Merge branch 'main' of https://github.com/rostools/prodigenr

.Rbuildignore

@@ -15,3 +15,4 @@
 ^CRAN-RELEASE$
 ^\.github$
 ^CRAN-SUBMISSION$
+^justfile$

.github/PULL_REQUEST_TEMPLATE.md

@@ -4,19 +4,7 @@ These changes are for PURPOSE, because REASON.
 
 Closes #
 
-## Reviewer Focus
-
-This PR needs a quick/an in-depth review.
-
-Focus on CHANGES.
-
 ## Checklist
 
-- [ ] Ran `devtools::document()`
-- [ ] Ran `devtools::test()`
-- [ ] Ran `devtools::spell_check()`
-- [ ] Ran `styler::style_pkg()`
-- [ ] Ran `devtools::lint()`
-- [ ] Ran `devtools::build_site()`
-- [ ] Ran `devtools::check()`
+- [ ] Ran `just run-all`
 - [ ] If docs were added, Markdown is formatted

.github/workflows/assign-pr-to-creator.yml

@@ -0,0 +1,24 @@
+name: Assign PR to creator
+
+on:
+  pull_request: 
+    types:
+      - reopened
+      - opened
+
+permissions:
+  pull-requests: write
+
+jobs:
+  assign-pr-to-creator:
+    name: Assign PR to creator
+    runs-on: ubuntu-latest
+    steps:
+      - name: Assign PR to creator
+        if: ${{ github.event_name == 'pull_request' }}
+        run: |
+          gh pr edit $PR --add-assignee $AUTHOR
+        env:
+          AUTHOR: ${{ github.event.pull_request.user.login }}
+          PR: ${{ github.event.pull_request.html_url }}
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.lintr

@@ -0,0 +1,4 @@
+linters: linters_with_defaults(
+    line_length_linter(100),
+    commented_code_linter = NULL
+  )

DESCRIPTION

@@ -20,11 +20,11 @@ Imports:
     withr,
     rlang,
     cli,
-    whisker
+    whisker,
+    gert
 Suggests: 
     testthat,
-    knitr,
-    gert
+    knitr
 VignetteBuilder: knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

NEWS.md

@@ -8,6 +8,9 @@
     `usethis::use_blank_slate("project")` (#144).
 -   New projects have Git added from the beginning, so don't need to use
     `setup_with_git()` (#148).
+-   Move `gert` to imports, since it makes more sense that it should be
+    a hard dependency as the project is an opinionated project creator
+    (#145).
 
 ## Fixes and improvements
 
@@ -17,6 +20,9 @@
 -   The `title` field in the `DESCRIPTION` file is needed by many
     usethis functions, so it is added to the created `DESCRIPTION` file
     (#137).
+-   It isn't always useful to have the report created when the project
+    is setup, so adding the report via `create_report()` is removed from
+    `project_setup()` (#142).
 
 # prodigenr 0.6.2
 
@@ -130,3 +136,4 @@
 -   Added a `NEWS.md` file to track changes to the package.
 -   Fixed a bug that prevented an Rproj file and the Rprofile files from
     being installed and created.
+

R/rstudio_setup.R

@@ -1,6 +1,5 @@
-
 rstudio_setup <- function(path, ...) {
-    # create project
-    setup_project(path = path)
-    invisible(NULL)
+  # create project
+  setup_project(path = path)
+  invisible(NULL)
 }

R/setup_project.R

@@ -18,33 +18,36 @@
 #' setup_with_git()
 #' }
 setup_project <-
-    function(path) {
-        stopifnot(is.character(path))
-        proj_path <- fs::path_abs(path)
-        proj_name <- fs::path_file(proj_path)
+  function(path) {
+    stopifnot(is.character(path))
+    proj_path <- fs::path_abs(path)
+    proj_name <- fs::path_file(proj_path)
 
-        if (grepl(" ", basename(proj_path))) {
-            rlang::warn("Project name has a space in it, replacing with a dash (-).")
-            proj_path <- path_remove_spaces(proj_path)
-        }
+    if (grepl(" ", basename(proj_path))) {
+      rlang::warn("Project name has a space in it, replacing with a dash (-).")
+      proj_path <- path_remove_spaces(proj_path)
+    }
 
-        if (fs::dir_exists(proj_path)) {
-            cli::cli_abort(c("The {.val {proj_path}} folder already exists, so project creation is canceled.",
-                         "i" = "Delete the folder or use another name (not {.val {proj_name}}) for your project."))
-        }
-        proj_template <- find_template("projects", "basic-analysis")
-        fs::dir_copy(proj_template, new_path = proj_path)
+    if (fs::dir_exists(proj_path)) {
+      cli::cli_abort(c(
+        "The {.val {proj_path}} folder already exists, so project creation is canceled.",
+        "i" = "Delete the folder or use another name (not {.val {proj_name}}) for your project."
+      ))
+    }
+    proj_template <- find_template("projects", "basic-analysis")
+    fs::dir_copy(proj_template, new_path = proj_path)
 
-        withr::with_dir(
-            new = proj_path,
-            code = {
-                update_template("DESCRIPTION", data = list(ProjectName = proj_name))
-                update_template("template-Rproj", paste0(proj_name, ".Rproj"))
-                fs::file_delete("template-Rproj")
-                update_template("README.md", data = list(ProjectName = proj_name))
+    withr::with_dir(
+      new = proj_path,
+      code = {
+        update_template("DESCRIPTION", data = list(ProjectName = proj_name))
+        update_template("template-Rproj", paste0(proj_name, ".Rproj"))
+        fs::file_delete("template-Rproj")
+        update_template("README.md", data = list(ProjectName = proj_name))
         gert::git_init()
       }
-    }
+    )
+  }
 
 # Git setup functions -------------------------------------------
 
@@ -53,32 +56,27 @@ setup_project <-
 #' Takes a lot of inspiration from the usethis `use_git()` function, except
 #' it only adds Git and nothing more (doesn't commit, doesn't restart RStudio
 #' automatically). Must run this function inside the project you created from
-#' [setup_project()]
+#' [setup_project()].
 #'
 #' @return Adds Git and `.gitignore` file to the project.
 #' @export
 #' @seealso [setup_project()] for starting the project.
 #'
 setup_with_git <- function() {
-    if (!requireNamespace("gert", quietly = TRUE)) {
-        cli::cli_abort(
-            c("This function relies on the gert package, please install it and then run the function again.",
-              "i" = "Install with: {.code install.packages('gert')}")
-        )
-    }
-
-    if (!is_rproj_folder())
-        cli::cli_abort(c("The folder does not contain an {.val .Rproj} file.",
-                         "i" = "Please use this function while in the project created from {.code prodigenr::setup_project().}"))
+  if (!is_rproj_folder()) {
+    cli::cli_abort(c("The folder does not contain an {.val .Rproj} file.",
+      "i" = "Please use this function while in the project created from {.code prodigenr::setup_project().}"
+    ))
+  }
 
-    if (has_git()) {
-        rlang::abort("The project already has Git added.")
-    }
+  if (has_git()) {
+    rlang::abort("The project already has Git added.")
+  }
 
-    gert::git_init()
-    set_git_ignore_files()
-    cli::cli_alert_info("You'll need to restart RStudio to see the Git pane.")
-    return(invisible(NULL))
+  gert::git_init()
+  set_git_ignore_files()
+  cli::cli_alert_info("You might need to restart RStudio to see the Git pane.")
+  return(invisible(NULL))
 }
 
 # Utilities -----------------------------------------------------
@@ -91,8 +89,8 @@ set_git_ignore_files <- function() {
 }
 
 path_remove_spaces <- function(path) {
-    path_as_vector <- fs::path_split(path)[[1]]
-    last_dir <- length(path_as_vector)
-    path_as_vector[last_dir] <- gsub(" +", "-", path_as_vector[last_dir])
-    fs::path_join(path_as_vector)
+  path_as_vector <- fs::path_split(path)[[1]]
+  last_dir <- length(path_as_vector)
+  path_as_vector[last_dir] <- gsub(" +", "-", path_as_vector[last_dir])
+  fs::path_join(path_as_vector)
 }

R/usethis-utils.R

@@ -12,7 +12,7 @@
 # copies of the Software, and to permit persons to whom the Software is
 # furnished to do so, subject to the following conditions:
 #
-#     The above copyright notice and this permission notice shall be included in all
+# The above copyright notice and this permission notice shall be included in all
 # copies or substantial portions of the Software.
 #
 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
@@ -27,25 +27,27 @@
 update_template <- function(template,
                             save_as = template,
                             data = list()) {
-    template_contents <-
-        base::strsplit(whisker::whisker.render(read_utf8(template),
-                                               data), "\n")[[1]]
-    new <- base::writeLines(template_contents, save_as)
-    invisible(new)
+  template_contents <-
+    base::strsplit(whisker::whisker.render(
+      read_utf8(template),
+      data
+    ), "\n")[[1]]
+  new <- base::writeLines(template_contents, save_as)
+  invisible(new)
 }
 
 # Taken from usethis package and modified to this package.
 find_template <- function(...) {
-    fs::path_package(package = "prodigenr", "templates", ...)
+  fs::path_package(package = "prodigenr", "templates", ...)
 }
 
 # Taken from usethis package
 read_utf8 <- function(path, n = -1L) {
-    base::readLines(path, n = n, encoding = "UTF-8", warn = FALSE)
+  base::readLines(path, n = n, encoding = "UTF-8", warn = FALSE)
 }
 
 # Taken from usethis:::uses_git
 has_git <- function(project_path = ".") {
-    repo <- tryCatch(gert::git_find(project_path), error = function(e) NULL)
-    !is.null(repo)
+  repo <- tryCatch(gert::git_find(project_path), error = function(e) NULL)
+  !is.null(repo)
 }

R/utils.R

@@ -1,8 +1,9 @@
 is_rproj_folder <- function() {
-    rprojroot::is.root_criterion(rprojroot::is_rstudio_project)
+  rprojroot::is.root_criterion(rprojroot::is_rstudio_project)
 }
 
 viz_project_tree <- function(path) {
-    withr::with_dir(fs::path_dir(path),
-                    {fs::dir_tree(basename(path), all = TRUE)})
+  withr::with_dir(fs::path_dir(path), {
+    fs::dir_tree(basename(path), all = TRUE)
+  })
 }

README.Rmd

@@ -13,7 +13,7 @@ knitr::opts_chunk$set(
 )
 ```
 
-# Project creation with prodigenr: A component of reproducible and open scientific projects <img src="man/figures/logo.png" style="text-align: right;"/>
+# Create projects with prodigenr <img src="man/figures/logo.png" style="text-align: right;" width="70"/>
 
 <!-- badges: start -->
 

README.md

@@ -1,7 +1,7 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# Project creation with prodigenr: A component of reproducible and open scientific projects <img src="man/figures/logo.png" style="text-align: right;"/>
+# Create projects with prodigenr <img src="man/figures/logo.png" style="text-align: right;" width="70"/>
 
 <!-- badges: start -->
 

justfile

@@ -1,32 +1,51 @@
-# These are for admin tasks that really only need to be done once or twice
-
 @_default:
-  just --list --unsorted
+    just --list --unsorted
 
-# Run build recipes and install the package
-build: style document test install-package check
+# Run all recipes
+run-all: install-package-dependencies document spell-check style lint test build-site check install-package
 
-# Install the package and its dependencies
-install-package:
+# Install package dependencies
+install-package-dependencies:
   #!/usr/bin/Rscript
-  devtools::install()
+  pak::pak(ask = FALSE)
+
+# Run document generators
+document: 
+  #!/usr/bin/Rscript
+  devtools::document()
 
 # Run tests
-test:
+test: 
   #!/usr/bin/Rscript
   devtools::test()
 
-# Re-build Roxygen docs
-document:
+# Check spelling
+spell-check: 
   #!/usr/bin/Rscript
-  devtools::document()
+  devtools::spell_check()
 
-# Run style formatter
-style:
+# Style all R code
+style: 
   #!/usr/bin/Rscript
   styler::style_pkg()
 
-# Run CRAN check
+# Run linter
+lint: 
+  #!/usr/bin/Rscript
+  devtools::lint(
+  )
+
+# Build pkgdown website
+build-site: 
+  #!/usr/bin/Rscript
+  devtools::build_site()
+
+# Run local CRAN checks
 check:
   #!/usr/bin/Rscript
   devtools::check()
+
+# Install prodigenr as a package
+install-package: install-package-dependencies
+  #!/usr/bin/Rscript
+  devtools::install()

prodigenr.Rproj

@@ -6,7 +6,7 @@ AlwaysSaveHistory: No
 
 EnableCodeIndexing: Yes
 UseSpacesForTab: Yes
-NumSpacesForTab: 4
+NumSpacesForTab: 2
 Encoding: UTF-8
 
 RnwWeave: knitr
@@ -19,3 +19,9 @@ BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
 PackageRoxygenize: rd,collate,namespace,vignette
+
+UseNativePipeOperator: Yes
+
+MarkdownWrap: Column
+MarkdownWrapAtColumn: 72
+MarkdownCanonical: Yes