[Bug]: The roxygen auto update commit does not delete files that are deleted by roxygen

[vedhav]

What happened?

In this PR the docs were not updated. The CI was able to identify this and commit the new docs. However, it did not commit the deletion of a file.

P.S It would be nice to re-run the CI because every time this happens we need to trigger the CI ourselves.

Which version(s) of R were you using?

No response

Relevant log output

No response

Code of Conduct

• I agree to follow this project's Code of Conduct.

Contribution Guidelines

• I agree to follow this project's Contribution Guidelines.

[cicdguy]

I'm pretty sure that roxygen2::roxygenize('.')'s actions are not strictly additive. It is capable of deleting files as well.

Eg:

rm R/hello.R

> roxygen2::roxygenize('.')
Writing NAMESPACE
ℹ Loading r.pkg.template
Warning: Objects listed as exports, but not present in
namespace:
• hello
• plumber_api
• shiny_app
Writing NAMESPACE
Deleting hello.Rd, plumber_api.Rd, and shiny_app.Rd

[cicdguy]

It would be nice to re-run the CI because every time this happens we need to trigger the CI ourselves.

Interestingly GitHub has introduced a new set of workarounds to auto-trigger workflows on bot commits, which was previously not allowed to prevent recursive runs: https://github.com/peter-evans/create-pull-request/blob/main/docs/concepts-guidelines.md#workarounds-to-trigger-further-workflow-runs

Maybe we can look into other alternatives. Will track that separately.

[cicdguy]

Done in #215