Closes #159 preserve_pr_websites: keep files on gh-pages

[bundfussr]

Pull Request

Use keep_files: true to avoid that existing files on the gh-pages branch are removed when the website is build and deployed.

Before you submit your pull request, take a look at the following checklist. Many thanks for your contribution!

• Title: Place Closes #<insert_issue_number> at the beginning of your PR title. Use the Edit button in the top-right if you need to update.
• Linked Issue: Ensure the related issue is linked in the "Development Section" on the right-hand side.
• First Contribution: If this is your first contribution, add yourself to the DESCRIPTION file.
• Impact on Examples: If your updates impact any examples, review locally for warnings or errors in the impacted example pages.
• Merge Conflicts: Developers should address any merge conflicts and merge upon successful review.
• New Packages: If new packages were used, ensure they are included in the DESCRIPTION file's Imports section.
• Landing Pages: If new packages were added or removed, update the package tables in the main landing page and the relevant section landing page(s) (sdtm/index.qmd, adam/index.qmd, tlg/index.qmd).
• Updated Examples: If you added or updated an example, ensure it runs on the latest CRAN release versions of all packages used.
• Testing Instructions: Provide instructions on how to test the code if necessary.

By default, a temporary website with the content of the PR is created. To avoid this add [skip website] to the title of the PR.

[github-actions]

The website is available at https://pharmaverse.github.io/examples/159_preserve_pr_websites.

[bundfussr]

Hi @pawelru , why is the website built and deployed every day?

Should we add a comment here why it is necessary?

[pawelru]

good question - I don't quite remember the rationale to be honest. Happy to change and make it more rarely

[bundfussr]

OK, I've removed the schedule event.

[bundfussr]

Hi @pawelru , could you have a look at this PR please?

[Gero1999]

LGTM! I think the code changes make sense, my only concern is that I cannot think of any other way of testing that it works than merging to main and checking. Let me know otherwise @bundfussr!

The main risk I can think of is that the old/stale PR previews will now accumulate on gh-pages and never get cleaned up. We may need a separate cleanup job that removes previews for closed/merged PRs (if there are any). But this is not relevant at all, seems like an easy task to address

[bundfussr]

The main risk I can think of is that the old/stale PR previews will now accumulate on gh-pages and never get cleaned up. We may need a separate cleanup job that removes previews for closed/merged PRs (if there are any). But this is not relevant at all, seems like an easy task to address

We have already a workflow which removes the PR previews when the PR is closed: https://github.com/pharmaverse/examples/blob/main/.github/workflows/remove_pr_website.yml

[bundfussr]

LGTM! I think the code changes make sense, my only concern is that I cannot think of any other way of testing that it works than merging to main and checking. Let me know otherwise @bundfussr!

I would merge it but I don't have the rights to merge. Could anyone else merge it?

[bms63]

merging in