Skip to content

Commit

Permalink
Update biocroxytest.Rmd
Browse files Browse the repository at this point in the history
  • Loading branch information
xec-cm committed Jan 17, 2024
1 parent 264de46 commit d18e849
Showing 1 changed file with 26 additions and 21 deletions.
47 changes: 26 additions & 21 deletions vignettes/biocroxytest.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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!
Expand Down

0 comments on commit d18e849

Please sign in to comment.