duplicate labels #375

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1. orbeckst

   added

   defectbugbug

   good-first-issue

   on Aug 15, 2024
2. mhmohona commented on Sep 22, 2024

   

   mhmohona

   on Sep 22, 2024

   Last edited by mhmohona

   Contributor

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   Hello @orbeckst, would you please share the command which showed these warning?

   I ran make html in doc folder and got following warning -

   /home/mona/Desktop/github/MDAnalysis-UserGuide/doc/source/formats/coordinates.rst:4: WARNING: duplicate label coordinate-readers, other instance in /home/mona/Desktop/github/MDAnalysis-UserGuide/doc/source/formats/index.rst
   /home/mona/Desktop/github/MDAnalysis-UserGuide/doc/source/formats/coordinates.rst:4: WARNING: duplicate label coordinate-readers, other instance in /home/mona/Desktop/github/MDAnalysis-UserGuide/doc/source/formats/coordinates.rst
   
   

   /home/mona/Desktop/github/MDAnalysis-UserGuide/doc/source/formats/coordinate_readers.txt:24: WARNING: undefined label: 'h5md-format'
   /home/mona/Desktop/github/MDAnalysis-UserGuide/doc/source/formats/coordinate_readers.txt:36: WARNING: undefined label: 'openmmapp-format'
   /home/mona/Desktop/github/MDAnalysis-UserGuide/doc/source/formats/coordinate_readers.txt:37: WARNING: undefined label: 'openmmsimulation-format'
   /home/mona/Desktop/github/MDAnalysis-UserGuide/doc/source/formats/coordinate_readers.txt:42: WARNING: undefined label: 'rdkit-format'
   /home/mona/Desktop/github/MDAnalysis-UserGuide/doc/source/formats/coordinate_readers.txt:45: WARNING: undefined label: 'trc-format'
   /home/mona/Desktop/github/MDAnalysis-UserGuide/doc/source/formats/format_overview.txt:24: WARNING: undefined label: 'h5md-format'
   /home/mona/Desktop/github/MDAnalysis-UserGuide/doc/source/formats/format_overview.txt:37: WARNING: undefined label: 'openmmapp-format'
   /home/mona/Desktop/github/MDAnalysis-UserGuide/doc/source/formats/format_overview.txt:38: WARNING: undefined label: 'openmmsimulation-format'
   /home/mona/Desktop/github/MDAnalysis-UserGuide/doc/source/formats/format_overview.txt:39: WARNING: undefined label: 'openmmtopology-format'
   /home/mona/Desktop/github/MDAnalysis-UserGuide/doc/source/formats/format_overview.txt:47: WARNING: undefined label: 'rdkit-format'
   /home/mona/Desktop/github/MDAnalysis-UserGuide/doc/source/formats/format_overview.txt:52: WARNING: undefined label: 'trc-format'
   /home/mona/Desktop/github/MDAnalysis-UserGuide/doc/source/formats/coordinate_readers.txt:24: WARNING: undefined label: 'h5md-format'
   /home/mona/Desktop/github/MDAnalysis-UserGuide/doc/source/formats/coordinate_readers.txt:36: WARNING: undefined label: 'openmmapp-format'
   /home/mona/Desktop/github/MDAnalysis-UserGuide/doc/source/formats/coordinate_readers.txt:37: WARNING: undefined label: 'openmmsimulation-format'
   /home/mona/Desktop/github/MDAnalysis-UserGuide/doc/source/formats/coordinate_readers.txt:42: WARNING: undefined label: 'rdkit-format'
   /home/mona/Desktop/github/MDAnalysis-UserGuide/doc/source/formats/coordinate_readers.txt:45: WARNING: undefined label: 'trc-format'
   
   

   I checked the warnings mentioned in issue description -

   > /home/runner/work/UserGuide/UserGuide/doc/source/examples/analysis/trajectory_similarity/README.rst:6: WARNING: duplicate label trajectory-similarity, other instance in /home/runner/work/UserGuide/UserGuide/doc/source/examples/analysis/README.rst
   

   For this error, in the 2nd file trajectory-similarity tag is not available.

   

   Same goes for second error as well-

   > /home/runner/work/UserGuide/UserGuide/doc/source/formats/coordinates.rst:4: WARNING: duplicate label coordinate-readers, other instance in /home/runner/work/UserGuide/UserGuide/doc/source/formats/coordinates.rst
   

   

   Now shall I proceed with the warning I got while running UserGuide locally?
3. orbeckst commented on Sep 24, 2024

   

   orbeckst

   on Sep 24, 2024

   MemberAuthor

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   Running make html locally is a good idea. I just looked at the CI https://github.com/MDAnalysis/UserGuide/actions, specifically the mda_gh_ci workflow and then in build_docs the build_docs step (eg https://github.com/MDAnalysis/UserGuide/actions/runs/11021678114/job/30609285468 ), which also runs make html.

   I am not sure how to fix this without looking at the problem in detail. If you can fix these warnings in any way, please put up a pull request (PR). Smaller PRs are better than big ones because then we can quickly review them.