pre-commit.ci does not work with our hooks

[lorenzwalthert]

https://pre-commit.ci is an upcoming CI/CD service by the creator of pre-commit that lets you run your pre-commit hooks via GitHub (and more to come). It does not work for script, system or local hooks as discussed in pre-commit-ci/issues#13 because the Rscript executable is not installed in the standard Docker image. For pre-commit to work with our R hooks on CI/CD, we must add support for R / renv as a language in pre-commit.

Alternative: https://github.com/openproblems-bio/openproblems/blob/main/.github/workflows/pre-commit.yml

[PelzKo]

Is the current status still to use the alternative or is R support in pre-commit.ci in sight?
Because when I tried to implement pre-commit.ci (free open source version), I got the error message "Executable Rscript not found"
Or is there just something specific to consider?

[lorenzwalthert]

Yes, I suggest to use this GitHub Action.

There is a pending issue (pre-commit-ci/runner-image#59) to support R out of the box. This will be through the language:r and will require {precommit} to also change the config from language: script to language: r.

[lorenzwalthert]

Now, R is supported as a language (pre-commit-ci/runner-image#80 (comment)). However, there are multiple problems:

• Because in our source installation, we chose to strip away the recommended packages, {Matrix} (which is a recursive dependency of {precommit}) can't be build because build-time-dependencies are not there at runtime. This needs a new image build that does contain the recommended packages.
• All packages that have system dependencies like {gert} won't work. System dependencies that are shipped with the package (like {git2r}) are possible if they are installed in /opt/r.
• We can get rid or the {usethis} -> {git2r} dependency for most of {precommit}, but not the roxygenize hook but using {cli} as we do for {touchstone}.
• the roxygen hook requires the ability to load the package, so all packages that have recursive system dependencies won't run.
• to install system dependencies, we could use pak::local_system_dependencies() or similar, but probably they won't be persistent with /opt/r.

[lorenzwalthert]

@PelzKo I opened #291 to maybe document the use of GitHub Actions + {precommit} to save everyone from trial and error. In #291, there is also a link to a very elaborated Github Action workflow file that you could probably adapt.