CI/CD Workshop | R in Pharma 2022

R in Pharma 2022 CI/CD workshop repository.

Full workshop video available here: https://www.youtube.com/watch?v=OcNzurpCCpY

Presentation video available here: https://www.youtube.com/watch?v=8HPpdv8crHo

Exercises

Exercise 1

Fix issues identified by R CMD check workflow.

<details><summary>Click here for a hint 🔎</summary> A unit test is failing for <code>hello.R</code>. </details> <br/> <details><summary>Click here for the solution ✅</summary> The expected message should be <code>Welcome to the R/Pharma CI/CD workshop!</code> (<code>R/Pharma</code> is missing from the message) in the <code>tests/testthat/test-hello.R</code> file. </details>

Exercise 2

Fix broken links after implementing the Check URLs workflow.

<details><summary>Click here for a hint 🔎</summary> An R/Pharma link is broken in the <code>NEWS.md</code> file. </details> <br/> <details><summary>Click here for the solution ✅</summary> The rinpharma website domain is incorrectly set as <code>.xcom</code>. It should be <code>.com</code>. </details>

Exercise 3

Find and fix all spelling errors determined by the Spellcheck workflow.

<details><summary>Click here for a hint 🔎</summary> One or more words are misspelled in the <code>NEWS.md</code> file. </details> <br/> <details><summary>Click here for the solution ✅</summary> The word <code>link</code> is misspelled as <code>linke</code> in <code>NEWS.md</code>. The word <code>strangephrase</code> should be <code>strange phrase</code> in <code>NEWS.md</code>. Fix the spelling first in the <code>NEWS.md</code> file. Next, simply run <code>spelling::update_wordlist(confirm="Yes")</code> to add technical jargon to the wordlist. </details>

Exercise 4

Fix code style errors implementing the Style workflow.

<details><summary>Click here for a hint 🔎</summary> There's a minor style issue in the <code>R/hello.R</code> file. </details> <br/> <details><summary>Click here for the solution ✅</summary> Simply run <code>styler::style_file("R/hello.R")</code> to automatically style the file. </details>

Exercise 5

Reduce the cyclomatic complexity identified by the Lint Code Base workflow.

<details><summary>Click here for a hint 🔎</summary> The issue is manifested in the <code>R/hello.R</code> file. </details> <br/> <details><summary>Click here for the solution ✅</summary> Reduce the number of if statements to reduce the cyclomatic complexity in the <code>R/hello.R</code> file for the <code>linter_ex()</code> function. Run <code>styler::style_file("R/hello.R")</code> to fix style issues, if any. Then, run <code>lintr::lint_package()</code> iteratively to determine whether the issue has been resolved. </details>

Exercise 6

Update man pages based on the errors reported by the ROxygen workflow.

<details><summary>Click here for a hint 🔎</summary> Function documentation is not up-to-date for <code>R/cicdworkshop-package.R</code> and the <code>linter_ex()</code> function. </details> <br/> <details><summary>Click here for the solution ✅</summary> Simply run <code>roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))</code> or <code>devtools::document()</code> to automatically update all man pages. </details>

Exercise 7

Increase code coverage for the package.

<details><summary>Click here for a hint 🔎</summary> Add a simple unit test for the <code>linter_ex()</code> function defined in the <code>R/hello.R</code> file. </details> <br/> <details><summary>Click here for the solution ✅</summary> Run <code>covr::package_coverage()</code> to note the current code coverage.

In the <code>tests/testthat/test-hello.R</code> file, add the following test:

<pre> test_that("linter_ex is surprised", { expect_message( linter_ex("lint"), "^Whoa!\\n" ) }) </pre>

Run tests locally by executing <code>devtools::test()</code> to make sure that the tests succeed.

Then, run <code>covr::package_coverage()</code> to see that the code coverage has increased.

</details>

Exercise 8

Publish a website for your package using GitHub Pages.

<details><summary>Click here for a hint 🔎</summary> Update the <code>_pkgdown.yml</code> and add the <b>pkgdown</b> workflow. </details> <br/> <details><summary>Click here for the solution ✅</summary> Update the <code>url</code> by replacing <code>pharmaverse</code> with your GitHub username and repository name. </details>