R/dependencies.R
In jimbrig/jimstemplates: Collection of templates
#' #' Create a Dockerfile for Shiny App
#' #'
#' #' Build a container containing your Shiny App.
#' #'
#' #' @inheritParams add_module
#' #' @param path path to the DESCRIPTION file to use as an input.
#' #' @param output name of the Dockerfile output.
#' #' @param from The FROM of the Dockerfile. Default is FROM rocker/r-ver:
#' #' with `R.Version()$major` and `R.Version()$minor`.
#' #' @param as The AS of the Dockerfile. Default it NULL.
#' #' @param port The `options('shiny.port')` on which to run the Shiny App.
#' #' Default is 80.
#' #' @param host The `options('shiny.host')` on which to run the Shiny App.
#' #' Default is 0.0.0.0.
#' #' @param sysreqs boolean to check the system requirements
#' #' @param repos character vector, the base URL of the repositories
#' #' @param expand boolean, if `TRUE` each system requirement will be known his own RUN line
#' #' @param open boolean, default is `TRUE` open the Dockerfile file
#' #' @param build_golem_from_source boolean, if `TRUE` no tar.gz Package is created and the Dockerfile directly mount the source folder to build it
#' #' @param update_tar_gz boolean, if `TRUE` and build_golem_from_source is also `TRUE` an updated tar.gz Package is created
#' #' @param extra_sysreqs extra debian system requirements as character vector. Will be installed with apt-get install
#' #' @export
#' #' @rdname dockerfiles
#' #' @importFrom usethis use_build_ignore
#' #' @importFrom desc desc_get_deps
#' #' @importFrom dockerfiler Dockerfile
#' #' @importFrom rstudioapi navigateToFile isAvailable
#' #' @importFrom fs path path_file
#' #' @examples
#' #' \donttest{
#' #' # Add a standard Dockerfile
#' #' if (interactive()){
#' #' add_dockerfile()
#' #' }
#' #' # Add a Dockerfile for ShinyProxy
#' #' if (interactive()){
#' #' add_dockerfile_shinyproxy()
#' #' }
#' #' # Add a Dockerfile for Heroku
#' #' if (interactive()){
#' #' add_dockerfile_heroku()
#' #' }
#' #'}
#' #'@return The `{dockerfiler}` object, invisibly.
#' add_dockerfile <- function(path = getwd(),
#' output = "Dockerfile",
#' pkg = get_golem_wd(),
#' from = paste0(
#' "rocker/r-ver:",
#' R.Version()$major,".",
#' R.Version()$minor),
#' as = NULL,
#' port = 80,
#' host = "0.0.0.0",
#' sysreqs = TRUE,
#' repos = c(CRAN="https://cran.rstudio.com/"),
#' expand = FALSE,
#' open = TRUE,
#' update_tar_gz = TRUE,
#' build_golem_from_source = TRUE,
#' extra_sysreqs = NULL) {
#'
#'
#'
#' }
#'
#'
#' desc_path <- fs::path(path, "DESCRIPTION")
#' if (fs::file_exists(desc_path)) {
#' usethis::ui_info("Detected a DESCRIPTION file to use for package dependencies.")
#' deps <- get_deps.pkg(path = desc_path)
#' }
#'
#'
#'
#'
#'
#'
#' where <- fs::path(pkg, output)
#'
#' #if ( !check_file_exist(where) ) return(invisible(FALSE))
#'
#' usethis::use_build_ignore(path_file(where))
#'
#' dock <- dock_from_desc(
#' path = path,
#' FROM = from,
#' AS = as,
#' sysreqs = sysreqs,
#' repos = repos,
#' expand = expand,
#' build_golem_from_source = build_golem_from_source,
#' update_tar_gz = update_tar_gz,
#' extra_sysreqs = extra_sysreqs
#' )
#'
#' dock$EXPOSE(port)
#'
#' dock$CMD(
#' sprintf(
#' "R -e \"options('shiny.port'=%s,shiny.host='%s');%s::run_app()\"",
#' port,
#' host,
#' read.dcf(path)[1]
#' )
#' )
#'
#' dock$write(output)
#'
#' if (open) {
#' if (rstudioapi::isAvailable()) {
#' rstudioapi::navigateToFile(output)
#' } else {
#' try(file.edit(output))
#' }
#' }
#' alert_build(
#' path = path,
#' output = output,
#' build_golem_from_source = build_golem_from_source
#' )
#'
#' return(invisible(dock))
#'
#' }
#'
#' #' @export
#' #' @rdname dockerfiles
#' #' @importFrom fs path path_file
#' add_dockerfile_shinyproxy <- function(
#' path = "DESCRIPTION",
#' output = "Dockerfile",
#' pkg = get_golem_wd(),
#' from = paste0(
#' "rocker/r-ver:",
#' R.Version()$major,".",
#' R.Version()$minor
#' ),
#' as = NULL,
#' sysreqs = TRUE,
#' repos = c(CRAN="https://cran.rstudio.com/"),
#' expand = FALSE,
#' open = TRUE,
#' update_tar_gz = TRUE,
#' build_golem_from_source = TRUE,
#' extra_sysreqs = NULL
#' ){
#'
#' where <- path(pkg, output)
#'
#' #if ( !check_file_exist(where) ) return(invisible(FALSE))
#'
#' usethis::use_build_ignore(output)
#'
#' dock <- dock_from_desc(
#' path = path,
#' FROM = from,
#' AS = as,
#' sysreqs = sysreqs,
#' repos = repos,
#' expand = expand,
#' build_golem_from_source = build_golem_from_source,
#' update_tar_gz = update_tar_gz,
#' extra_sysreqs = extra_sysreqs
#' )
#'
#' dock$EXPOSE(3838)
#' dock$CMD(sprintf(
#' " [\"R\", \"-e\", \"options('shiny.port'=3838,shiny.host='0.0.0.0');%s::run_app()\"]",
#' read.dcf(path)[1]
#' ))
#' dock$write(output)
#'
#' if (open) {
#' if (rstudioapi::isAvailable()) {
#' rstudioapi::navigateToFile(output)
#' } else {
#' try(file.edit(output))
#' }
#' }
#' alert_build(
#' path,
#' output,
#' build_golem_from_source = build_golem_from_source
#' )
#'
#' return(invisible(dock))
#'
#' }
#'
#' #' @export
#' #' @rdname dockerfiles
#' #' @importFrom fs path path_file
#' add_dockerfile_heroku <- function(
#' path = "DESCRIPTION",
#' output = "Dockerfile",
#' pkg = get_golem_wd(),
#' from = paste0(
#' "rocker/r-ver:",
#' R.Version()$major,".",
#' R.Version()$minor
#' ),
#' as = NULL,
#' sysreqs = TRUE,
#' repos = c(CRAN="https://cran.rstudio.com/"),
#' expand = FALSE,
#' open = TRUE,
#' update_tar_gz = TRUE,
#' build_golem_from_source = TRUE,
#' extra_sysreqs = NULL
#' ){
#' where <- path(pkg, output)
#'
#' #if ( !check_file_exist(where) ) return(invisible(FALSE))
#'
#' usethis::use_build_ignore(output)
#'
#' dock <- dock_from_desc(
#' path = path,
#' FROM = from,
#' AS = as,
#' sysreqs = sysreqs,
#' repos = repos,
#' expand = expand,
#' build_golem_from_source = build_golem_from_source,
#' update_tar_gz = update_tar_gz,
#' extra_sysreqs = extra_sysreqs
#' )
#'
#' dock$CMD(
#' sprintf(
#' "R -e \"options('shiny.port'=$PORT,shiny.host='0.0.0.0');%s::run_app()\"",
#' read.dcf(path)[1]
#' )
#' )
#' dock$write(output)
#'
#' alert_build(
#' path = path,
#' output = output,
#' build_golem_from_source = build_golem_from_source
#' )
#'
#' apps_h <- gsub(
#' "\\.", "-",
#' sprintf(
#' "%s-%s",
#' read.dcf(path)[1],
#' read.dcf(path)[1,][['Version']]
#' )
#' )
#'
#' cat_rule( "From your command line, run:" )
#' cat_line("heroku container:login")
#' cat_line(
#' sprintf("heroku create %s", apps_h)
#' )
#' cat_line(
#' sprintf("heroku container:push web --app %s", apps_h)
#' )
#' cat_line(
#' sprintf("heroku container:release web --app %s", apps_h)
#' )
#' cat_line(
#' sprintf("heroku open --app %s", apps_h)
#' )
#' cat_red_bullet("Be sure to have the heroku CLI installed.")
#' cat_red_bullet(
#' sprintf("You can replace %s with another app name.", apps_h)
#' )
#' if (open) {
#' if (rstudioapi::isAvailable()) {
#' rstudioapi::navigateToFile(output)
#' } else {
#' try(file.edit(output))
#' }
#' }
#' usethis::use_build_ignore(files = output)
#' return(invisible(dock))
#'
#' }
#'
#' alert_build <- function(
#' path,
#' output,
#' build_golem_from_source
#' ){
#' cat_created(output, "Dockerfile")
#' if ( ! build_golem_from_source ){
#' cat_red_bullet(
#' sprintf(
#' "Be sure to keep your %s_%s.tar.gz file (generated using `pkgbuild::build(vignettes = FALSE)` ) in the same folder as the %s file generated",
#' read.dcf(path)[1],
#' read.dcf(path)[1,][['Version']],
#' basename(output)
#' )
#' )
#' }
#' }
#'
#' #' Create Dockerfile from DESCRIPTION
#' #
#' #' @param path path to the DESCRIPTION file to use as an input.
#' #'
#' #' @param FROM The FROM of the Dockerfile. Default is FROM rocker/r-ver:
#' #' with `R.Version()$major` and `R.Version()$minor`.
#' #' @param AS The AS of the Dockerfile. Default it NULL.
#' #' @param sysreqs boolean to check the system requirements
#' #' @param repos character vector, the base URL of the repositories
#' #' @param expand boolean, if `TRUE` each system requirement will be known his own RUN line
#' #' @param update_tar_gz boolean, if `TRUE` and build_golem_from_source is also `TRUE` an updated tar.gz Package is created
#' #' @param build_golem_from_source boolean, if `TRUE` no tar.gz Package is created and the Dockerfile directly mount the source folder to build it
#' #' @param extra_sysreqs extra debian system requirements as character vector. Will be installed with apt-get install
#' #'
#' #' @importFrom utils installed.packages packageVersion
#' #' @importFrom remotes dev_package_deps
#' #' @importFrom desc desc_get_deps desc_get
#' #' @importFrom usethis use_build_ignore
#' #' @noRd
#' dock_from_desc <- function(
#' path = "DESCRIPTION",
#' FROM = paste0(
#' "rocker/r-ver:",
#' R.Version()$major,".",
#' R.Version()$minor
#' ),
#' AS = NULL,
#' sysreqs = TRUE,
#' repos = c(CRAN="https://cran.rstudio.com/"),
#' expand = FALSE,
#' update_tar_gz = TRUE,
#' build_golem_from_source = TRUE,
#' extra_sysreqs = NULL
#' ){
#'
#' packages <- desc::desc_get_deps(path)$package
#' packages <- packages[packages != "R"] # remove R
#' packages <- packages[ !packages %in% c(
#' "base", "boot", "class", "cluster",
#' "codetools", "compiler", "datasets",
#' "foreign", "graphics", "grDevices",
#' "grid", "KernSmooth", "lattice", "MASS",
#' "Matrix", "methods", "mgcv", "nlme",
#' "nnet", "parallel", "rpart", "spatial",
#' "splines", "stats", "stats4", "survival",
#' "tcltk", "tools", "utils"
#' )] # remove base and recommended
#'
#' if (sysreqs){
#' # please wait during system requirement calculation
#' cli::cat_bullet(
#' "Please wait while we compute system requirements...",
#' bullet = "info",
#' bullet_col = "green"
#' ) # TODO animated version ?
#' system_requirement <- unique(
#' get_sysreqs(packages = packages)
#' )
#' cat_green_tick("Done") # TODO animated version ?
#'
#' } else{
#' system_requirement <- NULL
#' }
#'
#' sr <- desc::desc_get(file = path,keys = "SystemRequirements" )
#'
#' if ( length(extra_sysreqs)>0 ){
#' system_requirement <- unique(c(system_requirement,extra_sysreqs))
#' } else if (!is.na(sr)) {
#' message(paste("the DESCRIPTION file contains the SystemRequirements bellow: ",sr))
#' message(paste("please check the Dockerfile created and if needed pass extra sysreqs using the extra_sysreqs param"))
#'
#' }
#'
#' remotes_deps <- remotes::package_deps(packages)
#' packages_on_cran <-
#' intersect(remotes_deps$package[remotes_deps$is_cran],packages)
#'
#' packages_not_on_cran <-
#' setdiff(packages,packages_on_cran)
#'
#' packages_with_version <- data.frame(
#' package=remotes_deps$package,
#' installed=remotes_deps$installed,
#' stringsAsFactors = FALSE
#' )
#' packages_with_version <- packages_with_version[
#' packages_with_version$package %in% packages_on_cran,
#' ]
#'
#' packages_on_cran <- set_name(
#' packages_with_version$installed,
#' packages_with_version$package
#' )
#'
#' dock <- dockerfiler::Dockerfile$new(FROM = FROM, AS = AS)
#'
#' if (length(system_requirement)>0){
#' if ( !expand ){
#' dock$RUN(
#' paste(
#' "apt-get update && apt-get install -y ",
#' paste(system_requirement, collapse = " "),
#' "&& rm -rf /var/lib/apt/lists/*"
#' )
#' )
#' } else {
#' dock$RUN("apt-get update")
#' for ( sr in system_requirement ){
#' dock$RUN( paste("apt-get install -y ", sr) )
#' }
#' dock$RUN("rm -rf /var/lib/apt/lists/*")
#' }
#' }
#'
#'
#' repos_as_character <- paste(capture.output(dput(repos)),collapse = "")
#' repos_as_character <- gsub(pattern = '\"',replacement = '\'',x=repos_as_character)
#'
#'
#' dock$RUN(
#' sprintf(
#' "echo \"options(repos = %s, download.file.method = 'libcurl')\" >> /usr/local/lib/R/etc/Rprofile.site",
#' repos_as_character
#' )
#' )
#'
#' dock$RUN("R -e 'install.packages(\"remotes\")'")
#'
#' if ( length(packages_on_cran>0)){
#' ping <- mapply(function(dock, ver, nm){
#' res <- dock$RUN(
#' sprintf(
#' "Rscript -e 'remotes::install_version(\"%s\",upgrade=\"never\", version = \"%s\")'",
#' nm,
#' ver
#' )
#' )
#' },
#' ver = packages_on_cran,
#' nm = names(packages_on_cran),
#' MoreArgs = list(dock = dock)
#' )
#' }
#'
#' if ( length(packages_not_on_cran > 0)){
#'
#' nn <-
#' as.data.frame(do.call(rbind,
#' lapply(remotes_deps$remote[!remotes_deps$is_cran],
#' function(.) {
#' .[c('repo', 'username', 'sha')]
#' })))
#'
#' nn <- sprintf(
#' "%s/%s@%s",
#' nn$username,
#' nn$repo,
#' nn$sha
#' )
#'
#'
#' pong <- mapply(function(dock, ver, nm){
#' res <- dock$RUN(
#' sprintf(
#' "Rscript -e 'remotes::install_github(\"%s\")'",
#' ver
#' )
#' )
#' },
#' ver = nn,
#' MoreArgs = list(dock = dock)
#' )
#' }
#'
#' if ( !build_golem_from_source){
#'
#' if ( update_tar_gz ){
#' old_version <- list.files(
#' pattern = sprintf("%s_.+.tar.gz", read.dcf(path)[1]),
#' full.names = TRUE
#' )
#'
#' if ( length(old_version) > 0){
#' lapply(old_version, file.remove)
#' lapply(old_version, unlink, force = TRUE)
#' cat_red_bullet(
#' sprintf(
#' "%s were removed from folder",
#' paste(old_version, collapse = ', ')
#' )
#' )
#' }
#'
#'
#' if (isTRUE(requireNamespace("pkgbuild", quietly = TRUE))) {
#' out <- pkgbuild::build(path = ".", dest_path = ".", vignettes = FALSE)
#' if (missing(out)){
#' cat_red_bullet("Error during tar.gz building" )
#'
#' } else {
#' usethis::use_build_ignore(files = out)
#' cat_green_tick(
#' sprintf(
#' " %s_%s.tar.gz created.",
#' read.dcf(path)[1],
#' read.dcf(path)[1,][['Version']]
#' )
#' )
#' }
#'
#' } else {
#' stop("please install {pkgbuild}")
#' }
#'
#'
#' }
#' # we use an already built tar.gz file
#'
#' dock$COPY(
#' from = paste0(read.dcf(path)[1], "_*.tar.gz"),
#' to = "/app.tar.gz"
#' )
#' dock$RUN("R -e 'remotes::install_local(\"/app.tar.gz\",upgrade=\"never\")'")
#' dock$RUN("rm /app.tar.gz")
#' } else {
#' dock$RUN("mkdir /build_zone")
#' dock$ADD(from = ".",to = "/build_zone")
#' dock$WORKDIR("/build_zone")
#' dock$RUN("R -e 'remotes::install_local(upgrade=\"never\")'")
#' dock$RUN("rm -rf /build_zone")
#' }
#' # Add a dockerignore
#' docker_ignore_add()
#'
#' dock
#' }
#'
#' docker_ignore_add <- function(
#' pkg = get_golem_wd()
#' ){
#' path <- fs::path(
#' pkg,
#' ".dockerignore"
#' )
#'
#' if (!fs::file_exists(
#' path
#' )){
#' fs::file_create(path)
#' }
#' write_ignore <- function(content){
#' write(content, path, append = TRUE)
#' }
#' for (i in c(
#' ".RData",
#' ".Rhistory",
#' ".git",
#' ".gitignore",
#' "manifest.json",
#' "rsconnect/",
#' "Rproj.user"
#' )) {
#' write_ignore(i)
#' }
#'
#' }
#'
#'
#'
#'
#'
#'
#'
#'
#'
#' # if (sysreqs)
#' #
#' # sysdeps <- {
#' # # please wait during system requirement calculation
#' # cli::cat_bullet(
#' # "Please wait while we compute system requirements...",
#' # bullet = "info",
#' # bullet_col = "green"
#' # ) # TODO animated version ?
#' # system_requirement <- unique(
#' # get_sysreqs(packages = packages)
#' # )
#' # cat_green_tick("Done") # TODO animated version ?
#' #
#' # } else{
#' # system_requirement <- NULL
#' # }
#' #
#' # docker_txt <- paste0(
#' # "FROM merlinoa/shiny_run_custom\n\nARG R_CONFIG_ACTIVE=default\n\n"
#' # )
#'
#'
#' # get_package_deps()
#'
#' #' @keywords internal
#' #' @noRd
#' #' @importFrom utils sessionInfo
#' detach_packages <- function() {
#'
#' all_attached <- paste("package:",
#' names(utils::sessionInfo()$otherPkgs),
#' sep = "")
#'
#' suppressWarnings(
#' invisible(
#' lapply(
#' all_attached, detach, character.only = TRUE, unload = TRUE
#' )
#' )
#' )
#'
#' }
#'
#' get_deps_full <- function(...) {
#'
#' deps <- get_deps()
#'
#' lapply(deps, get_package_details)
#'
#' }
#'
#' # bind_rows for df
#' # yaml::write_yaml
#' # R script using create_deps_r()
#'
#'
#'
#'
#'
#' #' Get Package Dependencies from DESCRIPTION or directory parsing
#' #'
#' #' @param path current projects root path; defaults to your current working
#' #' directory.
#' #' @param dput logical
#' #' @param field Depends, Imports, or Suggests
#' #'
#' #' @return character vector of package names
#' #'
#' #' @importFrom stringr str_replace_all str_trim
#' #' @importFrom stats setNames
#' #'
#' #' @keywords internal
#' #' @noRd
#' #'
#' #' @examples
#' #' \dontrun{
#' #' get_deps()
#' #' }
#' #' @importFrom fs dir_ls path
#' get_deps <- function(directory = getwd(), ...) {
#'
#' if ("DESCRIPTION" %in% basename(fs::dir_ls(directory))) {
#' hold <- get_deps.pkg(path = fs::path(directory, "DESCRIPTION"))
#' return(hold)
#' } else {
#' hold <- get_deps.dir(directory)
#' return(hold)
#' }
#'
#' }
#'
#' #' @keywords internal
#' #' @noRd
#' get_deps.dir <- function(directory = getwd()) {
#'
#' fls <- list.files(
#' path = directory,
#' pattern = "^.*\\.R$|^.*\\.Rmd$",
#' full.names = TRUE,
#' recursive = TRUE
#' )
#'
#' pkg_names <- unlist(sapply(fls, parse_packages))
#' pkg_names <- unique(pkg_names)
#'
#' if (length(pkg_names) == 0) {
#' message("warning: no packages found in specified directory")
#' return(invisible(NULL))
#' }
#'
#' return(unname(pkg_names))
#'
#' }
#'
#'
#' #' @keywords internal
#' #' @noRd
#' #' @importFrom stats setNames
#' #' @importFrom stringr str_replace_all str_trim
#' get_deps.pkg <- function(path = "DESCRIPTION",
#' dput = FALSE,
#' field = c("Depends", "Imports", "Suggests")) {
#'
#' init <- read.dcf(path)
#'
#' hold <- init[, intersect(colnames(init), field)] %>%
#' gsub(pattern = "\n", replacement = "") %>%
#' strsplit(",") %>%
#' unlist() %>%
#' stats::setNames(NULL)
#'
#' out <- hold[!grepl("^R [(]", hold)] %>%
#' stringr::str_replace_all("\\(.+\\)", "") %>%
#' stringr::str_trim() %>%
#' unique() %>%
#' sort()
#'
#' if (!dput) return(out)
#'
#' dput(out)
#'
#' }
#'
#'
#'
#'
#'
#'
#'
#' #' @keywords internal
#' #' @noRd
#' #' @importFrom desc description
#' #' @importFrom glue glue glue_collapse
#' #' @importFrom remotes install_github
#' #' @importFrom utils file.edit
#' create_deps_r <- function(path = "DESCRIPTION",
#' field = c("Depends",
#' "Imports"),
#' to = "inst/dependencies.R",
#' open_file = TRUE,
#' ignore_base = TRUE) {
#'
#' if (!dir.exists(dirname(to))) {
#' dir.create(dirname(to),
#' recursive = TRUE,
#' showWarnings = FALSE)
#' dir_to <- normalizePath(dirname(to))
#' } else {
#' dir_to <- normalizePath(dirname(to))
#' }
#'
#' ll <- get_deps.pkg()
#'
#' if (isTRUE(ignore_base)) {
#' to_remove <-
#' which(lapply(ll, packageDescription, field = "Priority") == "base")
#' if (length(to_remove) > 0) {
#' ll <- ll[-to_remove]
#' }
#' }
#'
#' desc <- desc::description$new(path)
#' remotes_orig <- desc$get_remotes()
#'
#' if (length(remotes_orig) != 0) {
#' remotes_orig_pkg <- gsub("^.*/", "", remotes_orig)
#' ll <- ll[!ll %in% remotes_orig_pkg]
#' inst_remotes <- remotes_orig
#' w.github <- !grepl("\\(", remotes_orig)
#' inst_remotes[w.github] <-
#' glue("remotes::install_github('{remotes_orig[w.github]}')")
#' inst_remotes[!w.github] <- remotes_orig[!w.github]
#' remotes_content <-
#' paste(
#' "# Remotes ----",
#' "install.packages(\"remotes\")",
#' paste(inst_remotes, collapse = "\n"),
#' sep = "\n"
#' )
#' }
#' else {
#' remotes_content <- "# No Remotes ----"
#' }
#' if (length(ll) != 0) {
#' content <-
#' glue::glue(
#' "*{remotes_content}*\n# Attachments ----\nto_install <- c(\"*{glue::glue_collapse(as.character(ll), sep=\"\\\", \\\"\")}*\")\n for (i in to_install) {\n message(paste(\"looking for \", i))\n if (!requireNamespace(i)) {\n message(paste(\" installing\", i))\n install.packages(i)\n }\n }\n\n",
#' .open = "*{",
#' .close = "}*"
#' )
#' }
#' else {
#' content <- glue::glue(
#' "*{remotes_content}*\n# No attachments ----\n \n\n",
#' .open = "*{",
#' .close = "}*"
#' )
#' }
#'
#' file <- file.path(dir_to, basename(to))
#' file.create(file)
#' cat(content, file = file)
#'
#' if (open_file) {
#' utils::file.edit(file, editor = "internal")
#' }
#' }
jimbrig/jimstemplates documentation built on Dec. 21, 2021, 12:05 a.m.
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#' #' Create a Dockerfile for Shiny App
#' #'
#' #' Build a container containing your Shiny App.
#' #'
#' #' @inheritParams add_module
#' #' @param path path to the DESCRIPTION file to use as an input.
#' #' @param output name of the Dockerfile output.
#' #' @param from The FROM of the Dockerfile. Default is FROM rocker/r-ver:
#' #' with `R.Version()$major` and `R.Version()$minor`.
#' #' @param as The AS of the Dockerfile. Default it NULL.
#' #' @param port The `options('shiny.port')` on which to run the Shiny App.
#' #' Default is 80.
#' #' @param host The `options('shiny.host')` on which to run the Shiny App.
#' #' Default is 0.0.0.0.
#' #' @param sysreqs boolean to check the system requirements
#' #' @param repos character vector, the base URL of the repositories
#' #' @param expand boolean, if `TRUE` each system requirement will be known his own RUN line
#' #' @param open boolean, default is `TRUE` open the Dockerfile file
#' #' @param build_golem_from_source boolean, if `TRUE` no tar.gz Package is created and the Dockerfile directly mount the source folder to build it
#' #' @param update_tar_gz boolean, if `TRUE` and build_golem_from_source is also `TRUE` an updated tar.gz Package is created
#' #' @param extra_sysreqs extra debian system requirements as character vector. Will be installed with apt-get install
#' #' @export
#' #' @rdname dockerfiles
#' #' @importFrom usethis use_build_ignore
#' #' @importFrom desc desc_get_deps
#' #' @importFrom dockerfiler Dockerfile
#' #' @importFrom rstudioapi navigateToFile isAvailable
#' #' @importFrom fs path path_file
#' #' @examples
#' #' \donttest{
#' #' # Add a standard Dockerfile
#' #' if (interactive()){
#' #' add_dockerfile()
#' #' }
#' #' # Add a Dockerfile for ShinyProxy
#' #' if (interactive()){
#' #' add_dockerfile_shinyproxy()
#' #' }
#' #' # Add a Dockerfile for Heroku
#' #' if (interactive()){
#' #' add_dockerfile_heroku()
#' #' }
#' #'}
#' #'@return The `{dockerfiler}` object, invisibly.
#' add_dockerfile <- function(path = getwd(),
#' output = "Dockerfile",
#' pkg = get_golem_wd(),
#' from = paste0(
#' "rocker/r-ver:",
#' R.Version()$major,".",
#' R.Version()$minor),
#' as = NULL,
#' port = 80,
#' host = "0.0.0.0",
#' sysreqs = TRUE,
#' repos = c(CRAN="https://cran.rstudio.com/"),
#' expand = FALSE,
#' open = TRUE,
#' update_tar_gz = TRUE,
#' build_golem_from_source = TRUE,
#' extra_sysreqs = NULL) {
#'
#'
#'
#' }
#'
#'
#' desc_path <- fs::path(path, "DESCRIPTION")
#' if (fs::file_exists(desc_path)) {
#' usethis::ui_info("Detected a DESCRIPTION file to use for package dependencies.")
#' deps <- get_deps.pkg(path = desc_path)
#' }
#'
#'
#'
#'
#'
#'
#' where <- fs::path(pkg, output)
#'
#' #if ( !check_file_exist(where) ) return(invisible(FALSE))
#'
#' usethis::use_build_ignore(path_file(where))
#'
#' dock <- dock_from_desc(
#' path = path,
#' FROM = from,
#' AS = as,
#' sysreqs = sysreqs,
#' repos = repos,
#' expand = expand,
#' build_golem_from_source = build_golem_from_source,
#' update_tar_gz = update_tar_gz,
#' extra_sysreqs = extra_sysreqs
#' )
#'
#' dock$EXPOSE(port)
#'
#' dock$CMD(
#' sprintf(
#' "R -e \"options('shiny.port'=%s,shiny.host='%s');%s::run_app()\"",
#' port,
#' host,
#' read.dcf(path)[1]
#' )
#' )
#'
#' dock$write(output)
#'
#' if (open) {
#' if (rstudioapi::isAvailable()) {
#' rstudioapi::navigateToFile(output)
#' } else {
#' try(file.edit(output))
#' }
#' }
#' alert_build(
#' path = path,
#' output = output,
#' build_golem_from_source = build_golem_from_source
#' )
#'
#' return(invisible(dock))
#'
#' }
#'
#' #' @export
#' #' @rdname dockerfiles
#' #' @importFrom fs path path_file
#' add_dockerfile_shinyproxy <- function(
#' path = "DESCRIPTION",
#' output = "Dockerfile",
#' pkg = get_golem_wd(),
#' from = paste0(
#' "rocker/r-ver:",
#' R.Version()$major,".",
#' R.Version()$minor
#' ),
#' as = NULL,
#' sysreqs = TRUE,
#' repos = c(CRAN="https://cran.rstudio.com/"),
#' expand = FALSE,
#' open = TRUE,
#' update_tar_gz = TRUE,
#' build_golem_from_source = TRUE,
#' extra_sysreqs = NULL
#' ){
#'
#' where <- path(pkg, output)
#'
#' #if ( !check_file_exist(where) ) return(invisible(FALSE))
#'
#' usethis::use_build_ignore(output)
#'
#' dock <- dock_from_desc(
#' path = path,
#' FROM = from,
#' AS = as,
#' sysreqs = sysreqs,
#' repos = repos,
#' expand = expand,
#' build_golem_from_source = build_golem_from_source,
#' update_tar_gz = update_tar_gz,
#' extra_sysreqs = extra_sysreqs
#' )
#'
#' dock$EXPOSE(3838)
#' dock$CMD(sprintf(
#' " [\"R\", \"-e\", \"options('shiny.port'=3838,shiny.host='0.0.0.0');%s::run_app()\"]",
#' read.dcf(path)[1]
#' ))
#' dock$write(output)
#'
#' if (open) {
#' if (rstudioapi::isAvailable()) {
#' rstudioapi::navigateToFile(output)
#' } else {
#' try(file.edit(output))
#' }
#' }
#' alert_build(
#' path,
#' output,
#' build_golem_from_source = build_golem_from_source
#' )
#'
#' return(invisible(dock))
#'
#' }
#'
#' #' @export
#' #' @rdname dockerfiles
#' #' @importFrom fs path path_file
#' add_dockerfile_heroku <- function(
#' path = "DESCRIPTION",
#' output = "Dockerfile",
#' pkg = get_golem_wd(),
#' from = paste0(
#' "rocker/r-ver:",
#' R.Version()$major,".",
#' R.Version()$minor
#' ),
#' as = NULL,
#' sysreqs = TRUE,
#' repos = c(CRAN="https://cran.rstudio.com/"),
#' expand = FALSE,
#' open = TRUE,
#' update_tar_gz = TRUE,
#' build_golem_from_source = TRUE,
#' extra_sysreqs = NULL
#' ){
#' where <- path(pkg, output)
#'
#' #if ( !check_file_exist(where) ) return(invisible(FALSE))
#'
#' usethis::use_build_ignore(output)
#'
#' dock <- dock_from_desc(
#' path = path,
#' FROM = from,
#' AS = as,
#' sysreqs = sysreqs,
#' repos = repos,
#' expand = expand,
#' build_golem_from_source = build_golem_from_source,
#' update_tar_gz = update_tar_gz,
#' extra_sysreqs = extra_sysreqs
#' )
#'
#' dock$CMD(
#' sprintf(
#' "R -e \"options('shiny.port'=$PORT,shiny.host='0.0.0.0');%s::run_app()\"",
#' read.dcf(path)[1]
#' )
#' )
#' dock$write(output)
#'
#' alert_build(
#' path = path,
#' output = output,
#' build_golem_from_source = build_golem_from_source
#' )
#'
#' apps_h <- gsub(
#' "\\.", "-",
#' sprintf(
#' "%s-%s",
#' read.dcf(path)[1],
#' read.dcf(path)[1,][['Version']]
#' )
#' )
#'
#' cat_rule( "From your command line, run:" )
#' cat_line("heroku container:login")
#' cat_line(
#' sprintf("heroku create %s", apps_h)
#' )
#' cat_line(
#' sprintf("heroku container:push web --app %s", apps_h)
#' )
#' cat_line(
#' sprintf("heroku container:release web --app %s", apps_h)
#' )
#' cat_line(
#' sprintf("heroku open --app %s", apps_h)
#' )
#' cat_red_bullet("Be sure to have the heroku CLI installed.")
#' cat_red_bullet(
#' sprintf("You can replace %s with another app name.", apps_h)
#' )
#' if (open) {
#' if (rstudioapi::isAvailable()) {
#' rstudioapi::navigateToFile(output)
#' } else {
#' try(file.edit(output))
#' }
#' }
#' usethis::use_build_ignore(files = output)
#' return(invisible(dock))
#'
#' }
#'
#' alert_build <- function(
#' path,
#' output,
#' build_golem_from_source
#' ){
#' cat_created(output, "Dockerfile")
#' if ( ! build_golem_from_source ){
#' cat_red_bullet(
#' sprintf(
#' "Be sure to keep your %s_%s.tar.gz file (generated using `pkgbuild::build(vignettes = FALSE)` ) in the same folder as the %s file generated",
#' read.dcf(path)[1],
#' read.dcf(path)[1,][['Version']],
#' basename(output)
#' )
#' )
#' }
#' }
#'
#' #' Create Dockerfile from DESCRIPTION
#' #
#' #' @param path path to the DESCRIPTION file to use as an input.
#' #'
#' #' @param FROM The FROM of the Dockerfile. Default is FROM rocker/r-ver:
#' #' with `R.Version()$major` and `R.Version()$minor`.
#' #' @param AS The AS of the Dockerfile. Default it NULL.
#' #' @param sysreqs boolean to check the system requirements
#' #' @param repos character vector, the base URL of the repositories
#' #' @param expand boolean, if `TRUE` each system requirement will be known his own RUN line
#' #' @param update_tar_gz boolean, if `TRUE` and build_golem_from_source is also `TRUE` an updated tar.gz Package is created
#' #' @param build_golem_from_source boolean, if `TRUE` no tar.gz Package is created and the Dockerfile directly mount the source folder to build it
#' #' @param extra_sysreqs extra debian system requirements as character vector. Will be installed with apt-get install
#' #'
#' #' @importFrom utils installed.packages packageVersion
#' #' @importFrom remotes dev_package_deps
#' #' @importFrom desc desc_get_deps desc_get
#' #' @importFrom usethis use_build_ignore
#' #' @noRd
#' dock_from_desc <- function(
#' path = "DESCRIPTION",
#' FROM = paste0(
#' "rocker/r-ver:",
#' R.Version()$major,".",
#' R.Version()$minor
#' ),
#' AS = NULL,
#' sysreqs = TRUE,
#' repos = c(CRAN="https://cran.rstudio.com/"),
#' expand = FALSE,
#' update_tar_gz = TRUE,
#' build_golem_from_source = TRUE,
#' extra_sysreqs = NULL
#' ){
#'
#' packages <- desc::desc_get_deps(path)$package
#' packages <- packages[packages != "R"] # remove R
#' packages <- packages[ !packages %in% c(
#' "base", "boot", "class", "cluster",
#' "codetools", "compiler", "datasets",
#' "foreign", "graphics", "grDevices",
#' "grid", "KernSmooth", "lattice", "MASS",
#' "Matrix", "methods", "mgcv", "nlme",
#' "nnet", "parallel", "rpart", "spatial",
#' "splines", "stats", "stats4", "survival",
#' "tcltk", "tools", "utils"
#' )] # remove base and recommended
#'
#' if (sysreqs){
#' # please wait during system requirement calculation
#' cli::cat_bullet(
#' "Please wait while we compute system requirements...",
#' bullet = "info",
#' bullet_col = "green"
#' ) # TODO animated version ?
#' system_requirement <- unique(
#' get_sysreqs(packages = packages)
#' )
#' cat_green_tick("Done") # TODO animated version ?
#'
#' } else{
#' system_requirement <- NULL
#' }
#'
#' sr <- desc::desc_get(file = path,keys = "SystemRequirements" )
#'
#' if ( length(extra_sysreqs)>0 ){
#' system_requirement <- unique(c(system_requirement,extra_sysreqs))
#' } else if (!is.na(sr)) {
#' message(paste("the DESCRIPTION file contains the SystemRequirements bellow: ",sr))
#' message(paste("please check the Dockerfile created and if needed pass extra sysreqs using the extra_sysreqs param"))
#'
#' }
#'
#' remotes_deps <- remotes::package_deps(packages)
#' packages_on_cran <-
#' intersect(remotes_deps$package[remotes_deps$is_cran],packages)
#'
#' packages_not_on_cran <-
#' setdiff(packages,packages_on_cran)
#'
#' packages_with_version <- data.frame(
#' package=remotes_deps$package,
#' installed=remotes_deps$installed,
#' stringsAsFactors = FALSE
#' )
#' packages_with_version <- packages_with_version[
#' packages_with_version$package %in% packages_on_cran,
#' ]
#'
#' packages_on_cran <- set_name(
#' packages_with_version$installed,
#' packages_with_version$package
#' )
#'
#' dock <- dockerfiler::Dockerfile$new(FROM = FROM, AS = AS)
#'
#' if (length(system_requirement)>0){
#' if ( !expand ){
#' dock$RUN(
#' paste(
#' "apt-get update && apt-get install -y ",
#' paste(system_requirement, collapse = " "),
#' "&& rm -rf /var/lib/apt/lists/*"
#' )
#' )
#' } else {
#' dock$RUN("apt-get update")
#' for ( sr in system_requirement ){
#' dock$RUN( paste("apt-get install -y ", sr) )
#' }
#' dock$RUN("rm -rf /var/lib/apt/lists/*")
#' }
#' }
#'
#'
#' repos_as_character <- paste(capture.output(dput(repos)),collapse = "")
#' repos_as_character <- gsub(pattern = '\"',replacement = '\'',x=repos_as_character)
#'
#'
#' dock$RUN(
#' sprintf(
#' "echo \"options(repos = %s, download.file.method = 'libcurl')\" >> /usr/local/lib/R/etc/Rprofile.site",
#' repos_as_character
#' )
#' )
#'
#' dock$RUN("R -e 'install.packages(\"remotes\")'")
#'
#' if ( length(packages_on_cran>0)){
#' ping <- mapply(function(dock, ver, nm){
#' res <- dock$RUN(
#' sprintf(
#' "Rscript -e 'remotes::install_version(\"%s\",upgrade=\"never\", version = \"%s\")'",
#' nm,
#' ver
#' )
#' )
#' },
#' ver = packages_on_cran,
#' nm = names(packages_on_cran),
#' MoreArgs = list(dock = dock)
#' )
#' }
#'
#' if ( length(packages_not_on_cran > 0)){
#'
#' nn <-
#' as.data.frame(do.call(rbind,
#' lapply(remotes_deps$remote[!remotes_deps$is_cran],
#' function(.) {
#' .[c('repo', 'username', 'sha')]
#' })))
#'
#' nn <- sprintf(
#' "%s/%s@%s",
#' nn$username,
#' nn$repo,
#' nn$sha
#' )
#'
#'
#' pong <- mapply(function(dock, ver, nm){
#' res <- dock$RUN(
#' sprintf(
#' "Rscript -e 'remotes::install_github(\"%s\")'",
#' ver
#' )
#' )
#' },
#' ver = nn,
#' MoreArgs = list(dock = dock)
#' )
#' }
#'
#' if ( !build_golem_from_source){
#'
#' if ( update_tar_gz ){
#' old_version <- list.files(
#' pattern = sprintf("%s_.+.tar.gz", read.dcf(path)[1]),
#' full.names = TRUE
#' )
#'
#' if ( length(old_version) > 0){
#' lapply(old_version, file.remove)
#' lapply(old_version, unlink, force = TRUE)
#' cat_red_bullet(
#' sprintf(
#' "%s were removed from folder",
#' paste(old_version, collapse = ', ')
#' )
#' )
#' }
#'
#'
#' if (isTRUE(requireNamespace("pkgbuild", quietly = TRUE))) {
#' out <- pkgbuild::build(path = ".", dest_path = ".", vignettes = FALSE)
#' if (missing(out)){
#' cat_red_bullet("Error during tar.gz building" )
#'
#' } else {
#' usethis::use_build_ignore(files = out)
#' cat_green_tick(
#' sprintf(
#' " %s_%s.tar.gz created.",
#' read.dcf(path)[1],
#' read.dcf(path)[1,][['Version']]
#' )
#' )
#' }
#'
#' } else {
#' stop("please install {pkgbuild}")
#' }
#'
#'
#' }
#' # we use an already built tar.gz file
#'
#' dock$COPY(
#' from = paste0(read.dcf(path)[1], "_*.tar.gz"),
#' to = "/app.tar.gz"
#' )
#' dock$RUN("R -e 'remotes::install_local(\"/app.tar.gz\",upgrade=\"never\")'")
#' dock$RUN("rm /app.tar.gz")
#' } else {
#' dock$RUN("mkdir /build_zone")
#' dock$ADD(from = ".",to = "/build_zone")
#' dock$WORKDIR("/build_zone")
#' dock$RUN("R -e 'remotes::install_local(upgrade=\"never\")'")
#' dock$RUN("rm -rf /build_zone")
#' }
#' # Add a dockerignore
#' docker_ignore_add()
#'
#' dock
#' }
#'
#' docker_ignore_add <- function(
#' pkg = get_golem_wd()
#' ){
#' path <- fs::path(
#' pkg,
#' ".dockerignore"
#' )
#'
#' if (!fs::file_exists(
#' path
#' )){
#' fs::file_create(path)
#' }
#' write_ignore <- function(content){
#' write(content, path, append = TRUE)
#' }
#' for (i in c(
#' ".RData",
#' ".Rhistory",
#' ".git",
#' ".gitignore",
#' "manifest.json",
#' "rsconnect/",
#' "Rproj.user"
#' )) {
#' write_ignore(i)
#' }
#'
#' }
#'
#'
#'
#'
#'
#'
#'
#'
#'
#' # if (sysreqs)
#' #
#' # sysdeps <- {
#' # # please wait during system requirement calculation
#' # cli::cat_bullet(
#' # "Please wait while we compute system requirements...",
#' # bullet = "info",
#' # bullet_col = "green"
#' # ) # TODO animated version ?
#' # system_requirement <- unique(
#' # get_sysreqs(packages = packages)
#' # )
#' # cat_green_tick("Done") # TODO animated version ?
#' #
#' # } else{
#' # system_requirement <- NULL
#' # }
#' #
#' # docker_txt <- paste0(
#' # "FROM merlinoa/shiny_run_custom\n\nARG R_CONFIG_ACTIVE=default\n\n"
#' # )
#'
#'
#' # get_package_deps()
#'
#' #' @keywords internal
#' #' @noRd
#' #' @importFrom utils sessionInfo
#' detach_packages <- function() {
#'
#' all_attached <- paste("package:",
#' names(utils::sessionInfo()$otherPkgs),
#' sep = "")
#'
#' suppressWarnings(
#' invisible(
#' lapply(
#' all_attached, detach, character.only = TRUE, unload = TRUE
#' )
#' )
#' )
#'
#' }
#'
#' get_deps_full <- function(...) {
#'
#' deps <- get_deps()
#'
#' lapply(deps, get_package_details)
#'
#' }
#'
#' # bind_rows for df
#' # yaml::write_yaml
#' # R script using create_deps_r()
#'
#'
#'
#'
#'
#' #' Get Package Dependencies from DESCRIPTION or directory parsing
#' #'
#' #' @param path current projects root path; defaults to your current working
#' #' directory.
#' #' @param dput logical
#' #' @param field Depends, Imports, or Suggests
#' #'
#' #' @return character vector of package names
#' #'
#' #' @importFrom stringr str_replace_all str_trim
#' #' @importFrom stats setNames
#' #'
#' #' @keywords internal
#' #' @noRd
#' #'
#' #' @examples
#' #' \dontrun{
#' #' get_deps()
#' #' }
#' #' @importFrom fs dir_ls path
#' get_deps <- function(directory = getwd(), ...) {
#'
#' if ("DESCRIPTION" %in% basename(fs::dir_ls(directory))) {
#' hold <- get_deps.pkg(path = fs::path(directory, "DESCRIPTION"))
#' return(hold)
#' } else {
#' hold <- get_deps.dir(directory)
#' return(hold)
#' }
#'
#' }
#'
#' #' @keywords internal
#' #' @noRd
#' get_deps.dir <- function(directory = getwd()) {
#'
#' fls <- list.files(
#' path = directory,
#' pattern = "^.*\\.R$|^.*\\.Rmd$",
#' full.names = TRUE,
#' recursive = TRUE
#' )
#'
#' pkg_names <- unlist(sapply(fls, parse_packages))
#' pkg_names <- unique(pkg_names)
#'
#' if (length(pkg_names) == 0) {
#' message("warning: no packages found in specified directory")
#' return(invisible(NULL))
#' }
#'
#' return(unname(pkg_names))
#'
#' }
#'
#'
#' #' @keywords internal
#' #' @noRd
#' #' @importFrom stats setNames
#' #' @importFrom stringr str_replace_all str_trim
#' get_deps.pkg <- function(path = "DESCRIPTION",
#' dput = FALSE,
#' field = c("Depends", "Imports", "Suggests")) {
#'
#' init <- read.dcf(path)
#'
#' hold <- init[, intersect(colnames(init), field)] %>%
#' gsub(pattern = "\n", replacement = "") %>%
#' strsplit(",") %>%
#' unlist() %>%
#' stats::setNames(NULL)
#'
#' out <- hold[!grepl("^R [(]", hold)] %>%
#' stringr::str_replace_all("\\(.+\\)", "") %>%
#' stringr::str_trim() %>%
#' unique() %>%
#' sort()
#'
#' if (!dput) return(out)
#'
#' dput(out)
#'
#' }
#'
#'
#'
#'
#'
#'
#'
#' #' @keywords internal
#' #' @noRd
#' #' @importFrom desc description
#' #' @importFrom glue glue glue_collapse
#' #' @importFrom remotes install_github
#' #' @importFrom utils file.edit
#' create_deps_r <- function(path = "DESCRIPTION",
#' field = c("Depends",
#' "Imports"),
#' to = "inst/dependencies.R",
#' open_file = TRUE,
#' ignore_base = TRUE) {
#'
#' if (!dir.exists(dirname(to))) {
#' dir.create(dirname(to),
#' recursive = TRUE,
#' showWarnings = FALSE)
#' dir_to <- normalizePath(dirname(to))
#' } else {
#' dir_to <- normalizePath(dirname(to))
#' }
#'
#' ll <- get_deps.pkg()
#'
#' if (isTRUE(ignore_base)) {
#' to_remove <-
#' which(lapply(ll, packageDescription, field = "Priority") == "base")
#' if (length(to_remove) > 0) {
#' ll <- ll[-to_remove]
#' }
#' }
#'
#' desc <- desc::description$new(path)
#' remotes_orig <- desc$get_remotes()
#'
#' if (length(remotes_orig) != 0) {
#' remotes_orig_pkg <- gsub("^.*/", "", remotes_orig)
#' ll <- ll[!ll %in% remotes_orig_pkg]
#' inst_remotes <- remotes_orig
#' w.github <- !grepl("\\(", remotes_orig)
#' inst_remotes[w.github] <-
#' glue("remotes::install_github('{remotes_orig[w.github]}')")
#' inst_remotes[!w.github] <- remotes_orig[!w.github]
#' remotes_content <-
#' paste(
#' "# Remotes ----",
#' "install.packages(\"remotes\")",
#' paste(inst_remotes, collapse = "\n"),
#' sep = "\n"
#' )
#' }
#' else {
#' remotes_content <- "# No Remotes ----"
#' }
#' if (length(ll) != 0) {
#' content <-
#' glue::glue(
#' "*{remotes_content}*\n# Attachments ----\nto_install <- c(\"*{glue::glue_collapse(as.character(ll), sep=\"\\\", \\\"\")}*\")\n for (i in to_install) {\n message(paste(\"looking for \", i))\n if (!requireNamespace(i)) {\n message(paste(\" installing\", i))\n install.packages(i)\n }\n }\n\n",
#' .open = "*{",
#' .close = "}*"
#' )
#' }
#' else {
#' content <- glue::glue(
#' "*{remotes_content}*\n# No attachments ----\n \n\n",
#' .open = "*{",
#' .close = "}*"
#' )
#' }
#'
#' file <- file.path(dir_to, basename(to))
#' file.create(file)
#' cat(content, file = file)
#'
#' if (open_file) {
#' utils::file.edit(file, editor = "internal")
#' }
#' }
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