Update

R/use_longtests.R

@@ -1,10 +1,19 @@
-
-
 #' Sets up overall longtests infrastructure
 #'
-#' Creates longtests/testthat directory and longtests/testthat.R file.
+#' This function is used to set up the environment for running long tests. It
+#' calls two helper functions: `setup_bboptions()` and `setup_longtetsts()`.
+#'
+#' @details The `use_longtests()` function is a wrapper function that calls
+#' `setup_bboptions()` and `setup_longtetsts()`. The `setup_bboptions()`
+#' function checks if the .BBSoptions file exists and creates it if it doesn't.
+#' It then checks the contents of the .BBSoptions file and adds or modifies the
+#' 'RunLongTests: TRUE' line as needed. The `setup_longtetsts()` function
+#' creates a 'longtests/testthat' directory if it doesn't exist and copies the
+#' 'tests/testthat.R' file into it. If the 'tests/testthat.R' file doesn't
+#' exist, it creates a new one with default content.
 #'
-#' @return Invisible
+#' @return This function does not return a value. It is used for its side
+#'   effects of setting up the environment for running long tests.
 #' @export
 #' @examples
 #' # Create the longtests directory and .BBSoptions file

README.Rmd

@@ -24,6 +24,8 @@ knitr::opts_chunk$set(
 [![GitHub pulls](https://img.shields.io/github/issues-pr/xec-cm/biocroxytest)](https://github.com/xec-cm/biocroxytest/pulls)
 <!-- badges: end -->
 
+<br>
+
 `r BiocStyle::Githubpkg("xec-cm/biocroxytest")` is an R package inspired by 
 `r BiocStyle::Githubpkg("mikldk/roxytest")`. It is specifically designed for 
 the development of Bioconductor packages that require tests with high execution 
@@ -41,6 +43,8 @@ improves the reliability of the package but also enhances its maintainability.
 Developers can easily locate, understand, and update these long tests as needed,
 leading to more robust and efficient code.
 
+<br>
+
 ## Installation instructions
 
 Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then 
@@ -62,6 +66,8 @@ And the development version from [GitHub](https://github.com/xec-cm/biocroxytest
 BiocManager::install("xec-cm/biocroxytest")
 ```
 
+<br>
+
 ## Example
 
 Here is how you can use `r BiocStyle::Githubpkg("xec-cm/biocroxytest")` to 
@@ -125,6 +131,8 @@ test_that("Function bar() @ L27", {
 })
 ```
 
+<br>
+
 ## Contributing
 
 - If you think you have encountered a bug, please [submit an issue](https://github.com/xec-cm/biocroxytest/issues).
@@ -133,6 +141,8 @@ test_that("Function bar() @ L27", {
 
 - Working on your first Pull Request? You can learn how from this *free* series [How to Contribute to an Open Source Project on GitHub](https://kcd.im/pull-request)
 
+<br>
+
 ## Code of Conduct
 
 Please note that the `r BiocStyle::Githubpkg("xec-cm/biocroxytest")` project is 

README.md

@@ -18,6 +18,8 @@ issues](https://img.shields.io/github/issues/xec-cm/biocroxytest)](https://githu
 pulls](https://img.shields.io/github/issues-pr/xec-cm/biocroxytest)](https://github.com/xec-cm/biocroxytest/pulls)
 <!-- badges: end -->
 
+<br>
+
 *[biocroxytest](https://github.com/xec-cm/biocroxytest)* is an R package
 inspired by *[roxytest](https://github.com/mikldk/roxytest)*. It is
 specifically designed for the development of Bioconductor packages that
@@ -37,6 +39,8 @@ reliability of the package but also enhances its maintainability.
 Developers can easily locate, understand, and update these long tests as
 needed, leading to more robust and efficient code.
 
+<br>
+
 ## Installation instructions
 
 Get the latest stable `R` release from
@@ -59,6 +63,8 @@ And the development version from
 BiocManager::install("xec-cm/biocroxytest")
 ```
 
+<br>
+
 ## Example
 
 Here is how you can use
@@ -123,6 +129,8 @@ test_that("Function bar() @ L27", {
 })
 ```
 
+<br>
+
 ## Contributing
 
 - If you think you have encountered a bug, please [submit an
@@ -137,6 +145,8 @@ test_that("Function bar() @ L27", {
   series [How to Contribute to an Open Source Project on
   GitHub](https://kcd.im/pull-request)
 
+<br>
+
 ## Code of Conduct
 
 Please note that the

vignettes/biocroxytest.Rmd

@@ -29,6 +29,7 @@ knitr::opts_chunk$set(
 options(digits = 3)
 ```
 
+<br>
 
 The `r BiocStyle::Githubpkg("xec-cm/biocroxytest")` package is a novel tool that enhances the efficiency of test writing in R, particularly for Bioconductor software packages. It leverages the structure of `r BiocStyle::Githubpkg("r-lib/roxygen2")` for test writing, which improves readability, code organization, and integrates seamlessly with package documentation.
 
@@ -38,6 +39,8 @@ In Bioconductor, daily tests are run as part of the nightly builds, with a maxim
 
 The `@longtests` roclet provides a dedicated space for extensive tests, ensuring they are easily accessible and well-documented. This not only improves the package's reliability but also its maintainability. Thus, `r BiocStyle::Githubpkg("xec-cm/biocroxytest")`  contributes to the creation of robust, reliable, and efficient Bioconductor packages. 
 
+<br>
+
 ## biocroxytest setup
 
 Once the `r BiocStyle::Githubpkg("xec-cm/biocroxytest")` package is installed, you need to carry out two steps to correctly set up long tests in your package:
@@ -61,6 +64,8 @@ biocroxytest::use_longtests()
 
 With these two steps, your package will be set up to write, document, and store long tests directly in your `r BiocStyle::Githubpkg("r-lib/roxygen2")` comments, improving the efficiency and organization of your test code.
 
+<br>
+
 ## Basic Process
 
 The `r BiocStyle::Githubpkg("xec-cm/biocroxytest")` package allows you to add extensive tests to your functions using the `@longtests` tag in your roxygen comments. Here's a more detailed explanation of how to use it:
@@ -106,6 +111,8 @@ testthat::test_that("Function foo() @ L11", {
 
 This file contains the long tests for the `foo()` function, ready to be run by `r BiocStyle::Githubpkg("r-lib/testthat")`.
 
+<br>
+
 ## Session info
 
 ```{r}