Overdue updates

.Rbuildignore

@@ -25,8 +25,8 @@
 ^src/framework/.git$
 # Files from the `framework` submodule
 
-^inc/.editorconfig$
-^inc/.git$
+^src/inc/.editorconfig$
+^src/inc/.git$
 # Files from the `inc` submodule
 
 ^vignettes/[^/]*\.pdf$

.gitmodules

@@ -2,7 +2,7 @@
 	path = src/framework
 	url = https://github.com/biocro/framework
 	branch = main
-[submodule "inc"]
-	path = inc
+[submodule "src/inc"]
+	path = src/inc
 	url = https://github.com/biocro/inc
 	branch = main

R/input_checking_functions.R

@@ -1,15 +1,16 @@
 # Checks whether `args_to_check` has names. The other checking functions require
 # names to give useful error messages.
 check_names <- function(args_to_check) {
-    if(is.null(names(args_to_check))) {
+    if (is.null(names(args_to_check))) {
         stop(paste0("`", substitute(args_to_check), "` must have names"))
     }
 }
 
-# Sends the error messages to the user in the proper format
-send_error_messages <- function(error_messages) {
+# Sends the error messages to the user in the proper format. Don't include the
+# call to `stop_and_send_error_messages` in the message itself.
+stop_and_send_error_messages <- function(error_messages) {
     if (length(error_messages) > 0) {
-        stop(paste(error_messages, collapse='  '))
+        stop(paste(error_messages, collapse='  '), call. = FALSE)
     }
 }
 

R/module_creators.R

@@ -10,7 +10,7 @@ module_creators <- function(module_names)
         check_element_length(list(module_names = module_names))
     )
 
-    send_error_messages(error_messages)
+    stop_and_send_error_messages(error_messages)
 
     # Make sure the module names are a vector
     module_names <- unlist(module_names)

docs/README.md

@@ -41,7 +41,7 @@ package:
       `Rscript module_library_setup.R`.
 
    In either case, you will be prompted for a module library name, which should
-   be 16 or fewer characters long and not contain any underscores; ideally this
+   be 12 or fewer characters long and not contain any underscores; ideally this
    would match the name of the newly-created repository. (If you might ever want
    to submit your package to CRAN, make sure your name is unique on CRAN and
    BioConductor; one way to help ensure this is to include `BML` in the name.)
@@ -117,23 +117,29 @@ skeleton module library in the future; every effort will be made to limit the
 frequency of these updates, but they will nevertheless occur. When there is an
 update to this repository, you can update your module library from it by taking
 the following steps:
-1. Make a new "development" branch for your repository (based on the main
-   branch) and make sure this branch is checked out in your working copy.
-2. Make sure you have a remote named `upstream` that points to the
+1. Check the
+   [skelBML news](https://github.com/biocro/skelBML/blob/main/skelBML_news.md)
+   for any version-specific notes about updating.
+2. Make a new branch for your repository and make sure this branch is checked
+   out in your working copy.
+3. Make sure you have a remote named `upstream` that points to the
    `biocro/skelBML` repository (_this_ repository). This can be done with the
    following command:
    ```
    git remote add upstream https://github.com/biocro/skelBML.git
    ```
    If the remote already exists, you will get an error, but there is no harm in
    running the command.
-3. Update from the remote using the commands
+4. Update from the remote using the commands
    ```
    git fetch upstream
    git merge upstream/main
    ```
-   You may need to address one or more merge conflicts at this point.
-4. Complete the update as follows:
+   You may need to address one or more merge conflicts at this point. One merge
+   conflict will be related to `skelBML_news.md`; this file will be deleted when
+   running the script in Step 5 below, so it does not matter how this conflict
+   is resolved.
+5. Complete the update as follows:
    1. Rerun the setup script, running it as described above.
    2. Any files that would be changed by the script will be backed up; for
       example, if the script would modify
@@ -145,15 +151,14 @@ the following steps:
       customizations that should be retained in the new version of those files,
       such as the table of modules, the package title, etc. Delete backups as
       you see fit.
-5. To confirm that everything worked, try building and checking the package on
-   the development branch with `R CMD build` and `R CMD check`.
-6. When everything is working, commit the changed files to the development
-   branch, and then merge the branch into the main branch of your repository
+6. To confirm that everything worked, try building and checking the package with
+   `R CMD build` and `R CMD check`.
+7. When everything is working, commit the changed files to the new branch, and
+   then merge the branch into the main or development branch of your repository
    (possibly by first creating a pull request if you are working with a team).
 
-Updating your repository on a development branch as described in these steps
-will allow you to test out the changes before committing them to your main
-branch.
+Updating your repository on a separate branch as described in these steps
+will allow you to safely test out the changes before finalizing them.
 
 ### Making contributions
 

script/module_library_setup.R

@@ -5,7 +5,7 @@
 
 ## function definitions
 
-name_length_limit <- 16
+name_length_limit <- 12
 
 stop_quietly <- function() {
   opt <- options(show.error.messages = FALSE)

script/templates/CITATION

@@ -0,0 +1,11 @@
+citHeader(
+    'When referencing the %1$s R package in a scientific publication, ',
+    'please cite the package itself or otherwise specify its version number.'
+)
+
+citation(auto = meta)
+
+citFooter(
+    'Because %1$s is a BioCro module library, please also reference the ',
+    'BioCro framework. Type citation("BioCro") for more details.'
+)

script/templates/DESCRIPTION

@@ -4,18 +4,24 @@ Title: YOUR TITLE HERE
 Description: YOUR DESCRIPTION HERE.
 Authors@R: c(
     person('Example', 'McAuthor', role = c('cre', 'aut'),
-          email = 'example@illinois.edu')
+          email = 'example@illinois.edu'),
+    person('%1$s authors', role = 'cph'),
+    person('BioCro authors', role = 'cph',
+           comment = 'Copyright holder of included BioCro C++ framework'),
+    person('Boost Organization', role = 'cph',
+           comment = 'Copyright holder of included Boost library')
     )
-Depends: R (>= 3.5.0)
+Depends: R (>= 4.1.0)
 Imports:
     stats
 Suggests:
     BioCro (>= 3.0.0),
-    testthat,
+    testthat (>= 3.2.0),
     knitr,
     lattice
 VignetteBuilder: knitr
-SystemRequirements: C++11, GNU make
+SystemRequirements: C++17, GNU make
 License: MIT + file LICENSE
 LazyData: true
 ByteCompile: TRUE
+Config/testthat/edition: 3

script/templates/LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2023
+YEAR: 2026
 COPYRIGHT HOLDER: %1$s authors

script/templates/LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2023 %1$s authors
+Copyright (c) 2026 %1$s authors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

script/templates/skeleton_version.h

@@ -8,7 +8,7 @@
 
 namespace %1$s
 {
-static const std::string skeleton_version = "2.1.3";
+static const std::string skeleton_version = "2.2.0";
 }
 
 #endif

script/templates/template_table

@@ -1,4 +1,5 @@
 template_file          destination_path
+CITATION               inst/CITATION
 DESCRIPTION            DESCRIPTION
 example_module.h       src/module_library/example_module.h
 init.cpp               src/init.cpp

skelBML_description

@@ -1,7 +1,7 @@
 ## WARNING: This file was included in this package by the BioCro skeleton module
 ## library and should not be manually edited.
 
-skelBML version 2.1.3 (https://github.com/biocro/skelBML)
+skelBML version 2.2.0 (https://github.com/biocro/skelBML)
 
 Created by Justin M. McGrath, Edward B. Lochocki, and Scott Rohde.
 

skelBML_license.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2023 skelBML authors
+Copyright (c) 2026 skelBML authors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

skelBML_news.md

@@ -16,6 +16,29 @@ Subsequent commits will then include a new "UNRELEASED" section in preparation
 for the next release.
 -->
 
+# skelBML VERSION 2.2.0
+
+- Several changes were made to better comply with CRAN policies and to better
+  match the BioCro framework R package:
+  - The included boost library was moved to `src/inc` from `inc` and updated to
+    version 1.89
+  - Copyright holders of included libraries were added to the description
+  - Citation guidelines were added
+  - The minimum supported version of R was changed to 4.1.0
+  - The C++ language specification was changed to C++17
+  - The character limit for package names was decreased from 16 to 12
+- Notes about updating to version 2.2.0:
+  - When running `git merge upstream/main` to update, you may be asked
+    `Unlink of file 'inc' failed. Should I try again? (y/n)`. Answer `n` to this
+    question.
+  - After completing the merge, you may need to run
+    `git submodule update --init` to initialize the `inc` submodule in its new
+    location.
+  - Any module libraries that were based on earlier versions of `skelBML` should
+    run `script/module_library_setup.R` when updating to version 2.1.4. In
+    particular, there are important updates to `DESCRIPTION`, `LICENSE`,
+    `LICENSE.md`, `inst/CITATION`, and `src/skeleton_version.h`.
+
 # skelBML VERSION 2.1.3
 
 - The boost library is now included as a git submodule, and has been updated to