Utilize usethis::proj_set() instead of usethis::local_project()

Second time writing this commit message since it got lost the first time =( I'm now writing this commit on a text editor window just to be safe. I see that `usethis::local_project()` runs `usethis::proj_set()` twice: first for the new `path`, then inside a `withr::defer()` call that restores the original path. I don't fully understand `withr::defer()`, but it seems to be triggered earlier that I would like it to. That's why I'm seeing on the README, some examples, and the vignette after r-lib/usethis#1108 (comment) paths that are not the one I expected (the one equivalent to `file.path(tempdir(), "biocthisexample")`). One option would be to rely on `usethis::with_project()` to get a similar behavior to what I had with `withr::with_dir()`, however like Jenny Bryan point out, this makes the code confusing for a new user to understand. That's why it seems to me that `usethis::proj_set()` is the better option to use in the examples, README and vignette code. I'm also now using a second example package name in the vignette to avoid clashing with the examples. The code doesn't overwrite the files by default, so if you run the code with the same example twice you don't get to see the output messages the second time.
lcolladotor · May 10, 2020 · dc38780 · jennybc · May 11, 2020 · lcolladotor
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diff --git a/R/bioc_style.R b/R/bioc_style.R
@@ -44,8 +44,8 @@
 #' ## Create the example package in a temporary location
 #' usethis::create_package(pkgdir)
 #'
-#' ## Set a local project to work with for the examples
-#' usethis::local_project(pkgdir)
+#' ## Set the project to use for the examples
+#' usethis::proj_set(pkgdir)
 #'
 #' ## Automatically style the example package
 #' styler::style_pkg(pkgdir, transformers = biocthis::bioc_style())

diff --git a/R/use_bioc_citation.R b/R/use_bioc_citation.R
@@ -25,8 +25,8 @@
 #' ## Create the example package in a temporary location
 #' usethis::create_package(pkgdir)
 #'
-#' ## Set a local project to work with for the examples
-#' usethis::local_project(pkgdir)
+#' ## Set the project to use for the examples
+#' usethis::proj_set(pkgdir)
 #'
 #' ## Create a template CITATION file that is Bioconductor-friendly
 #' biocthis::use_bioc_citation()

diff --git a/R/use_bioc_description.R b/R/use_bioc_description.R
@@ -35,8 +35,8 @@
 #' ## Create the example package in a temporary location
 #' usethis::create_package(pkgdir)
 #'
-#' ## Set a local project to work with for the examples
-#' usethis::local_project(pkgdir)
+#' ## Set the project to use for the examples
+#' usethis::proj_set(pkgdir)
 #'
 #' ## Setup up git
 #' usethis::use_git()

diff --git a/R/use_bioc_github_action.R b/R/use_bioc_github_action.R
@@ -36,8 +36,8 @@
 #' ## Create the example package in a temporary location
 #' usethis::create_package(pkgdir)
 #'
-#' ## Set a local project to work with for the examples
-#' usethis::local_project(pkgdir)
+#' ## Set the project to use for the examples
+#' usethis::proj_set(pkgdir)
 #'
 #' ## Create a GitHub Actions workflow that is Bioconductor-friendly
 #' biocthis::use_bioc_github_action()

diff --git a/R/use_bioc_issue_template.R b/R/use_bioc_issue_template.R
@@ -25,8 +25,8 @@
 #' ## Create the example package in a temporary location
 #' usethis::create_package(pkgdir)
 #'
-#' ## Set a local project to work with for the examples
-#' usethis::local_project(pkgdir)
+#' ## Set the project to use for the examples
+#' usethis::proj_set(pkgdir)
 #'
 #' ## Create a template GitHub issue file that is Bioconductor-friendly
 #' biocthis::use_bioc_issue_template()

diff --git a/R/use_bioc_news_md.R b/R/use_bioc_news_md.R
@@ -27,8 +27,8 @@
 #' ## Create the example package in a temporary location
 #' usethis::create_package(pkgdir)
 #'
-#' ## Set a local project to work with for the examples
-#' usethis::local_project(pkgdir)
+#' ## Set the project to use for the examples
+#' usethis::proj_set(pkgdir)
 #'
 #' ## Create a template NEWS.md file that is Bioconductor-friendly
 #' biocthis::use_bioc_news_md()

diff --git a/R/use_bioc_pkg_templates.R b/R/use_bioc_pkg_templates.R
@@ -41,8 +41,8 @@
 #' ## Create the example package in a temporary location
 #' usethis::create_package(pkgdir)
 #'
-#' ## Set a local project to work with for the examples
-#' usethis::local_project(pkgdir)
+#' ## Set the project to use for the examples
+#' usethis::proj_set(pkgdir)
 #'
 #' ## Create the biocthis templates
 #' biocthis::use_bioc_pkg_templates()

diff --git a/R/use_bioc_readme_rmd.R b/R/use_bioc_readme_rmd.R
@@ -30,8 +30,8 @@
 #' ## Create the example package in a temporary location
 #' usethis::create_package(pkgdir)
 #'
-#' ## Set a local project to work with for the examples
-#' usethis::local_project(pkgdir)
+#' ## Set the project to use for the examples
+#' usethis::proj_set(pkgdir)
 #'
 #' ## Setup up git
 #' usethis::use_git()

diff --git a/R/use_bioc_support.R b/R/use_bioc_support.R
@@ -25,8 +25,8 @@
 #' ## Create the example package in a temporary location
 #' usethis::create_package(pkgdir)
 #'
-#' ## Set a local project to work with for the examples
-#' usethis::local_project(pkgdir)
+#' ## Set the project to use for the examples
+#' usethis::proj_set(pkgdir)
 #'
 #' ## Create a template GitHub support file that is Bioconductor-friendly
 #' biocthis::use_bioc_support()

diff --git a/R/use_bioc_vignette.R b/R/use_bioc_vignette.R
@@ -33,8 +33,8 @@
 #' ## Create the example package in a temporary location
 #' usethis::create_package(pkgdir)
 #'
-#' ## Set a local project to work with for the examples
-#' usethis::local_project(pkgdir)
+#' ## Set the project to use for the examples
+#' usethis::proj_set(pkgdir)
 #'
 #' ## Create a template vignette file that is Bioconductor-friendly
 #' biocthis::use_bioc_vignette("biocthisexample", "Introduction to biocthisexample")

diff --git a/README.Rmd b/README.Rmd
@@ -61,8 +61,8 @@ pkgdir <- file.path(tempdir(), "biocthisexample")
 ## Create the example package in a temporary location
 usethis::create_package(pkgdir)
 
-## Set a local project to work with for the examples
-usethis::local_project(pkgdir)
+## Set the project to use for the examples
+usethis::proj_set(pkgdir)
 
 ## Create the bioc templates
 biocthis::use_bioc_pkg_templates()

diff --git a/README.md b/README.md
@@ -80,8 +80,8 @@ pkgdir <- file.path(tempdir(), "biocthisexample")
 
 ## Create the example package in a temporary location
 usethis::create_package(pkgdir)
-#> ✓ Creating '/var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T/RtmpSxZy15/biocthisexample/'
-#> ✓ Setting active project to '/private/var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T/RtmpSxZy15/biocthisexample'
+#> ✓ Creating '/var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T/RtmpPXAtNQ/biocthisexample/'
+#> ✓ Setting active project to '/private/var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T/RtmpPXAtNQ/biocthisexample'
 #> ✓ Creating 'R/'
 #> ✓ Writing 'DESCRIPTION'
 #> Package: biocthisexample
@@ -99,14 +99,18 @@ usethis::create_package(pkgdir)
 #> ✓ Writing 'NAMESPACE'
 #> ✓ Setting active project to '<no active project>'
 
-## Set a local project to work with for the examples
-usethis::local_project(pkgdir)
-#> ✓ Setting active project to '/private/var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T/RtmpSxZy15/biocthisexample'
-#> ✓ Setting active project to '<no active project>'
+## Set the project to use for the examples
+usethis::proj_set(pkgdir)
+#> ✓ Setting active project to '/private/var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T/RtmpPXAtNQ/biocthisexample'
 
 ## Create the bioc templates
 biocthis::use_bioc_pkg_templates()
-#> ✓ Setting active project to '/Users/lcollado/Dropbox/Code/biocthis'
+#> ✓ Creating 'dev/'
+#> ✓ Adding '^dev$' to '.Rbuildignore'
+#> ✓ Writing 'dev/01_create_pkg.R'
+#> ✓ Writing 'dev/02_git_github_setup.R'
+#> ✓ Writing 'dev/03_core_files.R'
+#> ✓ Writing 'dev/04_update.R'
 ```
 
 The template `dev` scripts include comments and steps you can follow for
@@ -120,12 +124,18 @@ subject](https://www.jimhester.com/talk/2020-rsc-github-actions/).
 ``` r
 ## Create a GitHub Actions workflow that is Bioconductor-friendly
 biocthis::use_bioc_github_action()
+#> ✓ Creating '.github/'
+#> ✓ Adding '^\\.github$' to '.Rbuildignore'
+#> ✓ Adding '*.html' to '.github/.gitignore'
+#> ✓ Creating '.github/workflows/'
+#> ✓ Writing '.github/workflows/check-bioc.yml'
 ```
 
 ``` r
 ## Alternatively, use the general GitHub Actions workflow maintained by
 ## r-lib/actions
 usethis::use_github_action("check-standard")
+#> ✓ Writing '.github/workflows/check-standard.yaml'
 
 ## Or use the biocthis GHA workflow without having to install biocthis
 usethis::use_github_action(

diff --git a/man/bioc_style.Rd b/man/bioc_style.Rd
diff --git a/man/use_bioc_citation.Rd b/man/use_bioc_citation.Rd
diff --git a/man/use_bioc_description.Rd b/man/use_bioc_description.Rd
diff --git a/man/use_bioc_github_action.Rd b/man/use_bioc_github_action.Rd
diff --git a/man/use_bioc_issue_template.Rd b/man/use_bioc_issue_template.Rd
diff --git a/man/use_bioc_news_md.Rd b/man/use_bioc_news_md.Rd
diff --git a/man/use_bioc_pkg_templates.Rd b/man/use_bioc_pkg_templates.Rd
diff --git a/man/use_bioc_readme_rmd.Rd b/man/use_bioc_readme_rmd.Rd
diff --git a/man/use_bioc_support.Rd b/man/use_bioc_support.Rd
diff --git a/man/use_bioc_vignette.Rd b/man/use_bioc_vignette.Rd
diff --git a/vignettes/biocthis.Rmd b/vignettes/biocthis.Rmd
@@ -120,18 +120,18 @@ library("styler")
 
 If you haven't made an R package yet, you can do so using `r CRANpkg("usethis")`. That is, utilize `usethis::create_package()` with the package name of your choice. If you are using [RStudio Desktop](https://www.rstudio.com/products/rstudio/download) this function will open a new RStudio window and open R in the correct location. Otherwise, you might need to use `setwd()` to change directories. 
 
-In this vignette we will create an example package called `biocthisexample` on a temporary directory and work in this directory using `usethis::local_project()` in order to illustrate how the functions work. In a real world scenario, you would not use `usethis::local_project()` yourself and instead you would be working inside your R package.
+In this vignette we will create an example package called `biocthispkg` on a temporary directory and work in this directory using `usethis::local_project()` in order to illustrate how the functions work. In a real world scenario, you would not use `usethis::local_project()` yourself and instead you would be working inside your R package.
 
 
 ```{r 'create_example_pkg'}
 ## Set the package name on a temporary directory
-pkgdir <- file.path(tempdir(), "biocthisexample")
+pkgdir <- file.path(tempdir(), "biocthispkg")
 
 ## Create the example package in a temporary location
 usethis::create_package(pkgdir)
 
-## Set a local project to work with for the examples
-usethis::local_project(pkgdir)
+## Set the project to use for the examples
+usethis::proj_set(pkgdir)
 ```
 
 Once you have created a package, you can use `use_bioc_pkg_templates()` to create a set of scripts in the `dev` (developer) directory.
@@ -282,7 +282,7 @@ biocthis::use_bioc_support()
 
 ```{r 'bioc_vignette'}
 ## Create a template vignette file that is Bioconductor-friendly
-biocthis::use_bioc_vignette("biocthisexample", "Introduction to biocthisexample")
+biocthis::use_bioc_vignette("biocthispkg", "Introduction to biocthispkg")
 ```
 
 # Acknowledgments