Merge pull request #272 from ThinkR-open/main-268

Fix linting errors in generated R files and bump version to 0.6.0.9005
ThinkR-open · Jan 30, 2025 · 062ca6a · 062ca6a
2 parents 1048139 + 56129e4
commit 062ca6a
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diff --git a/.github/workflows/R-CMD-check-devel.yaml b/.github/workflows/R-CMD-check-devel.yaml
@@ -54,19 +54,6 @@ jobs:
           remotes::install_github("ThinkR-open/lightparser", upgrade = "always")
         shell: Rscript {0}
 
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
-
       - name: Setup tmate session
         uses: mxschmitt/action-tmate@v3
         if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }} # Works on 'main' only

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, production-cran]
+    branches: [main, master, production-cran, main-268-test_x86]
   pull_request:
     branches: [main, master, production-cran]
 
@@ -23,6 +23,7 @@ jobs:
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: macos-13,   r: 'release'} #x86_64
           # - {os: ubuntu-20.04,   r: '3.6'}
           # - {os: ubuntu-20.04,   r: '3.5'} # with usethis >2.2
 

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,10 +1,12 @@
 Package: fusen
 Title: Build a Package from Rmarkdown Files
-Version: 0.6.0.9004
+Version: 0.7.1
 Authors@R: c(
-    person("Sebastien", "Rochette", , "[email protected]", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0002-1565-9313")),
-    person("Yohann", "Mansiaux", , "[email protected]", role = "aut"),
+    person("Sebastien", "Rochette", , "[email protected]", role = "aut",
+           comment = c(ORCID = "0000-0002-1565-9313", "creator")),
+    person("Vincent", "Guyader", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0003-0671-9270")),
+    person("Yohann", "Mansiaux", , "[email protected]", role = "aut"),
     person("ThinkR", role = "cph")
   )
 Description: Use Rmarkdown First method to build your package. Start your
@@ -50,7 +52,7 @@ Suggests:
     withr
 VignetteBuilder: 
     knitr
-Config/fusen/version: 0.6.0.9004
+Config/fusen/version: 0.7.0
 Config/testthat/edition: 3
 Config/testthat/parallel: false
 Encoding: UTF-8

diff --git a/NEWS.md b/NEWS.md
@@ -1,21 +1,24 @@
-# fusen (development version 0.6.0.9003)
+# fusen 0.7.1
 
-## New features
+## Bug fix
 
-- `inflate` and `inflate_all()` proposes to compute the package code coverage using `covr::package_coverage()` using the `codecov` parameter (default is FALSE)
+- Skip some tests on MacOS on CRAN to avoid errors
 
-# fusen (development version 0.6.0.9002)
+# fusen 0.7.0
 
 ## New features
 
+- Adding `sepuku()`, allowing to remove all traces of a fusen-related files and tags in the package (#257 #258 #259) @ymansiaux
+- `inflate` and `inflate_all()` proposes to compute the package code coverage using `covr::package_coverage()` using the `codecov` parameter (default is FALSE)
 - RStudio Addin "Fusen : Add fusen chunks" as well as `fusen::add_fusen_chunks()` add a development chunk in complement to the "function", "example" and "test" chunks already provided (#255) @ymansiaux
 
+## Minor changes
 
-# fusen (development version 0.6.0.9001)
+- Add `# nolint: line_length_linter` in created files to avoid line length linter warnings (#278) @LBeaulaton
 
-## New features
+## Bug fixes
 
-- Adding `sepuku()`, allowing to remove all traces of a fusen-related files and tags in the package (#257 #258 #259) @ymansiaux
+- Fix `grep()` calls in unit tests (#271) @statnmap
 
 # fusen 0.6.0
 

diff --git a/R/add_flat_template.R b/R/add_flat_template.R
@@ -1,4 +1,4 @@
-# WARNING - Generated by {fusen} from dev/flat_create_flat.Rmd: do not edit by hand
+# WARNING - Generated by {fusen} from dev/flat_create_flat.Rmd: do not edit by hand # nolint: line_length_linter.
 
 #' @rdname add_flat_template
 #' @export

diff --git a/R/build_fusen_chunks.R b/R/build_fusen_chunks.R
@@ -1,4 +1,4 @@
-# WARNING - Generated by {fusen} from dev/flat_addins.Rmd: do not edit by hand
+# WARNING - Generated by {fusen} from dev/flat_addins.Rmd: do not edit by hand # nolint: line_length_linter.
 
 #' Add 'fusen' chunks
 #'

diff --git a/R/deprecate_flat_file.R b/R/deprecate_flat_file.R
@@ -1,4 +1,4 @@
-# WARNING - Generated by {fusen} from dev/flat_deal_with_flat_files.Rmd: do not edit by hand
+# WARNING - Generated by {fusen} from dev/flat_deal_with_flat_files.Rmd: do not edit by hand # nolint: line_length_linter.
 
 #' Deprecate a flat file
 #'

diff --git a/R/get_all_created_funs.R b/R/get_all_created_funs.R
@@ -1,4 +1,4 @@
-# WARNING - Generated by {fusen} from dev/flat_get_package_structure.Rmd: do not edit by hand
+# WARNING - Generated by {fusen} from dev/flat_get_package_structure.Rmd: do not edit by hand # nolint: line_length_linter.
 
 #' Get all functions created in a R file
 #'

diff --git a/R/get_package_structure.R b/R/get_package_structure.R
@@ -1,4 +1,4 @@
-# WARNING - Generated by {fusen} from dev/flat_get_package_structure.Rmd: do not edit by hand
+# WARNING - Generated by {fusen} from dev/flat_get_package_structure.Rmd: do not edit by hand # nolint: line_length_linter.
 
 #' Get structure and information of a 'fusen' built package for developers
 #'

diff --git a/R/inflate-utils.R b/R/inflate-utils.R
@@ -284,7 +284,7 @@ parse_test <- function(x, pkg, relative_flat_file) { # x <- rmd_test[1,]
   }
 
   lines <- c(
-    sprintf("# WARNING - Generated by {fusen} from %s: do not edit by hand\n", relative_flat_file),
+    sprintf("# WARNING - Generated by {fusen} from %s: do not edit by hand # nolint: line_length_linter.\n", relative_flat_file),
     x[["code"]][[1]]
   )
   write_utf8(path = test_file, lines = lines)

diff --git a/R/inflate.R b/R/inflate.R
@@ -547,7 +547,7 @@ create_r_files <- function(fun_code, pkg, relative_flat_file) {
       cli::cli_alert_warning(paste(basename(r_file), "has been overwritten"))
     }
     lines <- c(
-      sprintf("# WARNING - Generated by {fusen} from %s: do not edit by hand\n", relative_flat_file),
+      sprintf("# WARNING - Generated by {fusen} from %s: do not edit by hand # nolint: line_length_linter.\n", relative_flat_file),
       unlist(fun_code[x, ][["code_example"]])
     )
     write_utf8(path = r_file, lines = lines)

diff --git a/R/inflate_all.R b/R/inflate_all.R
@@ -1,4 +1,4 @@
-# WARNING - Generated by {fusen} from dev/flat_inflate_all.Rmd: do not edit by hand
+# WARNING - Generated by {fusen} from dev/flat_inflate_all.Rmd: do not edit by hand # nolint: line_length_linter.
 
 #' Inflate all your flat files
 #'

diff --git a/R/inflate_all_utils.R b/R/inflate_all_utils.R
@@ -1,4 +1,4 @@
-# WARNING - Generated by {fusen} from dev/flat_inflate_all_utils.Rmd: do not edit by hand
+# WARNING - Generated by {fusen} from dev/flat_inflate_all_utils.Rmd: do not edit by hand # nolint: line_length_linter.
 
 #' This function evaluates whether flat files can or can not be inflated with `inflate_all()`
 #'

diff --git a/R/init_share_on_github.R b/R/init_share_on_github.R
@@ -1,4 +1,4 @@
-# WARNING - Generated by {fusen} from dev/flat_init_share_on_github.Rmd: do not edit by hand
+# WARNING - Generated by {fusen} from dev/flat_init_share_on_github.Rmd: do not edit by hand # nolint: line_length_linter.
 
 #' Initiate GitHub to share your package on a website
 #'

diff --git a/R/pre_inflate_all_diagnosis_eval.R b/R/pre_inflate_all_diagnosis_eval.R
@@ -1,4 +1,4 @@
-# WARNING - Generated by {fusen} from dev/flat_inflate_all_utils.Rmd: do not edit by hand
+# WARNING - Generated by {fusen} from dev/flat_inflate_all_utils.Rmd: do not edit by hand # nolint: line_length_linter.
 
 #' Eval message, warning and error from the diagnostic table
 #'

diff --git a/R/register_config_file.R b/R/register_config_file.R
@@ -1,4 +1,4 @@
-# WARNING - Generated by {fusen} from dev/flat_register_config_file.Rmd: do not edit by hand
+# WARNING - Generated by {fusen} from dev/flat_register_config_file.Rmd: do not edit by hand # nolint: line_length_linter.
 
 #' Show in a table files that are not already registered in the yaml config file
 #'

diff --git a/R/rename_flat_file.R b/R/rename_flat_file.R
@@ -1,4 +1,4 @@
-# WARNING - Generated by {fusen} from dev/flat_deal_with_flat_files.Rmd: do not edit by hand
+# WARNING - Generated by {fusen} from dev/flat_deal_with_flat_files.Rmd: do not edit by hand # nolint: line_length_linter.
 
 #' Rename a flat file
 #'

diff --git a/R/sepuku.R b/R/sepuku.R
@@ -1,8 +1,8 @@
-# WARNING - Generated by {fusen} from dev/flat_sepuku.Rmd: do not edit by hand
+# WARNING - Generated by {fusen} from dev/flat_sepuku.Rmd: do not edit by hand # nolint: line_length_linter.
 
 #' Clean a package from fusen-related files and tags
 #'
-#' This function will delete all the flat files (i.e files listed in the fusen configuration file, as well as rmd or qmd files starting with "flat" in the "dev/" and "dev/flat_history" folders). It will also remove the fusen-related tags added by calls to `fusen::inflate()` in files located in the "R/", "tests/" and "vignettes/" folders. Finally, it will also remove the fusen configuration file if it exists.
+#' This function will delete all the flat files (i.e files listed in the fusen configuration file, as well as Rmd or qmd files starting with "flat" in the "dev/" and "dev/flat_history" folders). It will also remove the fusen-related tags added by calls to `fusen::inflate()` in files located in the "R/", "tests/" and "vignettes/" folders. Finally, it will also remove the fusen configuration file if it exists.
 #'
 #' @param pkg Character. Path of the current package
 #' @param force logical. whether to force the cleaning or not, without asking if the user is sure about making this operation (default: FALSE)
@@ -127,9 +127,9 @@ sepuku <- function(
   config_file <- getOption("fusen.config_file", default = "dev/config_fusen.yaml")
 
   if (!file.exists(config_file)) {
-    cli_alert_info("No fusen configuration file found. The flat files to be deleted will be identified as rmd or qmd files starting with 'flat' in the dev/ and dev/flat_history folders.")
+    cli_alert_info("No fusen configuration file found. The flat files to be deleted will be identified as Rmd or qmd files starting with 'flat' in the dev/ and dev/flat_history folders.")
   } else {
-    cli_alert_info("A fusen configuration file was found. The flat files to be deleted will be identified as files listed in this configuration file as well as rmd or qmd files starting with 'flat' in the dev/ and dev/flat_history folders. The configuration file will also be deleted.")
+    cli_alert_info("A fusen configuration file was found. The flat files to be deleted will be identified as files listed in this configuration file as well as Rmd or qmd files starting with 'flat' in the dev/ and dev/flat_history folders. The configuration file will also be deleted.")
   }
 
   flat_files <- list_flat_files(pkg = pkg)

diff --git a/R/sepuku_utils.R b/R/sepuku_utils.R
@@ -1,4 +1,4 @@
-# WARNING - Generated by {fusen} from dev/flat_sepuku-utils.Rmd: do not edit by hand
+# WARNING - Generated by {fusen} from dev/flat_sepuku-utils.Rmd: do not edit by hand # nolint: line_length_linter.
 
 #' @importFrom yaml read_yaml
 #' @noRd
@@ -49,7 +49,7 @@ list_flat_files_in_dev_folder <- function(
 
 #' List all flat files present in the package
 #'
-#' Search for flat files listed in fusen config file, and for rmd and qmd files starting with "flat_" in dev/ folder, and dev/flat_history folder
+#' Search for flat files listed in fusen config file, and for Rmd and qmd files starting with "flat_" in dev/ folder, and dev/flat_history folder
 #'
 #' @param pkg Path to package
 #' @return a vector of flat files paths

diff --git a/README.Rmd b/README.Rmd
@@ -140,7 +140,7 @@ _Note that the `"flat*.Rmd"` files created with templates `full` and `teaching`
 There is a dedicated vignette to answer this: https://thinkr-open.github.io/fusen/articles/Maintain-packages-with-fusen.html
 
 - **Option 1**: After a first inflate of your flat file, you can continue developing in the "flat_template.Rmd" file, and then inflate it using `fusen::inflate_all()`
-- **Option 2**: After you're done with inflating, you can decide to deprecate your flat file with `fusen::deprecate_flat_file()` and develop in the package files directly, as for any other R package. 'fusen' has no impact on the structure of a classical package once inflated.
+- **Option 2**: After you're done with inflating, you can decide to deprecate your flat file with `fusen::deprecate_flat_file()` and develop in the package files directly, as for any other R package. 'fusen' has no impact on the structure of a classical package once inflated. You can even use `sepuku()` to remove all traces of 'fusen'.
 
 > Advice: Use git as soon as possible, this will avoid losing your work if you made some modifications in the wrong place
 
@@ -175,6 +175,7 @@ Write them all in the same file while you explore the possibilities and let {fus
 - Can I inflate a Quarto qmd file?
 - Can I use {fusen} with {golem}?
 - How can I know if R files were created from a flat or not ?
+- How can I get rid of everything related to 'fusen' in my package ?
 
 => See vignette Tips and Tricks: https://thinkr-open.github.io/fusen/articles/tips-and-tricks.html
 

diff --git a/README.md b/README.md
@@ -1,6 +1,5 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
-
 <!-- badges: start -->
 
 [![fusen status
@@ -174,7 +173,7 @@ There is a dedicated vignette to answer this:
   deprecate your flat file with `fusen::deprecate_flat_file()` and
   develop in the package files directly, as for any other R package.
   ‘fusen’ has no impact on the structure of a classical package once
-  inflated.
+  inflated. You can even use `sepuku()` to remove all traces of ‘fusen’.
 
 > Advice: Use git as soon as possible, this will avoid losing your work
 > if you made some modifications in the wrong place
@@ -233,6 +232,7 @@ place.
 - Can I inflate a Quarto qmd file?
 - Can I use {fusen} with {golem}?
 - How can I know if R files were created from a flat or not ?
+- How can I get rid of everything related to ‘fusen’ in my package ?
 
 =\> See vignette Tips and Tricks:
 <https://thinkr-open.github.io/fusen/articles/tips-and-tricks.html>
@@ -250,12 +250,9 @@ in a specific way so that at the end, you can magically `inflate()` it
 to let a nice package appear.
 
 <details>
-
 <summary>
-
 Click here to fold your {fusen}…
 </summary>
-
 <img src="man/figures/fusen-fold-origami.gif" />
 </details>
 

diff --git a/dev/cran-comments-history.md b/dev/cran-comments-history.md
@@ -1,11 +1,34 @@
+# v0.7.1
+## R CMD check results
+
+A new error appeared on CRAN for x86-64 MacOS architecture after the release of v0.7.0
+The present release fixes the problem
+
+0 errors | 0 warnings | 0 note
+
+* OK on GitHub Actions, rhub, winbuilder and macbuilder
+* Fixes error on CRAN checks: "DESCRIPTION file does not exist"
+
+# v0.7.0
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* Maintainer was changed for Vincent Guyader, instead Sébastien Rochette.
+* OK on GitHub Actions, rhub, winbuilder and macbuilder
+* Fixes error on CRAN checks: "invalid regular expression"
+
+
+
+
 # v0.6.0
 ## R CMD check results
 
 0 errors | 0 warnings | 1 note
 
 * Maintainer email was changed for my personal address, instead of my professional one.
 * OK on GitHub Actions, rhub, winbuilder and macbuilder
-
+* Fixes notes on CRAN checks: "Lost braces; missing escapes or markup?"
 
 # v0.5.2
 ## R CMD check results

diff --git a/dev/flat_create_flat.Rmd b/dev/flat_create_flat.Rmd
@@ -4,7 +4,7 @@ output: html_document
 editor_options: 
   chunk_output_type: console
 inflate:
-    state: deprecated?
+    state: active
 ---
 
 ```{r development, include=FALSE}
@@ -632,6 +632,7 @@ for (template in all_templates) {
     expect_true(sum(grepl(paste0("fusen::inflate\\(flat_file = \"dev/flat_", main_flat_file_name, ".Rmd\""), flat_lines)) == 1)
 
     withr::with_dir(dummypackage4, {
+      skip_on_os(os = "mac", arch = "x86_64")
       inflate_command <- paste0("fusen::inflate(flat_file = \"dev/flat_", main_flat_file_name, ".Rmd\", open_vignette = FALSE, check = FALSE)")
       expect_error(suppressMessages(eval(parse(text = inflate_command))), regexp = NA)
     })
@@ -640,6 +641,7 @@ for (template in all_templates) {
   # Now try to inflates a second time
   test_that("flat file inflates a second time", {
     withr::with_dir(dummypackage4, {
+      skip_on_os(os = "mac", arch = "x86_64")
       inflate_command_second <- paste0("fusen::inflate(flat_file = \"dev/flat_", main_flat_file_name, ".Rmd\", open_vignette = FALSE, check = FALSE, overwrite = TRUE)")
       expect_error(suppressMessages(eval(parse(text = inflate_command_second))), regexp = NA)
     })

diff --git a/dev/flat_deal_with_flat_files.Rmd b/dev/flat_deal_with_flat_files.Rmd
@@ -348,7 +348,7 @@ usethis::with_project(dummypackage, {
 
 ## Fully deprecate a flat file after inflate
 
-'fusen' serves as a framework to ensure that developers prioritize end-users during the function development process. By employing 'fusen' within Rmd/Qmd files, developers can conceptualize their product and articulate their ideas in plain text before initiating any code. This approach encourages consideration of the package's users: their intended actions, and the potential impact on their experiences. Consequently, developers can draft function documentation prior to its implementation, thinking about explaining what's behind the black box, as well as reminding that this may end into the vignette.
+'fusen' serves as a framework to ensure that developers prioritize end-users during the function development process. By employing 'fusen' within Rmd/qmd files, developers can conceptualize their product and articulate their ideas in plain text before initiating any code. This approach encourages consideration of the package's users: their intended actions, and the potential impact on their experiences. Consequently, developers can draft function documentation prior to its implementation, thinking about explaining what's behind the black box, as well as reminding that this may end into the vignette.
 
 Additionally, 'fusen' offers a minimal template comprising 'function', 'doc', and 'test' components. We advocate for Test Driven Development (TDD), where writing tests precedes function implementation. This practice aids in function design and enables anticipation of future behavior.
 

diff --git a/dev/flat_sepuku-utils.Rmd b/dev/flat_sepuku-utils.Rmd
@@ -165,7 +165,7 @@ usethis::with_project(dummypackage, {
   # Add licence
   usethis::use_mit_license("John Doe")
 
-  test_that("list_flat_files_in_dev_folder works for rmd and qmd files in dev folder starting with flat", {
+  test_that("list_flat_files_in_dev_folder works for Rmd and qmd files in dev folder starting with flat", {
     flat_file_with_bad_name <- "xxx_flat2.Rmd"
     file.create(file.path(dummypackage, "dev", flat_file_with_bad_name))
 
@@ -191,7 +191,7 @@ usethis::with_project(dummypackage, {
     )
   })
 
-  test_that("list_flat_files_in_dev_folder works for rmd and qmd files in flat_history folder starting with flat", {
+  test_that("list_flat_files_in_dev_folder works for Rmd and qmd files in flat_history folder starting with flat", {
     inflate(
       pkg = dummypackage,
       flat_file = flat_file1,
@@ -240,7 +240,7 @@ unlink(dummypackage, recursive = TRUE)
 ```{r function-list_flat_files}
 #' List all flat files present in the package
 #'
-#' Search for flat files listed in fusen config file, and for rmd and qmd files starting with "flat_" in dev/ folder, and dev/flat_history folder
+#' Search for flat files listed in fusen config file, and for Rmd and qmd files starting with "flat_" in dev/ folder, and dev/flat_history folder
 #'
 #' @param pkg Path to package
 #' @return a vector of flat files paths