Merge pull request #117 from ThinkR-open/att_from_examples

Att from examples

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: attachment
 Title: Deal with Dependencies
-Version: 0.4.2
+Version: 0.4.2.9000
 Authors@R: c(
     person("Sébastien", "Rochette", , "[email protected]", role = c("cre", "aut"),
            comment = c(ORCID = "0000-0002-1565-9313")),
@@ -31,7 +31,7 @@ Config/Needs/website: ThinkR-open/thinkrtemplate
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 Language: en-US
 Depends: 
     R (>= 3.4)

NAMESPACE

@@ -3,6 +3,7 @@
 export("%>%")
 export(att_amend_desc)
 export(att_from_description)
+export(att_from_examples)
 export(att_from_namespace)
 export(att_from_qmd)
 export(att_from_qmds)

NEWS.md

@@ -1,3 +1,14 @@
+# attachment (development version)
+
+## New features
+
+- Add `att_from_examples()` to get all packages called in examples from R files
+- `att_amend_desc` amend package DESCRIPTION file (Suggests) with the list of dependencies extracted from examples in R files.
+
+## Patch
+
+- Adding an example using a suggest package to the dummypackage
+
 # attachment 0.4.2
 
 ## New features
@@ -182,7 +193,7 @@ Minor
 * New function `install_from_description` to install all missing packages listed in the description file
 * Add an hex by @statnmap !
 * Allow for absence of vignette folder in `att_to_description`
-* Add `create_dependencies_file` to create a file listing all packages dependencies to install before your package
+* Add `create_dependencies_file` to create a file listing all packages dependencies to dinstall before your package
 * Allow for `pkg::fun` calls in R scripts with `att_from_functions`
 * Add option to run `devtools::document()` before `att_from_description`
 

R/add_from_examples.R

@@ -0,0 +1,34 @@
+#' Get all packages called in examples from R files
+#'
+#' @param dir.r path to directory with R scripts.
+#'
+#' @return Character vector of packages called with library or require.
+#'
+#' @examples
+#' dummypackage <- system.file("dummypackage",package = "attachment")
+#'
+#' # browseURL(dummypackage)
+#' att_from_examples(dir.r = file.path(dummypackage,"R"))
+
+#' @export
+att_from_examples <- function(dir.r = "R") {
+  rfiles <- list.files(dir.r, full.names = TRUE)
+
+  roxy_file <- tempfile("roxy.examples", fileext = ".R")
+
+  all_examples <- unlist(lapply(rfiles, function(the_file) {
+    file_roxytags <- roxygen2::parse_file(the_file)
+    res <- unlist(
+      lapply(file_roxytags,
+             function(x) roxygen2::block_get_tag_value(block = x, tag = "examples"))
+    )
+    res
+  }))
+  # Clean \dontrun and \donttest, and replace with '{' on next line
+  all_examples_clean <-
+    gsub(pattern = "\\\\dontrun\\s*\\{|\\\\donttest\\s*\\{", replacement = "#ICI\n{", x = all_examples)
+  cat(all_examples_clean, file = roxy_file, sep = "\n")
+  all_deps_examples <- attachment::att_from_rscript(roxy_file)
+  file.remove(roxy_file)
+  return(all_deps_examples)
+}

R/att_to_description.R

@@ -1,7 +1,7 @@
 #' Amend DESCRIPTION with dependencies read from package code parsing
 #'
 #' Amend package DESCRIPTION file with the list of dependencies extracted from
-#' R, tests, vignettes files.
+#' R, examples, tests, vignettes files.
 #' att_to_desc_from_pkg() is an alias of att_amend_desc(),
 #' for the correspondence with [att_to_desc_from_is()].
 #'
@@ -19,6 +19,7 @@
 #' @inheritParams att_from_namespace
 #' @inheritParams att_to_desc_from_is
 #' @inheritParams att_from_rmds
+#' @inheritParams att_from_examples
 #'
 #' @importFrom desc description
 #'
@@ -88,6 +89,8 @@ att_amend_desc <- function(path = ".",
     on.exit(setwd(old))
   }
 
+
+
   path <- normalizePath(path)
 
   # decide whether to use or update config file ----
@@ -196,6 +199,13 @@ att_amend_desc <- function(path = ".",
 
   # Suggests ----
   suggests <- NULL
+
+  # Get suggests in examples and remove if already in imports
+  if (dir.r != "") {
+    ex <- att_from_examples(dir.r = dir.r)
+    suggests <- c(suggests, ex[!ex %in% imports])
+  }
+
   # Get suggests in vignettes and remove if already in imports
   if (!grepl("^$|^\\s+$$", dir.v)) {
     vg <- att_from_rmds(dir.v, inside_rmd = inside_rmd)

inst/dummypackage/R/my_mean.R

@@ -4,6 +4,9 @@
 #'
 #' @export
 #' @importFrom magrittr %>%
+#' @examples
+#' # example code
+#' library(utils)
 my_mean <- function(x){
   x <- x %>% stats::na.omit()
   1+1

tests/testthat/test-amend-description.R

@@ -40,9 +40,10 @@ test_that("att_amend_desc updates description", {
   expect_equal(desc_file[w.depends + 6], "    glue,")
   expect_equal(desc_file[w.depends + 7], "    knitr,")
   expect_equal(desc_file[w.depends + 8], "    rmarkdown,")
-  expect_equal(desc_file[w.depends + 9], "    testthat")
-  expect_equal(desc_file[w.depends + 10], "LinkingTo:" )
-  expect_equal(desc_file[w.depends + 11], "    Rcpp")
+  expect_equal(desc_file[w.depends + 9], "    testthat,")
+  expect_equal(desc_file[w.depends + 10], "    utils")
+  expect_equal(desc_file[w.depends + 11], "LinkingTo:" )
+  expect_equal(desc_file[w.depends + 12], "    Rcpp")
   # base does not appear
   expect_false(all(grepl("base", desc_file)))
   # utils is removed
@@ -485,12 +486,105 @@ library(ggplot3)
   expect_equal(desc_file[w.depends + 7], "    glue,")
   expect_equal(desc_file[w.depends + 8], "    knitr,")
   expect_equal(desc_file[w.depends + 9], "    rmarkdown,")
-  expect_equal(desc_file[w.depends + 10], "    testthat")
-  expect_equal(desc_file[w.depends + 11], "LinkingTo:" )
-  expect_equal(desc_file[w.depends + 12], "    Rcpp")
+  expect_equal(desc_file[w.depends + 10], "    testthat,")
+  expect_equal(desc_file[w.depends + 11], "    utils")
+  expect_equal(desc_file[w.depends + 12], "LinkingTo:" )
+  expect_equal(desc_file[w.depends + 13], "    Rcpp")
 
 
   # Clean after
   unlink(dummypackage, recursive = TRUE)
 })
 
+
+# Test update desc when packages in examples ----
+test_that("if a package is used in an example, it is added to Suggests packages", {
+  # Copy package in a temporary directory
+  tmpdir <- tempfile("dummysuggestexamples")
+  dir.create(tmpdir)
+  file.copy(system.file("dummypackage",package = "attachment"), tmpdir, recursive = TRUE)
+  dummypackage <- file.path(tmpdir, "dummypackage")
+
+  r_file <- file.path(dummypackage, "R", "fun_manual.R")
+  file.create(r_file)
+  #> [1] TRUE
+  writeLines(
+    text = "#' @importFrom magrittr %>%
+#' @examples
+#' library(pkgfake)
+#' fakepkg::fun()
+#' @export
+my_length <- function(x) {
+  x %>% length()
+}",
+    con = r_file
+  )
+
+  attachment::att_amend_desc(path = dummypackage, check_if_suggests_is_installed = FALSE)
+
+
+  desc_file <- readLines(file.path(dummypackage, "DESCRIPTION"))
+
+  w.depends <- grep("Depends:", desc_file)
+  expect_length(w.depends, 1)
+  expect_equal(desc_file[w.depends + 5], "Suggests: ")
+  expect_equal(desc_file[w.depends + 6], "    fakepkg,")
+  expect_equal(desc_file[w.depends + 7], "    glue,")
+  expect_equal(desc_file[w.depends + 8], "    knitr,")
+  expect_equal(desc_file[w.depends + 9], "    pkgfake,")
+  expect_equal(desc_file[w.depends + 10], "    rmarkdown,")
+  expect_equal(desc_file[w.depends + 11], "    testthat,")
+  expect_equal(desc_file[w.depends + 12], "    utils")
+  # Clean after
+  unlink(dummypackage, recursive = TRUE)
+
+})
+
+
+test_that("if a package is used in an example has already been added to IMPORTS, it is not added to the suggests, it is added to Suggests packages", {
+  # Copy package in a temporary directory
+  tmpdir <- tempfile("dummysuggestexamples")
+  dir.create(tmpdir)
+  file.copy(system.file("dummypackage",package = "attachment"), tmpdir, recursive = TRUE)
+  dummypackage <- file.path(tmpdir, "dummypackage")
+
+  r_file <- file.path(dummypackage, "R", "fun_manual.R")
+  file.create(r_file)
+  #> [1] TRUE
+  writeLines(
+    text = "#' @importFrom magrittr %>%
+#' @examples
+#' library(magrittr)
+#' fakepkg::fun()
+#' @export
+my_length <- function(x) {
+  x %>% length()
+}",
+    con = r_file
+  )
+
+  attachment::att_amend_desc(path = dummypackage, check_if_suggests_is_installed = FALSE)
+
+
+  desc_file <- readLines(file.path(dummypackage, "DESCRIPTION"))
+
+  w.depends <- grep("Depends:", desc_file)
+  expect_length(w.depends, 1)
+  expect_equal(desc_file[w.depends + 1], "    R (>= 3.5.0)")
+  expect_equal(desc_file[w.depends + 2], "Imports: ")
+  expect_equal(desc_file[w.depends + 3], "    magrittr,")
+  expect_equal(desc_file[w.depends + 4], "    stats")
+  expect_equal(desc_file[w.depends + 5], "Suggests: ")
+  expect_equal(desc_file[w.depends + 6], "    fakepkg,")
+  expect_equal(desc_file[w.depends + 7], "    glue,")
+  expect_equal(desc_file[w.depends + 8], "    knitr,")
+  expect_equal(desc_file[w.depends + 9], "    rmarkdown,")
+  expect_equal(desc_file[w.depends + 10], "    testthat,")
+  expect_equal(desc_file[w.depends + 11], "    utils")
+  expect_equal(desc_file[w.depends + 12], "LinkingTo:" )
+  expect_equal(desc_file[w.depends + 13], "    Rcpp")
+
+  # Clean after
+  unlink(dummypackage, recursive = TRUE)
+
+})

tests/testthat/test-att_from_examples.R

@@ -0,0 +1,24 @@
+test_that("att_from_examples works", {
+  tmpdir <- tempfile("suggestexamples")
+
+  dir.create(file.path(tmpdir, "R"), recursive = TRUE)
+
+  r_file <- file.path(tmpdir, "R", "fun_manual.R")
+  file.create(r_file)
+
+  writeLines(
+    text = "#' @importFrom magrittr %>%
+#' @examples
+#' library(magrittr)
+#' fakepkg::fun()
+#' @export
+my_length <- function(x) {
+  x %>% length()
+}",
+    con = r_file
+  )
+
+  expect_equal(att_from_examples(dir.r = file.path(tmpdir, "R")),
+               c("magrittr", "fakepkg"))
+
+})

vignettes/a-fill-pkg-description.Rmd

@@ -221,13 +221,14 @@ for (i in to_install) {
 
 ## Other possibilities
 
-Of course, you can also use {attachment} out of a package to list all package dependencies of R scripts using `att_from_rscripts()` or Rmd files using `att_from_rmds()`.
+Of course, you can also use {attachment} out of a package to list all package dependencies of R scripts using `att_from_rscripts()`, Rmd files using `att_from_rmds()` or examples from R scripts using `att_from_examples()`.
 
 ```{r, eval=TRUE}
 dummypackage <- system.file("dummypackage", package = "attachment")
 
 att_from_rscripts(path = file.path(dummypackage, "R"))
 att_from_rmds(path = file.path(dummypackage, "vignettes"), inside_rmd = TRUE)
+att_from_examples(dir.r = file.path(dummypackage, "R"))
 ```
 
 

vignettes/b-bookdown-and-scripts.Rmd

@@ -106,6 +106,12 @@ This reads all files in directories of R scripts (default to `R` directory of a
 att_from_rscripts()
 ```
 
+Called in examples from R scripts: 
+
+```{r, eval=FALSE}
+att_from_examples()
+```
+
 ## Get all packages called in your Rmd
 If you have vignette, you may want to list extra libraries, not listed in your "Depends" list. This function applies to any Rmd file, of course.