Set up pre-commit yaml

[SaranjeetKaur]

• Use lintr and also set up pre-commit yaml file.
• Update .gitignore template
• Generate README.Rmd and convert it to README.md before commiting

[alexdewar]

I just came on here to post this because I noticed the pre-commit CI app was failing. Bigger picture, it's my fault for enabling it for every repo on the org unconditionally, but if you're going to use pre-commit anyway then that'll also fix things :smile:

Do you think I should disable it for new repos @jamesturner246? I mean, we don't have many repos on here and most of them do use pre-commit, but...

[SaranjeetKaur]

Hi @alexdewar, I am planning to include pre-commit on this repo. I would have done that by now but I am running into some errors and will be catching up with James shortly today to work on it

[SaranjeetKaur]

Steps to autogenerate .pre-commit-config.yaml in RStudio on Windows:

• pip install pre-commit --user (macOS, Linux and Windows) outside a conda or virtual environment. (Alternatively, test a work around with zipapp)
• `install.packages("precommit") on RStudio console
• check whether the path to the pre-commit executable is available on RStudio using precommit::path_precommit_exec()
• If the pre-commit executable is not discoverable, then find its location on your local machine and set it for RStudio as follows:

1. precommit_path <- "C:/Users/ssbhogal/.pyenv/pyenv-win/versions/3.11.0/Scripts/pre-commit.exe" # path to the pre-commit executable
2. options(precommit.executable = precommit_path) # set R options
3. getOption("precommit.executable") should return the path to the executable, if everything is ok. In this case, it will return "C:/Users/ssbhogal/.pyenv/pyenv-win/versions/3.11.0/Scripts/pre-commit.exe". The same output will also be returned if instead you use precommit::path_precommit_exec().
4. use precommit::use_precommit() to autogenerate .pre-commit-config.yaml

5. If you are using the roxygenize hook, then this requires further edits in your .pre-commit-config.yaml, please run precommit::snippet_generate('additional-deps-roxygenize') to proceed with the same. It will generate the following snippet:

   
   Generating snippet using CRAN versions. If you need another source, specify with syntax that `renv::install()` understands (see examples in help file). 
   
   -   id: roxygenize
       # roxygen requires loading pkg -> add dependencies from DESCRIPTION
       additional_dependencies:
       -    ggplot2
       -    grDevices

• Replace the id: roxygenize key in .pre-commit-config.yaml with the above code. ℹ Note that CI services like have build-time restrictions and installing the above dependencies may exceed those, resulting in a timeout. In addition, system dependencies are not supported for . See vignette("ci", package = "precommit") for details and solutions.

[jamesturner246]

Ideally we will use it in all repos, eventually, but I'm not against changing it if it prevents issues.