Switch to automatically set up GITHUB_TOKEN

[js2264]

Currently the rworkflows.yml requires a specific "PAT_GITHUB" secret to be set up in each repo using the GHA.
However, GitHub automatically sets up {{ secrets.GITHUB_TOKEN }} for any GHA job, without needing to set it up manually, so this could be used instead of a manually set up "PAT_GITHUB".

This requires adding permissions set for contents: write for any job relying on {{ secrets.GITHUB_TOKEN }}, otherwise JamesIves deploy GHA won't work (see here: https://github.com/JamesIves/github-pages-deploy-action#:~:text=If%20you%20do,permissions%20it%20needs.)

More here: https://docs.github.com/en/actions/security-guides/automatic-token-authentication

[js2264]

Not sure how the checks here work in a PR, and whose secrets they inherit?
I have not actually changed any workflow file (in .github/workflows/), so I doubt the error would be due to my changes? The error seems to be related to a missing GITHUB_PAT for remotes (note, a missing GITHUB_PAT, not the PAT_GITHUB mentioned in the package and in my comment above). I have reverted part of my modifications to retain the storing of this GITHUB_PAT ("GITHUB_PAT=${{ inputs.GITHUB_TOKEN }}"). Maybe I'm missing something else here?

[js2264]

Just to confirm things should work, here is my rworkflows results:

• before updating the yml: https://github.com/js2264/plyinteractions/actions/runs/6042308201/job/16397129358
• after updating the yml: https://github.com/js2264/plyinteractions/actions/runs/6042789772/job/16398618280

The only commit in-between, with only changes to the yml: js2264/plyinteractions@dc2e62a

And AFAIK I have no secret set up for this repo.

[bschilder]

Thanks so much for the PR @js2264 , this has been a point of confusion for me for a long time. Ideally I'd like to get rid of any additional setup steps outside of the rworkflows::use_workflow function, so this would definitely be a step towards that. Let me double check what's going on with the checks and I'll get back to you ASAP.

Also thanks for being an early adopter of rworkflows! I've seen you're using it in a number of your packages. If you have any other PRs/suggestions/feature requests do let me know and I'd be happy to work with you to make it happen.

All the best,
Brian

[bschilder]

Oh also, I'm going to try to switch this PR to the dev branch, so that we can play around with these changes without affecting other users just yet. The dev branch will then be run using this workflow:
https://github.com/neurogenomics/rworkflows/blob/master/.github/workflows/rworkflows_dev.yml

[js2264]

🎉🎉 https://github.com/neurogenomics/rworkflows/actions/runs/6048293406/job/16413370380

[bschilder]

🎉🎉 https://github.com/neurogenomics/rworkflows/actions/runs/6048293406/job/16413370380

Awesome work @js2264 , everything is now merged and working great. This goes a long way towards making rworkflows even easier to use!

Thanks again,
Brian