To do an initial conversion of vignettes of a package from Rnw to Rmd:
- Click "Use this template" - "Create a new repository" above
- Give the new repository the name of the Bioconductor package whose Rnw vignettes you would like to convert to Rmd
- In the new repository, under settings go to "Actions - General" then the section "Workflow permissions" to select:
- "Read and write permissions"
- "Allow GitHub Actions to create and approve pull requests"
- Click on "Actions", click on the "Initial commit" job, and click "Re-run all jobs". This seems to be necessary to have the new permissions take effect.
- Once the GitHub Action has finished (~10 minutes), click on the "Pull requests" tab to merge the pull request it created.
- Check and edit the Rmd vignettes of the new repository until they work
- Optional: activate GitHub Pages on the new repository; it will already have pkgdown running in its GitHub Action. (TODO: add pkgdown Action and instructions)