Merge pull request #97 from ThinkR-open/att_config

fix: stop if parameters are not used

Author: statnmap

NEWS.md

@@ -1,14 +1,22 @@
 # attachment 0.3.1.XXXX
 
+## Breaking changes
+
+- When using `att_amend_desc()` without the default parameters, like `pkg_ignore = "x"` will now require `att_amend_desc(pkg_ignore = "x", update.config = TRUE)`, otherwise, it will fail. This allows for the use of parameters stored in the config file when running `att_amend_desc()` directly in the console.
+Recommendation: Run `att_amend_desc(pkg_ignore = "x", update.config = TRUE)` if you have to update your config, run `att_amend_desc()` daily as you'll want to use what is stored in the config file.
+
+- `create_dependencies_file()` gets parameter `install_only_if_missing = FALSE` by default to complete the installation instructions packages only if missing. (@MurielleDelmotte) 
+
 ## New features
 
 - `att_amend_desc()` can run with the last set of parameters stored in a configuration file, without having to call them all each time. See vignettes and documentation of parameters `update.config = FALSE`, `use.config = FALSE` and `path.c = "dev/config_attachment.yaml"`. (@dagousket)
 - `create_dependencies_file()` now takes other sources into account (git, gitlab, github, bioc, local). (@MurielleDelmotte)
-- `create_dependencies_file()` gets parameter `install_only_if_missing = FALSE` by default to complete the installation instructions packages only if missing. (@MurielleDelmotte) 
+- Use `create_dependencies_file(to = NULL)` to only get the output as character and do not create a file
 
 ## Bug fixes 
 
 - `att_amend_desc()` does not modify user `options("warn")` level anymore (#94)
+- `att_amend_desc()` allows "Remotes" field to contain `@ref` (#67)
 
 # attachment 0.3.1
 
@@ -19,7 +27,7 @@
 ## Minor changes
 
 - a new parameters `check_if_suggests_is_installed` in `att_amend_desc()` allow not to check if suggested package is installed. (thanks to @yogat3ch)
-- `create_renv_for_prod()` dont look anymore for suggested packages
+- `create_renv_for_prod()` don't look anymore for suggested packages
 - Clean a maximum of temp directories after examples and unit tests
 
 # attachment 0.3.0

R/amend_with_config.R

@@ -1,5 +1,48 @@
 # WARNING - Generated by {fusen} from dev/flat_save_att_params.Rmd: do not edit by hand
 
+#' Compare input from the user to config file or default inputs
+#'
+#' @param local_att_params List of parameters called by the user
+#' @inheritParams att_amend_desc
+#'
+#' @noRd
+
+compare_inputs_load_or_save <- function(path.c, local_att_params, use.config, update.config) {
+
+    if (isTRUE(use.config) & file.exists(path.c)) {
+      # reassign input value to saved parameters
+      saved_att_params <- load_att_params(path_to_yaml = path.c)
+      # Check if different from config and as defaults
+      diff_config <- lapply(names(local_att_params), function(x) {setdiff(local_att_params[x], saved_att_params[x])})
+      diff_default <- lapply(names(local_att_params), function(x) {setdiff(local_att_params[x], formals(att_amend_desc)[x])})
+
+      if (any(lengths(diff_config) != 0) & any(lengths(diff_default) != 0)) {
+        stop(c("Params in your `att_amend_desc()` and the one in the config file are different. ",
+             "Please choose among `update.config = TRUE` or `use.config = FALSE`"))
+      }
+      
+      params_to_load <- saved_att_params
+      # for (param_name in names(saved_att_params)){
+      #   assign(param_name, saved_att_params[[param_name]])
+      # }
+      # message(c("Documentation parameters were restored from attachment config file.\n"))
+    } else if (isTRUE(update.config) | !file.exists(path.c)) {
+      # save current parameters to yaml config - overwrite if already exist
+      save_att_params(
+        param_list = local_att_params,
+        path_to_yaml = path.c,
+        overwrite = TRUE)
+      
+      params_to_load <- NULL
+    } else {
+      message("attachment config file was not updated. Parameters used this time won't be stored.")
+      
+      params_to_load <- local_att_params
+    }
+
+    return(params_to_load)
+  }
+
 #' load_att_params
 #' 
 #' @param path_to_yaml character The path to the yaml file

R/att_to_description.R

@@ -24,15 +24,43 @@
 #'
 #' @return Update DESCRIPTION file.
 #'
+#' @details
+#'
+#' Your daily use is to run `att_amend_desc()`, as is.
+#' You will want to run this function sometimes with some extra information like
+#' `att_amend_desc(pkg_ignore = "x", update.config = TRUE)` if you have to update
+#' the configuration file.
+#' Next time `att_amend_desc()` will use these parameters from the configuration
+#' file directly.
+#'
+#'
 #' @export
 #' @examples
+#'
+#' # Run on an external "dummypackage" as an example
+#' # For your local use, you do not have to specify the `path` as below
+#' # By default, `att_amend_desc()` will run on the current working directory
+#'
+#' # Create a fake package for the example
 #' tmpdir <- tempfile(pattern = "description")
 #' dir.create(tmpdir)
 #' file.copy(system.file("dummypackage",package = "attachment"), tmpdir,
 #'  recursive = TRUE)
 #' dummypackage <- file.path(tmpdir, "dummypackage")
-#' # browseURL(dummypackage)
-#' att_amend_desc(path = tmpdir)
+#'
+#' # Update documentation and dependencies
+#' att_amend_desc(path = dummypackage)
+#'
+#' # You can look at the content of this external package
+#' #' # browseURL(dummypackage)
+#'
+#' # Update the config file with extra parameters
+#' # We recommend that you store this code in a file in your "dev/" directory
+#' # to run it when needed
+#' att_amend_desc(path = dummypackage, extra.suggests = "testthat", update.config = TRUE)
+#'
+#' # Next time, in your daily development
+#' att_amend_desc(path = dummypackage)
 #'
 #' # Clean after examples
 #' unlink(tmpdir, recursive = TRUE)
@@ -73,22 +101,17 @@ att_amend_desc <- function(path = ".",
   att_params <- att_params[!att_params %in% c("path", "update.config", "use.config", "path.c")]
   local_att_params <- mget(att_params)
 
-  if (isTRUE(use.config) & file.exists(path.c)) {
-      # reassign input value to saved parameters
-      saved_att_params <- load_att_params(path_to_yaml = path.c)
-      for (param_name in names(saved_att_params)){
-        assign(param_name, saved_att_params[[param_name]])
-      }
-      message(c("Documentation parameters were restored from attachment config file.\n",
-                "See `use.config` and `update.config` for other behaviour with `att_amend_desc()`\n"))
-  } else if (isTRUE(update.config) | !file.exists(path.c)) {
-    # save current parameters to yaml config - overwrite if already exist
-    save_att_params(
-      param_list = local_att_params,
-      path_to_yaml = path.c,
-      overwrite = TRUE)
-  } else {
-    message("attachment config file was not updated. Parameters used this time won't be stored.")
+  params_to_load <- compare_inputs_load_or_save(
+    path.c = path.c,
+    local_att_params = local_att_params,
+    use.config = use.config,
+    update.config = update.config)
+
+  if (!is.null(params_to_load)) {
+    for (param_name in names(params_to_load)){
+      assign(param_name, params_to_load[[param_name]])
+    }
+    message(c("Documentation parameters were restored from attachment config file."))
   }
 
   # Save all open files ----
@@ -314,7 +337,7 @@ att_to_desc_from_is <- function(path.d = "DESCRIPTION", imports = NULL,
 
   remotes_orig <- desc$get_remotes()
   if (length(remotes_orig) != 0) {
-    remotes_orig_pkg <- gsub("^.*/|[.]git", "", remotes_orig)
+    remotes_orig_pkg <- gsub("^.*/|[.]git|@.*$", "", remotes_orig)
   } else {
     remotes_orig_pkg <- NULL
   }

R/create_dependencies_file.R

@@ -1,80 +1,93 @@
 # WARNING - Generated by {fusen} from dev/flat_create_dependencies_file.Rmd: do not edit by hand
 
-#' Create a dependencies.R in the `inst` folder
+#' Create the list of instructions to install dependencies from a DESCRIPTION file
+#' 
+#' Outputs the list of instructions and a "dependencies.R" file with instructions in the "inst/" directory
 #'
 #' @param path path to the DESCRIPTION file
 #' @param field DESCRIPTION field to parse, "Import" and "Depends" by default. Can add "Suggests"
-#' @param to path to dependencies.R. "inst/dependencies.R" by default
+#' @param to path where to save the dependencies file. Set to "inst/dependencies.R" by default. Set to `NULL` if you do not want the file, but only the instructions as a list of character.
 #' @param open_file Logical. Open the file created in an editor
 #' @param ignore_base Logical. Whether to ignore package coming with base, as they cannot be installed (default TRUE)
 #' @param install_only_if_missing Logical Modify the installation instructions to check, beforehand, if the packages are missing . (default FALSE)
 #' @export
-#' @return Used for side effect. Shows a message with installation instructions and
-#' creates a R file containing these instructions.
+#' @return List of R instructions to install all dependencies from a DESCRIPTION file. Side effect: creates a R file containing these instructions.
 #' @importFrom glue glue glue_collapse
 #' @importFrom desc description
 #' @importFrom utils packageDescription
 #'
 #' @examples
-#' \dontrun{
-#'   tmpdir <- tempfile(pattern = "depsfile")
-#'   dir.create(tmpdir)
-#'   file.copy(system.file("dummypackage",package = "attachment"), tmpdir,
-#'    recursive = TRUE)
-#'   dummypackage <- file.path(tmpdir, "dummypackage")
-#'   
-#'   # browseURL(dummypackage)
-#'   create_dependencies_file(path = file.path(dummypackage,"DESCRIPTION"),
+#' # Create a fake package
+#' tmpdir <- tempfile(pattern = "depsfile")
+#' dir.create(tmpdir)
+#' file.copy(system.file("dummypackage",package = "attachment"), tmpdir,
+#'           recursive = TRUE)
+#' dummypackage <- file.path(tmpdir, "dummypackage")
+#' 
+#' # Create the dependencies commands but no file
+#' create_dependencies_file(
+#'   path = file.path(dummypackage,"DESCRIPTION"),
+#'   to = NULL,
+#'   open_file = FALSE)
+#' 
+#' # Create the dependencies files in the package
+#' create_dependencies_file(
+#'   path = file.path(dummypackage,"DESCRIPTION"),
 #'   to = file.path(dummypackage, "inst/dependencies.R"),
 #'   open_file = FALSE)
-#'   
-#'   # Clean temp files after this example
-#'   unlink(tmpdir, recursive = TRUE)
-#' }
+#' list.files(file.path(dummypackage, "inst"))
+#' # browseURL(dummypackage)
+#' 
+#' # Clean temp files after this example
+#' unlink(tmpdir, recursive = TRUE)
 create_dependencies_file <- function(path = "DESCRIPTION",
                                      field = c("Depends", "Imports"),
                                      to = "inst/dependencies.R", 
                                      open_file = TRUE,
                                      ignore_base = TRUE,
                                      install_only_if_missing = FALSE) {
 
-  if (!dir.exists(dirname(to))) {
-    dir.create(dirname(to), recursive = TRUE, showWarnings = FALSE)
-    dir_to <- normalizePath(dirname(to))
-  } else {
-    dir_to <- normalizePath(dirname(to))
-  }
-
   # get all packages
   ll <- att_from_description(path = path, field = field)
   # get pkg in remotes
   if (isTRUE(ignore_base)) {
-    to_remove<- which(lapply(ll,packageDescription,field="Priority")=="base")
-    if (length(to_remove)>0){
-     ll<- ll[-to_remove]
+    to_remove <-
+      which(lapply(ll , packageDescription, field = "Priority") == "base")
+    if (length(to_remove) > 0) {
+      ll <- ll[-to_remove]
     }
 
   }
 
   desc <- description$new(path)
   # Get previous dependencies in Description in case version is set
-  # deps_orig <- desc$get_deps()
   remotes_orig <- desc$get_remotes()
 
   content <- dependencies_file_text(ll = ll,
                          remotes_orig = remotes_orig,
                          install_only_if_missing = install_only_if_missing)
 
-  # file <- normalizePath(to, mustWork = FALSE)
-  file <- file.path(dir_to, basename(to))
-  file.create(file)
-
-  cat(unlist(content), sep  = "\n", file = file)
+  if (!is.null(to)) {
+    if (!dir.exists(dirname(to))) {
+      dir.create(dirname(to), recursive = TRUE, showWarnings = FALSE)
+      dir_to <- normalizePath(dirname(to))
+    } else {
+      dir_to <- normalizePath(dirname(to))
+    }
+    
+    the_file <- file.path(dir_to, basename(to))
+    # file.create(the_file)
+    cat(unlist(content), sep  = "\n", file = the_file)
 
-  if (interactive() && open_file) {
-    utils::file.edit(file, editor = "internal")
+    if (interactive() && open_file) {
+      utils::file.edit(file, editor = "internal")
+    }
+    
+    return(invisible(content))
+  } else {
+    return(content)
   }
 
-  return(invisible(content))
+
 }
 

R/create_renv.R

@@ -40,6 +40,7 @@ extra_dev_pkg <- c(
 #'
 #' @examples
 #' \dontrun{
+#' # Writes a renv.lock a file in the user directory
 #' create_renv_for_dev()
 #' create_renv_for_dev(dev_pkg = "attachment")
 #' create_renv_for_prod()
@@ -68,7 +69,21 @@ create_renv_for_dev <- function(path = ".",
   }
 
   if (isTRUE(document)) {
-    att_amend_desc(path, check_if_suggests_is_installed = check_if_suggests_is_installed)
+    # Use a temporary config_file for renv
+    config_file <- file.path(path, "dev", "config_attachment.yaml")
+    if (file.exists(config_file)) {
+      yaml_params <- load_att_params(path_to_yaml = config_file)
+      yaml_params[["check_if_suggests_is_installed"]] <- check_if_suggests_is_installed
+      yamlfile <- tempfile(fileext = ".yaml")
+      save_att_params(path_to_yaml = yamlfile, param_list = yaml_params)
+      att_amend_desc(path,
+                     use.config = TRUE,
+                     path.c = yamlfile)
+    } else {
+      att_amend_desc(path,
+                     check_if_suggests_is_installed = check_if_suggests_is_installed,
+                     use.config = FALSE)
+    }
   }
 
   if ( isTRUE(check_if_suggests_is_installed)){

R/dependencies_file_text.R

@@ -1,4 +1,4 @@
-# WARNING - Generated by {fusen} from /dev/flat_create_dependencies_file.Rmd: do not edit by hand
+# WARNING - Generated by {fusen} from dev/flat_create_dependencies_file.Rmd: do not edit by hand
 
 #' dependencies_file_text
 #' 

R/install_from_description.R

@@ -7,10 +7,11 @@
 #' @return Used for side effect. Installs R packages from DESCRIPTION file if missing.
 #' @examples
 #' \dontrun{
+#' # This will install packages on your system
 #' dummypackage <- system.file("dummypackage", package = "attachment")
 #' # browseURL(dummypackage)
 #'
-#' install_from_description(path = file.path(dummypackage,"DESCRIPTION"))
+#' install_from_description(path = file.path(dummypackage, "DESCRIPTION"))
 #' }
 
 install_from_description <- function(path = "DESCRIPTION", field = c("Depends", "Imports", "Suggests"), ...) {
@@ -30,7 +31,8 @@ install_from_description <- function(path = "DESCRIPTION", field = c("Depends",
 #' @return Used for side effect. Install missing packages from the character vector input.
 #' @examples
 #' \dontrun{
-#' install_if_missing(c("dplyr","fcuk","rusk"))
+#' # This will install packages on your system
+#' install_if_missing(c("dplyr", "fcuk", "rusk"))
 #' }
 #'
 install_if_missing <- function(to_be_installed, ...) {

R/set_remotes.R

@@ -11,11 +11,13 @@
 #' @examples
 #' # Find from vector of packages
 #' find_remotes(pkg = c("attachment", "desc", "glue"))
+#'
 #' # Find from Description file
 #' dummypackage <- system.file("dummypackage", package = "attachment")
 #' att_from_description(
 #' path = file.path(dummypackage, "DESCRIPTION")) %>%
 #' find_remotes()
+#'
 #' \dontrun{
 #' # For the current package directory
 #' att_from_description() %>% find_remotes()

dev/config_attachment.yaml

@@ -35,6 +35,7 @@ pkg_ignore:
   - ggplot3
   - svn
   - pkgload
+  - bookdown
 document: yes
 normalize: no
 inside_rmd: no