Merge pull request #118 from ThinkR-open/att_from_data

Att from data
ThinkR-open · Aug 5, 2024 · 6565c35 · 6565c35
2 parents fe48132 + 22fa437
commit 6565c35
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: attachment
 Title: Deal with Dependencies
-Version: 0.4.2.9000
+Version: 0.4.2.9001
 Authors@R: c(
     person("Sébastien", "Rochette", , "[email protected]", role = c("cre", "aut"),
            comment = c(ORCID = "0000-0002-1565-9313")),
@@ -24,9 +24,8 @@ License: GPL-3
 URL: https://thinkr-open.github.io/attachment/,
     https://github.com/ThinkR-open/attachment
 BugReports: https://github.com/ThinkR-open/attachment/issues
-VignetteBuilder:
-    knitr
-Config/fusen/version: 0.5.0.9006
+VignetteBuilder: knitr
+Config/fusen/version: 0.6.0
 Config/Needs/website: ThinkR-open/thinkrtemplate
 Config/testthat/edition: 3
 Encoding: UTF-8

diff --git a/NAMESPACE b/NAMESPACE
@@ -2,6 +2,7 @@
 
 export("%>%")
 export(att_amend_desc)
+export(att_from_data)
 export(att_from_description)
 export(att_from_examples)
 export(att_from_namespace)
@@ -27,6 +28,8 @@ importFrom(glue,glue)
 importFrom(glue,glue_collapse)
 importFrom(knitr,purl)
 importFrom(magrittr,"%>%")
+importFrom(roxygen2,block_get_tag_value)
+importFrom(roxygen2,parse_file)
 importFrom(roxygen2,roxygenise)
 importFrom(stats,na.omit)
 importFrom(stats,setNames)

diff --git a/NEWS.md b/NEWS.md
@@ -3,11 +3,12 @@
 ## New features
 
 - Add `att_from_examples()` to get all packages called in examples from R files
+- Add `att_from_data()` to look for functions called in data loading code
 - `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
+- Adding an example using suggest packages to the dummypackage
 
 # attachment 0.4.2
 

diff --git a/R/add_from_examples.R b/R/add_from_examples.R
@@ -3,7 +3,7 @@
 #' @param dir.r path to directory with R scripts.
 #'
 #' @return Character vector of packages called with library or require.
-#'
+#' @importFrom roxygen2 parse_file block_get_tag_value
 #' @examples
 #' dummypackage <- system.file("dummypackage",package = "attachment")
 #'
@@ -28,7 +28,14 @@ att_from_examples <- function(dir.r = "R") {
   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_data <- attachment::att_from_data(all_examples_clean)
+
   all_deps_examples <- attachment::att_from_rscript(roxy_file)
+
   file.remove(roxy_file)
-  return(all_deps_examples)
+
+  all_deps <- unique(c(all_deps_examples, all_deps_examples_data))
+
+  return(all_deps)
 }
diff --git a/R/att_from_data.R b/R/att_from_data.R
@@ -0,0 +1,20 @@
+#' Look for functions called in data loading code
+#'
+#' @param chr A character vector containing the code as a string. The code should follow the pattern used for loading data with `data()`, specifying the dataset and package.
+#' @return A character vector containing the names of the packages from which datasets are being loaded.
+#' @importFrom stringr str_extract_all
+#' @export
+#' @examples
+#'
+#' vec_char <- 'data("starwars", package = "dplyr")'
+#' att_from_data(vec_char)
+att_from_data <- function(chr) {
+  pkg <-
+    str_extract_all(
+      chr,
+      '(?<=data\\(\\".{1,100}\\"\\,\\s{0,5}package\\s{0,5}\\=\\s{0,5}\\\")[[:alnum:]\\.]+(?=\\\"\\))'
+    ) |>
+    unlist()
+  return(pkg)
+
+}
diff --git a/R/create_dependencies_file.R b/R/create_dependencies_file.R
@@ -23,21 +23,21 @@
 #' 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)
 #' list.files(file.path(dummypackage, "inst"))
 #' # browseURL(dummypackage)
-#' 
+#'
 #' # Clean temp files after this example
 #' unlink(tmpdir, recursive = TRUE)
 create_dependencies_file <- function(path = "DESCRIPTION",

diff --git a/R/set_remotes.R b/R/set_remotes.R
@@ -15,12 +15,12 @@
 #' # Find from Description file
 #' dummypackage <- system.file("dummypackage", package = "attachment")
 #' att_from_description(
-#' path = file.path(dummypackage, "DESCRIPTION")) %>%
+#' path = file.path(dummypackage, "DESCRIPTION")) |>
 #' find_remotes()
 #'
 #' \dontrun{
 #' # For the current package directory
-#' att_from_description() %>% find_remotes()
+#' att_from_description() |> find_remotes()
 #' }
 #'
 #' \donttest{
@@ -69,15 +69,15 @@ find_remotes <- function(pkg) {
 #'  recursive = TRUE)
 #' dummypackage <- file.path(tmpdir, "dummypackage")
 #' # Add remotes field if there are Remotes locally
-#' att_amend_desc(dummypackage) %>%
+#' att_amend_desc(dummypackage) |>
 #'   set_remotes_to_desc()
 #'
 #' # Clean temp files after this example
 #' unlink(tmpdir, recursive = TRUE)
 #'
 #' \dontrun{
 #' # For your current package
-#' att_amend_desc() %>%
+#' att_amend_desc() |>
 #'   set_remotes_to_desc()
 #' }
 set_remotes_to_desc <- function(path.d = "DESCRIPTION", stop.local = FALSE,

diff --git a/dev/config_attachment.yaml b/dev/config_attachment.yaml
@@ -36,6 +36,9 @@ pkg_ignore:
   - svn
   - pkgload
   - bookdown
+  - pkgfake
+  - fakepkg
+  - dplyr
 document: yes
 normalize: no
 inside_rmd: no

diff --git a/dev/config_fusen.yaml b/dev/config_fusen.yaml
@@ -8,6 +8,14 @@ flat_create_dependencies_file.Rmd:
   - tests/testthat/test-dependencies_file_text.R
   - tests/testthat/test-create_dependencies_file.R
   vignettes: vignettes/create-dependencies-file.Rmd
+  inflate:
+    flat_file: dev/flat_create_dependencies_file.Rmd
+    vignette_name: Create dependencies file
+    open_vignette: false
+    check: false
+    document: true
+    overwrite: 'yes'
+    clean: ask
 flat_save_att_params.Rmd:
   path: dev/flat_save_att_params.Rmd
   state: active

diff --git a/dev/flat_create_dependencies_file.Rmd b/dev/flat_create_dependencies_file.Rmd
@@ -291,7 +291,7 @@ dep_file_without_remotes <- readLines(file.path(dummypackage, "inst", "dependenc
 
 test_that("create-dependencies-file works without remotes", {
   expect_equal(dep_file_without_remotes[1], "# No Remotes ----")
-  expect_equal(dep_file_without_remotes[3], "to_install <- c(\"knitr\", \"magrittr\", \"rmarkdown\", \"testthat\")")
+  expect_equal(dep_file_without_remotes[3], "to_install <- c(\"glue\", \"knitr\", \"magrittr\", \"rmarkdown\", \"stringr\", \"testthat\")")
 })
   
 
@@ -326,7 +326,7 @@ test_that("create-dependencies-file works with remotes", {
   expect_equal(dep_file_with_remotes[7], "remotes::install_git('https://github.com/fakepkggit.git')")
   expect_equal(dep_file_with_remotes[8], "remotes::install_git('https://MyForge.com/fakepkggit2r')")
   expect_equal(dep_file_with_remotes[9], "remotes::install_github('ThinkR-open/fusen')")
-  expect_equal(dep_file_with_remotes[11], "to_install <- c(\"knitr\", \"magrittr\", \"rmarkdown\", \"testthat\")")
+  expect_equal(dep_file_with_remotes[11], "to_install <- c(\"glue\", \"knitr\", \"magrittr\", \"rmarkdown\", \"stringr\", \"testthat\")")
 })
 
 
@@ -347,7 +347,7 @@ test_that("create-dependencies-file works with remotes install_only_if_missing",
   expect_equal(dep_file_with_remotes_install_only_if_missing[7], "if(isFALSE(requireNamespace('fakepkggit', quietly = TRUE))) {message('installation of fakepkggit');remotes::install_git('https://github.com/fakepkggit.git')}")
   expect_equal(dep_file_with_remotes_install_only_if_missing[8],  "if(isFALSE(requireNamespace('fakepkggit2r', quietly = TRUE))) {message('installation of fakepkggit2r');remotes::install_git('https://MyForge.com/fakepkggit2r')}")
   expect_equal(dep_file_with_remotes_install_only_if_missing[9], "if(isFALSE(requireNamespace('fusen', quietly = TRUE))) {message('installation of fusen');remotes::install_github('ThinkR-open/fusen')}")
-  expect_equal(dep_file_with_remotes_install_only_if_missing[11], "to_install <- c(\"knitr\", \"magrittr\", \"rmarkdown\", \"testthat\")")
+  expect_equal(dep_file_with_remotes_install_only_if_missing[11], "to_install <- c(\"glue\", \"knitr\", \"magrittr\", \"rmarkdown\", \"stringr\", \"testthat\")")
 })
 
 # Clean temp files after this example

diff --git a/inst/dummypackage/DESCRIPTION b/inst/dummypackage/DESCRIPTION
@@ -9,14 +9,18 @@ Depends:
     R (>= 3.5.0)
 Imports: 
     magrittr,
-    utils
+    stats
+Suggests: 
+    glue,
+    knitr,
+    rmarkdown,
+    testthat,
+    utils,
+    stringr
 LinkingTo:
     Rcpp
+VignetteBuilder: 
+    knitr
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.0
-Suggests: 
-    knitr,
-    rmarkdown,
-    testthat
-VignetteBuilder: knitr
+RoxygenNote: 7.3.1
diff --git a/inst/dummypackage/R/my_mean.R b/inst/dummypackage/R/my_mean.R
@@ -7,6 +7,7 @@
 #' @examples
 #' # example code
 #' library(utils)
+#' data("fruit", package = "stringr")
 my_mean <- function(x){
   x <- x %>% stats::na.omit()
   1+1

diff --git a/inst/dummypackage/man/my_mean.Rd b/inst/dummypackage/man/my_mean.Rd
diff --git a/man/att_from_data.Rd b/man/att_from_data.Rd
diff --git a/man/find_remotes.Rd b/man/find_remotes.Rd
diff --git a/man/set_remotes_to_desc.Rd b/man/set_remotes_to_desc.Rd
diff --git a/tests/testthat/test-amend-description.R b/tests/testthat/test-amend-description.R
@@ -40,10 +40,11 @@ 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], "    utils")
-  expect_equal(desc_file[w.depends + 11], "LinkingTo:" )
-  expect_equal(desc_file[w.depends + 12], "    Rcpp")
+  expect_equal(desc_file[w.depends + 9], "    stringr,")
+  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")
   # base does not appear
   expect_false(all(grepl("base", desc_file)))
   # utils is removed
@@ -486,10 +487,11 @@ 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], "    utils")
-  expect_equal(desc_file[w.depends + 12], "LinkingTo:" )
-  expect_equal(desc_file[w.depends + 13], "    Rcpp")
+  expect_equal(desc_file[w.depends + 10], "    stringr,")
+  expect_equal(desc_file[w.depends + 11], "    testthat,")
+  expect_equal(desc_file[w.depends + 12], "    utils")
+  expect_equal(desc_file[w.depends + 13], "LinkingTo:" )
+  expect_equal(desc_file[w.depends + 14], "    Rcpp")
 
 
   # Clean after
@@ -533,8 +535,9 @@ my_length <- function(x) {
   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")
+  expect_equal(desc_file[w.depends + 11], "    stringr,")
+  expect_equal(desc_file[w.depends + 12], "    testthat,")
+  expect_equal(desc_file[w.depends + 13], "    utils")
   # Clean after
   unlink(dummypackage, recursive = TRUE)
 
@@ -579,10 +582,11 @@ my_length <- function(x) {
   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")
+  expect_equal(desc_file[w.depends + 10], "    stringr,")
+  expect_equal(desc_file[w.depends + 11], "    testthat,")
+  expect_equal(desc_file[w.depends + 12], "    utils")
+  expect_equal(desc_file[w.depends + 13], "LinkingTo:" )
+  expect_equal(desc_file[w.depends + 14], "    Rcpp")
 
   # Clean after
   unlink(dummypackage, recursive = TRUE)

diff --git a/tests/testthat/test-att_from_data.R b/tests/testthat/test-att_from_data.R
@@ -0,0 +1,21 @@
+test_that("att_from_data works with a single package", {
+
+  input1 <- 'data("starwars", package = "dplyr")'
+  expect_equal(att_from_data(input1), "dplyr")
+
+})
+
+test_that("att_from_data works with multi package", {
+
+  input1 <- 'data("starwars", package = "dplyr")data("dataset", package = "pkgfake")'
+  expect_equal(att_from_data(input1), c("dplyr", "pkgfake"))
+
+})
+
+
+test_that("att_from_data works with extra spaces", {
+
+  input1 <- 'data("starwars",package    = "dplyr")'
+  expect_equal(att_from_data(input1), "dplyr")
+
+})