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Migrate unmaintained mkdocs to Sphinx + PyData theme#41

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JAlvarezJarreta merged 4 commits into
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jalvarez/sphinx-pydata
May 1, 2026
Merged

Migrate unmaintained mkdocs to Sphinx + PyData theme#41
JAlvarezJarreta merged 4 commits into
mainfrom
jalvarez/sphinx-pydata

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@JAlvarezJarreta

@JAlvarezJarreta JAlvarezJarreta commented Apr 23, 2026

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After more than 1 year of not being maintained and the news that v2 is going to go on a different direction, keeping our documentation based on mkdocs is not reliable anymore. We could opt to choose for many different alternatives, but I have opted to rely on Sphinx with PyData theme (for version control), which is a much more stable system (still maintained and does not look it is going anywhere any time soon). Obviously this has mean quite a few changes in the coverage and documentation structure, but I believe the final result is quite similar (and even better in some parts) than what we had already.

Note: once approved I will produce a similar update on our Python template repository.

@JAlvarezJarreta JAlvarezJarreta self-assigned this Apr 23, 2026
@JAlvarezJarreta JAlvarezJarreta added the enhancement New feature or request label Apr 23, 2026
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github-actions Bot commented Apr 23, 2026

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Coverage

Coverage Report
FileStmtsMissBranchBrPartCoverMissing
src/ensembl/utils
   __init__.py5000100% 
   archive.py31040100% 
   argparse.py990321100% 
   checksums.py12000100% 
   logging.py2512096%56
   plugin.py72414294%79–80, 219–220
   rloader.py460120100% 
src/ensembl/utils/database
   __init__.py3000100% 
   dbconnection.py98710492%216, 218, 220, 223–224, 228–229
   unittestdb.py701030985%98, 102, 124–125, 144, 168–171, 173
TOTAL461221041695% 

Tests Skipped Failures Errors Time
91 0 💤 0 ❌ 0 🔥 1.395s ⏱️

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license-eye has checked 61 files.

Valid Invalid Ignored Fixed
33 2 26 0
Click to see the invalid file list
  • docs/_static/custom-icons.js
  • docs/_static/switcher.json
Use this command to fix any missing license headers
```bash

docker run -it --rm -v $(pwd):/github/workspace apache/skywalking-eyes header fix

</details>

Comment thread docs/_static/custom-icons.js
ens-sb
ens-sb previously approved these changes Apr 24, 2026
@JAlvarezJarreta JAlvarezJarreta force-pushed the jalvarez/sphinx-pydata branch from 8e59547 to c4b9041 Compare April 24, 2026 10:54
@JAlvarezJarreta JAlvarezJarreta merged commit cee8498 into main May 1, 2026
5 checks passed
@JAlvarezJarreta JAlvarezJarreta deleted the jalvarez/sphinx-pydata branch May 1, 2026 14:19
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2 participants