feat: add additional args to yaml files

[Bai-Li-NOAA]

This PR addresses issue #144

• update the following YAML files to support additional arguments on Windows, macOS, and Ubuntu: .github/workflows/build-pkgdown.yml, .github/workflows/r-cmd-check.yml, and .github/workflows/update-pkgdown.yml
• allow additional arguments to be specified after checking out the repo and before setting up R
• add a helper function validate_additional_args() to validate additional arguments for R functions
• add a helper function add_args() to include platform-specific additional arguments in a YAML file
• add additional_args to use_r_cmd_check(), use_update_pkgdown(), and use_build_pkgdown() to pass additional arguments to YAML files (e.g., call_*.yml)
• add unit and integration tests to verify the new feature

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 99.36709% with 1 line in your changes missing coverage. Please review.

Project coverage is 95.19%. Comparing base (d1ca9b5) to head (29b7717).

Files with missing lines	Patch %	Lines
R/use_r_workflows.R	99.20%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #147      +/-   ##
==========================================
+ Coverage   94.01%   95.19%   +1.18%     
==========================================
  Files           3        4       +1     
  Lines         167      208      +41     
==========================================
+ Hits          157      198      +41     
  Misses         10       10              

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[Bai-Li-NOAA]

@e-perl-NOAA, could you review this pull request? I will do a final cleanup after the review before merging the changes into the main branch.

Also, could you test the new feature using SS3 repos? For example:

• Copy and paste the following code chunk into the call-r-cmd-check.yml file. See an example here

    uses: nmfs-fish-tools/ghactions4r/.github/workflows/r-cmd-check.yml@add-additional-args-to-yaml
    # uses: nmfs-fish-tools/ghactions4r/.github/workflows/r-cmd-check.yml@main
    with:
      additional_args_ubuntu: |
        sudo apt-get update
        sudo apt-get install -y libcurl4-openssl-dev
        sudo add-apt-repository ppa:ubuntu-toolchain-r/test
        sudo apt-get install --only-upgrade libstdc++6

• Use the R code below to modify the YAML file. See an example here

use_update_pkgdown(
  workflow_name = "call-update-pkgdown.yml",
  additional_args = list(
    "ubuntu" = c(
      "sudo apt-get update",
      "sudo apt-get install -y libcurl4-openssl-dev",
      "sudo add-apt-repository ppa:ubuntu-toolchain-r/test",
      "sudo apt-get install --only-upgrade libstdc++6"
    )
  )
)

Let me know if you have any questions!

[e-perl-NOAA]

Okay, I just added things in the r4ss repo which calls these workflows. It will take awhile for the tests to run and confirm that they work but I will let you know when they do. The r function to update the workflow does work (at least for the ubuntu additions) though of course I did have to change the branch once added from main to this one so that it will work when the github actions are running right now.

[e-perl-NOAA]

Ummm, so I keep getting this result which is weird because I'm pretty sure everything is right. Idk if this is just one of those situations (like many other things these days) where everything has decided to stop working properly or something else

[Bai-Li-NOAA]

@e-perl-NOAA, my bad! I gave the wrong branch name. The correct one is add-additional-args-to-yaml

uses: nmfs-fish-tools/ghactions4r/.github/workflows/r-cmd-check.yml@add-additional-args-to-yaml
    # uses: nmfs-fish-tools/ghactions4r/.github/workflows/r-cmd-check.yml@main

[e-perl-NOAA]

Okay it's working in r4ss (there is a problem with the macos run but that's a me problem with gh and APIs and github enterprise with single sign on, not a you problem)!

[e-perl-NOAA]

@Bai-Li-NOAA would it be too much trouble to add an input for env portion to the r-cmd-check for me to test out? I might not be able to get it to do what I want it to and thus it may not matter in the end. This could also be done in another branch not associated with this PR.

[e-perl-NOAA]

The env is to try to deal with API calls to the mac github actions runner.

[Bai-Li-NOAA]

@e-perl-NOAA Feel free to add an input of env to test in this branch or another branch, either works for me. I am not entirely sure about the desired input format for env portion, but let me know the details of the user case if you would like me to work on it.

[e-perl-NOAA]

Actually nevermind on the env, it already uses it. It looks like macs will just always cause strife in my life.

[e-perl-NOAA]

I assume that you will re-run with spell check before you merge.

[e-perl-NOAA]

I tried adding it and then realized that you already had the GITHUB_TOKEN in there which is what I wanted to try. Its nothing for you to worry about.

[Bai-Li-NOAA]

@e-perl-NOAA, okay, thanks for the update! I will do a final cleanup, including fixing the spell check GHA, before merging the PR.

[Bai-Li-NOAA]

@e-perl-NOAA I have merged the PR. You might need to update some GHA workflows in the SS3 repositories. Let me know if you have any questions!