Default is `FALSE`.
17 | #'
18 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
19 | #' `FALSE`.
20 | #'
21 | #' @return No return value.
22 | #'
23 | #' @export
24 | #'
25 | #' @family development functions
26 | #'
27 | #' @examples
28 | #' \dontrun{
29 | #' add_github_actions_codemeta()
30 | #' }
31 |
32 | add_github_actions_codemeta <- function(open = FALSE, overwrite = FALSE,
33 | quiet = FALSE) {
34 |
35 |
36 | stop_if_not_logical(open, overwrite, quiet)
37 |
38 | if (!dir.exists(file.path(path_proj(), ".git"))) {
39 | stop("The project is not versioning with git.")
40 | }
41 |
42 |
43 | path <- file.path(path_proj(), ".github", "workflows", "update-codemeta.yaml")
44 |
45 |
46 | ## Do not replace current file but open it if required ----
47 |
48 | if (file.exists(path) && !overwrite) {
49 |
50 | if (!open) {
51 |
52 | stop("An '.github/workflows/update-codemeta.yaml' file is already ",
53 | "present. If you want to replace it, please use `overwrite = TRUE`.")
54 |
55 | } else {
56 |
57 | edit_file(path)
58 |
59 | return(invisible(NULL))
60 | }
61 | }
62 |
63 |
64 | ## Copy Template ----
65 |
66 | dir.create(file.path(path_proj(), ".github", "workflows"),
67 | showWarnings = FALSE, recursive = TRUE)
68 |
69 | add_to_buildignore(".github", quiet = FALSE)
70 |
71 | invisible(
72 | file.copy(system.file(file.path("templates", "update-codemeta.yaml"),
73 | package = "rcompendium"), path))
74 |
75 |
76 | if (!quiet)
77 | ui_done(paste0("Writing {ui_value('.github/workflows/",
78 | "update-codemeta.yaml')} file"))
79 |
80 |
81 | ## Add codemeta.json file ----
82 |
83 | codemetar::write_codemeta(verbose = FALSE)
84 |
85 |
86 | ## Messages ----
87 |
88 | if (!quiet) ui_done("Writing {ui_value('codemeta.json')} file")
89 |
90 | if (open) edit_file(path)
91 |
92 | invisible(NULL)
93 | }
94 |
--------------------------------------------------------------------------------
/R/add_github_actions_document.R:
--------------------------------------------------------------------------------
1 | #' Setup GitHub Actions to document package
2 | #'
3 | #' @description
4 | #' This function creates a configuration file (`.yaml`) to setup GitHub Actions
5 | #' to document the package and update the `Rd` files in the `man/`, the
6 | #' `NAMESPACE` and `DESCRIPTION` files.
7 | #' This workflow is derived
8 | #' from \url{https://github.com/r-lib/actions/tree/v2-branch/examples}.
9 | #' This file will be written as `.github/workflows/document-package.yaml`.
10 | #'
11 | #' @param open A logical value. If `TRUE` (default) the file is opened in the
12 | #' editor.
13 | #'
14 | #' @param overwrite A logical value. If this file is already present and
15 | #' `overwrite = TRUE`, it will be erased and replaced. Default is `FALSE`.
16 | #'
17 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
18 | #' `FALSE`.
19 | #'
20 | #' @return No return value.
21 | #'
22 | #' @export
23 | #'
24 | #' @family development functions
25 | #'
26 | #' @examples
27 | #' \dontrun{
28 | #' add_github_actions_document()
29 | #' }
30 |
31 | add_github_actions_document <- function(open = FALSE, overwrite = FALSE,
32 | quiet = FALSE) {
33 |
34 |
35 | stop_if_not_logical(open, overwrite, quiet)
36 |
37 | if (!dir.exists(file.path(path_proj(), ".git"))) {
38 | stop("The project is not versioning with git.")
39 | }
40 |
41 |
42 | path <- file.path(path_proj(), ".github", "workflows",
43 | "document-package.yaml")
44 |
45 |
46 | ## Do not replace current file but open it if required ----
47 |
48 | if (file.exists(path) && !overwrite) {
49 |
50 | if (!open) {
51 |
52 | stop("An '.github/workflows/document-package.yaml' file is already ",
53 | "present. If you want to replace it, please use `overwrite = TRUE`.")
54 |
55 | } else {
56 |
57 | edit_file(path)
58 | return(invisible(NULL))
59 | }
60 | }
61 |
62 |
63 | ## Copy Template ----
64 |
65 | dir.create(file.path(path_proj(), ".github", "workflows"),
66 | showWarnings = FALSE, recursive = TRUE)
67 |
68 | add_to_buildignore(".github", quiet = FALSE)
69 |
70 | invisible(
71 | file.copy(system.file(file.path("templates", "document-package.yaml"),
72 | package = "rcompendium"), path))
73 |
74 |
75 | if (!quiet) {
76 | ui_done(paste0("Writing ",
77 | "{ui_value('.github/workflows/document-package.yaml')} ",
78 | "file"))
79 | }
80 |
81 |
82 | if (open) edit_file(path)
83 |
84 | invisible(NULL)
85 | }
86 |
--------------------------------------------------------------------------------
/R/add_github_actions_pkgdown.R:
--------------------------------------------------------------------------------
1 | #' Setup GitHub Actions to build and deploy package website
2 | #'
3 | #' @description
4 | #' This function creates a configuration file (`.yaml`) to setup GitHub Actions
5 | #' to automatically build and deploy the website using
6 | #' [`pkgdown`](https://pkgdown.r-lib.org/index.html). This workflow is derived
7 | #' from \url{https://github.com/r-lib/actions/tree/v2-branch/examples}.
8 | #' This file will be written as `.github/workflows/pkgdown.yaml`.
9 | #' An additional empty file (`_pkgdown.yaml`) will also be written: it can be
10 | #' used to customize the website.
11 | #'
12 | #' @param open A logical value. If `TRUE` (default) the file is opened in the
13 | #' editor.
14 | #'
15 | #' @param overwrite A logical value. If this file is already present and
16 | #' `overwrite = TRUE`, it will be erased and replaced. Default is `FALSE`.
17 | #'
18 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
19 | #' `FALSE`.
20 | #'
21 | #' @return No return value.
22 | #'
23 | #' @export
24 | #'
25 | #' @family development functions
26 | #'
27 | #' @examples
28 | #' \dontrun{
29 | #' add_github_actions_pkgdown()
30 | #' }
31 |
32 | add_github_actions_pkgdown <- function(open = FALSE, overwrite = FALSE,
33 | quiet = FALSE) {
34 |
35 |
36 | stop_if_not_logical(open, overwrite, quiet)
37 |
38 | if (!dir.exists(file.path(path_proj(), ".git"))) {
39 | stop("The project is not versioning with git.")
40 | }
41 |
42 | path <- file.path(path_proj(), ".github", "workflows", "pkgdown.yaml")
43 |
44 |
45 | ## Do not replace current file but open it if required ----
46 |
47 | if (file.exists(path) && !overwrite) {
48 |
49 | if (!open) {
50 |
51 | stop("An '.github/workflows/pkgdown.yaml' file is already present. ",
52 | "If you want to replace it, please use `overwrite = TRUE`.")
53 |
54 | } else {
55 |
56 | edit_file(path)
57 | return(invisible(NULL))
58 | }
59 | }
60 |
61 |
62 | ## Copy Template ----
63 |
64 | dir.create(file.path(path_proj(), ".github", "workflows"),
65 | showWarnings = FALSE, recursive = TRUE)
66 |
67 | add_to_buildignore(".github", quiet = FALSE)
68 |
69 | invisible(
70 | file.copy(system.file(file.path("templates", "pkgdown.yaml"),
71 | package = "rcompendium"), path))
72 |
73 |
74 | if (!quiet)
75 | ui_done("Writing {ui_value('.github/workflows/pkgdown.yaml')} file")
76 |
77 |
78 | ## Write (Empty) Custom Config file ---
79 |
80 | if (!file.exists(file.path(path_proj(), "_pkgdown.yaml"))) {
81 | file.create(file.path(path_proj(), "_pkgdown.yaml"))
82 | add_to_buildignore("_pkgdown.yaml", quiet = quiet)
83 | }
84 |
85 |
86 | if (open) edit_file(path)
87 |
88 | invisible(NULL)
89 | }
90 |
--------------------------------------------------------------------------------
/R/add_github_actions_pkgdown_badge.R:
--------------------------------------------------------------------------------
1 | #' Add a Website badge
2 | #'
3 | #' @description
4 | #' This function adds a **Website** badge to the `README.Rmd`. This function
5 | #' must be run after [add_github_actions_pkgdown()] which will setup
6 | #' GitHub Actions to build and deploy the package website.
7 | #'
8 | #' Make sure that 1) a `README.Rmd` file exists at the project root and 2) it
9 | #' contains a block starting with the line `` and ending
10 | #' with the line ``.
11 | #'
12 | #' Don't forget to re-render the `README.md`.
13 | #'
14 | #' @param organisation A character of length 1. The name of the GitHub
15 | #' organisation to host the package. If `NULL` (default) the GitHub account
16 | #' will be used.
17 | #'
18 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
19 | #' `FALSE`.
20 | #'
21 | #' @return A badge as a markdown expression.
22 | #'
23 | #' @export
24 | #'
25 | #' @family adding badges
26 | #'
27 | #' @examples
28 | #' \dontrun{
29 | #' add_github_actions_pkgdown_badge()
30 | #' }
31 |
32 | add_github_actions_pkgdown_badge <- function(organisation = NULL,
33 | quiet = FALSE) {
34 |
35 |
36 | stop_if_not_logical(quiet)
37 |
38 | ## Check if GH Actions are set ----
39 |
40 | if (!file.exists(file.path(path_proj(), ".github", "workflows",
41 | "pkgdown.yaml"))) {
42 | stop("Please run `add_github_actions_pkgdown()` to setup GitHub Actions.")
43 | }
44 |
45 |
46 | ## Retrieve GitHub pseudo/organization ----
47 |
48 | if (!is.null(organisation)) {
49 |
50 | github <- organisation
51 |
52 | } else {
53 |
54 | github <- gh::gh_whoami()$"login"
55 |
56 | if (is.null(github)) {
57 | stop("Unable to find GitHub username. Please run ",
58 | "`?gert::git_config_global` for more information.")
59 | }
60 | }
61 |
62 | stop_if_not_string(github)
63 |
64 |
65 | ## Check URL ----
66 |
67 | is_gh_user()
68 |
69 | project_name <- get_package_name()
70 |
71 |
72 | ## Create Badge Markdown Expression ----
73 |
74 | alt <- "Website"
75 | href <- paste("https://github.com", github, project_name,
76 | "actions/workflows/pkgdown.yaml", sep = "/")
77 | img <- paste("https://github.com", github, project_name,
78 | "actions/workflows/pkgdown.yaml/badge.svg", sep = "/")
79 |
80 | badge <- paste0("[![", alt, "](", img, ")](", href, ")")
81 |
82 |
83 | ## Add Badge ----
84 |
85 | add_badge(badge, pattern = alt)
86 |
87 | if (!quiet) {
88 | ui_done(paste0("Adding {ui_field('Website deployment')} badge to ",
89 | "{ui_value('README.Rmd')}"))
90 | }
91 |
92 |
93 | invisible(badge)
94 | }
95 |
--------------------------------------------------------------------------------
/R/add_github_actions_render.R:
--------------------------------------------------------------------------------
1 | #' Setup GitHub Actions to render README
2 | #'
3 | #' @description
4 | #' This function creates a configuration file (`.yaml`) to setup GitHub Actions
5 | #' to automatically knit the `README.Rmd` after a push. This workflow will be
6 | #' triggered only if the `README.Rmd` has been modified since the last commit.
7 | #' This workflow is derived
8 | #' from \url{https://github.com/r-lib/actions/tree/v2-branch/examples}.
9 | #' This file will be written as `.github/workflows/render-README.yaml`.
10 | #'
11 | #' @param open A logical value. If `TRUE` (default) the file is opened in the
12 | #' editor.
13 | #'
14 | #' @param overwrite A logical value. If this file is already present and
15 | #' `overwrite = TRUE`, it will be erased and replaced. Default is `FALSE`.
16 | #'
17 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
18 | #' `FALSE`.
19 | #'
20 | #' @return No return value.
21 | #'
22 | #' @export
23 | #'
24 | #' @family development functions
25 | #'
26 | #' @examples
27 | #' \dontrun{
28 | #' add_github_actions_render()
29 | #' }
30 |
31 | add_github_actions_render <- function(open = FALSE, overwrite = FALSE,
32 | quiet = FALSE) {
33 |
34 |
35 | stop_if_not_logical(open, overwrite, quiet)
36 |
37 | if (!dir.exists(file.path(path_proj(), ".git"))) {
38 | stop("The project is not versioning with git.")
39 | }
40 |
41 |
42 | path <- file.path(path_proj(), ".github", "workflows", "render-README.yaml")
43 |
44 |
45 | ## Do not replace current file but open it if required ----
46 |
47 | if (file.exists(path) && !overwrite) {
48 |
49 | if (!open) {
50 |
51 | stop("An '.github/workflows/render-README.yaml' file is already present.",
52 | " If you want to replace it, please use `overwrite = TRUE`.")
53 |
54 | } else {
55 |
56 | edit_file(path)
57 | return(invisible(NULL))
58 | }
59 | }
60 |
61 |
62 | ## Copy Template ----
63 |
64 | dir.create(file.path(path_proj(), ".github", "workflows"),
65 | showWarnings = FALSE, recursive = TRUE)
66 |
67 | add_to_buildignore(".github", quiet = FALSE)
68 |
69 | invisible(
70 | file.copy(system.file(file.path("templates", "render-README.yaml"),
71 | package = "rcompendium"), path))
72 |
73 |
74 | if (!quiet)
75 | ui_done("Writing {ui_value('.github/workflows/render-README.yaml')} file")
76 |
77 | if (open) edit_file(path)
78 |
79 | invisible(NULL)
80 | }
81 |
--------------------------------------------------------------------------------
/R/add_license_badge.R:
--------------------------------------------------------------------------------
1 | #' Add a License badge
2 | #'
3 | #' @description
4 | #' This function adds or updates the **License** badge to the `README.Rmd`.
5 | #' This function reads the `License` field of the `DESCRIPTION` file. Ensure
6 | #' that this field is correctly defined. See [add_license()] for further detail.
7 | #'
8 | #' This function requires the presence of a `DESCRIPTION` file at the project
9 | #' root. See [add_description()] for further detail.
10 | #'
11 | #' Make sure that 1) a `README.Rmd` file exists at the project root and 2) it
12 | #' contains a block starting with the line `` and ending
13 | #' with the line ``.
14 | #'
15 | #' Don't forget to re-render the `README.md`.
16 | #'
17 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
18 | #' `FALSE`.
19 | #'
20 | #' @return A badge as a markdown expression.
21 | #'
22 | #' @export
23 | #'
24 | #' @family adding badges
25 | #'
26 | #' @examples
27 | #' \dontrun{
28 | #' add_license_badge()
29 | #' }
30 |
31 | add_license_badge <- function(quiet = FALSE) {
32 |
33 |
34 | ## Checks ----
35 |
36 | stop_if_not_logical(quiet)
37 |
38 | user_license <- read_descr()$"License"
39 | user_license <- gsub(" \\+ file LICENSE", "", user_license)
40 |
41 |
42 | if (!is.null(user_license)) {
43 |
44 | if (user_license %in% licenses$"tag") {
45 |
46 |
47 | ## Create Badge Markdown Expression ----
48 |
49 | color <- licenses[which(licenses$tag == user_license), "color"]
50 |
51 | user_license_encoded <- gsub("-", " v", user_license)
52 | user_license_encoded <- gsub("\\s", "%20", user_license_encoded)
53 | user_license_encoded <- gsub("\\(", "%28", user_license_encoded)
54 | user_license_encoded <- gsub("\\)", "%29", user_license_encoded)
55 | user_license_encoded <- gsub(">", "%3E", user_license_encoded)
56 | user_license_encoded <- gsub("=", "%3D", user_license_encoded)
57 |
58 | alt <- paste0("License: ", user_license)
59 | href <- licenses[which(licenses$tag == user_license), "url"]
60 | img <- paste0("https://img.shields.io/badge/License-",
61 | user_license_encoded, "-", color, ".svg")
62 |
63 | badge <- paste0("[![", alt, "](", img, ")](", href, ")")
64 |
65 |
66 | ## Add Badge ----
67 |
68 | add_badge(badge, pattern = "License")
69 |
70 | if (!quiet) {
71 | ui_done(paste0("Adding {ui_field('License')} badge to ",
72 | "{ui_value('README.Rmd')}"))
73 | }
74 |
75 | } else {
76 |
77 | ui_oops("Unknow {ui_field('License')} type in {ui_value('DESCRIPTION')}")
78 | ui_todo("See {ui_code('?add_license()')} for further information")
79 | }
80 |
81 | } else {
82 |
83 | ui_oops("No {ui_field('License')} field in {ui_value('DESCRIPTION')}")
84 | ui_todo("See {ui_code('?add_license()')} for further information")
85 | }
86 |
87 | invisible(badge)
88 | }
89 |
--------------------------------------------------------------------------------
/R/add_lifecycle_badge.R:
--------------------------------------------------------------------------------
1 | #' Add a Life Cycle badge
2 | #'
3 | #' @description
4 | #' This function adds or updates the **Life Cycle** badge to the `README.Rmd`.
5 | #' It is based on the standard defined at
6 | #' \url{https://lifecycle.r-lib.org/articles/stages.html}.
7 | #'
8 | #' Make sure that 1) a `README.Rmd` file exists at the project root and 2) it
9 | #' contains a block starting with the line `` and ending
10 | #' with the line ``.
11 | #'
12 | #' Don't forget to re-render the `README.md`.
13 | #'
14 | #' @param lifecycle A character of length 1. Accepted stages are:
15 | #' `'experimental'` (default), `'stable'`, `'deprecated'`, or `'superseded'`.
16 | #'
17 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
18 | #' `FALSE`.
19 | #'
20 | #' @details
21 | #' The project can have the following life cycle stage:
22 | #' \itemize{
23 | #' \item **Experimental** - An experimental project is made available so user
24 | #' can try it out and provide feedback, but come with no promises for long
25 | #' term stability.
26 | #' \item **Stable** - A project is considered stable when the author is happy
27 | #' with its interface, does not see major issues, and is happy to share it
28 | #' with the world.
29 | #' \item **Superseded** - A superseded project has a known better
30 | #' alternative, and it is not going away. Superseded project will not receive
31 | #' new features, but will receive any critical bug fixes needed to keep it
32 | #' working.
33 | #' \item **Deprecated** - A deprecated project has a better alternative
34 | #' available and is scheduled for removal.
35 | #' }
36 | #'
37 | #' @return A badge as a markdown expression.
38 | #'
39 | #' @export
40 | #'
41 | #' @family adding badges
42 | #'
43 | #' @examples
44 | #' \dontrun{
45 | #' add_lifecycle_badge()
46 | #' add_lifecycle_badge(lifecycle = "stable")
47 | #' }
48 |
49 | add_lifecycle_badge <- function(lifecycle = "experimental", quiet = FALSE) {
50 |
51 |
52 | ## Checks ----
53 |
54 | stop_if_not_logical(quiet)
55 |
56 | stop_if_not_string(lifecycle)
57 |
58 | if (!(tolower(lifecycle) %in% c("experimental", "stable", "deprecated",
59 | "superseded"))) {
60 | stop("Argument 'lifecycle' must be of among 'experimental', 'stable', ",
61 | "'deprecated', or 'superseded'.")
62 | }
63 |
64 |
65 | if (!file.exists(file.path(path_proj(), "README.Rmd"))) {
66 | stop("The file 'README.Rmd' cannot be found.")
67 | }
68 |
69 |
70 | ## Create Badge Markdown Expression ----
71 |
72 | color <- switch(lifecycle,
73 | `stable` = "green",
74 | `experimental` = "orange",
75 | `deprecated` = "orange",
76 | `superseded` = "blue")
77 |
78 | alt <- "LifeCycle"
79 |
80 | href <- paste0("https://lifecycle.r-lib.org/articles/stages.html#",
81 | lifecycle)
82 |
83 | img <- paste0("https://img.shields.io/badge/lifecycle-", lifecycle, "-",
84 | color)
85 |
86 | badge <- paste0("[![", alt, "](", img, ")](", href, ")")
87 |
88 |
89 | ## Add Badge ----
90 |
91 | add_badge(badge, pattern = alt)
92 |
93 |
94 | if (!quiet) {
95 | ui_done(paste0("Adding {ui_field('Lifecycle')} badge to ",
96 | "{ui_value('README.Rmd')}"))
97 | }
98 |
99 | invisible(badge)
100 | }
101 |
--------------------------------------------------------------------------------
/R/add_makefile.R:
--------------------------------------------------------------------------------
1 | #' Create a Make-like R file
2 | #'
3 | #' @description
4 | #' This function creates a Make-like R file (`make.R`) at the root of the
5 | #' project based on a template. To be used only if the project is a research
6 | #' compendium. The content of this file provides some guidelines. See also
7 | #' [new_compendium()] for further information.
8 | #'
9 | #' @param open A logical value. If `TRUE` (default) the file is opened in the
10 | #' editor.
11 | #'
12 | #' @param overwrite A logical value. If this file is already present and
13 | #' `overwrite = TRUE`, it will be erased and replaced. Default is `FALSE`.
14 | #'
15 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
16 | #' `FALSE`.
17 | #'
18 | #' @inheritParams set_credentials
19 | #'
20 | #' @return No return value.
21 | #'
22 | #' @export
23 | #'
24 | #' @family create files
25 | #'
26 | #' @examples
27 | #' \dontrun{
28 | #' add_makefile()
29 | #' }
30 |
31 | add_makefile <- function(given = NULL, family = NULL, email = NULL,
32 | open = TRUE, overwrite = FALSE, quiet = FALSE) {
33 |
34 |
35 | stop_if_not_logical(open, overwrite, quiet)
36 |
37 | path <- file.path(path_proj(), "make.R")
38 |
39 |
40 | ## Do not replace current file but open it if required ----
41 |
42 | if (file.exists(path) && !overwrite) {
43 |
44 | if (!open) {
45 |
46 | stop("A 'make.R' file is already present. If you want to ",
47 | "replace it, please use `overwrite = TRUE`.")
48 |
49 | } else {
50 |
51 | edit_file(path)
52 | return(invisible(NULL))
53 | }
54 | }
55 |
56 |
57 | ## Get fields values ----
58 |
59 | if (is.null(given)) given <- getOption("given")
60 | if (is.null(family)) family <- getOption("family")
61 | if (is.null(email)) email <- getOption("email")
62 |
63 | stop_if_not_string(given, family, email)
64 |
65 |
66 | project_name <- get_package_name()
67 | today <- format(Sys.time(), "%Y/%m/%d")
68 |
69 |
70 | ## Copy Template ----
71 |
72 | invisible(
73 | file.copy(system.file(file.path("templates", "make.R"),
74 | package = "rcompendium"), path, overwrite = TRUE))
75 |
76 |
77 | ## Update default values ----
78 |
79 |
80 | xfun::gsub_file(path, "{{date}}", today, fixed = TRUE)
81 | xfun::gsub_file(path, "{{project_name}}", project_name, fixed = TRUE)
82 | xfun::gsub_file(path, "{{given}}", given, fixed = TRUE)
83 | xfun::gsub_file(path, "{{family}}", family, fixed = TRUE)
84 | xfun::gsub_file(path, "{{email}}", email, fixed = TRUE)
85 |
86 |
87 | ## Message ----
88 |
89 | if (!quiet) ui_done("Writing {ui_value('make.R')} file")
90 |
91 | add_to_buildignore("make.R", quiet = quiet)
92 |
93 | if (open) edit_file(path)
94 |
95 | invisible(NULL)
96 | }
97 |
--------------------------------------------------------------------------------
/R/add_package_doc.R:
--------------------------------------------------------------------------------
1 | #' Create a package-level documentation file
2 | #'
3 | #' @description
4 | #' This function adds a package-level documentation file (`pkg-package.R`) in
5 | #' the `R/` folder. This file will make help available to the user via `?pkg`
6 | #' (where `pkg` is the name of the package). It a good place to put general
7 | #' directives like `@import` and `@importFrom`.
8 | #'
9 | #' @param open A logical value. If `TRUE` (default) the file is opened in the
10 | #' editor.
11 | #'
12 | #' @param overwrite A logical value. If this file is already present and
13 | #' `overwrite = TRUE`, it will be erased and replaced. Default is `FALSE`.
14 | #'
15 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
16 | #' `FALSE`.
17 | #'
18 | #' @return No return value.
19 | #'
20 | #' @export
21 | #'
22 | #' @family create files
23 | #'
24 | #' @examples
25 | #' \dontrun{
26 | #' add_package_doc()
27 | #' }
28 |
29 | add_package_doc <- function(open = TRUE, overwrite = FALSE, quiet = FALSE) {
30 |
31 |
32 | stop_if_not_logical(open, overwrite, quiet)
33 |
34 | filename <- paste0(get_package_name(), "-package.R")
35 | path <- file.path(path_proj(), "R", filename)
36 |
37 |
38 | ## Do not replace current file but open it if required ----
39 |
40 | if (file.exists(path) && !overwrite) {
41 |
42 | if (!open) {
43 |
44 | stop("A 'R/", filename, "' file is already present. If you want to ",
45 | "replace it, please use `overwrite = TRUE`.")
46 |
47 | } else {
48 |
49 | edit_file(path)
50 | return(invisible(NULL))
51 | }
52 | }
53 |
54 |
55 | if (!dir.exists(file.path(path_proj(), "R")))
56 | dir.create(file.path(path_proj(), "R"), showWarnings = FALSE)
57 |
58 | invisible(
59 | file.copy(system.file(file.path("templates", "package-package.R"),
60 | package = "rcompendium"), path, overwrite = TRUE))
61 |
62 |
63 | if (!quiet) ui_done("Writing {ui_value(paste0('R/', filename))} file")
64 |
65 | if (open) edit_file(path)
66 |
67 | invisible(NULL)
68 | }
69 |
--------------------------------------------------------------------------------
/R/add_r_depend.R:
--------------------------------------------------------------------------------
1 | #' Add minimal R version to DESCRIPTION
2 | #'
3 | #' @description
4 | #' This function adds the minimal R version to the `Depends` field of the
5 | #' `DESCRIPTION` file. This version corresponds to the higher version of R
6 | #' among all dependencies. If no dependencies mentions minimal R version, the
7 | #' `DESCRIPTION` is not modified.
8 | #'
9 | #' @return No return value.
10 | #'
11 | #' @export
12 | #'
13 | #' @family development functions
14 | #'
15 | #' @examples
16 | #' \dontrun{
17 | #' add_r_depend()
18 | #' }
19 |
20 | add_r_depend <- function() {
21 |
22 | r_version <- get_minimal_r_version()
23 |
24 | if (!is.null(r_version)) {
25 |
26 | r_version <- paste0("R (>= ", r_version, ")")
27 |
28 | descr <- read_descr()
29 |
30 | if (is.null(descr$"Depends")) { # No Depends field
31 |
32 | descr$"Depends" <- r_version
33 |
34 | } else {
35 |
36 | depends <- unlist(strsplit(descr$"Depends", "\n\\s+|,|,\\s+"))
37 |
38 | is_r <- grep("R \\(.*\\)", depends)
39 |
40 | if (length(is_r)) { # No R version mentioned
41 |
42 | depends[is_r] <- r_version
43 |
44 | } else { # R version mentioned
45 |
46 | depends <- c(r_version, depends)
47 | }
48 |
49 | descr$"Depends" <- paste0(depends, collapse = ", ")
50 | }
51 |
52 | write_descr(descr)
53 | ui_done(paste0("Adding the following line to {ui_value('DESCRIPTION')}: ",
54 | "{ui_code(paste('Depends:', r_version))}"))
55 |
56 | } else {
57 |
58 | ui_done(paste0("No minimal R version detected"))
59 | }
60 |
61 | invisible(NULL)
62 | }
63 |
--------------------------------------------------------------------------------
/R/add_renv.R:
--------------------------------------------------------------------------------
1 | #' Initialize renv
2 | #'
3 | #' @description
4 | #' This function initializes an `renv` environment for the project by running
5 | #' [renv::init()]. See \url{https://rstudio.github.io/renv/} for further detail.
6 | #'
7 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
8 | #' `FALSE`.
9 | #'
10 | #' @return No return value.
11 | #'
12 | #' @export
13 | #'
14 | #' @family create files
15 | #'
16 | #' @examples
17 | #' \dontrun{
18 | #' add_renv()
19 | #' }
20 |
21 | add_renv <- function(quiet = FALSE) {
22 |
23 | stop_if_not_logical(quiet)
24 |
25 | if (!file.exists(file.path(path_proj(), "renv.lock"))) {
26 |
27 |
28 | ## Disable renv messages ----
29 |
30 | renv_verbose <- options()$"renv.verbose"
31 | on.exit(options("renv.verbose" = renv_verbose))
32 | options("renv.verbose" = FALSE)
33 |
34 |
35 | ## Init renv ----
36 |
37 | renv::init(bare = FALSE, restart = FALSE)
38 |
39 | if (!quiet) {
40 |
41 | ui_done("Creating {ui_value('renv/')}")
42 | ui_done("Writing {ui_value('.Rprofile')}")
43 | ui_done("Writing {ui_value('renv.lock')}")
44 | cli::cat_line()
45 | ui_todo("Call {ui_code('renv::install()')} to install packages")
46 | ui_todo("Call {ui_code('renv::snapshot()')} to update the lockfile")
47 | }
48 |
49 |
50 | ## Add renv files to .Rbuildignore ----
51 |
52 | add_to_buildignore("renv/")
53 | add_to_buildignore(".Rprofile")
54 | add_to_buildignore("renv.lock")
55 |
56 |
57 | ## Add renv files to .Rbuildignore ----
58 |
59 | add_to_gitignore("renv/")
60 | add_to_gitignore(".Rprofile")
61 |
62 |
63 | ## Add renv to Import tag in DESCRIPTION ----
64 |
65 | descr <- read_descr()
66 |
67 | deps <- c(get_deps_in_depends(), read_descr()$"Imports",
68 | read_descr()$"Suggests", read_descr()$"LinkingTo")
69 |
70 | deps_to_add <- c("renv")
71 |
72 | if (!is.null(deps)) {
73 |
74 | deps <- unlist(strsplit(deps, "\n\\s+|,|,\\s+"))
75 | deps <- deps[!(deps == "")]
76 | deps_to_add <- deps_to_add[!(deps_to_add %in% deps)]
77 | }
78 |
79 |
80 | if (length(deps_to_add)) {
81 |
82 | if (!is.null(descr$"Imports")) {
83 |
84 | deps_in_imports <- unlist(strsplit(descr$"Imports", "\n\\s+|,|,\\s+"))
85 | deps_in_imports <- deps_in_imports[!(deps_in_imports == "")]
86 |
87 | } else {
88 |
89 | deps_in_imports <- character(0)
90 | }
91 |
92 | deps_in_imports <- sort(unique(c(deps_in_imports, deps_to_add)))
93 | deps_in_imports <- paste0(deps_in_imports, collapse = ",\n ")
94 |
95 | descr$"Imports" <- paste0("\n ", deps_in_imports)
96 |
97 | if (!quiet) {
98 | msg <- paste0("Imports: ", gsub(",\n ", ", ", deps_in_imports))
99 | ui_done(paste0("Adding the following line in ",
100 | "{ui_value('DESCRIPTION')}: {ui_code(msg)}"))
101 | }
102 | }
103 |
104 | write_descr(descr)
105 |
106 |
107 | ## Update makefile ----
108 |
109 | path <- file.path(path_proj(), "make.R")
110 |
111 | if (file.exists(path)) {
112 |
113 | xfun::gsub_file(path, "devtools::install_deps(upgrade = \"never\")",
114 | "renv::restore()", fixed = TRUE)
115 | }
116 | }
117 |
118 | invisible(NULL)
119 | }
120 |
--------------------------------------------------------------------------------
/R/add_repostatus_badge.R:
--------------------------------------------------------------------------------
1 | #' Add a Repository Status badge
2 | #'
3 | #' @description
4 | #' This function adds or updates the **Repository Status** badge of the project
5 | #' to the `README.Rmd`. It is based on the standard defined by the
6 | #' \url{https://www.repostatus.org} project.
7 | #'
8 | #' Make sure that 1) a `README.Rmd` file exists at the project root and 2) it
9 | #' contains a block starting with the line `` and ending
10 | #' with the line ``.
11 | #'
12 | #' Don't forget to re-render the `README.md`.
13 | #'
14 | #' @param status A character of length 1. Accepted status are: `'concept'`
15 | #' (default), `'wip'`, `'suspended'`, `'abandoned'`, `'active'`,
16 | #' `'inactive'`, or `'unsupported'`.
17 | #'
18 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
19 | #' `FALSE`.
20 | #'
21 | #' @details
22 | #' The project can have the following status:
23 | #' \itemize{
24 | #' \item **Concept** - Minimal or no implementation has been done yet, or the
25 | #' repository is only intended to be a limited example, demo, or
26 | #' proof-of-concept.
27 | #' \item **WIP** - Initial development is in progress, but there has not yet
28 | #' been a stable, usable release suitable for the public.
29 | #' \item **Suspended** - Initial development has started, but there has not
30 | #' yet been a stable, usable release; work has been stopped for the time
31 | #' being but the author(s) intend on resuming work.
32 | #' \item **Abandoned** - Initial development has started, but there has not
33 | #' yet been a stable, usable release; the project has been abandoned and the
34 | #' author(s) do not intend on continuing development.
35 | #' \item **Active** - The project has reached a stable, usable state and is
36 | #' being actively developed.
37 | #' \item **Inactive** - The project has reached a stable, usable state but is
38 | #' no longer being actively developed; support/maintenance will be provided
39 | #' as time allows.
40 | #' \item **Unsupported** - The project has reached a stable, usable state but
41 | #' the author(s) have ceased all work on it. A new maintainer may be desired.
42 | #' }
43 | #'
44 | #' @return A badge as a markdown expression.
45 | #'
46 | #' @export
47 | #'
48 | #' @family adding badges
49 | #'
50 | #' @examples
51 | #' \dontrun{
52 | #' add_repostatus_badge()
53 | #' add_repostatus_badge(status = "active")
54 | #' }
55 |
56 | add_repostatus_badge <- function(status = "concept", quiet = FALSE) {
57 |
58 |
59 | ## Checks ----
60 |
61 | stop_if_not_logical(quiet)
62 |
63 | stop_if_not_string(status)
64 |
65 | if (!(tolower(status) %in% c("concept", "wip", "suspended", "abandoned",
66 | "active", "inactive", "unsupported"))) {
67 |
68 | stop("Argument 'status' must be of among 'concept', 'wip', 'suspended', ",
69 | "'abandoned', 'active', 'inactive', or 'unsupported'.")
70 | }
71 |
72 | if (!file.exists(file.path(path_proj(), "README.Rmd"))) {
73 | stop("The file 'README.Rmd' cannot be found.")
74 | }
75 |
76 |
77 | ## Create Badge Markdown Expression ----
78 |
79 | status <- paste0(
80 | toupper(substr(status, 1, 1)),
81 | tolower(substr(status, 2, nchar(status))))
82 |
83 | status <- ifelse(status == "Wip", "WIP", status)
84 |
85 | alt <- paste0("Project Status: ",
86 | status)
87 | href <- paste0("https://www.repostatus.org/#",
88 | tolower(status))
89 | img <- paste0("https://www.repostatus.org/badges/latest/",
90 | tolower(status), ".svg")
91 |
92 | badge <- paste0("[![", alt, "](", img, ")](", href, ")")
93 |
94 |
95 | ## Add Badge ----
96 |
97 | add_badge(badge, pattern = "Project Status")
98 |
99 |
100 | if (!quiet) {
101 | ui_done(paste0("Adding {ui_field('Repo Status')} badge to ",
102 | "{ui_value('README.Rmd')}"))
103 | }
104 |
105 | invisible(badge)
106 | }
107 |
--------------------------------------------------------------------------------
/R/add_testthat.R:
--------------------------------------------------------------------------------
1 | #' Initialize units tests
2 | #'
3 | #' @description
4 | #' This function initializes units tests settings by running
5 | #' [usethis::use_testthat()] and by adding an example units tests file
6 | #' `tests/testthat/test-demo.R`. The sample file will test a demo function
7 | #' created in `R/fun-demo.R`.
8 | #'
9 | #' @return No return value.
10 | #'
11 | #' @export
12 | #'
13 | #' @family create files
14 | #'
15 | #' @examples
16 | #' \dontrun{
17 | #' add_testthat()
18 | #' }
19 |
20 | add_testthat <- function() {
21 |
22 | if (!file.exists(file.path(path_proj(), "tests", "testthat.R"))) {
23 |
24 | usethis::use_testthat()
25 |
26 | path <- file.path(path_proj(), "tests", "testthat", "test-demo.R")
27 |
28 | if (!file.exists(path)) {
29 |
30 | invisible(
31 | file.copy(system.file(file.path("templates", "test-demo.R"),
32 | package = "rcompendium"), path,
33 | overwrite = TRUE))
34 | }
35 | }
36 |
37 | invisible(NULL)
38 | }
39 |
--------------------------------------------------------------------------------
/R/add_to_buildignore.R:
--------------------------------------------------------------------------------
1 | #' Add to the .Rbuildignore file
2 | #'
3 | #' @description
4 | #' This function adds files/folders to the `.Rbuildignore` file. If a
5 | #' `.Rbuildignore` is already present, files to be ignored while checking
6 | #' package are just added to this file. Otherwise a new file is created.
7 | #'
8 | #' @param x A character vector. One or several files/folders names to be added
9 | #' to the `.Rbuildignore`. This argument is mandatory.
10 | #'
11 | #' @param open A logical value. If `TRUE` the `.Rbuildignore` file is opened in
12 | #' the editor. Default is `FALSE`.
13 | #'
14 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
15 | #' `FALSE`.
16 | #'
17 | #' @return No return value.
18 | #'
19 | #' @export
20 | #'
21 | #' @family development functions
22 | #'
23 | #' @examples
24 | #' \dontrun{
25 | #' add_to_buildignore(open = TRUE)
26 | #' add_to_buildignore(".DS_Store")
27 | #' }
28 |
29 | add_to_buildignore <- function(x, open = FALSE, quiet = FALSE) {
30 |
31 |
32 | if (missing(x) && !open) stop("Argument 'x' is missing.")
33 |
34 | stop_if_not_logical(open, quiet)
35 |
36 |
37 | path <- file.path(path_proj(), ".Rbuildignore")
38 |
39 |
40 | ## Create new file (if missing) ----
41 |
42 | if (!file.exists(path)) {
43 |
44 | invisible(file.create(path))
45 |
46 | if (!quiet) ui_done("Writing {ui_value('.Rbuildignore')} file")
47 | }
48 |
49 |
50 | ## Add file/folder ----
51 |
52 | if (!missing(x)) {
53 |
54 | stopifnot(is.character(x))
55 |
56 |
57 | ## Escape files ----
58 |
59 | x <- gsub("\\.", "\\\\.", x)
60 | x <- gsub("/$", "", x)
61 | x <- paste0("^", x, "$")
62 |
63 |
64 | ## Add files/folders to .Rbuildignore ----
65 |
66 | build_ignore <- readLines(path)
67 |
68 | x <- x[!(x %in% build_ignore)]
69 |
70 | if (length(x)) {
71 |
72 | build_ignore <- c(build_ignore, x)
73 |
74 | writeLines(build_ignore, con = path)
75 |
76 | if (!quiet)
77 | ui_done(paste0("Adding {ui_value(paste0(x, collapse = ", "))} to ",
78 | "{ui_value('.Rbuildignore')}"))
79 | }
80 | }
81 |
82 | if (open) edit_file(path)
83 |
84 | invisible(NULL)
85 | }
86 |
--------------------------------------------------------------------------------
/R/add_to_gitignore.R:
--------------------------------------------------------------------------------
1 | #' Add to the .gitignore file
2 | #'
3 | #' @description
4 | #' This function creates a `.gitignore` file at the root of the project based on
5 | #' a template (specific to R). If a `.gitignore` is already present, files to
6 | #' be untracked by **git** are just added to this file.
7 | #'
8 | #' @param x A character vector. One or several files/folders names to be added
9 | #' to the `.gitignore`.
10 | #'
11 | #' @param open A logical value. If `TRUE` the `.gitignore` file is opened in
12 | #' the editor. Default is `FALSE`.
13 | #'
14 | #' @param quiet A logical value. If `TRUE` messages are deleted. Default is
15 | #' `FALSE`.
16 | #'
17 | #' @return No return value.
18 | #'
19 | #' @export
20 | #'
21 | #' @family development functions
22 | #'
23 | #' @examples
24 | #' \dontrun{
25 | #' add_to_gitignore(open = TRUE)
26 | #' add_to_gitignore(".DS_Store")
27 | #' }
28 |
29 | add_to_gitignore <- function(x, open = FALSE, quiet = FALSE) {
30 |
31 |
32 | stop_if_not_logical(open, quiet)
33 |
34 | path <- file.path(path_proj(), ".gitignore")
35 |
36 |
37 | ## Copy Template ----
38 |
39 | if (!file.exists(path)) {
40 |
41 | invisible(
42 | file.copy(system.file(file.path("templates", "gitignore"),
43 | package = "rcompendium"), path))
44 |
45 | if (!quiet) ui_done("Writing {ui_value('.gitignore')} file")
46 | }
47 |
48 |
49 | ## Add files/folders to .gitignore ----
50 |
51 | if (!missing(x)) {
52 |
53 | stopifnot(is.character(x))
54 |
55 | git_ignore <- readLines(path)
56 |
57 | x <- x[!(x %in% git_ignore)]
58 |
59 | if (length(x)) {
60 |
61 | git_ignore <- c(git_ignore, x)
62 |
63 | writeLines(git_ignore, con = path)
64 |
65 | if (!quiet)
66 | ui_done(paste0("Adding {ui_value(paste0(x, collapse = ", "))} to ",
67 | "{ui_value('.gitignore')}"))
68 | }
69 | }
70 |
71 | if (open) edit_file(path)
72 |
73 | invisible(NULL)
74 | }
75 |
--------------------------------------------------------------------------------
/R/get_all_dependencies.R:
--------------------------------------------------------------------------------
1 | #' Get all external dependencies
2 | #'
3 | #' @description
4 | #' This function gets all the external packages that the project needs. It is
5 | #' used the generate the _Dependencies_ badge ([add_dependencies_badge()]).
6 | #'
7 | #' @param pkg A character of length 1. The name of a CRAN package or `NULL`
8 | #' (default). If `NULL` get dependencies of the local (uninstalled) project
9 | #' (package or compendium).
10 | #'
11 | #' @return A list of three vectors:
12 | #' * `base_deps`, a vector of base packages;
13 | #' * `direct_deps`, a vector of direct packages;
14 | #' * `all_deps`, a vector of all dependencies (recursively obtained).
15 | #'
16 | #' @export
17 | #'
18 | #' @family utilities functions
19 | #'
20 | #' @examples
21 | #' \dontrun{
22 | #' ## Update dependencies ----
23 | #' add_dependencies()
24 | #'
25 | #' ## Get all dependencies ----
26 | #' deps <- get_all_dependencies()
27 | #' unlist(lapply(deps, length))
28 | #'
29 | #' ## Can be used for a CRAN package ----
30 | #' deps <- get_all_dependencies("usethis")
31 | #' unlist(lapply(deps, length))
32 | #' }
33 |
34 | get_all_dependencies <- function(pkg = NULL) {
35 |
36 | if (is.null(pkg)) {
37 |
38 | ## Dev package ----
39 |
40 | direct_deps <- c(get_deps_in_depends(), read_descr()$"Imports",
41 | read_descr()$"LinkingTo")
42 |
43 | if (!is.null(direct_deps)) {
44 |
45 | direct_deps <- unlist(strsplit(direct_deps, "\n\\s+|,|,\\s+"))
46 | direct_deps <- direct_deps[!(direct_deps == "")]
47 |
48 | pkg <- direct_deps
49 |
50 | } else {
51 |
52 | return(list("base_deps" = character(0),
53 | "direct_deps" = character(0),
54 | "all_deps" = character(0)))
55 | }
56 |
57 | } else {
58 |
59 | ## CRAN package ----
60 |
61 | if (length(pkg) > 1) stop("Argument `pkg` must be of length 1 or `NULL`.")
62 |
63 | deps <- utils::available.packages()
64 | deps <- deps[deps[ , "Package"] %in% pkg, ]
65 |
66 | deps <- deps[c("Depends", "Imports", "LinkingTo")]
67 |
68 | deps_depends <- unlist(strsplit(deps["Depends"], ", "))
69 | deps_depends <- deps_depends[!grep("^R\\s\\(", deps_depends)]
70 | deps_imports <- unlist(strsplit(deps["Imports"], ", "))
71 | deps_linkingto <- unlist(strsplit(deps["LinkingTo"], ", "))
72 |
73 | direct_deps <- c(deps_depends, deps_imports, deps_linkingto)
74 | direct_deps <- direct_deps[!is.na(direct_deps)]
75 | direct_deps <- gsub("\\s\\(.+\\)|\\n", "", direct_deps)
76 |
77 | direct_deps <- unlist(strsplit(direct_deps, ","))
78 | }
79 |
80 |
81 | ## List of base packages ----
82 |
83 | base_deps <- c("base", "compiler", "datasets", "graphics", "grDevices",
84 | "grid", "methods", "parallel", "splines", "stats", "stats4",
85 | "tcltk", "tools", "utils")
86 |
87 |
88 | ## List of all dependencies (on which pkg depends) ----
89 |
90 | all_deps <- gtools::getDependencies(pkg, installed = FALSE,
91 | available = FALSE, base = FALSE)
92 | all_deps <- gsub("\\s\\(.+\\)", "", all_deps)
93 | names(all_deps) <- NULL
94 |
95 | basic_deps <- direct_deps[direct_deps %in% base_deps]
96 | names(basic_deps) <- NULL
97 |
98 | direct_deps <- direct_deps[!(direct_deps %in% base_deps)]
99 | names(direct_deps) <- NULL
100 |
101 | list("base_deps" = sort(unique(basic_deps)),
102 | "direct_deps" = sort(unique(direct_deps)),
103 | "all_deps" = sort(unique(all_deps)))
104 | }
105 |
--------------------------------------------------------------------------------
/R/get_all_functions.R:
--------------------------------------------------------------------------------
1 | #' List all functions in the package
2 | #'
3 | #' @description
4 | #' This function returns a list of all the functions (exported and internal)
5 | #' available with the package. As this function scans the `NAMESPACE` and the
6 | #' `R/` folder, it is recommended to run [devtools::document()] before.
7 | #'
8 | #' @return A list of two vectors:
9 | #' * `external`, a vector of exported functions name;
10 | #' * `internal`, a vector of internal functions name.
11 | #'
12 | #' @export
13 | #'
14 | #' @family utilities functions
15 | #'
16 | #' @examples
17 | #' \dontrun{
18 | #' ## Update NAMESPACE ----
19 | #' devtools::document()
20 | #'
21 | #' ## List all implemented functions ----
22 | #' get_all_functions()
23 | #' }
24 |
25 | get_all_functions <- function() {
26 |
27 | if (!dir.exists(file.path(path_proj(), "R"))) {
28 | stop("The directory 'R/' cannot be found.")
29 | }
30 |
31 |
32 | x <- list.files(path = file.path(path_proj(), "R"), pattern = "\\.R$",
33 | full.names = TRUE, ignore.case = TRUE)
34 |
35 |
36 | if (!length(x)) {
37 |
38 | ui_oops("The {ui_value('R/')} folder is empty")
39 |
40 | return(NULL)
41 |
42 | } else {
43 |
44 |
45 | ## Read R files ----
46 |
47 | x <- lapply(x, function(x) readLines(con = x, warn = FALSE))
48 |
49 |
50 | ## Extract function names ----
51 |
52 | x <- lapply(x, function(x) x[grep("\\s{0,}(<-|=)\\s{0,}function\\s{0,}\\(",
53 | x)])
54 | x <- lapply(x, function(x) gsub("\\s{0,}(<-|=)\\s{0,}function.*", "", x))
55 |
56 | x <- unlist(x)
57 | x <- gsub("\\s", "", x)
58 | x <- sort(unique(x))
59 |
60 |
61 | if (length(x)) {
62 |
63 | if (file.exists(file.path(path_proj(), "NAMESPACE"))) {
64 |
65 | namespace <- readLines(con = file.path(path_proj(), "NAMESPACE"),
66 | warn = FALSE)
67 |
68 | exports <- gsub("export\\(|\\)", "",
69 | namespace[grep("^export", namespace)])
70 |
71 | funs <- list("external" = character(0), "internal" = character(0))
72 |
73 | if (length(exports)) {
74 |
75 | funs$"external" <- paste0(x[ (x %in% exports)], "()")
76 | funs$"internal" <- paste0(x[!(x %in% exports)], "()")
77 |
78 | } else {
79 |
80 | funs$"internal" <- paste0(x, "()")
81 | }
82 |
83 | } else {
84 |
85 | funs$"internal" <- paste0(x, "()")
86 | }
87 |
88 | return(funs)
89 |
90 | } else {
91 |
92 | return(NULL)
93 | }
94 | }
95 | }
96 |
--------------------------------------------------------------------------------
/R/get_licenses.R:
--------------------------------------------------------------------------------
1 | #' List all available licenses
2 | #'
3 | #' @description
4 | #' This function returns a list of all available licenses. This is particularly
5 | #' useful to get the right spelling of the license to be passed to
6 | #' [new_package()], [new_compendium()], or [add_license()].
7 | #'
8 | #' @return A `data.frame` with the following two variables:
9 | #' * `tag`, the license name to be used with [add_license()];
10 | #' * `url`, the URL of the license description.
11 | #'
12 | #' @export
13 | #'
14 | #' @family utilities functions
15 | #'
16 | #' @examples
17 | #' get_licenses()
18 |
19 | get_licenses <- function() licenses[ , c("tag", "url")]
20 |
--------------------------------------------------------------------------------
/R/get_minimal_r_version.R:
--------------------------------------------------------------------------------
1 | #' Get required minimal R version
2 | #'
3 | #' @description
4 | #' This function detects the minimal required R version for the project based
5 | #' on minimal required R version of its dependencies. It can be used to update
6 | #' the `Depends` field of the `DESCRIPTION` file.
7 | #'
8 | #' @param pkg A character of length 1. The name of a CRAN package or `NULL`
9 | #' (default). If `NULL` get minimal required R version of the local
10 | #' (uninstalled) project (package or compendium).
11 | #'
12 | #' @return A character with the minimal required R version.
13 | #'
14 | #' @export
15 | #'
16 | #' @family utilities functions
17 | #'
18 | #' @examples
19 | #' \dontrun{
20 | #' ## Update dependencies ----
21 | #' add_dependencies()
22 | #'
23 | #' ## Minimal R version of a project ----
24 | #' get_minimal_r_version()
25 | #'
26 | #' ## Minimal R version of a CRAN package ----
27 | #' get_minimal_r_version("usethis")
28 | #' }
29 |
30 | get_minimal_r_version <- function(pkg = NULL) {
31 |
32 | if (is.null(pkg)) {
33 |
34 | ## Dev package ----
35 |
36 | direct_deps <- c(get_deps_in_depends(), read_descr()$"Imports",
37 | read_descr()$"LinkingTo")
38 |
39 | direct_deps <- unlist(strsplit(direct_deps, "\n\\s+|,|,\\s+"))
40 | direct_deps <- direct_deps[!(direct_deps == "")]
41 |
42 | pkg <- direct_deps
43 |
44 | } else {
45 |
46 | ## CRAN package ----
47 |
48 | if (length(pkg) > 1) stop("Argument `pkg` must be of length 1 or `NULL`.")
49 |
50 | }
51 |
52 | deps <- gtools::getDependencies(pkg, installed = FALSE, available = FALSE)
53 |
54 | if (length(deps)) {
55 |
56 | pkgs <- utils::available.packages()
57 |
58 | r_versions <- pkgs[pkgs[ , "Package"] %in% deps, "Depends"]
59 | r_versions <- unlist(stringr::str_extract_all(string = r_versions,
60 | pattern = "^R \\(.[^,]+\\)$"))
61 | r_versions <- gsub("R \\(|\\)|>|=|\\s", "", r_versions)
62 | r_versions <- r_versions[!is.na(r_versions)]
63 |
64 | r_version <- max(numeric_version(r_versions))
65 | r_version <- strsplit(as.character(r_version), "\\.")[[1]]
66 |
67 | return(paste(r_version[1], r_version[2], sep = "."))
68 |
69 | } else {
70 |
71 | return(NULL)
72 | }
73 | }
74 |
--------------------------------------------------------------------------------
/R/refresh.R:
--------------------------------------------------------------------------------
1 | #' Refresh a package/research compendium
2 | #'
3 | #' @description
4 | #' **This function is about to be removed from `rcompendium`.**
5 | #'
6 | #' This function refreshes a package/research compendium. It will:
7 | #' * Update `.Rd` files and `NAMESPACE` by using [devtools::document()];
8 | #' * Update external packages (in `DESCRIPTION` file) by using
9 | #' [add_dependencies()];
10 | #' * Update badges in `README.Rmd` (if already present);
11 | #' * Re-knitr the `README.Rmd` by using [rmarkdown::render()];
12 | #' * Check package integrity by using [devtools::check()];
13 | #' * Run analysis by sourcing `make.R` (only for compendium).
14 | #'
15 | #' @param make A logical value. If `TRUE` the Make-like R file `make.R` is
16 | #' sourced. Only for research compendium created with [new_compendium()].
17 | #' Default is `FALSE`.
18 | #'
19 | #' @param check A logical value. If `TRUE` package integrity is checked using
20 | #' [devtools::check()].
21 | #' Default is `FALSE`.
22 | #'
23 | #' @param quiet A logical value. If `TRUE` (default) message are deleted.
24 | #'
25 | #' @inheritParams add_dependencies
26 | #'
27 | #' @return No return value.
28 | #'
29 | #' @export
30 | #'
31 | #' @family setup functions
32 | #'
33 | #' @examples
34 | #' \dontrun{
35 | #' library(rcompendium)
36 | #'
37 | #' ## Create an R package ----
38 | #' new_package()
39 | #'
40 | #' ## Start developing functions ----
41 | #' ## ...
42 | #'
43 | #' ## Update package (documentation, dependencies, README) ----
44 | #' refresh()
45 | #' }
46 |
47 | refresh <- function(compendium = NULL, make = FALSE, check = FALSE,
48 | quiet = FALSE) {
49 |
50 |
51 | .Deprecated(msg = "This function is about to be removed from 'rcompendium'")
52 |
53 | is_package()
54 |
55 | stop_if_not_logical(make, check, quiet)
56 |
57 |
58 | ## Loading Project ----
59 |
60 | ui_title("Loading Project")
61 |
62 | suppressMessages(devtools::load_all(quiet = TRUE))
63 |
64 | if (!quiet) {
65 | ui_done("Loading {ui_value(get_package_name())}")
66 | }
67 |
68 |
69 | ## Update Rd files and NAMESPACE ----
70 |
71 | ui_title("Updating Documentation")
72 |
73 | suppressMessages(devtools::document(quiet = TRUE))
74 |
75 | if (!quiet) {
76 | ui_done("Updating {ui_value('Rd files')} and {ui_value('NAMESPACE')}")
77 | }
78 |
79 |
80 | ## Update Dependencies ----
81 |
82 | ui_title("Updating Dependencies")
83 |
84 | add_dependencies(compendium)
85 |
86 |
87 | ## Update Badges ----
88 |
89 | if (file.exists(file.path(path_proj(), "README.Rmd"))) {
90 |
91 | ui_title("Updating Badges")
92 |
93 | read_me <- readLines(con = file.path(path_proj(), "README.Rmd"))
94 |
95 | if (length(grep(paste0("^\\s{0,}\\[!\\[Dependencies"), read_me))) {
96 |
97 | add_dependencies_badge()
98 | }
99 |
100 | if (length(grep(paste0("^\\s{0,}\\[!\\[License"), read_me))) {
101 |
102 | add_license_badge()
103 | }
104 | }
105 |
106 |
107 | ## Update README.md ----
108 |
109 | if (file.exists(file.path(path_proj(), "README.Rmd"))) {
110 |
111 | ui_title("Updating README")
112 |
113 | rmarkdown::render(file.path(path_proj(), "README.Rmd"),
114 | output_format = "md_document", quiet = TRUE)
115 |
116 | if (!quiet)
117 | ui_done("Re-kniting {ui_value('README.Rmd')}")
118 | }
119 |
120 |
121 | ## Check package integrity ----
122 |
123 | if (check) {
124 |
125 | ui_title("Checking Package")
126 |
127 | dev_msg <- suppressMessages(devtools::check(quiet = TRUE))
128 |
129 | print(dev_msg)
130 | }
131 |
132 |
133 | ## Run project (research compendium) ----
134 |
135 | if (make) {
136 |
137 | ui_title("Running Analysis")
138 |
139 | if (file.exists(file.path(path_proj(), "make.R"))) {
140 |
141 | if (!quiet)
142 | ui_info("Sourcing 'make.R'}")
143 |
144 | source(file.path(path_proj(), "make.R"))
145 |
146 | if (!quiet)
147 | ui_done("Done!")
148 |
149 | } else {
150 |
151 | ui_oops("Unable to find {ui_value('make.R')}")
152 | }
153 | }
154 |
155 |
156 | invisible(NULL)
157 | }
158 |
--------------------------------------------------------------------------------
/R/set_credentials.R:
--------------------------------------------------------------------------------
1 | #' Store credentials to the .Rprofile
2 | #'
3 | #' @description
4 | #' This function is used to store user credentials in the `.Rprofile` file.
5 | #' Accepted credentials are listed below. This function is useful if user
6 | #' creates a lot of packages and/or research compendiums.
7 | #'
8 | #' If the `.Rprofile` file does not exist this function will create it. Users
9 | #' need to paste the content of the clipboard to this file.
10 | #'
11 | #' @param given A character of length 1. The given name of the project
12 | #' maintainer.
13 | #'
14 | #' @param family A character of length 1. The family name of the project
15 | #' maintainer.
16 | #'
17 | #' @param email A character of length 1. The email address of the project
18 | #' maintainer.
19 | #'
20 | #' @param orcid A character of length 1. The ORCID of the project maintainer.
21 | #'
22 | #' @param protocol A character of length 1. The GIT protocol used to
23 | #' communicate with the GitHub remote. One of `'https'` or `'ssh'`. If you
24 | #' don't know, keep the default value (i.e. `NULL`) and the protocol will be
25 | #' `'https'`.
26 | #'
27 | #' @return No return value.
28 | #'
29 | #' @export
30 | #'
31 | #' @family setup functions
32 | #'
33 | #' @examples
34 | #' \dontrun{
35 | #' library(rcompendium)
36 | #'
37 | #'
38 | #' ## Define **ONCE FOR ALL** your credentials ----
39 | #'
40 | #' set_credentials("John", "Doe", "john.doe@domain.com",
41 | #' orcid = "9999-9999-9999-9999", protocol = "https")
42 | #' }
43 |
44 | set_credentials <- function(given = NULL, family = NULL, email = NULL,
45 | orcid = NULL, protocol = NULL) {
46 |
47 |
48 | credentials <- as.list(match.call())[-1]
49 |
50 | if (length(credentials)) {
51 |
52 | r_prof <- "## RCompendium Credentials ----"
53 |
54 |
55 | ## Check remote protocol ----
56 |
57 | protocol <- credentials["protocol"]$protocol
58 |
59 | if (!is.null(protocol)) {
60 |
61 | stop_if_not_string(protocol)
62 |
63 | if (!(protocol %in% c("https", "ssh"))) {
64 |
65 | protocol <- NULL
66 | stop("Argument 'protocol' must one among 'https' and 'ssh'.")
67 | }
68 |
69 |
70 | if (!is.null(protocol)) {
71 |
72 | usethis_protocol <- getOption("usethis.protocol")
73 |
74 | if (!is.null(usethis_protocol)) {
75 |
76 | if (usethis_protocol == protocol) {
77 |
78 | ui_oops("Protocol is already set to {ui_value(protocol)}")
79 | protocol <- NULL
80 | }
81 | }
82 | }
83 | }
84 |
85 |
86 | ## Check user credentials ----
87 |
88 | credentials <- credentials[!(names(credentials) %in% "protocol")]
89 |
90 | if (!is.null(credentials)) {
91 |
92 | invisible(lapply(credentials, stop_if_not_string))
93 |
94 | opts <- paste0(names(credentials), " = \"", unlist(credentials), "\"")
95 | opts <- paste0(opts, collapse = ", ")
96 |
97 | r_prof <- c(r_prof, paste0("options(", opts, ")", ""))
98 | }
99 |
100 | if (!is.null(protocol)) {
101 |
102 | opts <- paste0("usethis.protocol = \"", protocol, "\"")
103 | r_prof <- c(r_prof, paste0("options(", opts, ")", ""))
104 | }
105 |
106 |
107 | ## Re-write .Rprofile ----
108 |
109 | ui_todo("Please paste the following lines to the {ui_value('.Rprofile')}:")
110 | usethis::ui_code_block(r_prof)
111 | }
112 |
113 | usethis::edit_r_profile()
114 |
115 | invisible(NULL)
116 | }
117 |
--------------------------------------------------------------------------------
/R/sysdata.rda:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/FRBCesab/rcompendium/c50e80d8a693cef53280d46edbb2e544b5744b22/R/sysdata.rda
--------------------------------------------------------------------------------
/R/utils-checks.R:
--------------------------------------------------------------------------------
1 | ## Utilities functions - Inputs Checks ----
2 |
3 |
4 |
5 | #' **Check if arguments are logical of length 1**
6 | #'
7 | #' @param ... one or several arguments
8 | #'
9 | #' @noRd
10 |
11 | stop_if_not_logical <- function(...) {
12 |
13 | args_values <- list(...)
14 | names(args_values) <- as.list(match.call())[-1]
15 |
16 | if (length(args_values)) {
17 |
18 | is_logical <- unlist(lapply(args_values, length))
19 |
20 | if (any(is_logical != 1)) {
21 | stop("Argument '", names(is_logical[is_logical != 1])[1],
22 | "' must be a logical of length 1.")
23 | }
24 |
25 | is_logical <- unlist(lapply(args_values, is.logical))
26 |
27 | if (any(!is_logical)) {
28 | stop("Argument '", names(is_logical[!is_logical])[1],
29 | "' must be a logical of length 1.")
30 | }
31 | }
32 |
33 | invisible(NULL)
34 | }
35 |
36 |
37 |
38 | #' **Check if arguments are character of length 1**
39 | #'
40 | #' @param ... one or several arguments
41 | #'
42 | #' @noRd
43 |
44 | stop_if_not_string <- function(...) {
45 |
46 | args_values <- list(...)
47 | names(args_values) <- as.list(match.call())[-1]
48 |
49 | if (length(args_values)) {
50 |
51 | is_string <- unlist(lapply(args_values, length))
52 |
53 | if (any(is_string != 1)) {
54 | stop("Argument '", names(is_string[is_string != 1])[1],
55 | "' must be a character of length 1.")
56 | }
57 |
58 | is_string <- unlist(lapply(args_values, is.character))
59 |
60 | if (any(!is_string)) {
61 | stop("Argument '", names(is_string[!is_string])[1],
62 | "' must be a character of length 1.")
63 | }
64 | }
65 |
66 | invisible(NULL)
67 | }
68 |
69 |
70 |
71 | #' **Check if arguments are numeric of length 1**
72 | #'
73 | #' @param ... one or several arguments
74 | #'
75 | #' @noRd
76 |
77 | stop_if_not_numeric <- function(...) {
78 |
79 | args_values <- list(...)
80 | names(args_values) <- as.list(match.call())[-1]
81 |
82 | if (length(args_values)) {
83 |
84 | is_numeric <- unlist(lapply(args_values, length))
85 |
86 | if (any(is_numeric != 1)) {
87 | stop("Argument '", names(is_numeric[is_numeric != 1])[1],
88 | "' must be a numeric of length 1.")
89 | }
90 |
91 | is_numeric <- unlist(lapply(args_values, is.numeric))
92 |
93 | if (any(!is_numeric)) {
94 | stop("Argument '", names(is_numeric[!is_numeric])[1],
95 | "' must be a numeric of length 1.")
96 | }
97 | }
98 |
99 | invisible(NULL)
100 | }
101 |
--------------------------------------------------------------------------------
/_pkgdown.yml:
--------------------------------------------------------------------------------
1 | url: https://frbcesab.github.io/rcompendium
2 |
3 | template:
4 | bootstrap: 5
5 |
6 | reference:
7 | - title: Prerequisites
8 | desc: |
9 | High level overview of the package
10 | contents:
11 | - rcompendium
12 |
13 | - title: Setup functions
14 | desc: |
15 | These four functions are usually the only ones user needs to run. The use of
16 | `set_credentials` is strongly recommended to permanently store user
17 | information (name, email, orcid, etc.) in the `.Rprofile`. This function
18 | must be run one time. The function `new_package` must be used to create an
19 | R package structure whereas `new_compendium` creates a new research
20 | compendium structure (i.e. R package structure with some additional
21 | files/folders). After that user can start to develop his/her project and
22 | run `refresh` to frequently update the package/compendium components (`Rd`
23 | files, `NAMESPACE`, dependencies, badges, `README.md`, etc.)
24 | contents:
25 | - set_credentials
26 | - new_package
27 | - new_compendium
28 | - refresh
29 |
30 | - title: Create files
31 | desc: |
32 | These function write files specific to R package and research compendium
33 | (`add_makefile`). They are called by the main functions `new_package`,
34 | `new_compendium`, and `refresh` but they also can be used to overwrite files
35 | (with `overwrite = TRUE`) in case of broken code. When `open = TRUE` and
36 | `overwrite = FALSE` (default) files are open in the editor.
37 | contents:
38 | - add_description
39 | - add_license
40 | - add_package_doc
41 | - add_citation
42 | - add_code_of_conduct
43 | - add_contributing
44 | - add_testthat
45 | - add_vignette
46 | - add_readme_rmd
47 | - add_compendium
48 | - add_makefile
49 | - add_renv
50 | - add_dockerfile
51 |
52 | - title: README badges
53 | desc: |
54 | These functions add badges to the `README.Rmd`. They are called by the main
55 | functions `new_package`, `new_compendium`, and `refresh` but they also can
56 | be used to update badges if license, lifecycle, repository status change or
57 | to update number of dependencies (`add_dependencies_badge`).
58 | contents:
59 | - add_cran_badge
60 | - add_dependencies_badge
61 | - add_license_badge
62 | - add_lifecycle_badge
63 | - add_repostatus_badge
64 | - add_github_actions_check_badge
65 | - add_github_actions_pkgdown_badge
66 | - add_github_actions_codecov_badge
67 | - add_codecov_badge
68 |
69 | - title: Advanced functions
70 | desc: |
71 | These functions update fields in `DESCRIPTION` (`add_dependencies` and
72 | `add_r_depend`), edit files (`add_to_gitignore` and `add_to_buildignore`),
73 | or write configuration files (`add_github_actions_check`,
74 | `add_github_actions_pkgdown`, `add_github_actions_codecov`, and
75 | `add_github_actions_render`).
76 | contents:
77 | - add_dependencies
78 | - add_r_depend
79 | - add_to_gitignore
80 | - add_to_buildignore
81 | - add_github_actions_check
82 | - add_github_actions_pkgdown
83 | - add_github_actions_codecov
84 | - add_github_actions_render
85 | - add_github_actions_citation
86 | - add_github_actions_codemeta
87 | - add_github_actions_document
88 |
89 | - title: Utilities functions
90 | desc: |
91 | These functions return objects but do not edit any file.
92 | contents:
93 | - get_licenses
94 | - get_all_dependencies
95 | - get_all_functions
96 | - get_minimal_r_version
97 |
--------------------------------------------------------------------------------
/inst/CITATION:
--------------------------------------------------------------------------------
1 | citHeader("To cite rcompendium in publications use:")
2 |
3 | bibentry(
4 | bibtype = "Manual",
5 | title = "{rcompendium}: {An} {R} package to create a package or research compendium structure",
6 | author = c(person("Casajus N.")),
7 | year = "2023",
8 | note = "R package version 1.3",
9 | url = "https://github.com/FRBCesab/rcompendium"
10 | )
11 |
--------------------------------------------------------------------------------
/inst/hexsticker/hexsticker.R:
--------------------------------------------------------------------------------
1 | #'
2 | #' Create an Hexagonal Sticker for the Package
3 | #'
4 |
5 | hexSticker::sticker(
6 |
7 | subplot = here::here("inst", "hexsticker", "icon.png"),
8 | package = "rcompendium",
9 | filename = here::here("man", "figures", "hexsticker.png"),
10 | dpi = 600,
11 |
12 | p_size = 6.0, # Title
13 | u_size = 1.2, # URL
14 | p_family = "Aller_Rg",
15 |
16 | p_color = "#722F26", # Title
17 | h_fill = "#B0987D", # Background
18 | h_color = "#722F26", # Border
19 | u_color = "#433625", # URL
20 |
21 | p_x = 1.00, # Title
22 | p_y = 0.65, # Title
23 | s_x = 1.00, # Subplot
24 | s_y = 1.25, # Subplot
25 |
26 | s_width = 0.50, # Subplot
27 |
28 | url = "https://frbcesab.github.io/rcompendium"
29 | )
30 |
--------------------------------------------------------------------------------
/inst/hexsticker/icon.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/FRBCesab/rcompendium/c50e80d8a693cef53280d46edbb2e544b5744b22/inst/hexsticker/icon.png
--------------------------------------------------------------------------------
/inst/licenses/copyright-mit:
--------------------------------------------------------------------------------
1 | YEAR: {{year}}
2 | COPYRIGHT HOLDER: {{given}} {{family}}
3 |
--------------------------------------------------------------------------------
/inst/licenses/license-mit:
--------------------------------------------------------------------------------
1 | # MIT License
2 |
3 | Copyright (c) {{year}} {{given}} {{family}}
4 |
5 | Permission is hereby granted, free of charge, to any person obtaining a copy
6 | of this software and associated documentation files (the "Software"), to deal
7 | in the Software without restriction, including without limitation the rights
8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 |
12 | The above copyright notice and this permission notice shall be included in all
13 | copies or substantial portions of the Software.
14 |
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21 | SOFTWARE.
22 |
--------------------------------------------------------------------------------
/inst/templates/DESCRIPTION:
--------------------------------------------------------------------------------
1 | Package: {{project_name}}
2 | Type: Package
3 | Title: The Title of the Project
4 | Version: 0.0.0.9000
5 | Authors@R: c(
6 | person(given = "{{given}}",
7 | family = "{{family}}",
8 | role = c("aut", "cre", "cph"),
9 | email = "{{email}}",
10 | comment = c(ORCID = "{{orcid}}")))
11 | Description: A paragraph providing a full description of the project (on
12 | several lines...)
13 | URL: https://github.com/{{github}}/{{project_name}}
14 | BugReports: https://github.com/{{github}}/{{project_name}}/issues
15 | License: {{license}}
16 | Encoding: UTF-8
17 | Roxygen: list(markdown = TRUE)
18 | RoxygenNote: {{roxygen2_version}}
19 |
--------------------------------------------------------------------------------
/inst/templates/Dockerfile:
--------------------------------------------------------------------------------
1 | ## Based on the image RStudio with R {{r_version}} ----
2 |
3 | FROM rocker/rstudio:{{r_version}}
4 |
5 | MAINTAINER {{given}} {{family}} <{{email}}>
6 |
7 |
8 | ## Install system dependencies ----
9 |
10 | RUN sudo apt update -yq \
11 | && sudo apt install --no-install-recommends libxml2-dev -yq \
12 | && sudo apt clean all \
13 | && sudo apt purge \
14 | && sudo rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
15 |
16 |
17 | ## Copy local project ----
18 |
19 | ENV folder="/home/rstudio/"
20 |
21 | COPY . $folder
22 | RUN chown -R rstudio:rstudio $folder
23 |
24 |
25 | ## Set working directory ----
26 |
27 | WORKDIR $folder
28 |
29 |
30 | ## Install R packages ----
31 |
32 | {{install_packages}}
33 |
--------------------------------------------------------------------------------
/inst/templates/R-CMD-check.yaml:
--------------------------------------------------------------------------------
1 | # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
2 | # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
3 |
4 | on:
5 | push:
6 | branches: [main, master]
7 | pull_request:
8 | branches: [main, master]
9 |
10 | name: R CMD Check
11 |
12 | jobs:
13 | R-CMD-check:
14 | runs-on: ${{ matrix.config.os }}
15 |
16 | name: ${{ matrix.config.os }} (${{ matrix.config.r }})
17 |
18 | strategy:
19 | fail-fast: false
20 | matrix:
21 | config:
22 | - {os: macos-latest, r: 'release'}
23 | - {os: windows-latest, r: 'release'}
24 | - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
25 | - {os: ubuntu-latest, r: 'release'}
26 | - {os: ubuntu-latest, r: 'oldrel-1'}
27 |
28 | env:
29 | GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
30 | R_KEEP_PKG_SOURCE: yes
31 |
32 | steps:
33 | - uses: actions/checkout@v4
34 |
35 | - uses: r-lib/actions/setup-pandoc@v2
36 |
37 | - uses: r-lib/actions/setup-r@v2
38 | with:
39 | r-version: ${{ matrix.config.r }}
40 | http-user-agent: ${{ matrix.config.http-user-agent }}
41 | use-public-rspm: true
42 |
43 | - uses: r-lib/actions/setup-r-dependencies@v2
44 | with:
45 | extra-packages: any::rcmdcheck
46 | needs: check
47 |
48 | - uses: r-lib/actions/check-r-package@v2
49 | with:
50 | upload-snapshots: true
51 | build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
52 |
--------------------------------------------------------------------------------
/inst/templates/README-comp.Rmd:
--------------------------------------------------------------------------------
1 | ---
2 | output: github_document
3 | ---
4 |
5 |
6 |
7 |
8 | ```{r, include = FALSE}
9 | knitr::opts_chunk$set(collapse = TRUE,
10 | comment = "#>",
11 | fig.path = "figures/readme/",
12 | out.width = "100%")
13 | ```
14 |
15 |
16 |
17 | {{project_name}} 
18 | =========================================================
19 |
20 |
21 |
22 |
23 |
24 |
25 |
26 | • Overview
27 | • Data sources
28 | • Workflow
29 | • Content
30 | • Installation
31 | • Usage
32 | • Citation
33 | • Contributing
34 | • Acknowledgments
35 | • References
36 |
37 |
38 |
39 |
40 | ## Overview
41 |
42 | This project is dedicated to... **{{ DESCRIBE YOUR PROJECT }}**
43 |
44 |
45 |
46 | ## Data sources
47 |
48 | This project uses the following databases:
49 |
50 | **{{ DESCRIBE THE DATA SOURCES }}**
51 |
52 |
57 |
58 |
59 | ## Workflow
60 |
61 | The analysis pipeline follows these steps:
62 |
63 | **{{ DESCRIBE THE PIPELINE }}**
64 |
65 |
66 | ## Content
67 |
68 | This repository is structured as follow:
69 |
70 | - [`DESCRIPTION`](https://github.com/{{github}}/{{project_name}}/tree/{{branch}}/DESCRIPTION):
71 | contains project metadata (authors, date, dependencies, etc.)
72 |
73 | - [`make.R`](https://github.com/{{github}}/{{project_name}}/tree/{{branch}}/make.R):
74 | main R script to run the entire project
75 |
76 | - [`R/`](https://github.com/{{github}}/{{project_name}}/tree/{{branch}}/R):
77 | contains R functions developed especially for this project
78 |
79 | **{{ LIST ADDITIONAL FILES/FOLDER }}**
80 |
81 |
82 |
83 | ## Installation
84 |
85 | To install this compendium:
86 |
87 | - [Fork](https://docs.github.com/en/get-started/quickstart/contributing-to-projects)
88 | this repository using the GitHub interface.
89 | - [Clone](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository)
90 | your fork using `git clone fork-url` (replace `fork-url` by the URL of your fork).
91 | Alternatively, open [RStudio IDE](https://posit.co/products/open-source/rstudio/)
92 | and create a New Project from Version Control.
93 |
94 |
95 |
96 | ## Usage
97 |
98 | Launch the [`make.R`](https://github.com/{{github}}/{{project_name}}/tree/{{branch}}/make.R)
99 | file with:
100 |
101 | ```{r eval=FALSE}
102 | source("make.R")
103 | ```
104 |
105 | **Notes**
106 |
107 | - All required packages listed in the `DESCRIPTION` file will be installed (if necessary)
108 | - All required packages and R functions will be loaded
109 | - Some analyses listed in the `make.R` might take time
110 |
111 |
112 |
113 | ## Citation
114 |
115 | Please use the following citation:
116 |
117 | > **{{ ADD A CITATION }}**
118 |
119 |
120 |
121 | ## Contributing
122 |
123 | All types of contributions are encouraged and valued. For more information,
124 | check out our [Contributor Guidelines](https://github.com/{{github}}/{{project_name}}/blob/main/CONTRIBUTING.md).
125 |
126 | Please note that this project is released with a
127 | [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html).
128 | By contributing to this project, you agree to abide by its terms.
129 |
130 |
131 |
132 | ## Acknowledgments
133 |
134 | **{{ OPTIONAL SECTION }}**
135 |
136 |
137 |
138 | ## References
139 |
140 | **{{ OPTIONAL SECTION }}**
141 |
--------------------------------------------------------------------------------
/inst/templates/README-pkg.Rmd:
--------------------------------------------------------------------------------
1 | ---
2 | output: github_document
3 | ---
4 |
5 |
6 |
7 |
8 | ```{r, include = FALSE}
9 | knitr::opts_chunk$set(collapse = TRUE,
10 | comment = "#>",
11 | fig.path = "man/figures/",
12 | out.width = "100%")
13 | ```
14 |
15 |
16 |
17 | {{project_name}} 
18 | =========================================================
19 |
20 |
21 |
22 |
23 |
24 |
25 |
26 | • Overview
27 | • Features
28 | • Installation
29 | • Get started
30 | • Long-form documentations
31 | • Citation
32 | • Contributing
33 | • Acknowledgments
34 | • References
35 |
36 |
37 |
38 |
39 | ## Overview
40 |
41 |
42 | The R package `{{project_name}}`... **{{ DESCRIBE YOUR PACKAGE }}**
43 |
44 |
45 |
46 | ## Features
47 |
48 | The main purpose of `{{project_name}}` is to... **{{ DESCRIBE THE MAIN FEATURES }}**
49 |
50 |
51 |
52 | ## Installation
53 |
54 | You can install the development version from [GitHub](https://github.com/) with:
55 |
56 | ```{r eval=FALSE}
57 | ## Install < remotes > package (if not already installed) ----
58 | if (!requireNamespace("remotes", quietly = TRUE)) {
59 | install.packages("remotes")
60 | }
61 |
62 | ## Install < {{project_name}} > from GitHub ----
63 | remotes::install_github("{{github}}/{{project_name}}")
64 | ```
65 |
66 | Then you can attach the package `{{project_name}}`:
67 |
68 | ```{r eval=FALSE}
69 | library("{{project_name}}")
70 | ```
71 |
72 |
73 |
74 | ## Get started
75 |
76 | For an overview of the main features of `{{project_name}}`, please read the
77 | [Get started](https://{{github}}.github.io/{{project_name}}/articles/{{project_name}}.html)
78 | vignette.
79 |
80 |
81 |
82 | ## Long-form documentations
83 |
84 | `{{project_name}}` provides **{{ NUMBER OF VIGNETTES }}** vignettes to learn more about the package:
85 |
86 | - the [Get started](https://{{github}}.github.io/{{project_name}}/articles/{{project_name}}.html)
87 | vignette describes the core features of the package
88 | - **{{ LIST ADDITIONAL VIGNETTES }}**
89 |
90 |
91 |
92 | ## Citation
93 |
94 | Please cite `{{project_name}}` as:
95 |
96 | > {{family}} {{given}} (`r format(Sys.Date(), "%Y")`) {{project_name}}: An R
97 | package to **{{ TITLE }}**. R package version {{pkg_version}}.
98 |
99 |
100 |
101 |
102 | ## Contributing
103 |
104 | All types of contributions are encouraged and valued. For more information,
105 | check out our [Contributor Guidelines](https://github.com/{{github}}/{{project_name}}/blob/main/CONTRIBUTING.md).
106 |
107 | Please note that the `{{project_name}}` project is released with a
108 | [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html).
109 | By contributing to this project, you agree to abide by its terms.
110 |
111 |
112 |
113 | ## Acknowledgments
114 |
115 | **{{ OPTIONAL SECTION }}**
116 |
117 |
118 |
119 | ## References
120 |
121 | **{{ OPTIONAL SECTION }}**
122 |
--------------------------------------------------------------------------------
/inst/templates/bug_report.md:
--------------------------------------------------------------------------------
1 | ---
2 | name: Bug report
3 | about: Standard bug report template
4 | title: ''
5 | labels: 'bug'
6 | ---
7 |
8 | **Bug description**
9 |
10 | A clear and concise description of what the bug is.
11 |
12 |
13 | **Reproducible example**
14 |
15 | It is easier for developers to help if they can reproduce the problem.
16 | Could you please provide a minimal reproducible example?
17 |
18 |
19 | **Additional context**
20 |
21 | Add any other context about the problem here.
22 |
23 |
24 |
25 | ```r
26 | # Output of sessionInfo()
27 | ```
28 |
29 |
--------------------------------------------------------------------------------
/inst/templates/citation:
--------------------------------------------------------------------------------
1 | citHeader("To cite {{project_name}} in publications use:")
2 |
3 | bibentry(
4 | bibtype = "Manual",
5 | title = "{{project_name}}: {An} {R} package to ...",
6 | author = c(person("{{family}} {{given}}")),
7 | year = "{{year}}",
8 | note = "R package version {{pkg_version}}",
9 | url = "https://github.com/{{github}}/{{project_name}}"
10 | )
11 |
--------------------------------------------------------------------------------
/inst/templates/compendium-sticker.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/FRBCesab/rcompendium/c50e80d8a693cef53280d46edbb2e544b5744b22/inst/templates/compendium-sticker.png
--------------------------------------------------------------------------------
/inst/templates/dockerignore:
--------------------------------------------------------------------------------
1 | # macOS files ----
2 | .DS_Store
3 |
4 | # Large files ----
5 | .git
6 | renv/library
7 | renv/local
8 |
9 | # History files ----
10 | .Rhistory
11 | .Rapp.history
12 |
13 | # Session Data files ----
14 | .RData
15 | .Ruserdata
16 |
17 | # RStudio files ----
18 | *.Rproj
19 | .Rproj.user/
20 |
--------------------------------------------------------------------------------
/inst/templates/document-package.yaml:
--------------------------------------------------------------------------------
1 | # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
2 | # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
3 | on:
4 | push:
5 | paths: ["R/**"]
6 |
7 | name: Document
8 |
9 | jobs:
10 | document:
11 | runs-on: ubuntu-latest
12 | env:
13 | GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
14 | steps:
15 | - name: Checkout repo
16 | uses: actions/checkout@v4
17 | with:
18 | fetch-depth: 0
19 |
20 | - name: Setup R
21 | uses: r-lib/actions/setup-r@v2
22 | with:
23 | use-public-rspm: true
24 |
25 | - name: Install dependencies
26 | uses: r-lib/actions/setup-r-dependencies@v2
27 | with:
28 | extra-packages: any::roxygen2
29 | needs: roxygen2
30 |
31 | - name: Document
32 | run: roxygen2::roxygenise()
33 | shell: Rscript {0}
34 |
35 | - name: Commit and push changes
36 | run: |
37 | git config --local user.name "$GITHUB_ACTOR"
38 | git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
39 | git add man/\* NAMESPACE DESCRIPTION
40 | git commit -m "doc: update documentation" || echo "No changes to commit"
41 | git pull --ff-only
42 | git push origin
43 |
--------------------------------------------------------------------------------
/inst/templates/feature_request.md:
--------------------------------------------------------------------------------
1 | ---
2 | name: Feature request
3 | about: Standard feature request template
4 | title: ''
5 | labels: 'enhancement'
6 | ---
7 |
8 | **Feature description**
9 |
10 | A clear and complete description of what the requested feature is.
11 |
--------------------------------------------------------------------------------
/inst/templates/fun-demo.R:
--------------------------------------------------------------------------------
1 | #' Print a message
2 | #'
3 | #' @description
4 | #' This function prints a simple message. This is a demo function to show good
5 | #' practices in writing and documenting R function. If you delete this function
6 | #' do not forget to delete the corresponding test file
7 | #' `tests/testthat/test-demo.R` if you used `new_package(test = TRUE)`.
8 | #'
9 | #' @param x a character of length 1. Default is `'Hello world'`.
10 | #'
11 | #' @return The value of `x` (only if the result is assigned to a variable).
12 | #'
13 | #' @export
14 | #'
15 | #' @examples
16 | #' print_msg()
17 | #' print_msg("Bonjour le monde")
18 | #'
19 | #' x <- print_msg("Bonjour le monde")
20 | #' x
21 |
22 | print_msg <- function(x = "Hello world") {
23 |
24 | if (!is.character(x) || length(x) != 1)
25 | stop("Argument 'x' must be a character of length 1.")
26 |
27 | cat(x, "\n")
28 |
29 | invisible(x)
30 | }
31 |
--------------------------------------------------------------------------------
/inst/templates/gitignore:
--------------------------------------------------------------------------------
1 | # macOS files ----
2 | .DS_Store
3 |
4 | # History files ----
5 | .Rhistory
6 | .Rapp.history
7 |
8 | # Session Data files ----
9 | .RData
10 | .Ruserdata
11 |
12 | # RStudio files ----
13 | *.Rproj
14 | .Rproj.user/
15 |
16 | # R Environment Variables ----
17 | .Renviron
18 |
19 | # User-specific files ----
20 | README.html
21 | inst/doc
22 |
--------------------------------------------------------------------------------
/inst/templates/make.R:
--------------------------------------------------------------------------------
1 | #' {{project_name}}: A Research Compendium
2 | #'
3 | #' @description
4 | #' A paragraph providing a full description of the project and describing each
5 | #' step of the workflow.
6 | #'
7 | #' @author {{given}} {{family}} \email{{{email}}}
8 | #'
9 | #' @date {{date}}
10 |
11 |
12 |
13 | ## Install Dependencies (listed in DESCRIPTION) ----
14 |
15 | devtools::install_deps(upgrade = "never")
16 |
17 |
18 | ## Load Project Addins (R Functions and Packages) ----
19 |
20 | devtools::load_all(here::here())
21 |
22 |
23 | ## Global Variables ----
24 |
25 | # You can list global variables here (or in a separate R script)
26 |
27 |
28 | ## Run Project ----
29 |
30 | # List all R scripts in a sequential order and using the following form:
31 | # source(here::here("analyses", "script_X.R"))
32 |
--------------------------------------------------------------------------------
/inst/templates/other_issue.md:
--------------------------------------------------------------------------------
1 | ---
2 | name: Other issue
3 | about: Template for other issue types
4 | title: ''
5 | labels: ''
6 | ---
7 |
--------------------------------------------------------------------------------
/inst/templates/package-package.R:
--------------------------------------------------------------------------------
1 | #' @keywords internal
2 | "_PACKAGE"
3 |
4 | # Imports: start ----
5 | # Imports: end ----
6 |
7 | NULL
8 |
--------------------------------------------------------------------------------
/inst/templates/package-sticker.R:
--------------------------------------------------------------------------------
1 | #'
2 | #' Create an Hexagonal Sticker for the Package
3 | #'
4 |
5 |
6 | # install.packages(c("png", "ggplot2", "hexSticker", "grid", "ggpubr"))
7 |
8 |
9 | rlogo <- png::readPNG(here::here("inst", "package-sticker", "r_logo.png"))
10 | rlogo <- grid::rasterGrob(rlogo, interpolate = TRUE)
11 |
12 | p <- ggplot2::ggplot() +
13 | ggplot2::annotation_custom(rlogo, xmin = -Inf, xmax = Inf, ymin = -Inf,
14 | ymax = Inf) +
15 | ggplot2::theme_void() +
16 | ggpubr::theme_transparent()
17 |
18 | hexSticker::sticker(
19 |
20 | subplot = p,
21 | package = "R Package",
22 | filename = here::here("man", "figures", "package-sticker.png"),
23 | dpi = 600,
24 |
25 | p_size = 28.0, # Title
26 | u_size = 5.0, # URL
27 | p_family = "Aller_Rg",
28 |
29 | p_color = "#32436F", # Title
30 | h_fill = "#FFFFFF", # Background
31 | h_color = "#1064B2", # Border
32 | u_color = "#32436F", # URL
33 |
34 | p_x = 1.00, # Title
35 | p_y = 0.60, # Title
36 | s_x = 1.00, # Subplot
37 | s_y = 1.25, # Subplot
38 |
39 | s_width = 1.25, # Subplot
40 | s_height = 1.25, # Subplot
41 |
42 | url = "https://github.com/",
43 |
44 | spotlight = TRUE,
45 | l_alpha = 0.10,
46 | l_width = 4,
47 | l_height = 4
48 | )
49 |
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/inst/templates/package-sticker.png:
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https://raw.githubusercontent.com/FRBCesab/rcompendium/c50e80d8a693cef53280d46edbb2e544b5744b22/inst/templates/package-sticker.png
--------------------------------------------------------------------------------
/inst/templates/package-vignette.Rmd:
--------------------------------------------------------------------------------
1 | ---
2 | title: "{{title}}"
3 | output: rmarkdown::html_vignette
4 | vignette: >
5 | %\VignetteIndexEntry{{{title}}}
6 | %\VignetteEngine{knitr::rmarkdown}
7 | %\VignetteEncoding{UTF-8}
8 | ---
9 |
10 | ```{r, include = FALSE}
11 | knitr::opts_chunk$set(collapse = TRUE,
12 | comment = "#>")
13 | ```
14 |
15 |
16 | ```{r setup}
17 | library({{project_name}})
18 | ```
19 |
20 |
--------------------------------------------------------------------------------
/inst/templates/pkgdown.yaml:
--------------------------------------------------------------------------------
1 | # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
2 | # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
3 |
4 | on:
5 | push:
6 | branches: [main, master]
7 | pull_request:
8 | branches: [main, master]
9 | release:
10 | types: [published]
11 | workflow_dispatch:
12 |
13 | name: Website
14 |
15 | jobs:
16 | pkgdown:
17 | runs-on: ubuntu-latest
18 | # Only restrict concurrency for non-PR jobs
19 | concurrency:
20 | group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
21 | env:
22 | GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
23 | permissions:
24 | contents: write
25 | steps:
26 | - uses: actions/checkout@v4
27 |
28 | - uses: r-lib/actions/setup-pandoc@v2
29 |
30 | - uses: r-lib/actions/setup-r@v2
31 | with:
32 | use-public-rspm: true
33 |
34 | - uses: r-lib/actions/setup-r-dependencies@v2
35 | with:
36 | extra-packages: any::pkgdown, local::.
37 | needs: website
38 |
39 | - name: Build site
40 | run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
41 | shell: Rscript {0}
42 |
43 | - name: Deploy to GitHub pages
44 | if: github.event_name != 'pull_request'
45 | uses: JamesIves/github-pages-deploy-action@v4.4.1
46 | with:
47 | clean: false
48 | branch: gh-pages
49 | folder: docs
50 |
--------------------------------------------------------------------------------
/inst/templates/r_logo.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/FRBCesab/rcompendium/c50e80d8a693cef53280d46edbb2e544b5744b22/inst/templates/r_logo.png
--------------------------------------------------------------------------------
/inst/templates/render-README.yaml:
--------------------------------------------------------------------------------
1 | # Workflow derived from https://github.com/r-lib/actions/blob/v2-branch/examples/render-rmarkdown.yaml
2 |
3 | on:
4 | push:
5 | paths: 'README.Rmd'
6 |
7 | name: Render README
8 |
9 | jobs:
10 | render-readme:
11 | runs-on: ubuntu-latest
12 | env:
13 | GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
14 | steps:
15 | - name: Checkout repo
16 | uses: actions/checkout@v4
17 | with:
18 | fetch-depth: 0
19 |
20 | - uses: r-lib/actions/setup-pandoc@v2
21 | - uses: r-lib/actions/setup-r@v2
22 |
23 | - name: Install Rmarkdown
24 | run: Rscript -e 'install.packages("rmarkdown")'
25 |
26 | - name: Render README
27 | run: |
28 | RMD_PATH=($(git diff --name-only ${{ github.event.before }} ${{ github.sha }} | grep '^README.Rmd$'))
29 | Rscript -e 'for (f in commandArgs(TRUE)) if (file.exists(f)) rmarkdown::render(f)' ${RMD_PATH[*]}
30 |
31 | - name: Commit results
32 | run: |
33 | git config --local user.name "$GITHUB_ACTOR"
34 | git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
35 | git commit README.md -m 'doc: render README' || echo "No changes to commit"
36 | git push origin || echo "No changes to commit"
37 |
--------------------------------------------------------------------------------
/inst/templates/test-coverage.yaml:
--------------------------------------------------------------------------------
1 | # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
2 | # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
3 |
4 | on:
5 | push:
6 | branches: [main, master]
7 | pull_request:
8 | branches: [main, master]
9 |
10 | name: Test coverage
11 |
12 | jobs:
13 | test-coverage:
14 | runs-on: ubuntu-latest
15 | env:
16 | GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
17 |
18 | steps:
19 | - uses: actions/checkout@v4
20 |
21 | - uses: r-lib/actions/setup-r@v2
22 | with:
23 | use-public-rspm: true
24 |
25 | - uses: r-lib/actions/setup-r-dependencies@v2
26 | with:
27 | extra-packages: any::covr
28 | needs: coverage
29 |
30 | - name: Test coverage
31 | run: |
32 | covr::codecov(
33 | quiet = FALSE,
34 | clean = FALSE,
35 | install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
36 | )
37 | shell: Rscript {0}
38 |
39 | - name: Show testthat output
40 | if: always()
41 | run: |
42 | ## --------------------------------------------------------------------
43 | find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
44 | shell: bash
45 |
46 | - name: Upload test results
47 | if: failure()
48 | uses: actions/upload-artifact@v4
49 | with:
50 | name: coverage-test-failures
51 | path: ${{ runner.temp }}/package
52 |
--------------------------------------------------------------------------------
/inst/templates/test-demo.R:
--------------------------------------------------------------------------------
1 | ## Test demo ----
2 |
3 | test_that("Test demo", {
4 | expect_invisible(print_msg())
5 |
6 | x <- print_msg()
7 | expect_equal(x, "Hello world")
8 |
9 | x <- print_msg("Bonjour le monde")
10 | expect_equal(x, "Bonjour le monde")
11 |
12 | expect_error(print_msg(c("Hello", "world")))
13 | expect_error(print_msg(1), "Argument 'x' must be a character of length 1.")
14 | })
15 |
--------------------------------------------------------------------------------
/inst/templates/update-citation-cff.yaml:
--------------------------------------------------------------------------------
1 | # Workflow derived from https://github.com/r-lib/actions/tree/master/examples
2 |
3 | on:
4 | release:
5 | types: [published]
6 | push:
7 | branches: [master, main]
8 | paths:
9 | - DESCRIPTION
10 | - inst/CITATION
11 | workflow_dispatch:
12 |
13 | name: Update CITATION.cff
14 |
15 | jobs:
16 | update-citation-cff:
17 | runs-on: macos-latest
18 | env:
19 | GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
20 | steps:
21 | - uses: actions/checkout@v4
22 | - uses: r-lib/actions/setup-r@v2
23 | - uses: r-lib/actions/setup-r-dependencies@v2
24 | with:
25 | extra-packages: |
26 | any::cffr
27 | any::V8
28 |
29 | - name: Update CITATION.cff
30 | run: |
31 | # Update CITATION.cff file
32 | cffr::cff_write(keys = list())
33 | shell: Rscript {0}
34 |
35 | - name: Commit results
36 | run: |
37 | git config --local user.name "$GITHUB_ACTOR"
38 | git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
39 | git add CITATION.cff
40 | git commit -m 'doc: update CITATION.cff' || echo "No changes to commit"
41 | git push origin || echo "No changes to commit"
42 |
--------------------------------------------------------------------------------
/inst/templates/update-codemeta.yaml:
--------------------------------------------------------------------------------
1 | on:
2 | release:
3 | types: [published]
4 | push:
5 | branches: [master, main]
6 | paths:
7 | - DESCRIPTION
8 | - inst/CITATION
9 | - README.md
10 | workflow_dispatch:
11 |
12 | name: Update codemeta.json
13 |
14 | jobs:
15 | update-codemeta:
16 | runs-on: macos-latest
17 | env:
18 | GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
19 | steps:
20 | - uses: actions/checkout@v4
21 | - uses: r-lib/actions/setup-r@v2
22 | - uses: r-lib/actions/setup-r-dependencies@v2
23 | with:
24 | extra-packages: |
25 | any::codemetar
26 |
27 | - name: Update codemeta.json
28 | run: codemetar::write_codemeta()
29 | shell: Rscript {0}
30 |
31 | - name: Commit results
32 | run: |
33 | git config --local user.name "$GITHUB_ACTOR"
34 | git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
35 | git add codemeta.json
36 | git commit -m 'Update codemeta.json' || echo "No changes to commit"
37 | git push origin || echo "No changes to commit"
38 |
--------------------------------------------------------------------------------
/man/add_citation.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_citation.R
3 | \name{add_citation}
4 | \alias{add_citation}
5 | \title{Create a CITATION file}
6 | \usage{
7 | add_citation(
8 | given = NULL,
9 | family = NULL,
10 | organisation = NULL,
11 | open = TRUE,
12 | overwrite = FALSE,
13 | quiet = FALSE
14 | )
15 | }
16 | \arguments{
17 | \item{given}{A character of length 1. The given name of the project
18 | maintainer.}
19 |
20 | \item{family}{A character of length 1. The family name of the project
21 | maintainer.}
22 |
23 | \item{organisation}{A character of length 1. The name of the GitHub
24 | organisation to host the package. If \code{NULL} (default) the GitHub account
25 | will be used. This argument is used to set the URL of the package
26 | (hosted on GitHub).}
27 |
28 | \item{open}{A logical value. If \code{TRUE} (default) the file is opened in the
29 | editor.}
30 |
31 | \item{overwrite}{A logical value. If this file is already present and
32 | \code{overwrite = TRUE}, it will be erased and replaced. Default is \code{FALSE}.}
33 |
34 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
35 | \code{FALSE}.}
36 | }
37 | \value{
38 | No return value.
39 | }
40 | \description{
41 | This function creates a \code{CITATION} file in the folder \verb{inst/}. This file
42 | contains a BiBTeX entry to cite the package as a manual. User will need to
43 | edit by hand some information (title, version, etc.).
44 | }
45 | \examples{
46 | \dontrun{
47 | add_citation()
48 | readCitationFile("inst/CITATION")
49 | citation("pkg") # If you have installed your package
50 | }
51 | }
52 | \seealso{
53 | Other create files:
54 | \code{\link{add_code_of_conduct}()},
55 | \code{\link{add_compendium}()},
56 | \code{\link{add_contributing}()},
57 | \code{\link{add_description}()},
58 | \code{\link{add_dockerfile}()},
59 | \code{\link{add_license}()},
60 | \code{\link{add_makefile}()},
61 | \code{\link{add_package_doc}()},
62 | \code{\link{add_readme_rmd}()},
63 | \code{\link{add_renv}()},
64 | \code{\link{add_testthat}()},
65 | \code{\link{add_vignette}()}
66 | }
67 | \concept{create files}
68 |
--------------------------------------------------------------------------------
/man/add_code_of_conduct.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_code_of_conduct.R
3 | \name{add_code_of_conduct}
4 | \alias{add_code_of_conduct}
5 | \title{Add code of conduct}
6 | \usage{
7 | add_code_of_conduct(
8 | email = NULL,
9 | open = TRUE,
10 | overwrite = FALSE,
11 | quiet = FALSE
12 | )
13 | }
14 | \arguments{
15 | \item{email}{A character of length 1. The email address of the project
16 | maintainer.}
17 |
18 | \item{open}{A logical value. If \code{TRUE} (default) the \code{CONTRIBUTING.md} file
19 | is opened in the editor.}
20 |
21 | \item{overwrite}{A logical value. If files are already present and
22 | \code{overwrite = TRUE}, they will be erased and replaced. Default is \code{FALSE}.}
23 |
24 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
25 | \code{FALSE}.}
26 | }
27 | \value{
28 | No return value.
29 | }
30 | \description{
31 | This function creates a \code{CODE_OF_CONDUCT.md} file adapted from the
32 | Contributor Covenant, version 2.1 available at
33 | \url{https://www.contributor-covenant.org/version/2/1/code_of_conduct.html}.
34 | }
35 | \examples{
36 | \dontrun{
37 | add_code_of_conduct()
38 | }
39 | }
40 | \seealso{
41 | Other create files:
42 | \code{\link{add_citation}()},
43 | \code{\link{add_compendium}()},
44 | \code{\link{add_contributing}()},
45 | \code{\link{add_description}()},
46 | \code{\link{add_dockerfile}()},
47 | \code{\link{add_license}()},
48 | \code{\link{add_makefile}()},
49 | \code{\link{add_package_doc}()},
50 | \code{\link{add_readme_rmd}()},
51 | \code{\link{add_renv}()},
52 | \code{\link{add_testthat}()},
53 | \code{\link{add_vignette}()}
54 | }
55 | \concept{create files}
56 |
--------------------------------------------------------------------------------
/man/add_codecov_badge.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_codecov_badge.R
3 | \name{add_codecov_badge}
4 | \alias{add_codecov_badge}
5 | \title{Add a Codecov badge}
6 | \usage{
7 | add_codecov_badge(organisation = NULL, quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{organisation}{A character of length 1. The name of the GitHub
11 | organisation to host the package. If \code{NULL} (default) the GitHub account
12 | will be used.}
13 |
14 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
15 | \code{FALSE}.}
16 | }
17 | \value{
18 | A badge as a markdown expression.
19 | }
20 | \description{
21 | This function adds a \strong{Code coverage} badge to the \code{README.Rmd}, i.e. the
22 | percentage of code cover by units tests. This percentage is computed by
23 | the codecov.io service.
24 |
25 | \strong{Note:} this service must be manually activated for the package by visiting
26 | \url{https://about.codecov.io/}.
27 |
28 | Make sure that 1) a \code{README.Rmd} file exists at the project root and 2) it
29 | contains a block starting with the line \verb{} and ending
30 | with the line \verb{}.
31 |
32 | Don't forget to re-render the \code{README.md}.
33 | }
34 | \examples{
35 | \dontrun{
36 | add_codecov_badge()
37 | }
38 | }
39 | \seealso{
40 | Other adding badges:
41 | \code{\link{add_cran_badge}()},
42 | \code{\link{add_dependencies_badge}()},
43 | \code{\link{add_github_actions_check_badge}()},
44 | \code{\link{add_github_actions_codecov_badge}()},
45 | \code{\link{add_github_actions_pkgdown_badge}()},
46 | \code{\link{add_license_badge}()},
47 | \code{\link{add_lifecycle_badge}()},
48 | \code{\link{add_repostatus_badge}()}
49 | }
50 | \concept{adding badges}
51 |
--------------------------------------------------------------------------------
/man/add_compendium.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_compendium.R
3 | \name{add_compendium}
4 | \alias{add_compendium}
5 | \title{Create additional folders}
6 | \usage{
7 | add_compendium(compendium = NULL, quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{compendium}{A character vector specifying the folders to be created.}
11 |
12 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
13 | \code{FALSE}.}
14 | }
15 | \value{
16 | No return value.
17 | }
18 | \description{
19 | This function creates a compendium, i.e. additional folders to a package
20 | structure. By default, the following directories are created:
21 | \code{data}, \verb{analyses/}, \verb{outputs/}, and \verb{figures/}. A \code{README.md} is added to
22 | each folder and must be edited. The argument \code{compendium} allows user to
23 | hoose its own compendium structure. All theses folders are added to the
24 | \code{.Rbuildignore} file.
25 | }
26 | \examples{
27 | \dontrun{
28 | add_compendium()
29 | add_compendium(compendium = "paper")
30 | add_compendium(compendium = c("data", "outputs", "code", "manuscript"))
31 | }
32 | }
33 | \seealso{
34 | Other create files:
35 | \code{\link{add_citation}()},
36 | \code{\link{add_code_of_conduct}()},
37 | \code{\link{add_contributing}()},
38 | \code{\link{add_description}()},
39 | \code{\link{add_dockerfile}()},
40 | \code{\link{add_license}()},
41 | \code{\link{add_makefile}()},
42 | \code{\link{add_package_doc}()},
43 | \code{\link{add_readme_rmd}()},
44 | \code{\link{add_renv}()},
45 | \code{\link{add_testthat}()},
46 | \code{\link{add_vignette}()}
47 | }
48 | \concept{create files}
49 |
--------------------------------------------------------------------------------
/man/add_contributing.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_contributing.R
3 | \name{add_contributing}
4 | \alias{add_contributing}
5 | \title{Add contribution guidelines}
6 | \usage{
7 | add_contributing(
8 | email = NULL,
9 | organisation = NULL,
10 | open = TRUE,
11 | overwrite = FALSE,
12 | quiet = FALSE
13 | )
14 | }
15 | \arguments{
16 | \item{email}{A character of length 1. The email address of the project
17 | maintainer.}
18 |
19 | \item{organisation}{A character of length 1. The name of the GitHub
20 | organisation to host the package. If \code{NULL} (default) the GitHub account
21 | will be used. This argument is used to set the URL of the package
22 | (hosted on GitHub).}
23 |
24 | \item{open}{A logical value. If \code{TRUE} (default) the \code{CONTRIBUTING.md} file
25 | is opened in the editor.}
26 |
27 | \item{overwrite}{A logical value. If files are already present and
28 | \code{overwrite = TRUE}, they will be erased and replaced. Default is \code{FALSE}.}
29 |
30 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
31 | \code{FALSE}.}
32 | }
33 | \value{
34 | No return value.
35 | }
36 | \description{
37 | This function creates several files to help the user to learn how to
38 | contribute to the project:
39 | \itemize{
40 | \item \code{CONTRIBUTING.md}: general guidelines outlining the best way to contribute
41 | to the project (can be modified);
42 | \item \code{.github/ISSUE_TEMPLATE/bug_report.md}: an issue template to report a bug
43 | (can be modified);
44 | \item \code{.github/ISSUE_TEMPLATE/feature_request.md}: an issue template to suggest
45 | a new feature (can be modified);
46 | \item \code{.github/ISSUE_TEMPLATE/other_issue.md}: an issue template for all other
47 | types of issue (can be modified).
48 | }
49 | }
50 | \examples{
51 | \dontrun{
52 | add_contributing()
53 | }
54 | }
55 | \seealso{
56 | Other create files:
57 | \code{\link{add_citation}()},
58 | \code{\link{add_code_of_conduct}()},
59 | \code{\link{add_compendium}()},
60 | \code{\link{add_description}()},
61 | \code{\link{add_dockerfile}()},
62 | \code{\link{add_license}()},
63 | \code{\link{add_makefile}()},
64 | \code{\link{add_package_doc}()},
65 | \code{\link{add_readme_rmd}()},
66 | \code{\link{add_renv}()},
67 | \code{\link{add_testthat}()},
68 | \code{\link{add_vignette}()}
69 | }
70 | \concept{create files}
71 |
--------------------------------------------------------------------------------
/man/add_cran_badge.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_cran_badge.R
3 | \name{add_cran_badge}
4 | \alias{add_cran_badge}
5 | \title{Add a CRAN Status badge}
6 | \usage{
7 | add_cran_badge(quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
11 | \code{FALSE}.}
12 | }
13 | \value{
14 | A badge as a markdown expression.
15 | }
16 | \description{
17 | This function adds a \strong{CRAN Status} badge to the \code{README.Rmd}. If the
18 | package is not hosted on the CRAN the badge will indicate
19 | \emph{not published on the CRAN}.
20 |
21 | Make sure that 1) a \code{README.Rmd} file exists at the project root and 2) it
22 | contains a block starting with the line \verb{} and ending
23 | with the line \verb{}.
24 |
25 | Don't forget to re-render the \code{README.md}.
26 | }
27 | \examples{
28 | \dontrun{
29 | add_cran_badge()
30 | }
31 | }
32 | \seealso{
33 | Other adding badges:
34 | \code{\link{add_codecov_badge}()},
35 | \code{\link{add_dependencies_badge}()},
36 | \code{\link{add_github_actions_check_badge}()},
37 | \code{\link{add_github_actions_codecov_badge}()},
38 | \code{\link{add_github_actions_pkgdown_badge}()},
39 | \code{\link{add_license_badge}()},
40 | \code{\link{add_lifecycle_badge}()},
41 | \code{\link{add_repostatus_badge}()}
42 | }
43 | \concept{adding badges}
44 |
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/man/add_dependencies.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_dependencies.R
3 | \name{add_dependencies}
4 | \alias{add_dependencies}
5 | \title{Add dependencies in DESCRIPTION}
6 | \usage{
7 | add_dependencies(compendium = NULL)
8 | }
9 | \arguments{
10 | \item{compendium}{A character of length 1. The name of the folder to
11 | recursively detect dependencies to be added to the \code{Imports} field of
12 | \code{DESCRIPTION} file. It can be \code{'analysis/'} (if additional folders, i.e.
13 | \verb{data/}, \verb{outputs/}, \verb{figures/}, etc. have been created in this folder),
14 | \code{'.'} (if folders \verb{data/}, \verb{outputs/}, \verb{figures/}, etc. have been created
15 | at the root of the project), etc.
16 | See \code{\link[=new_compendium]{new_compendium()}} for further information.
17 |
18 | Default is \code{compendium = NULL} (i.e. no additional folder are inspected
19 | but \verb{R/}, \code{NAMESPACE}, \verb{vignettes/}, and \verb{tests/} are still inspected).}
20 | }
21 | \value{
22 | No return value.
23 | }
24 | \description{
25 | This function detects external dependencies used in \verb{R/}, \code{NAMESPACE}, and
26 | \verb{@examples} sections of \code{roxygen2} headers and automatically adds these
27 | dependencies in the \code{Imports} section of the \code{DESCRIPTION} file.
28 |
29 | In the \code{NAMESPACE} this function detects dependencies mentioned as
30 | \code{import(pkg)} and \code{importFrom(pkg,fun)}.
31 |
32 | In the \verb{R/} folder it detects functions called as \code{pkg::fun()} in the code
33 | of each R files. In \verb{@examples} sections it also detects packages attached
34 | by \code{library()} or \code{require()}.
35 |
36 | The \verb{vignettes/} folder is also inspected and detected dependencies
37 | (\code{pkg::fun()}, \code{library()} or \code{require()}) are added to the \code{Suggests}
38 | field of the \code{DESCRIPTION} file (in addition to the packages
39 | \href{https://yihui.org/knitr/}{\code{knitr}} and
40 | \href{https://rmarkdown.rstudio.com/}{\code{rmarkdown}}).
41 |
42 | If the project is a research compendium user can also inspect additional
43 | folder(s) with the argument \code{compendium} to add dependencies to the
44 | \code{Imports} section of the \code{DESCRIPTION} file. The detection process is the
45 | same as the one used for \verb{vignettes/}.
46 |
47 | The \verb{tests/} folder is also inspected and detected dependencies
48 | (\code{pkg::fun()}, \code{library()} or \code{require()}) are added to the \code{Suggests}
49 | field of the \code{DESCRIPTION} file (in addition to the package
50 | \href{https://testthat.r-lib.org}{\code{testthat}}).
51 | }
52 | \examples{
53 | \dontrun{
54 | add_dependencies()
55 | }
56 | }
57 | \seealso{
58 | Other development functions:
59 | \code{\link{add_github_actions_check}()},
60 | \code{\link{add_github_actions_citation}()},
61 | \code{\link{add_github_actions_codecov}()},
62 | \code{\link{add_github_actions_codemeta}()},
63 | \code{\link{add_github_actions_document}()},
64 | \code{\link{add_github_actions_pkgdown}()},
65 | \code{\link{add_github_actions_render}()},
66 | \code{\link{add_r_depend}()},
67 | \code{\link{add_to_buildignore}()},
68 | \code{\link{add_to_gitignore}()}
69 | }
70 | \concept{development functions}
71 |
--------------------------------------------------------------------------------
/man/add_dependencies_badge.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_dependencies_badge.R
3 | \name{add_dependencies_badge}
4 | \alias{add_dependencies_badge}
5 | \title{Add a Dependencies badge}
6 | \usage{
7 | add_dependencies_badge(quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
11 | \code{FALSE}.}
12 | }
13 | \value{
14 | A badge as a markdown expression.
15 | }
16 | \description{
17 | This function adds or updates the \strong{Dependencies} badge to the \code{README.Rmd}.
18 | The first number corresponds to the direct dependencies and the second to the
19 | recursive dependencies.
20 |
21 | \strong{Note:} this function can work with packages not published on the CRAN
22 | and is based on the function \code{\link[gtools:getDependencies]{gtools::getDependencies()}}. See also the
23 | function \code{\link[=get_all_dependencies]{get_all_dependencies()}}.
24 |
25 | Make sure that 1) a \code{README.Rmd} file exists at the project root and 2) it
26 | contains a block starting with the line \verb{} and ending
27 | with the line \verb{}.
28 |
29 | Don't forget to re-render the \code{README.md}.
30 | }
31 | \examples{
32 | \dontrun{
33 | add_dependencies_badge()
34 | }
35 | }
36 | \seealso{
37 | Other adding badges:
38 | \code{\link{add_codecov_badge}()},
39 | \code{\link{add_cran_badge}()},
40 | \code{\link{add_github_actions_check_badge}()},
41 | \code{\link{add_github_actions_codecov_badge}()},
42 | \code{\link{add_github_actions_pkgdown_badge}()},
43 | \code{\link{add_license_badge}()},
44 | \code{\link{add_lifecycle_badge}()},
45 | \code{\link{add_repostatus_badge}()}
46 | }
47 | \concept{adding badges}
48 |
--------------------------------------------------------------------------------
/man/add_description.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_description.R
3 | \name{add_description}
4 | \alias{add_description}
5 | \title{Create a DESCRIPTION file}
6 | \usage{
7 | add_description(
8 | given = NULL,
9 | family = NULL,
10 | email = NULL,
11 | orcid = NULL,
12 | organisation = NULL,
13 | open = TRUE,
14 | overwrite = FALSE,
15 | quiet = FALSE
16 | )
17 | }
18 | \arguments{
19 | \item{given}{A character of length 1. The given name of the project
20 | maintainer.}
21 |
22 | \item{family}{A character of length 1. The family name of the project
23 | maintainer.}
24 |
25 | \item{email}{A character of length 1. The email address of the project
26 | maintainer.}
27 |
28 | \item{orcid}{A character of length 1. The ORCID of the project maintainer.}
29 |
30 | \item{organisation}{A character of length 1. The name of the GitHub
31 | organisation to host the package. If \code{NULL} (default) the GitHub account
32 | will be used.}
33 |
34 | \item{open}{A logical value. If \code{TRUE} (default) the file is opened in the
35 | editor.}
36 |
37 | \item{overwrite}{A logical value. If a \code{DESCRIPTION} is already present and
38 | \code{overwrite = TRUE}, this file will be erased and replaced. Default is
39 | \code{FALSE}.}
40 |
41 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
42 | \code{FALSE}.}
43 | }
44 | \value{
45 | No return value.
46 | }
47 | \description{
48 | This function creates a \code{DESCRIPTION} file at the root of the project. This
49 | file contains metadata of the project. Some information (title, description,
50 | version, etc.) must be edited by hand. For more information:
51 | \url{https://r-pkgs.org/description.html}.
52 | User credentials can be passed as arguments but it is recommended to store
53 | them in the \code{.Rprofile} file with \code{\link[=set_credentials]{set_credentials()}}.
54 | }
55 | \examples{
56 | \dontrun{
57 | add_description(organisation = "MySociety")
58 | }
59 | }
60 | \seealso{
61 | Other create files:
62 | \code{\link{add_citation}()},
63 | \code{\link{add_code_of_conduct}()},
64 | \code{\link{add_compendium}()},
65 | \code{\link{add_contributing}()},
66 | \code{\link{add_dockerfile}()},
67 | \code{\link{add_license}()},
68 | \code{\link{add_makefile}()},
69 | \code{\link{add_package_doc}()},
70 | \code{\link{add_readme_rmd}()},
71 | \code{\link{add_renv}()},
72 | \code{\link{add_testthat}()},
73 | \code{\link{add_vignette}()}
74 | }
75 | \concept{create files}
76 |
--------------------------------------------------------------------------------
/man/add_dockerfile.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_dockerfile.R
3 | \name{add_dockerfile}
4 | \alias{add_dockerfile}
5 | \title{Create a Dockerfile}
6 | \usage{
7 | add_dockerfile(
8 | given = NULL,
9 | family = NULL,
10 | email = NULL,
11 | open = TRUE,
12 | overwrite = FALSE,
13 | quiet = FALSE
14 | )
15 | }
16 | \arguments{
17 | \item{given}{A character of length 1. The given name of the project
18 | maintainer.}
19 |
20 | \item{family}{A character of length 1. The family name of the project
21 | maintainer.}
22 |
23 | \item{email}{A character of length 1. The email address of the project
24 | maintainer.}
25 |
26 | \item{open}{A logical value. If \code{TRUE} (default) the \code{Dockerfile} is opened
27 | in the editor.}
28 |
29 | \item{overwrite}{A logical value. If this file is already present and
30 | \code{overwrite = TRUE}, it will be erased and replaced. Default is \code{FALSE}.}
31 |
32 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
33 | \code{FALSE}.}
34 | }
35 | \value{
36 | No return value.
37 | }
38 | \description{
39 | This function creates a \code{Dockerfile} at the root of the project based on a
40 | template. The Docker image is based on
41 | \href{https://hub.docker.com/r/rocker/rstudio}{rocker/rstudio}. The whole project
42 | will be copied in the image and R packages will be installed (using
43 | \code{\link[renv:restore]{renv::restore()}} or \code{\link[remotes:install_deps]{remotes::install_deps()}}).
44 |
45 | In addition a \code{.dockerignore} file is added to ignore some files/folders
46 | while building the image.
47 |
48 | User can customize this \code{Dockerfile} (e.g. system dependencies). He/she
49 | can also use a different default Docker image (i.e. \code{tidyverse}, \code{verse},
50 | \code{geospatial}, etc.). For more information:
51 | https://github.com/rocker-org/rocker-versioned2
52 |
53 | By default the versions of R and \code{renv} (if applicable) specified in the
54 | \code{Dockerfile} are the same as the local system.
55 |
56 | Once the project is ready to be released, user must build the Docker image by
57 | running: \verb{docker build -t "image_name" .}
58 |
59 | Then to run a container, user must run:
60 | \verb{docker run --rm -p 127.0.0.1:8787:8787 -e DISABLE_AUTH=true image_name}
61 |
62 | A new instance of RStudio Server is available on the Web browser at the URL:
63 | \verb{127.0.0.1:8787}.
64 | }
65 | \examples{
66 | \dontrun{
67 | add_dockerfile()
68 | }
69 | }
70 | \seealso{
71 | Other create files:
72 | \code{\link{add_citation}()},
73 | \code{\link{add_code_of_conduct}()},
74 | \code{\link{add_compendium}()},
75 | \code{\link{add_contributing}()},
76 | \code{\link{add_description}()},
77 | \code{\link{add_license}()},
78 | \code{\link{add_makefile}()},
79 | \code{\link{add_package_doc}()},
80 | \code{\link{add_readme_rmd}()},
81 | \code{\link{add_renv}()},
82 | \code{\link{add_testthat}()},
83 | \code{\link{add_vignette}()}
84 | }
85 | \concept{create files}
86 |
--------------------------------------------------------------------------------
/man/add_github_actions_check.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_github_actions_check.R
3 | \name{add_github_actions_check}
4 | \alias{add_github_actions_check}
5 | \title{Setup GitHub Actions to check package}
6 | \usage{
7 | add_github_actions_check(open = FALSE, overwrite = FALSE, quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{open}{A logical value. If \code{TRUE} (default) the file is opened in the
11 | editor.}
12 |
13 | \item{overwrite}{A logical value. If this file is already present and
14 | \code{overwrite = TRUE}, it will be erased and replaced. Default is \code{FALSE}.}
15 |
16 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
17 | \code{FALSE}.}
18 | }
19 | \value{
20 | No return value.
21 | }
22 | \description{
23 | This function creates a configuration file (\code{.yaml}) to setup GitHub Actions
24 | to check the package.
25 | This workflow is derived
26 | from \url{https://github.com/r-lib/actions/tree/v2-branch/examples}.
27 | This file will be written as \code{.github/workflows/R-CMD-check.yaml}.
28 | }
29 | \details{
30 | This workflow runs \verb{R CMD check} on the three major operating systems
31 | (Ubuntu, macOS, and Windows) using the latest release of R. The package is
32 | also checked on Ubuntu (latest version) using the development and previous
33 | versions of R.
34 | }
35 | \examples{
36 | \dontrun{
37 | add_github_actions_check()
38 | }
39 | }
40 | \seealso{
41 | Other development functions:
42 | \code{\link{add_dependencies}()},
43 | \code{\link{add_github_actions_citation}()},
44 | \code{\link{add_github_actions_codecov}()},
45 | \code{\link{add_github_actions_codemeta}()},
46 | \code{\link{add_github_actions_document}()},
47 | \code{\link{add_github_actions_pkgdown}()},
48 | \code{\link{add_github_actions_render}()},
49 | \code{\link{add_r_depend}()},
50 | \code{\link{add_to_buildignore}()},
51 | \code{\link{add_to_gitignore}()}
52 | }
53 | \concept{development functions}
54 |
--------------------------------------------------------------------------------
/man/add_github_actions_check_badge.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_github_actions_check_badge.R
3 | \name{add_github_actions_check_badge}
4 | \alias{add_github_actions_check_badge}
5 | \title{Add a R CMD Check badge}
6 | \usage{
7 | add_github_actions_check_badge(organisation = NULL, quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{organisation}{A character of length 1. The name of the GitHub
11 | organisation to host the package. If \code{NULL} (default) the GitHub account
12 | will be used.}
13 |
14 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
15 | \code{FALSE}.}
16 | }
17 | \value{
18 | A badge as a markdown expression.
19 | }
20 | \description{
21 | This function adds a \strong{R CMD Check} badge to the \code{README.Rmd}. This function
22 | must be run after \code{\link[=add_github_actions_check]{add_github_actions_check()}} which will setup GitHub
23 | Actions to check and test the package.
24 |
25 | Make sure that 1) a \code{README.Rmd} file exists at the project root and 2) it
26 | contains a block starting with the line \verb{} and ending
27 | with the line \verb{}.
28 |
29 | Don't forget to re-render the \code{README.md}.
30 | }
31 | \examples{
32 | \dontrun{
33 | add_github_actions_check_badge()
34 | }
35 | }
36 | \seealso{
37 | Other adding badges:
38 | \code{\link{add_codecov_badge}()},
39 | \code{\link{add_cran_badge}()},
40 | \code{\link{add_dependencies_badge}()},
41 | \code{\link{add_github_actions_codecov_badge}()},
42 | \code{\link{add_github_actions_pkgdown_badge}()},
43 | \code{\link{add_license_badge}()},
44 | \code{\link{add_lifecycle_badge}()},
45 | \code{\link{add_repostatus_badge}()}
46 | }
47 | \concept{adding badges}
48 |
--------------------------------------------------------------------------------
/man/add_github_actions_citation.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_github_actions_citation.R
3 | \name{add_github_actions_citation}
4 | \alias{add_github_actions_citation}
5 | \title{Setup GitHub Actions to update CITATION.cff}
6 | \usage{
7 | add_github_actions_citation(open = FALSE, overwrite = FALSE, quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{open}{A logical value. If \code{TRUE} (default) the file is opened in the
11 | editor.}
12 |
13 | \item{overwrite}{A logical value. If this file is already present and
14 | \code{overwrite = TRUE}, it will be erased and replaced. Default is \code{FALSE}.}
15 |
16 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
17 | \code{FALSE}.}
18 | }
19 | \value{
20 | No return value.
21 | }
22 | \description{
23 | This function creates a configuration file (\code{.yaml}) to setup GitHub Actions
24 | to update the \code{CITATION.cff}.
25 | This workflow is derived
26 | from \url{https://github.com/r-lib/actions/tree/v2-branch/examples}.
27 | This file will be written as \code{.github/workflows/update-citation-cff.yaml}.
28 |
29 | This function also create the \code{CITATION.cff} using the package \link{cffr}.
30 | }
31 | \examples{
32 | \dontrun{
33 | add_github_actions_citation()
34 | }
35 | }
36 | \seealso{
37 | Other development functions:
38 | \code{\link{add_dependencies}()},
39 | \code{\link{add_github_actions_check}()},
40 | \code{\link{add_github_actions_codecov}()},
41 | \code{\link{add_github_actions_codemeta}()},
42 | \code{\link{add_github_actions_document}()},
43 | \code{\link{add_github_actions_pkgdown}()},
44 | \code{\link{add_github_actions_render}()},
45 | \code{\link{add_r_depend}()},
46 | \code{\link{add_to_buildignore}()},
47 | \code{\link{add_to_gitignore}()}
48 | }
49 | \concept{development functions}
50 |
--------------------------------------------------------------------------------
/man/add_github_actions_codecov.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_github_actions_codecov.R
3 | \name{add_github_actions_codecov}
4 | \alias{add_github_actions_codecov}
5 | \title{Setup GitHub Actions to report code coverage}
6 | \usage{
7 | add_github_actions_codecov(open = FALSE, overwrite = FALSE, quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{open}{A logical value. If \code{TRUE} (default) the file is opened in the
11 | editor.}
12 |
13 | \item{overwrite}{A logical value. If this file is already present and
14 | \code{overwrite = TRUE}, it will be erased and replaced. Default is \code{FALSE}.}
15 |
16 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
17 | \code{FALSE}.}
18 | }
19 | \value{
20 | No return value.
21 | }
22 | \description{
23 | This function creates a configuration file (\code{.yaml}) to setup GitHub Actions
24 | to report code coverage when testing the package.
25 | This workflow is derived
26 | from \url{https://github.com/r-lib/actions/tree/v2-branch/examples}.
27 | This file will be written as \code{.github/workflows/test-coverage.yaml}.
28 | }
29 | \examples{
30 | \dontrun{
31 | add_github_actions_codecov()
32 | }
33 | }
34 | \seealso{
35 | Other development functions:
36 | \code{\link{add_dependencies}()},
37 | \code{\link{add_github_actions_check}()},
38 | \code{\link{add_github_actions_citation}()},
39 | \code{\link{add_github_actions_codemeta}()},
40 | \code{\link{add_github_actions_document}()},
41 | \code{\link{add_github_actions_pkgdown}()},
42 | \code{\link{add_github_actions_render}()},
43 | \code{\link{add_r_depend}()},
44 | \code{\link{add_to_buildignore}()},
45 | \code{\link{add_to_gitignore}()}
46 | }
47 | \concept{development functions}
48 |
--------------------------------------------------------------------------------
/man/add_github_actions_codecov_badge.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_github_actions_codecov_badge.R
3 | \name{add_github_actions_codecov_badge}
4 | \alias{add_github_actions_codecov_badge}
5 | \title{Add a Test coverage badge}
6 | \usage{
7 | add_github_actions_codecov_badge(organisation = NULL, quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{organisation}{A character of length 1. The name of the GitHub
11 | organisation to host the package. If \code{NULL} (default) the GitHub account
12 | will be used.}
13 |
14 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
15 | \code{FALSE}.}
16 | }
17 | \value{
18 | A badge as a markdown expression.
19 | }
20 | \description{
21 | This function adds a \strong{Test coverage} badge to the \code{README.Rmd}. This
22 | function must be run after \code{\link[=add_github_actions_codecov]{add_github_actions_codecov()}} which will setup
23 | GitHub Actions to report the percentage of code cover by units tests.
24 |
25 | Make sure that 1) a \code{README.Rmd} file exists at the project root and 2) it
26 | contains a block starting with the line \verb{} and ending
27 | with the line \verb{}.
28 |
29 | Don't forget to re-render the \code{README.md}.
30 | }
31 | \examples{
32 | \dontrun{
33 | add_github_actions_codecov_badge()
34 | }
35 | }
36 | \seealso{
37 | Other adding badges:
38 | \code{\link{add_codecov_badge}()},
39 | \code{\link{add_cran_badge}()},
40 | \code{\link{add_dependencies_badge}()},
41 | \code{\link{add_github_actions_check_badge}()},
42 | \code{\link{add_github_actions_pkgdown_badge}()},
43 | \code{\link{add_license_badge}()},
44 | \code{\link{add_lifecycle_badge}()},
45 | \code{\link{add_repostatus_badge}()}
46 | }
47 | \concept{adding badges}
48 |
--------------------------------------------------------------------------------
/man/add_github_actions_codemeta.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_github_actions_codemeta.R
3 | \name{add_github_actions_codemeta}
4 | \alias{add_github_actions_codemeta}
5 | \title{Setup GitHub Actions to update codemeta.json}
6 | \usage{
7 | add_github_actions_codemeta(open = FALSE, overwrite = FALSE, quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{open}{A logical value. If \code{TRUE} (default) the file is opened in the
11 | editor.}
12 |
13 | \item{overwrite}{A logical value. If this file is already present and
14 | \code{overwrite = TRUE}, it will be erased and replaced. Default is \code{FALSE}.}
15 |
16 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
17 | \code{FALSE}.}
18 | }
19 | \value{
20 | No return value.
21 | }
22 | \description{
23 | This function creates a configuration file (\code{.yaml}) to setup GitHub Actions
24 | to update the \code{codemeta.json}.
25 | This workflow is derived
26 | from \url{https://github.com/r-lib/actions/tree/v2-branch/examples}.
27 | This file will be written as \code{.github/workflows/update-citation-cff.yaml}.
28 |
29 | This function also create the \code{codemeta.json} using the package \link{codemetar}.
30 | }
31 | \examples{
32 | \dontrun{
33 | add_github_actions_codemeta()
34 | }
35 | }
36 | \seealso{
37 | Other development functions:
38 | \code{\link{add_dependencies}()},
39 | \code{\link{add_github_actions_check}()},
40 | \code{\link{add_github_actions_citation}()},
41 | \code{\link{add_github_actions_codecov}()},
42 | \code{\link{add_github_actions_document}()},
43 | \code{\link{add_github_actions_pkgdown}()},
44 | \code{\link{add_github_actions_render}()},
45 | \code{\link{add_r_depend}()},
46 | \code{\link{add_to_buildignore}()},
47 | \code{\link{add_to_gitignore}()}
48 | }
49 | \concept{development functions}
50 |
--------------------------------------------------------------------------------
/man/add_github_actions_document.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_github_actions_document.R
3 | \name{add_github_actions_document}
4 | \alias{add_github_actions_document}
5 | \title{Setup GitHub Actions to document package}
6 | \usage{
7 | add_github_actions_document(open = FALSE, overwrite = FALSE, quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{open}{A logical value. If \code{TRUE} (default) the file is opened in the
11 | editor.}
12 |
13 | \item{overwrite}{A logical value. If this file is already present and
14 | \code{overwrite = TRUE}, it will be erased and replaced. Default is \code{FALSE}.}
15 |
16 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
17 | \code{FALSE}.}
18 | }
19 | \value{
20 | No return value.
21 | }
22 | \description{
23 | This function creates a configuration file (\code{.yaml}) to setup GitHub Actions
24 | to document the package and update the \code{Rd} files in the \verb{man/}, the
25 | \code{NAMESPACE} and \code{DESCRIPTION} files.
26 | This workflow is derived
27 | from \url{https://github.com/r-lib/actions/tree/v2-branch/examples}.
28 | This file will be written as \code{.github/workflows/document-package.yaml}.
29 | }
30 | \examples{
31 | \dontrun{
32 | add_github_actions_document()
33 | }
34 | }
35 | \seealso{
36 | Other development functions:
37 | \code{\link{add_dependencies}()},
38 | \code{\link{add_github_actions_check}()},
39 | \code{\link{add_github_actions_citation}()},
40 | \code{\link{add_github_actions_codecov}()},
41 | \code{\link{add_github_actions_codemeta}()},
42 | \code{\link{add_github_actions_pkgdown}()},
43 | \code{\link{add_github_actions_render}()},
44 | \code{\link{add_r_depend}()},
45 | \code{\link{add_to_buildignore}()},
46 | \code{\link{add_to_gitignore}()}
47 | }
48 | \concept{development functions}
49 |
--------------------------------------------------------------------------------
/man/add_github_actions_pkgdown.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_github_actions_pkgdown.R
3 | \name{add_github_actions_pkgdown}
4 | \alias{add_github_actions_pkgdown}
5 | \title{Setup GitHub Actions to build and deploy package website}
6 | \usage{
7 | add_github_actions_pkgdown(open = FALSE, overwrite = FALSE, quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{open}{A logical value. If \code{TRUE} (default) the file is opened in the
11 | editor.}
12 |
13 | \item{overwrite}{A logical value. If this file is already present and
14 | \code{overwrite = TRUE}, it will be erased and replaced. Default is \code{FALSE}.}
15 |
16 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
17 | \code{FALSE}.}
18 | }
19 | \value{
20 | No return value.
21 | }
22 | \description{
23 | This function creates a configuration file (\code{.yaml}) to setup GitHub Actions
24 | to automatically build and deploy the website using
25 | \href{https://pkgdown.r-lib.org/index.html}{\code{pkgdown}}. This workflow is derived
26 | from \url{https://github.com/r-lib/actions/tree/v2-branch/examples}.
27 | This file will be written as \code{.github/workflows/pkgdown.yaml}.
28 | An additional empty file (\verb{_pkgdown.yaml}) will also be written: it can be
29 | used to customize the website.
30 | }
31 | \examples{
32 | \dontrun{
33 | add_github_actions_pkgdown()
34 | }
35 | }
36 | \seealso{
37 | Other development functions:
38 | \code{\link{add_dependencies}()},
39 | \code{\link{add_github_actions_check}()},
40 | \code{\link{add_github_actions_citation}()},
41 | \code{\link{add_github_actions_codecov}()},
42 | \code{\link{add_github_actions_codemeta}()},
43 | \code{\link{add_github_actions_document}()},
44 | \code{\link{add_github_actions_render}()},
45 | \code{\link{add_r_depend}()},
46 | \code{\link{add_to_buildignore}()},
47 | \code{\link{add_to_gitignore}()}
48 | }
49 | \concept{development functions}
50 |
--------------------------------------------------------------------------------
/man/add_github_actions_pkgdown_badge.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_github_actions_pkgdown_badge.R
3 | \name{add_github_actions_pkgdown_badge}
4 | \alias{add_github_actions_pkgdown_badge}
5 | \title{Add a Website badge}
6 | \usage{
7 | add_github_actions_pkgdown_badge(organisation = NULL, quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{organisation}{A character of length 1. The name of the GitHub
11 | organisation to host the package. If \code{NULL} (default) the GitHub account
12 | will be used.}
13 |
14 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
15 | \code{FALSE}.}
16 | }
17 | \value{
18 | A badge as a markdown expression.
19 | }
20 | \description{
21 | This function adds a \strong{Website} badge to the \code{README.Rmd}. This function
22 | must be run after \code{\link[=add_github_actions_pkgdown]{add_github_actions_pkgdown()}} which will setup
23 | GitHub Actions to build and deploy the package website.
24 |
25 | Make sure that 1) a \code{README.Rmd} file exists at the project root and 2) it
26 | contains a block starting with the line \verb{} and ending
27 | with the line \verb{}.
28 |
29 | Don't forget to re-render the \code{README.md}.
30 | }
31 | \examples{
32 | \dontrun{
33 | add_github_actions_pkgdown_badge()
34 | }
35 | }
36 | \seealso{
37 | Other adding badges:
38 | \code{\link{add_codecov_badge}()},
39 | \code{\link{add_cran_badge}()},
40 | \code{\link{add_dependencies_badge}()},
41 | \code{\link{add_github_actions_check_badge}()},
42 | \code{\link{add_github_actions_codecov_badge}()},
43 | \code{\link{add_license_badge}()},
44 | \code{\link{add_lifecycle_badge}()},
45 | \code{\link{add_repostatus_badge}()}
46 | }
47 | \concept{adding badges}
48 |
--------------------------------------------------------------------------------
/man/add_github_actions_render.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_github_actions_render.R
3 | \name{add_github_actions_render}
4 | \alias{add_github_actions_render}
5 | \title{Setup GitHub Actions to render README}
6 | \usage{
7 | add_github_actions_render(open = FALSE, overwrite = FALSE, quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{open}{A logical value. If \code{TRUE} (default) the file is opened in the
11 | editor.}
12 |
13 | \item{overwrite}{A logical value. If this file is already present and
14 | \code{overwrite = TRUE}, it will be erased and replaced. Default is \code{FALSE}.}
15 |
16 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
17 | \code{FALSE}.}
18 | }
19 | \value{
20 | No return value.
21 | }
22 | \description{
23 | This function creates a configuration file (\code{.yaml}) to setup GitHub Actions
24 | to automatically knit the \code{README.Rmd} after a push. This workflow will be
25 | triggered only if the \code{README.Rmd} has been modified since the last commit.
26 | This workflow is derived
27 | from \url{https://github.com/r-lib/actions/tree/v2-branch/examples}.
28 | This file will be written as \code{.github/workflows/render-README.yaml}.
29 | }
30 | \examples{
31 | \dontrun{
32 | add_github_actions_render()
33 | }
34 | }
35 | \seealso{
36 | Other development functions:
37 | \code{\link{add_dependencies}()},
38 | \code{\link{add_github_actions_check}()},
39 | \code{\link{add_github_actions_citation}()},
40 | \code{\link{add_github_actions_codecov}()},
41 | \code{\link{add_github_actions_codemeta}()},
42 | \code{\link{add_github_actions_document}()},
43 | \code{\link{add_github_actions_pkgdown}()},
44 | \code{\link{add_r_depend}()},
45 | \code{\link{add_to_buildignore}()},
46 | \code{\link{add_to_gitignore}()}
47 | }
48 | \concept{development functions}
49 |
--------------------------------------------------------------------------------
/man/add_license.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_license.R
3 | \name{add_license}
4 | \alias{add_license}
5 | \title{Add a LICENSE}
6 | \usage{
7 | add_license(license = NULL, given = NULL, family = NULL, quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{license}{A character of length 1. The chosen license.
11 | Run \code{\link[=get_licenses]{get_licenses()}}) to select an appropriate one.}
12 |
13 | \item{given}{A character of length 1. The given name of the copyright holder.
14 | Only required if \code{license = 'MIT'}. If is \code{NULL} (default) and
15 | \code{license = 'MIT'}, this function will try to retrieve the value of this
16 | parameter from the \code{.Rprofile} file (edited with \code{\link[=set_credentials]{set_credentials()}}).}
17 |
18 | \item{family}{A character of length 1. The family name of the copyright
19 | holder. Only required if \code{license = 'MIT'}. If is \code{NULL} (default) and
20 | \code{license = 'MIT'}, this function will try to retrieve the value of this
21 | parameter from the \code{.Rprofile} file (edited with \code{\link[=set_credentials]{set_credentials()}}).}
22 |
23 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
24 | \code{FALSE}.}
25 | }
26 | \value{
27 | No return value.
28 | }
29 | \description{
30 | This function adds a license to the project. It will add the license name
31 | in the \code{License} field of the \code{DESCRIPTION} file and write the content of
32 | the license in the \code{License.md} file.
33 | }
34 | \examples{
35 | \dontrun{
36 | add_license(license = "MIT")
37 | add_license(license = "GPL (>= 2)")
38 | }
39 | }
40 | \seealso{
41 | Other create files:
42 | \code{\link{add_citation}()},
43 | \code{\link{add_code_of_conduct}()},
44 | \code{\link{add_compendium}()},
45 | \code{\link{add_contributing}()},
46 | \code{\link{add_description}()},
47 | \code{\link{add_dockerfile}()},
48 | \code{\link{add_makefile}()},
49 | \code{\link{add_package_doc}()},
50 | \code{\link{add_readme_rmd}()},
51 | \code{\link{add_renv}()},
52 | \code{\link{add_testthat}()},
53 | \code{\link{add_vignette}()}
54 | }
55 | \concept{create files}
56 |
--------------------------------------------------------------------------------
/man/add_license_badge.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_license_badge.R
3 | \name{add_license_badge}
4 | \alias{add_license_badge}
5 | \title{Add a License badge}
6 | \usage{
7 | add_license_badge(quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
11 | \code{FALSE}.}
12 | }
13 | \value{
14 | A badge as a markdown expression.
15 | }
16 | \description{
17 | This function adds or updates the \strong{License} badge to the \code{README.Rmd}.
18 | This function reads the \code{License} field of the \code{DESCRIPTION} file. Ensure
19 | that this field is correctly defined. See \code{\link[=add_license]{add_license()}} for further detail.
20 |
21 | This function requires the presence of a \code{DESCRIPTION} file at the project
22 | root. See \code{\link[=add_description]{add_description()}} for further detail.
23 |
24 | Make sure that 1) a \code{README.Rmd} file exists at the project root and 2) it
25 | contains a block starting with the line \verb{} and ending
26 | with the line \verb{}.
27 |
28 | Don't forget to re-render the \code{README.md}.
29 | }
30 | \examples{
31 | \dontrun{
32 | add_license_badge()
33 | }
34 | }
35 | \seealso{
36 | Other adding badges:
37 | \code{\link{add_codecov_badge}()},
38 | \code{\link{add_cran_badge}()},
39 | \code{\link{add_dependencies_badge}()},
40 | \code{\link{add_github_actions_check_badge}()},
41 | \code{\link{add_github_actions_codecov_badge}()},
42 | \code{\link{add_github_actions_pkgdown_badge}()},
43 | \code{\link{add_lifecycle_badge}()},
44 | \code{\link{add_repostatus_badge}()}
45 | }
46 | \concept{adding badges}
47 |
--------------------------------------------------------------------------------
/man/add_lifecycle_badge.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_lifecycle_badge.R
3 | \name{add_lifecycle_badge}
4 | \alias{add_lifecycle_badge}
5 | \title{Add a Life Cycle badge}
6 | \usage{
7 | add_lifecycle_badge(lifecycle = "experimental", quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{lifecycle}{A character of length 1. Accepted stages are:
11 | \code{'experimental'} (default), \code{'stable'}, \code{'deprecated'}, or \code{'superseded'}.}
12 |
13 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
14 | \code{FALSE}.}
15 | }
16 | \value{
17 | A badge as a markdown expression.
18 | }
19 | \description{
20 | This function adds or updates the \strong{Life Cycle} badge to the \code{README.Rmd}.
21 | It is based on the standard defined at
22 | \url{https://lifecycle.r-lib.org/articles/stages.html}.
23 |
24 | Make sure that 1) a \code{README.Rmd} file exists at the project root and 2) it
25 | contains a block starting with the line \verb{} and ending
26 | with the line \verb{}.
27 |
28 | Don't forget to re-render the \code{README.md}.
29 | }
30 | \details{
31 | The project can have the following life cycle stage:
32 | \itemize{
33 | \item \strong{Experimental} - An experimental project is made available so user
34 | can try it out and provide feedback, but come with no promises for long
35 | term stability.
36 | \item \strong{Stable} - A project is considered stable when the author is happy
37 | with its interface, does not see major issues, and is happy to share it
38 | with the world.
39 | \item \strong{Superseded} - A superseded project has a known better
40 | alternative, and it is not going away. Superseded project will not receive
41 | new features, but will receive any critical bug fixes needed to keep it
42 | working.
43 | \item \strong{Deprecated} - A deprecated project has a better alternative
44 | available and is scheduled for removal.
45 | }
46 | }
47 | \examples{
48 | \dontrun{
49 | add_lifecycle_badge()
50 | add_lifecycle_badge(lifecycle = "stable")
51 | }
52 | }
53 | \seealso{
54 | Other adding badges:
55 | \code{\link{add_codecov_badge}()},
56 | \code{\link{add_cran_badge}()},
57 | \code{\link{add_dependencies_badge}()},
58 | \code{\link{add_github_actions_check_badge}()},
59 | \code{\link{add_github_actions_codecov_badge}()},
60 | \code{\link{add_github_actions_pkgdown_badge}()},
61 | \code{\link{add_license_badge}()},
62 | \code{\link{add_repostatus_badge}()}
63 | }
64 | \concept{adding badges}
65 |
--------------------------------------------------------------------------------
/man/add_makefile.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_makefile.R
3 | \name{add_makefile}
4 | \alias{add_makefile}
5 | \title{Create a Make-like R file}
6 | \usage{
7 | add_makefile(
8 | given = NULL,
9 | family = NULL,
10 | email = NULL,
11 | open = TRUE,
12 | overwrite = FALSE,
13 | quiet = FALSE
14 | )
15 | }
16 | \arguments{
17 | \item{given}{A character of length 1. The given name of the project
18 | maintainer.}
19 |
20 | \item{family}{A character of length 1. The family name of the project
21 | maintainer.}
22 |
23 | \item{email}{A character of length 1. The email address of the project
24 | maintainer.}
25 |
26 | \item{open}{A logical value. If \code{TRUE} (default) the file is opened in the
27 | editor.}
28 |
29 | \item{overwrite}{A logical value. If this file is already present and
30 | \code{overwrite = TRUE}, it will be erased and replaced. Default is \code{FALSE}.}
31 |
32 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
33 | \code{FALSE}.}
34 | }
35 | \value{
36 | No return value.
37 | }
38 | \description{
39 | This function creates a Make-like R file (\code{make.R}) at the root of the
40 | project based on a template. To be used only if the project is a research
41 | compendium. The content of this file provides some guidelines. See also
42 | \code{\link[=new_compendium]{new_compendium()}} for further information.
43 | }
44 | \examples{
45 | \dontrun{
46 | add_makefile()
47 | }
48 | }
49 | \seealso{
50 | Other create files:
51 | \code{\link{add_citation}()},
52 | \code{\link{add_code_of_conduct}()},
53 | \code{\link{add_compendium}()},
54 | \code{\link{add_contributing}()},
55 | \code{\link{add_description}()},
56 | \code{\link{add_dockerfile}()},
57 | \code{\link{add_license}()},
58 | \code{\link{add_package_doc}()},
59 | \code{\link{add_readme_rmd}()},
60 | \code{\link{add_renv}()},
61 | \code{\link{add_testthat}()},
62 | \code{\link{add_vignette}()}
63 | }
64 | \concept{create files}
65 |
--------------------------------------------------------------------------------
/man/add_package_doc.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_package_doc.R
3 | \name{add_package_doc}
4 | \alias{add_package_doc}
5 | \title{Create a package-level documentation file}
6 | \usage{
7 | add_package_doc(open = TRUE, overwrite = FALSE, quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{open}{A logical value. If \code{TRUE} (default) the file is opened in the
11 | editor.}
12 |
13 | \item{overwrite}{A logical value. If this file is already present and
14 | \code{overwrite = TRUE}, it will be erased and replaced. Default is \code{FALSE}.}
15 |
16 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
17 | \code{FALSE}.}
18 | }
19 | \value{
20 | No return value.
21 | }
22 | \description{
23 | This function adds a package-level documentation file (\code{pkg-package.R}) in
24 | the \verb{R/} folder. This file will make help available to the user via \code{?pkg}
25 | (where \code{pkg} is the name of the package). It a good place to put general
26 | directives like \verb{@import} and \verb{@importFrom}.
27 | }
28 | \examples{
29 | \dontrun{
30 | add_package_doc()
31 | }
32 | }
33 | \seealso{
34 | Other create files:
35 | \code{\link{add_citation}()},
36 | \code{\link{add_code_of_conduct}()},
37 | \code{\link{add_compendium}()},
38 | \code{\link{add_contributing}()},
39 | \code{\link{add_description}()},
40 | \code{\link{add_dockerfile}()},
41 | \code{\link{add_license}()},
42 | \code{\link{add_makefile}()},
43 | \code{\link{add_readme_rmd}()},
44 | \code{\link{add_renv}()},
45 | \code{\link{add_testthat}()},
46 | \code{\link{add_vignette}()}
47 | }
48 | \concept{create files}
49 |
--------------------------------------------------------------------------------
/man/add_r_depend.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_r_depend.R
3 | \name{add_r_depend}
4 | \alias{add_r_depend}
5 | \title{Add minimal R version to DESCRIPTION}
6 | \usage{
7 | add_r_depend()
8 | }
9 | \value{
10 | No return value.
11 | }
12 | \description{
13 | This function adds the minimal R version to the \code{Depends} field of the
14 | \code{DESCRIPTION} file. This version corresponds to the higher version of R
15 | among all dependencies. If no dependencies mentions minimal R version, the
16 | \code{DESCRIPTION} is not modified.
17 | }
18 | \examples{
19 | \dontrun{
20 | add_r_depend()
21 | }
22 | }
23 | \seealso{
24 | Other development functions:
25 | \code{\link{add_dependencies}()},
26 | \code{\link{add_github_actions_check}()},
27 | \code{\link{add_github_actions_citation}()},
28 | \code{\link{add_github_actions_codecov}()},
29 | \code{\link{add_github_actions_codemeta}()},
30 | \code{\link{add_github_actions_document}()},
31 | \code{\link{add_github_actions_pkgdown}()},
32 | \code{\link{add_github_actions_render}()},
33 | \code{\link{add_to_buildignore}()},
34 | \code{\link{add_to_gitignore}()}
35 | }
36 | \concept{development functions}
37 |
--------------------------------------------------------------------------------
/man/add_readme_rmd.Rd:
--------------------------------------------------------------------------------
1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_readme_rmd.R
3 | \name{add_readme_rmd}
4 | \alias{add_readme_rmd}
5 | \title{Create a README file}
6 | \usage{
7 | add_readme_rmd(
8 | type = "package",
9 | given = NULL,
10 | family = NULL,
11 | organisation = NULL,
12 | open = TRUE,
13 | overwrite = FALSE,
14 | quiet = FALSE
15 | )
16 | }
17 | \arguments{
18 | \item{type}{A character of length 1. If \code{package} (default) a GitHub
19 | \code{README.Rmd} specific to an R package will be created. If \code{compendium} a
20 | GitHub \code{README.Rmd} specific to a research compendium will be created.}
21 |
22 | \item{given}{A character of length 1. The given name of the project
23 | maintainer.}
24 |
25 | \item{family}{A character of length 1. The family name of the project
26 | maintainer.}
27 |
28 | \item{organisation}{A character of length 1. The name of the GitHub
29 | organisation to host the package. If \code{NULL} (default) the GitHub account
30 | will be used. This argument is used to set the URL of the package
31 | (hosted on GitHub).}
32 |
33 | \item{open}{A logical value. If \code{TRUE} (default) the file is opened in the
34 | editor.}
35 |
36 | \item{overwrite}{A logical value. If this file is already present and
37 | \code{overwrite = TRUE}, it will be erased and replaced. Default is \code{FALSE}.}
38 |
39 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
40 | \code{FALSE}.}
41 | }
42 | \value{
43 | No return value.
44 | }
45 | \description{
46 | This function creates a \code{README.Rmd} file at the root of the project based
47 | on a template. Once edited user needs to knit it into a \code{README.md}
48 | (or use the function \code{\link[=refresh]{refresh()}}).
49 | }
50 | \examples{
51 | \dontrun{
52 | add_readme_rmd(type = "package")
53 | }
54 | }
55 | \seealso{
56 | Other create files:
57 | \code{\link{add_citation}()},
58 | \code{\link{add_code_of_conduct}()},
59 | \code{\link{add_compendium}()},
60 | \code{\link{add_contributing}()},
61 | \code{\link{add_description}()},
62 | \code{\link{add_dockerfile}()},
63 | \code{\link{add_license}()},
64 | \code{\link{add_makefile}()},
65 | \code{\link{add_package_doc}()},
66 | \code{\link{add_renv}()},
67 | \code{\link{add_testthat}()},
68 | \code{\link{add_vignette}()}
69 | }
70 | \concept{create files}
71 |
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/man/add_renv.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_renv.R
3 | \name{add_renv}
4 | \alias{add_renv}
5 | \title{Initialize renv}
6 | \usage{
7 | add_renv(quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
11 | \code{FALSE}.}
12 | }
13 | \value{
14 | No return value.
15 | }
16 | \description{
17 | This function initializes an \code{renv} environment for the project by running
18 | \code{\link[renv:init]{renv::init()}}. See \url{https://rstudio.github.io/renv/} for further detail.
19 | }
20 | \examples{
21 | \dontrun{
22 | add_renv()
23 | }
24 | }
25 | \seealso{
26 | Other create files:
27 | \code{\link{add_citation}()},
28 | \code{\link{add_code_of_conduct}()},
29 | \code{\link{add_compendium}()},
30 | \code{\link{add_contributing}()},
31 | \code{\link{add_description}()},
32 | \code{\link{add_dockerfile}()},
33 | \code{\link{add_license}()},
34 | \code{\link{add_makefile}()},
35 | \code{\link{add_package_doc}()},
36 | \code{\link{add_readme_rmd}()},
37 | \code{\link{add_testthat}()},
38 | \code{\link{add_vignette}()}
39 | }
40 | \concept{create files}
41 |
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/man/add_repostatus_badge.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_repostatus_badge.R
3 | \name{add_repostatus_badge}
4 | \alias{add_repostatus_badge}
5 | \title{Add a Repository Status badge}
6 | \usage{
7 | add_repostatus_badge(status = "concept", quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{status}{A character of length 1. Accepted status are: \code{'concept'}
11 | (default), \code{'wip'}, \code{'suspended'}, \code{'abandoned'}, \code{'active'},
12 | \code{'inactive'}, or \code{'unsupported'}.}
13 |
14 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
15 | \code{FALSE}.}
16 | }
17 | \value{
18 | A badge as a markdown expression.
19 | }
20 | \description{
21 | This function adds or updates the \strong{Repository Status} badge of the project
22 | to the \code{README.Rmd}. It is based on the standard defined by the
23 | \url{https://www.repostatus.org} project.
24 |
25 | Make sure that 1) a \code{README.Rmd} file exists at the project root and 2) it
26 | contains a block starting with the line \verb{} and ending
27 | with the line \verb{}.
28 |
29 | Don't forget to re-render the \code{README.md}.
30 | }
31 | \details{
32 | The project can have the following status:
33 | \itemize{
34 | \item \strong{Concept} - Minimal or no implementation has been done yet, or the
35 | repository is only intended to be a limited example, demo, or
36 | proof-of-concept.
37 | \item \strong{WIP} - Initial development is in progress, but there has not yet
38 | been a stable, usable release suitable for the public.
39 | \item \strong{Suspended} - Initial development has started, but there has not
40 | yet been a stable, usable release; work has been stopped for the time
41 | being but the author(s) intend on resuming work.
42 | \item \strong{Abandoned} - Initial development has started, but there has not
43 | yet been a stable, usable release; the project has been abandoned and the
44 | author(s) do not intend on continuing development.
45 | \item \strong{Active} - The project has reached a stable, usable state and is
46 | being actively developed.
47 | \item \strong{Inactive} - The project has reached a stable, usable state but is
48 | no longer being actively developed; support/maintenance will be provided
49 | as time allows.
50 | \item \strong{Unsupported} - The project has reached a stable, usable state but
51 | the author(s) have ceased all work on it. A new maintainer may be desired.
52 | }
53 | }
54 | \examples{
55 | \dontrun{
56 | add_repostatus_badge()
57 | add_repostatus_badge(status = "active")
58 | }
59 | }
60 | \seealso{
61 | Other adding badges:
62 | \code{\link{add_codecov_badge}()},
63 | \code{\link{add_cran_badge}()},
64 | \code{\link{add_dependencies_badge}()},
65 | \code{\link{add_github_actions_check_badge}()},
66 | \code{\link{add_github_actions_codecov_badge}()},
67 | \code{\link{add_github_actions_pkgdown_badge}()},
68 | \code{\link{add_license_badge}()},
69 | \code{\link{add_lifecycle_badge}()}
70 | }
71 | \concept{adding badges}
72 |
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/man/add_testthat.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_testthat.R
3 | \name{add_testthat}
4 | \alias{add_testthat}
5 | \title{Initialize units tests}
6 | \usage{
7 | add_testthat()
8 | }
9 | \value{
10 | No return value.
11 | }
12 | \description{
13 | This function initializes units tests settings by running
14 | \code{\link[usethis:use_testthat]{usethis::use_testthat()}} and by adding an example units tests file
15 | \code{tests/testthat/test-demo.R}. The sample file will test a demo function
16 | created in \code{R/fun-demo.R}.
17 | }
18 | \examples{
19 | \dontrun{
20 | add_testthat()
21 | }
22 | }
23 | \seealso{
24 | Other create files:
25 | \code{\link{add_citation}()},
26 | \code{\link{add_code_of_conduct}()},
27 | \code{\link{add_compendium}()},
28 | \code{\link{add_contributing}()},
29 | \code{\link{add_description}()},
30 | \code{\link{add_dockerfile}()},
31 | \code{\link{add_license}()},
32 | \code{\link{add_makefile}()},
33 | \code{\link{add_package_doc}()},
34 | \code{\link{add_readme_rmd}()},
35 | \code{\link{add_renv}()},
36 | \code{\link{add_vignette}()}
37 | }
38 | \concept{create files}
39 |
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/man/add_to_buildignore.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_to_buildignore.R
3 | \name{add_to_buildignore}
4 | \alias{add_to_buildignore}
5 | \title{Add to the .Rbuildignore file}
6 | \usage{
7 | add_to_buildignore(x, open = FALSE, quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{x}{A character vector. One or several files/folders names to be added
11 | to the \code{.Rbuildignore}. This argument is mandatory.}
12 |
13 | \item{open}{A logical value. If \code{TRUE} the \code{.Rbuildignore} file is opened in
14 | the editor. Default is \code{FALSE}.}
15 |
16 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
17 | \code{FALSE}.}
18 | }
19 | \value{
20 | No return value.
21 | }
22 | \description{
23 | This function adds files/folders to the \code{.Rbuildignore} file. If a
24 | \code{.Rbuildignore} is already present, files to be ignored while checking
25 | package are just added to this file. Otherwise a new file is created.
26 | }
27 | \examples{
28 | \dontrun{
29 | add_to_buildignore(open = TRUE)
30 | add_to_buildignore(".DS_Store")
31 | }
32 | }
33 | \seealso{
34 | Other development functions:
35 | \code{\link{add_dependencies}()},
36 | \code{\link{add_github_actions_check}()},
37 | \code{\link{add_github_actions_citation}()},
38 | \code{\link{add_github_actions_codecov}()},
39 | \code{\link{add_github_actions_codemeta}()},
40 | \code{\link{add_github_actions_document}()},
41 | \code{\link{add_github_actions_pkgdown}()},
42 | \code{\link{add_github_actions_render}()},
43 | \code{\link{add_r_depend}()},
44 | \code{\link{add_to_gitignore}()}
45 | }
46 | \concept{development functions}
47 |
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/man/add_to_gitignore.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_to_gitignore.R
3 | \name{add_to_gitignore}
4 | \alias{add_to_gitignore}
5 | \title{Add to the .gitignore file}
6 | \usage{
7 | add_to_gitignore(x, open = FALSE, quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{x}{A character vector. One or several files/folders names to be added
11 | to the \code{.gitignore}.}
12 |
13 | \item{open}{A logical value. If \code{TRUE} the \code{.gitignore} file is opened in
14 | the editor. Default is \code{FALSE}.}
15 |
16 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
17 | \code{FALSE}.}
18 | }
19 | \value{
20 | No return value.
21 | }
22 | \description{
23 | This function creates a \code{.gitignore} file at the root of the project based on
24 | a template (specific to R). If a \code{.gitignore} is already present, files to
25 | be untracked by \strong{git} are just added to this file.
26 | }
27 | \examples{
28 | \dontrun{
29 | add_to_gitignore(open = TRUE)
30 | add_to_gitignore(".DS_Store")
31 | }
32 | }
33 | \seealso{
34 | Other development functions:
35 | \code{\link{add_dependencies}()},
36 | \code{\link{add_github_actions_check}()},
37 | \code{\link{add_github_actions_citation}()},
38 | \code{\link{add_github_actions_codecov}()},
39 | \code{\link{add_github_actions_codemeta}()},
40 | \code{\link{add_github_actions_document}()},
41 | \code{\link{add_github_actions_pkgdown}()},
42 | \code{\link{add_github_actions_render}()},
43 | \code{\link{add_r_depend}()},
44 | \code{\link{add_to_buildignore}()}
45 | }
46 | \concept{development functions}
47 |
--------------------------------------------------------------------------------
/man/add_vignette.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/add_vignette.R
3 | \name{add_vignette}
4 | \alias{add_vignette}
5 | \title{Create a vignette document}
6 | \usage{
7 | add_vignette(
8 | filename = NULL,
9 | title = NULL,
10 | open = TRUE,
11 | overwrite = FALSE,
12 | quiet = FALSE
13 | )
14 | }
15 | \arguments{
16 | \item{filename}{A character of length 1. The name of the \code{.Rmd} file to be
17 | created. If \code{NULL} (default ) the \code{.Rmd} file will be named \code{pkg.Rmd}
18 | where \code{pkg} is your package name.}
19 |
20 | \item{title}{A character of length 1. The title of the vignette. If \code{NULL}
21 | (default) the title will be \verb{Get started}.}
22 |
23 | \item{open}{A logical value. If \code{TRUE} (default) the file is opened in the
24 | editor.}
25 |
26 | \item{overwrite}{A logical value. If this file is already present and
27 | \code{overwrite = TRUE}, it will be erased and replaced. Default is \code{FALSE}.}
28 |
29 | \item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
30 | \code{FALSE}.}
31 | }
32 | \value{
33 | No return value.
34 | }
35 | \description{
36 | This function adds a vignette in the folder \verb{vignettes/}. It also adds
37 | dependencies \href{https://yihui.org/knitr/}{\code{knitr}} and
38 | \href{https://rmarkdown.rstudio.com/}{\code{rmarkdown}} in the
39 | field \code{Suggests} of the \code{DESCRIPTION} file (if not already present in
40 | fields \code{Imports}).
41 | }
42 | \examples{
43 | \dontrun{
44 | ## Default vignette ----
45 | add_vignette()
46 |
47 | ## Default vignette ----
48 | add_vignette(filename = "pkg", title = "Get started")
49 | }
50 | }
51 | \seealso{
52 | Other create files:
53 | \code{\link{add_citation}()},
54 | \code{\link{add_code_of_conduct}()},
55 | \code{\link{add_compendium}()},
56 | \code{\link{add_contributing}()},
57 | \code{\link{add_description}()},
58 | \code{\link{add_dockerfile}()},
59 | \code{\link{add_license}()},
60 | \code{\link{add_makefile}()},
61 | \code{\link{add_package_doc}()},
62 | \code{\link{add_readme_rmd}()},
63 | \code{\link{add_renv}()},
64 | \code{\link{add_testthat}()}
65 | }
66 | \concept{create files}
67 |
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/man/figures/logo.png:
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https://raw.githubusercontent.com/FRBCesab/rcompendium/c50e80d8a693cef53280d46edbb2e544b5744b22/man/figures/logo.png
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/man/get_all_dependencies.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/get_all_dependencies.R
3 | \name{get_all_dependencies}
4 | \alias{get_all_dependencies}
5 | \title{Get all external dependencies}
6 | \usage{
7 | get_all_dependencies(pkg = NULL)
8 | }
9 | \arguments{
10 | \item{pkg}{A character of length 1. The name of a CRAN package or \code{NULL}
11 | (default). If \code{NULL} get dependencies of the local (uninstalled) project
12 | (package or compendium).}
13 | }
14 | \value{
15 | A list of three vectors:
16 | \itemize{
17 | \item \code{base_deps}, a vector of base packages;
18 | \item \code{direct_deps}, a vector of direct packages;
19 | \item \code{all_deps}, a vector of all dependencies (recursively obtained).
20 | }
21 | }
22 | \description{
23 | This function gets all the external packages that the project needs. It is
24 | used the generate the \emph{Dependencies} badge (\code{\link[=add_dependencies_badge]{add_dependencies_badge()}}).
25 | }
26 | \examples{
27 | \dontrun{
28 | ## Update dependencies ----
29 | add_dependencies()
30 |
31 | ## Get all dependencies ----
32 | deps <- get_all_dependencies()
33 | unlist(lapply(deps, length))
34 |
35 | ## Can be used for a CRAN package ----
36 | deps <- get_all_dependencies("usethis")
37 | unlist(lapply(deps, length))
38 | }
39 | }
40 | \seealso{
41 | Other utilities functions:
42 | \code{\link{get_all_functions}()},
43 | \code{\link{get_licenses}()},
44 | \code{\link{get_minimal_r_version}()}
45 | }
46 | \concept{utilities functions}
47 |
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/man/get_all_functions.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/get_all_functions.R
3 | \name{get_all_functions}
4 | \alias{get_all_functions}
5 | \title{List all functions in the package}
6 | \usage{
7 | get_all_functions()
8 | }
9 | \value{
10 | A list of two vectors:
11 | \itemize{
12 | \item \code{external}, a vector of exported functions name;
13 | \item \code{internal}, a vector of internal functions name.
14 | }
15 | }
16 | \description{
17 | This function returns a list of all the functions (exported and internal)
18 | available with the package. As this function scans the \code{NAMESPACE} and the
19 | \verb{R/} folder, it is recommended to run \code{\link[devtools:document]{devtools::document()}} before.
20 | }
21 | \examples{
22 | \dontrun{
23 | ## Update NAMESPACE ----
24 | devtools::document()
25 |
26 | ## List all implemented functions ----
27 | get_all_functions()
28 | }
29 | }
30 | \seealso{
31 | Other utilities functions:
32 | \code{\link{get_all_dependencies}()},
33 | \code{\link{get_licenses}()},
34 | \code{\link{get_minimal_r_version}()}
35 | }
36 | \concept{utilities functions}
37 |
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/man/get_licenses.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/get_licenses.R
3 | \name{get_licenses}
4 | \alias{get_licenses}
5 | \title{List all available licenses}
6 | \usage{
7 | get_licenses()
8 | }
9 | \value{
10 | A \code{data.frame} with the following two variables:
11 | \itemize{
12 | \item \code{tag}, the license name to be used with \code{\link[=add_license]{add_license()}};
13 | \item \code{url}, the URL of the license description.
14 | }
15 | }
16 | \description{
17 | This function returns a list of all available licenses. This is particularly
18 | useful to get the right spelling of the license to be passed to
19 | \code{\link[=new_package]{new_package()}}, \code{\link[=new_compendium]{new_compendium()}}, or \code{\link[=add_license]{add_license()}}.
20 | }
21 | \examples{
22 | get_licenses()
23 | }
24 | \seealso{
25 | Other utilities functions:
26 | \code{\link{get_all_dependencies}()},
27 | \code{\link{get_all_functions}()},
28 | \code{\link{get_minimal_r_version}()}
29 | }
30 | \concept{utilities functions}
31 |
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/man/get_minimal_r_version.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/get_minimal_r_version.R
3 | \name{get_minimal_r_version}
4 | \alias{get_minimal_r_version}
5 | \title{Get required minimal R version}
6 | \usage{
7 | get_minimal_r_version(pkg = NULL)
8 | }
9 | \arguments{
10 | \item{pkg}{A character of length 1. The name of a CRAN package or \code{NULL}
11 | (default). If \code{NULL} get minimal required R version of the local
12 | (uninstalled) project (package or compendium).}
13 | }
14 | \value{
15 | A character with the minimal required R version.
16 | }
17 | \description{
18 | This function detects the minimal required R version for the project based
19 | on minimal required R version of its dependencies. It can be used to update
20 | the \code{Depends} field of the \code{DESCRIPTION} file.
21 | }
22 | \examples{
23 | \dontrun{
24 | ## Update dependencies ----
25 | add_dependencies()
26 |
27 | ## Minimal R version of a project ----
28 | get_minimal_r_version()
29 |
30 | ## Minimal R version of a CRAN package ----
31 | get_minimal_r_version("usethis")
32 | }
33 | }
34 | \seealso{
35 | Other utilities functions:
36 | \code{\link{get_all_dependencies}()},
37 | \code{\link{get_all_functions}()},
38 | \code{\link{get_licenses}()}
39 | }
40 | \concept{utilities functions}
41 |
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/man/refresh.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/refresh.R
3 | \name{refresh}
4 | \alias{refresh}
5 | \title{Refresh a package/research compendium}
6 | \usage{
7 | refresh(compendium = NULL, make = FALSE, check = FALSE, quiet = FALSE)
8 | }
9 | \arguments{
10 | \item{compendium}{A character of length 1. The name of the folder to
11 | recursively detect dependencies to be added to the \code{Imports} field of
12 | \code{DESCRIPTION} file. It can be \code{'analysis/'} (if additional folders, i.e.
13 | \verb{data/}, \verb{outputs/}, \verb{figures/}, etc. have been created in this folder),
14 | \code{'.'} (if folders \verb{data/}, \verb{outputs/}, \verb{figures/}, etc. have been created
15 | at the root of the project), etc.
16 | See \code{\link[=new_compendium]{new_compendium()}} for further information.
17 |
18 | Default is \code{compendium = NULL} (i.e. no additional folder are inspected
19 | but \verb{R/}, \code{NAMESPACE}, \verb{vignettes/}, and \verb{tests/} are still inspected).}
20 |
21 | \item{make}{A logical value. If \code{TRUE} the Make-like R file \code{make.R} is
22 | sourced. Only for research compendium created with \code{\link[=new_compendium]{new_compendium()}}.
23 | Default is \code{FALSE}.}
24 |
25 | \item{check}{A logical value. If \code{TRUE} package integrity is checked using
26 | \code{\link[devtools:check]{devtools::check()}}.
27 | Default is \code{FALSE}.}
28 |
29 | \item{quiet}{A logical value. If \code{TRUE} (default) message are deleted.}
30 | }
31 | \value{
32 | No return value.
33 | }
34 | \description{
35 | \strong{This function is about to be removed from \code{rcompendium}.}
36 |
37 | This function refreshes a package/research compendium. It will:
38 | \itemize{
39 | \item Update \code{.Rd} files and \code{NAMESPACE} by using \code{\link[devtools:document]{devtools::document()}};
40 | \item Update external packages (in \code{DESCRIPTION} file) by using
41 | \code{\link[=add_dependencies]{add_dependencies()}};
42 | \item Update badges in \code{README.Rmd} (if already present);
43 | \item Re-knitr the \code{README.Rmd} by using \code{\link[rmarkdown:render]{rmarkdown::render()}};
44 | \item Check package integrity by using \code{\link[devtools:check]{devtools::check()}};
45 | \item Run analysis by sourcing \code{make.R} (only for compendium).
46 | }
47 | }
48 | \examples{
49 | \dontrun{
50 | library(rcompendium)
51 |
52 | ## Create an R package ----
53 | new_package()
54 |
55 | ## Start developing functions ----
56 | ## ...
57 |
58 | ## Update package (documentation, dependencies, README) ----
59 | refresh()
60 | }
61 | }
62 | \seealso{
63 | Other setup functions:
64 | \code{\link{new_compendium}()},
65 | \code{\link{new_package}()},
66 | \code{\link{set_credentials}()}
67 | }
68 | \concept{setup functions}
69 |
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/man/set_credentials.Rd:
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1 | % Generated by roxygen2: do not edit by hand
2 | % Please edit documentation in R/set_credentials.R
3 | \name{set_credentials}
4 | \alias{set_credentials}
5 | \title{Store credentials to the .Rprofile}
6 | \usage{
7 | set_credentials(
8 | given = NULL,
9 | family = NULL,
10 | email = NULL,
11 | orcid = NULL,
12 | protocol = NULL
13 | )
14 | }
15 | \arguments{
16 | \item{given}{A character of length 1. The given name of the project
17 | maintainer.}
18 |
19 | \item{family}{A character of length 1. The family name of the project
20 | maintainer.}
21 |
22 | \item{email}{A character of length 1. The email address of the project
23 | maintainer.}
24 |
25 | \item{orcid}{A character of length 1. The ORCID of the project maintainer.}
26 |
27 | \item{protocol}{A character of length 1. The GIT protocol used to
28 | communicate with the GitHub remote. One of \code{'https'} or \code{'ssh'}. If you
29 | don't know, keep the default value (i.e. \code{NULL}) and the protocol will be
30 | \code{'https'}.}
31 | }
32 | \value{
33 | No return value.
34 | }
35 | \description{
36 | This function is used to store user credentials in the \code{.Rprofile} file.
37 | Accepted credentials are listed below. This function is useful if user
38 | creates a lot of packages and/or research compendiums.
39 |
40 | If the \code{.Rprofile} file does not exist this function will create it. Users
41 | need to paste the content of the clipboard to this file.
42 | }
43 | \examples{
44 | \dontrun{
45 | library(rcompendium)
46 |
47 |
48 | ## Define **ONCE FOR ALL** your credentials ----
49 |
50 | set_credentials("John", "Doe", "john.doe@domain.com",
51 | orcid = "9999-9999-9999-9999", protocol = "https")
52 | }
53 | }
54 | \seealso{
55 | Other setup functions:
56 | \code{\link{new_compendium}()},
57 | \code{\link{new_package}()},
58 | \code{\link{refresh}()}
59 | }
60 | \concept{setup functions}
61 |
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/tests/testthat.R:
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1 | library(testthat)
2 | library(rcompendium)
3 |
4 | test_check("rcompendium")
5 |
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/tests/testthat/setup-tests.R:
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1 | #' Setup Tests Infrastructure
2 | #'
3 |
4 | ## Temporary Directory ----
5 |
6 | create_temp_compendium <- function(pkg = file.path(tempdir(), "pkgtest")) {
7 |
8 | old_wd <- getwd()
9 |
10 | withr::defer(fs::dir_delete(pkg), envir = parent.frame())
11 |
12 | dir.create(pkg)
13 |
14 | setwd(pkg)
15 | invisible(file.create(".here"))
16 |
17 | withr::defer(setwd(old_wd), envir = parent.frame())
18 |
19 | invisible(pkg)
20 | }
21 |
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/tests/testthat/test-01-proj.R:
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1 | ## PROJECT ---
2 |
3 | test_that("Check Project Found", {
4 |
5 | create_temp_compendium()
6 |
7 | expect_equal(get_package_name(), "pkgtest")
8 | })
9 |
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/tests/testthat/test-03-license.R:
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1 | ## LICENSE FILE ----
2 |
3 | test_that("Check Inputs", {
4 |
5 | # Simulation of no Rprofile...
6 | withr::local_options(list("given" = NULL, "family" = NULL, "email" = NULL,
7 | "orcid" = NULL, "github" = NULL))
8 |
9 | expect_error(add_license(quiet = TRUE), "No 'DESCRIPTION' file found.")
10 |
11 | create_temp_compendium()
12 | add_description("John", "Doe", "john.doe@gmail.com", "9999-9999-9999-9999",
13 | organisation = "society", open = FALSE, overwrite = FALSE,
14 | quiet = TRUE)
15 |
16 | expect_error(add_license(quiet = TRUE))
17 | expect_error(add_license(license = NA, quiet = TRUE))
18 | expect_error(add_license(license = numeric(0), quiet = TRUE))
19 | expect_error(add_license(license = c("MIT", "GPL-2"), quiet = TRUE))
20 | expect_error(add_license(license = "GPL2", quiet = TRUE))
21 | expect_error(add_license(license = "GPL 2", quiet = TRUE))
22 |
23 | expect_error(add_license(quiet = 0))
24 | expect_error(add_license(quiet = NULL))
25 | expect_error(add_license(quiet = "false"))
26 |
27 | expect_error(add_license(license = "MIT", quiet = TRUE))
28 | expect_error(add_license(license = "MIT", "John", quiet = TRUE))
29 | expect_error(add_license(license = "MIT", "John Doe", quiet = TRUE))
30 | expect_error(add_license(license = "MIT", c("John", "Doe"), quiet = TRUE))
31 | expect_error(add_license(license = "MIT", family = "Doe", quiet = TRUE))
32 |
33 | expect_invisible(add_license(license = "MIT", "John", "Doe", quiet = TRUE))
34 | })
35 |
36 |
37 | test_that("Check Credentials", {
38 |
39 | withr::local_options(list("given" = "john", "family" = "doe",
40 | "email" = "john.doe@gmail.com",
41 | "orcid" = "9999-9999-9999-9999"))
42 |
43 | create_temp_compendium()
44 | add_description(organisation = "society", open = FALSE, overwrite = FALSE,
45 | quiet = TRUE)
46 |
47 | expect_invisible(add_license(license = "MIT", quiet = TRUE))
48 | })
49 |
50 |
51 | test_that("Check Files and Overwrite", {
52 |
53 | withr::local_options(list("given" = "john", "family" = "doe",
54 | "email" = "john.doe@gmail.com",
55 | "orcid" = "9999-9999-9999-9999"))
56 |
57 | create_temp_compendium()
58 | add_description(organisation = "society", open = FALSE, overwrite = FALSE,
59 | quiet = TRUE)
60 |
61 | add_license(license = "MIT", quiet = TRUE)
62 |
63 | expect_true("LICENSE" %in% list.files(getwd()))
64 | expect_true("LICENSE.md" %in% list.files(getwd()))
65 |
66 | content <- readLines("LICENSE.md")
67 | expect_length(grep("MIT License", content[1]), n = 1)
68 |
69 |
70 | add_license(license = "GPL-2", quiet = TRUE)
71 |
72 | expect_false("LICENSE" %in% list.files(getwd()))
73 |
74 | content <- readLines("LICENSE.md")
75 | expect_length(grep("GNU General Public License", content[1]), n = 1)
76 | })
77 |
78 | test_that("Check DESCRIPTION Fields", {
79 |
80 | withr::local_options(list("given" = "john", "family" = "doe",
81 | "email" = "john.doe@gmail.com",
82 | "orcid" = "9999-9999-9999-9999"))
83 |
84 | create_temp_compendium()
85 | add_description(organisation = "society", open = FALSE, overwrite = FALSE,
86 | quiet = TRUE)
87 |
88 | add_license(license = "MIT", quiet = TRUE)
89 | expect_equal(read_descr()$"License", "MIT + file LICENSE")
90 |
91 | add_license(license = "LGPL (>= 3)", quiet = TRUE)
92 | expect_equal(read_descr()$"License", "LGPL (>= 3)")
93 | })
94 |
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/vignettes/.gitignore:
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1 | *.html
2 | *.R
3 |
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