Fix bugs in documentation generation workflow

[nwiltsie]

Description

This fixes four issues with the documentation generation:

1. backfill.py tries to push to ghpages and not gh-pages 🤦
2. Repeated headings trip an assertion failure
3. Bad anchor links cause the process to crash
   • Sub-issue Handle headings with embedded links #19 is that the parsed anchor for a heading with an embedded link is somethink like please-see-list-of-contributorshttpsgithubcomuclahs-cdspipeline-call-mtsnvgraphscontributors-at-github instead of please-see-list-of-contributors-at-github
   • Older versions of call-mtSNV just have plain ol' broken links in them, like https://github.com/uclahs-cds/pipeline-call-mtSNV/tree/2.0.0?tab=readme-ov-file#2-Align-mt-Reads-with-MToolBox
4. Headings with Markdown formatting (links, emphasis, whatever) have that formatting show up in the table of contents:

The first problem was a one-character fix.

I walked right into the second problem (#22) by assuming that, because headings get anchor links, they of course must always be unique. Obviously untrue, and GitHub handles that by appending numbers to repeated headings (see this README for an example). The generated docs will now behave the same way, with anchor links repeat, repeat-1, repeat-2, etc.

For the last two problems, I added a strip_markdown function that uses some custom rules for a markdown-it renderer to strip away all inline formatting. That function is used for both the anchor links and the page titles - that ensures that the links work as expected, the table of contents looks correct, but the formatting persists on the actual pages:

Finally, actually incorrect anchor links are just left broken. That means that instead of being properly re-written to point to the correct page, like http://localhost:8000/latest/pipeline-steps/#3-Call-mtSNV-with-mitoCaller, they are left as bad anchors on the root page, like http://localhost:8000/latest/#2-Align-mt-Reads-with-MToolBox. A warning annotation will show up on the workflow run's summary, but nobody will notice unless they specifically go looking for it.

Closes #19, closes #22

Checklist

• This PR does NOT contain Protected Health Information (PHI). A repo may need to be deleted if such data is uploaded.
  Disclosing PHI is a major problem¹ - Even a small leak can be costly².

• This PR does NOT contain germline genetic data³, RNA-Seq, DNA methylation, microbiome or other molecular data⁴.

• This PR does NOT contain other non-plain text files, such as: compressed files, images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other output files.

  To automatically exclude such files using a .gitignore file, see here for example.

• I have read the code review guidelines and the code review best practice on GitHub check-list.

• I have set up or verified the main branch protection rule following the github standards before opening this pull request.

• The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].

• I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

Footnotes

1. UCLA Health reaches $7.5m settlement over 2015 breach of 4.5m patient records ↩

2. The average healthcare data breach costs $2.2 million, despite the majority of breaches releasing fewer than 500 records. ↩

3. Genetic information is considered PHI.
   Forensic assays can identify patients with as few as 21 SNPs ↩

4. RNA-Seq, DNA methylation, microbiome, or other molecular data can be used to predict genotypes (PHI) and reveal a patient's identity. ↩

[yashpatel6]

Looks good!

Changes made

[yashpatel6]

Still looks good!