Merge pull request #227 from ThinkR-open/v0.5.2-before-cran

V0.5.2 before cran

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: fusen
 Title: Build a Package from Rmarkdown Files
-Version: 0.5.1
+Version: 0.5.2
 Authors@R: c(
     person("Sebastien", "Rochette", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-1565-9313")),
@@ -47,10 +47,10 @@ Suggests:
     withr
 VignetteBuilder: 
     knitr
-Config/fusen/version: 0.5.1
+Config/fusen/version: 0.5.2
 Config/Needs/website: ThinkR-open/thinkrtemplate
 Config/testthat/edition: 3
-Config/testthat/parallel: true
+Config/testthat/parallel: false
 Encoding: UTF-8
 Language: en-US
 LazyData: true

R/add_flat_template.R

@@ -129,7 +129,7 @@ create_fusen_choices <- c("full", "minimal", "teaching", "dev_history")
 #'
 #' @examples
 #' # Create a new project
-#' dummypackage <- tempfile("dummypackage")
+#' dummypackage <- tempfile("dummy.package.flat")
 #' dir.create(dummypackage)
 #'
 #' # Add

R/create_fusen_rsproject.R

@@ -125,7 +125,7 @@ create_fusen_gui <- function(path,
                              flat_name = template,
                              with_git) {
   create_fusen(
-    path = file.path(getwd(), path),
+    path = file.path(normalize_path_winslash(getwd()), path),
     template = template,
     flat_name = flat_name,
     open = FALSE, # Project opening is done spontaneously by Rstudio Project Wizard

R/fill_description.R

@@ -12,7 +12,7 @@
 #'
 #' @examples
 #' # Create a new project
-#' dummypackage <- tempfile("dummypackage")
+#' dummypackage <- tempfile("dummy.package.desc")
 #' dir.create(dummypackage)
 #'
 #' fill_description(

R/inflate.R

@@ -42,7 +42,7 @@ regex_example <- paste(regex_example_vec, collapse = "|")
 #'
 #' @examples
 #' # Create a new project
-#' dummypackage <- tempfile("dummypackage")
+#' dummypackage <- tempfile("dummy.package")
 #' dir.create(dummypackage)
 #'
 #' # {fusen} steps
@@ -127,11 +127,21 @@ inflate <- function(pkg = ".", flat_file,
   }
 
   old <- setwd(pkg)
-  on.exit(setwd(old))
+  if (normalizePath(old, mustWork = FALSE) != normalizePath(pkg, mustWork = FALSE)) {
+    if (dir.exists(old)) {
+      on.exit(setwd(old))
+    } else {
+      on.exit(here::here())
+    }
+  }
 
   old_proj <- usethis::proj_get()
-  if (normalizePath(old_proj) != normalizePath(pkg)) {
-    on.exit(usethis::proj_set(old_proj))
+  if (normalizePath(old_proj, mustWork = FALSE) != normalizePath(pkg, mustWork = FALSE)) {
+    if (dir.exists(old_proj)) {
+      on.exit(usethis::proj_set(old_proj))
+    } else {
+      on.exit(usethis::proj_set(here::here()))
+    }
     usethis::proj_set(pkg)
   }
 

R/inflate_all.R

@@ -40,7 +40,7 @@
 #'
 #' # You can also inflate_all flats of another package as follows
 #' # Example with a dummy package with a flat file
-#' dummypackage <- tempfile("inflateall")
+#' dummypackage <- tempfile("inflateall.otherpkg")
 #' dir.create(dummypackage)
 #' fill_description(pkg = dummypackage, fields = list(Title = "Dummy Package"))
 #' flat_files <- add_minimal_package(

R/register_config_file.R

@@ -58,7 +58,7 @@
 #' })
 #' unlink(dummypackage, recursive = TRUE)
 check_not_registered_files <- function(path = ".", guess = TRUE, to_csv = TRUE, open = FALSE) {
-  path <- normalizePath(path, winslash = "/")
+  path <- normalize_path_winslash(path)
 
   all_r <- list.files(file.path(path, "R"), pattern = "[.]R$|[.]r$", full.names = TRUE)
   all_test <- list.files(file.path(path, "tests", "testthat"), pattern = "[.]R$|[.]r$", full.names = TRUE)
@@ -86,7 +86,7 @@ check_not_registered_files <- function(path = ".", guess = TRUE, to_csv = TRUE,
   if (file.exists(config_file)) {
     # Read config file, and remove those already there
     config_list <- yaml::read_yaml(config_file)
-    config_list_path <- normalizePath(get_list_paths(config_list), mustWork = FALSE, winslash = "/")
+    config_list_path <- normalize_path_winslash(get_list_paths(config_list), mustWork = FALSE)
     res_existing <- res[res$path %in% config_list_path, ]
     res_new <- res[!res$path %in% config_list_path, ]
     config_flat_paths <- sapply(config_list, function(x) x[["path"]])
@@ -121,11 +121,11 @@ check_not_registered_files <- function(path = ".", guess = TRUE, to_csv = TRUE,
   }
 
   # TODO go back to relative path
-  res_new$path <- gsub(paste0(getwd(), "/"), "", normalize_path_winslash(res_new$path, mustWork = TRUE), fixed = TRUE)
+  res_new$path <- gsub(paste0(normalize_path_winslash(getwd()), "/"), "", normalize_path_winslash(res_new$path, mustWork = TRUE), fixed = TRUE)
 
   # config_file may not exist already
   csv_file <- file.path(
-    gsub(paste0(getwd(), "/"), "", dirname(normalize_path_winslash(config_file, mustWork = FALSE)), fixed = TRUE), "config_not_registered.csv"
+    gsub(paste0(normalize_path_winslash(getwd()), "/"), "", dirname(normalize_path_winslash(config_file, mustWork = FALSE)), fixed = TRUE), "config_not_registered.csv"
   )
 
   # Save for manual modification
@@ -174,9 +174,12 @@ guess_flat_origin <- function(path) {
     lines[grep("(G|g)enerated by \\{fusen\\} from", lines)][1]
   )
 
-  guess_path <- normalizePath(guess_path, mustWork = FALSE, winslash = "/")
+  guess_path <- normalize_path_winslash(guess_path, mustWork = FALSE)
   if (file.exists(guess_path)) {
-    guess_path <- gsub(paste0(getwd(), "/"), "", normalizePath(guess_path, mustWork = FALSE, winslash = "/"))
+    guess_path <- gsub(
+      paste0(normalize_path_winslash(getwd()), "/"), "",
+      normalize_path_winslash(guess_path, mustWork = FALSE)
+    )
     return(guess_path)
   } else {
     return("No existing source path found.")
@@ -638,7 +641,7 @@ register_all_to_config <- function(pkg = ".") {
 
   # Delete out_df
   csv_file <- file.path(
-    gsub(paste0(getwd(), "/"), "", dirname(normalize_path_winslash(config_file, mustWork = FALSE)), fixed = TRUE), "config_not_registered.csv"
+    gsub(paste0(normalize_path_winslash(getwd()), "/"), "", dirname(normalize_path_winslash(config_file, mustWork = FALSE)), fixed = TRUE), "config_not_registered.csv"
   )
   if (file.exists(csv_file)) {
     cli::cat_rule(paste("Delete", csv_file))

dev/dev_history.R

@@ -194,6 +194,7 @@ testthat::test_file("tests/testthat/test-add_flat_template.R")
 testthat::test_file("tests/testthat/test-skeleton.R")
 Sys.setenv("NOT_CRAN" = "false")
 
+# Run line by line
 Sys.setenv("FUSEN_TEST_PUBLISH" = "TRUE")
 testthat::test_file("tests/testthat/test-init_share_on_github.R")
 Sys.setenv("FUSEN_TEST_PUBLISH" = "FALSE")
@@ -206,32 +207,6 @@ Sys.setenv("FUSEN_TEST_PUBLISH" = "FALSE")
 # Run examples in interactive mode too
 devtools::run_examples()
 
-local <- utils::fileSnapshot(".", timestamp = tempfile("timestamp"), md5sum = TRUE)
-home <- utils::fileSnapshot("~", timestamp = tempfile("timestamp"), md5sum = TRUE)
-
-# run tests or whatever, then ...
-# x <- autotest::autotest_package(test = TRUE)
-devtools::test()
-devtools::run_examples()
-# vignettes
-dircheck <- tempfile("check")
-dir.create(dircheck)
-rcmdcheck::rcmdcheck(check_dir = dircheck)
-# browseURL(dircheck)
-
-the_dir <- list.files(file.path(dircheck), pattern = ".Rcheck", full.names = TRUE)
-# Same tests, no new files
-all(list.files(file.path(the_dir, "tests", "testthat")) %in%
-  list.files(file.path(".", "tests", "testthat")))
-
-devtools::build_vignettes()
-devtools::clean_vignettes()
-
-utils::changedFiles(local, md5sum = TRUE)
-utils::changedFiles(home, md5sum = TRUE)
-
-DT::datatable(x)
-
 # Check package as CRAN
 rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"))
 devtools::check(args = c("--no-manual", "--as-cran"))
@@ -240,9 +215,12 @@ devtools::check(args = c("--no-manual", "--as-cran"))
 # remotes::install_github("ThinkR-open/checkhelper")
 tags <- checkhelper::find_missing_tags()
 View(tags$functions)
+
+# Remettre: Config/testthat/parallel: false dans DESCRIPTION
 out <- checkhelper::check_clean_userspace(pkg = ".")
 out
 checkhelper::check_as_cran()
+# Remettre: Config/testthat/parallel: true dans DESCRIPTION
 
 # Check spelling
 # usethis::use_spell_check()
@@ -260,7 +238,7 @@ usethis::use_version(which = c("patch", "minor", "major", "dev")[2])
 # _rhub
 devtools::check_rhub()
 rhub::platforms()
-rhub::check_on_windows(check_args = "--force-multiarch")
+rhub::check_on_windows(check_args = "--force-multiarch", show_status = FALSE)
 rhub::check_on_solaris(show_status = FALSE)
 rhub::check(platform = "debian-clang-devel", show_status = FALSE)
 rhub::check(platform = "debian-gcc-devel", show_status = FALSE)

dev/flat_create_flat.Rmd

@@ -249,7 +249,7 @@ local_file_ignore <- function(file, ignores) {
 
 ```{r examples-1}
 # Create a new project
-dummypackage <- tempfile("dummypackage")
+dummypackage <- tempfile("dummy.package.flat")
 dir.create(dummypackage)
 
 # Add
@@ -461,7 +461,7 @@ for (template in all_templates) {
     main_flat_file_name <- "teaching"
   }
 
-  dummypackage4 <- tempfile(pattern = "all.templates.knit")
+  dummypackage4 <- tempfile(pattern = paste0("all.templates.knit", gsub("_", ".", template)))
   dir.create(dummypackage4)
 
   orig.proj <- here::here()

dev/flat_inflate_all.Rmd

@@ -194,7 +194,7 @@ inflate_all(stylers = styler::style_pkg)
 
 # You can also inflate_all flats of another package as follows
 # Example with a dummy package with a flat file
-dummypackage <- tempfile("inflateall")
+dummypackage <- tempfile("inflateall.otherpkg")
 dir.create(dummypackage)
 fill_description(pkg = dummypackage, fields = list(Title = "Dummy Package"))
 flat_files <- add_minimal_package(
@@ -241,7 +241,7 @@ unlink(dummypackage, recursive = TRUE)
 
 ```{r tests-inflate_all}
 # unlink(dummypackage, recursive = TRUE)
-dummypackage <- tempfile("inflateall")
+dummypackage <- tempfile("inflateall.first")
 dir.create(dummypackage)
 fill_description(pkg = dummypackage, fields = list(Title = "Dummy Package"))
 dev_file <- suppressMessages(add_minimal_package(pkg = dummypackage, overwrite = TRUE, open = FALSE))
@@ -484,7 +484,7 @@ unlink(dummypackage, recursive = TRUE)
 
 # You can also inflate_all flats of another package as follows
 # Example with a dummy package with a flat file
-dummypackage <- tempfile("inflateall")
+dummypackage <- tempfile("inflateall.other.pkg")
 dir.create(dummypackage)
 suppressMessages(fill_description(pkg = dummypackage, fields = list(Title = "Dummy Package")))
 flat_files <- add_minimal_package(
@@ -540,7 +540,7 @@ usethis::with_project(dummypackage, {
 unlink(dummypackage, recursive = TRUE)
 
 # Test inflate_all_no_check vs inflate_all with check ----
-dummypackage <- tempfile("inflateall")
+dummypackage <- tempfile("inflateall.nocheck")
 dir.create(dummypackage)
 suppressMessages(fill_description(pkg = dummypackage, fields = list(Title = "Dummy Package")))
 dev_file <- suppressMessages(add_minimal_package(pkg = dummypackage, overwrite = TRUE, open = FALSE))

dev/flat_register_config_file.Rmd

@@ -154,7 +154,7 @@ Have a look at the configuration file at the end of the process to check that ev
 #'
 #' @export
 check_not_registered_files <- function(path = ".", guess = TRUE, to_csv = TRUE, open = FALSE) {
-  path <- normalizePath(path, winslash = "/")
+  path <- normalize_path_winslash(path)
 
   all_r <- list.files(file.path(path, "R"), pattern = "[.]R$|[.]r$", full.names = TRUE)
   all_test <- list.files(file.path(path, "tests", "testthat"), pattern = "[.]R$|[.]r$", full.names = TRUE)
@@ -182,7 +182,7 @@ check_not_registered_files <- function(path = ".", guess = TRUE, to_csv = TRUE,
   if (file.exists(config_file)) {
     # Read config file, and remove those already there
     config_list <- yaml::read_yaml(config_file)
-    config_list_path <- normalizePath(get_list_paths(config_list), mustWork = FALSE, winslash = "/")
+    config_list_path <- normalize_path_winslash(get_list_paths(config_list), mustWork = FALSE)
     res_existing <- res[res$path %in% config_list_path, ]
     res_new <- res[!res$path %in% config_list_path, ]
     config_flat_paths <- sapply(config_list, function(x) x[["path"]])
@@ -217,11 +217,11 @@ check_not_registered_files <- function(path = ".", guess = TRUE, to_csv = TRUE,
   }
 
   # TODO go back to relative path
-  res_new$path <- gsub(paste0(getwd(), "/"), "", normalize_path_winslash(res_new$path, mustWork = TRUE), fixed = TRUE)
+  res_new$path <- gsub(paste0(normalize_path_winslash(getwd()), "/"), "", normalize_path_winslash(res_new$path, mustWork = TRUE), fixed = TRUE)
 
   # config_file may not exist already
   csv_file <- file.path(
-    gsub(paste0(getwd(), "/"), "", dirname(normalize_path_winslash(config_file, mustWork = FALSE)), fixed = TRUE), "config_not_registered.csv"
+    gsub(paste0(normalize_path_winslash(getwd()), "/"), "", dirname(normalize_path_winslash(config_file, mustWork = FALSE)), fixed = TRUE), "config_not_registered.csv"
   )
 
   # Save for manual modification
@@ -270,9 +270,12 @@ guess_flat_origin <- function(path) {
     lines[grep("(G|g)enerated by \\{fusen\\} from", lines)][1]
   )
 
-  guess_path <- normalizePath(guess_path, mustWork = FALSE, winslash = "/")
+  guess_path <- normalize_path_winslash(guess_path, mustWork = FALSE)
   if (file.exists(guess_path)) {
-    guess_path <- gsub(paste0(getwd(), "/"), "", normalizePath(guess_path, mustWork = FALSE, winslash = "/"))
+    guess_path <- gsub(
+      paste0(normalize_path_winslash(getwd()), "/"), "",
+      normalize_path_winslash(guess_path, mustWork = FALSE)
+    )
     return(guess_path)
   } else {
     return("No existing source path found.")
@@ -521,7 +524,7 @@ register_all_to_config <- function(pkg = ".") {
 
   # Delete out_df
   csv_file <- file.path(
-    gsub(paste0(getwd(), "/"), "", dirname(normalize_path_winslash(config_file, mustWork = FALSE)), fixed = TRUE), "config_not_registered.csv"
+    gsub(paste0(normalize_path_winslash(getwd()), "/"), "", dirname(normalize_path_winslash(config_file, mustWork = FALSE)), fixed = TRUE), "config_not_registered.csv"
   )
   if (file.exists(csv_file)) {
     cli::cat_rule(paste("Delete", csv_file))

tests/testthat/test-add_flat_template.R

@@ -182,7 +182,7 @@ for (template in all_templates) {
     main_flat_file_name <- "teaching"
   }
 
-  dummypackage4 <- tempfile(pattern = "all.templates.knit")
+  dummypackage4 <- tempfile(pattern = paste0("all.templates.knit", gsub("_", ".", template)))
   dir.create(dummypackage4)
 
   orig.proj <- here::here()

tests/testthat/test-inflate-part2.R

@@ -53,9 +53,9 @@ unlink(dummypackage, recursive = TRUE)
 alltemp <- tempfile("all.templates.inflate")
 dir.create(alltemp)
 
-# for (pkgname in c("full", "teaching", "minimal")) {
 create_choices_test <- fusen:::create_fusen_choices[!grepl("dev_history", fusen:::create_fusen_choices)]
 for (pkgname in create_choices_test) {
+  # pkgname <- create_choices_test[1]
   # No "additional" with create_fusen
   # {fusen} steps
   path_foosen <- normalize_path_winslash(file.path(alltemp, pkgname), mustWork = FALSE)
@@ -64,7 +64,7 @@ for (pkgname in create_choices_test) {
 
   usethis::with_project(path_foosen, {
     fill_description(pkg = path_foosen, fields = list(Title = "Dummy Package"))
-    usethis::use_gpl_license()
+    suppressMessages(usethis::use_gpl_license())
 
     test_that("description is good", {
       expect_true(file.exists(file.path(path_foosen, "DESCRIPTION")))
@@ -154,7 +154,9 @@ for (pkgname in create_choices_test) {
       skip_if_not(interactive())
       # Needs MASS, lattice, Matrix installed
       # quiet and checkdir
-      checkdir <- file.path(alltemp, paste0("checkout", pkgname))
+      checkdir <- normalize_path_winslash(
+        file.path(alltemp, paste0("checkout", pkgname)),
+        mustWork = FALSE)
       extra_params <- glue(
         'fusen::inflate(pkg = "{path_foosen}",
       check = TRUE, check_dir = "{checkdir}",