From d18e849c7f3fe05c5807473ba34dabe18107aadd Mon Sep 17 00:00:00 2001
From: xec-cm <fcatala@irsicaixa.es>
Date: Wed, 17 Jan 2024 13:48:30 +0100
Subject: [PATCH] Update biocroxytest.Rmd

---
 vignettes/biocroxytest.Rmd | 47 +++++++++++++++++++++-----------------
 1 file changed, 26 insertions(+), 21 deletions(-)

diff --git a/vignettes/biocroxytest.Rmd b/vignettes/biocroxytest.Rmd
index dc992b4..1f58689 100644
--- a/vignettes/biocroxytest.Rmd
+++ b/vignettes/biocroxytest.Rmd
@@ -53,21 +53,24 @@ robust, reliable, and efficient Bioconductor packages.
 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:
 
-**1 - Add the new roclet to your Description file:** You need to add 
-`biocroxytest::longtests_roclet` to the Roxygen section of your Description file. 
-This will enable `roxygen2::roxygenize()` to generate long tests from the 
-`@longtest` tag. Your Description file should have a line similar to this:
+**1 - Add the new roclet to your Description file:** 
+
+You need to add `biocroxytest::longtests_roclet` to the Roxygen section of your 
+Description file. This will enable `roxygen2::roxygenize()` to generate long 
+tests from the `@longtest` tag. Your Description file should have a line similar 
+to this:
 
 ```
 Roxygen: list(roclets = c("namespace", "rd", "biocroxytest::longtests_roclet"))
 ```
 
-**2 - Run the `biocroxytest::use_longtests()` function:** This function sets up 
-the overall infrastructure for long tests. When run, it creates the 
-`longtests/testthat` directory and the `longtests/testthat.R` file, which are 
-necessary for storing and running your long tests. Additionally, it generates a 
-file named `.BBSoptions` that contains the `RunLongTests: TRUE` parameter, 
-indicating that long tests should be run on the Bioconductor servers.
+**2 - Run the `biocroxytest::use_longtests()` function:** 
+
+This function sets up the overall infrastructure for long tests. When run, it 
+creates the `longtests/testthat` directory and the `longtests/testthat.R` file, 
+which are necessary for storing and running your long tests. Additionally, it
+generates a file named `.BBSoptions` that contains the `RunLongTests: TRUE` 
+parameter, indicating that long tests should be run on the Bioconductor server.
 
 ```{r}
 # Create the longtests directory and .BBSoptions file
@@ -84,10 +87,10 @@ 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:
 
-**1 - Add the `@longtests` tag to your function documentation**: In your roxygen 
-comments for each function, you can add a `@longtests` tag followed by the tests 
-you want to run. These tests should be written as if they were in a 
-`testthat::test_that()` call. For example:
+**1 - Add the `@longtests` tag to your function documentation**: 
+
+In your roxygen comments for each function, you can add a `@longtests` tag 
+followed by the tests you want to run. These tests should be written as if they were in a `testthat::test_that()` call. For example:
 
 ```{r}
 #' A function to do x
@@ -107,15 +110,17 @@ foo <- function(x) {
 In this example, the function `foo()` has two long tests associated with it: 
 `expect_equal(foo(2),    sqrt(2))` and `expect_error(foo("a string"))`.
 
-**2 - Run `roxygen2::roxygenise()`:** After adding the `@longtests` tags to your 
-functions, you need to run `roxygen2::roxygenise()`. This will generate a new 
-file in the `longtests/testthat` directory for each R script that contains 
-functions with `@longtests` tags. The generated files will contain 
-`testthat::test_that()` calls for each set of long tests. 
+**2 - Run `roxygen2::roxygenise()`:** 
+
+After adding the `@longtests` tags to your functions, you need to run 
+`roxygen2::roxygenise()`. This will generate a new file in the `longtests/testthat` 
+directory for each R script that contains functions with `@longtests` tags. The 
+generated files will contain `testthat::test_that()` calls for each set of long 
+tests. 
 
 For instance, if you have the `foo()` function in a file named `R/functions.R`,
-`roxygen2::roxygenise()` will generate a file named 
-`longtests/test-biocroxytest-tests-functions.R` with the following content:
+`roxygen2::roxygenise()` will generate a file named `longtests/test-biocroxytest-tests-functions.R` 
+with the following content:
 
 ```{r results='hide'}
 # Generated by biocroxytest: do not edit by hand!