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Docs for WaterBridgeAnalysis incorrectly formatted/do not show up #3259

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orbeckst opened this issue May 4, 2021 · 5 comments · Fixed by #3258
Closed

Docs for WaterBridgeAnalysis incorrectly formatted/do not show up #3259

orbeckst opened this issue May 4, 2021 · 5 comments · Fixed by #3258
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@orbeckst
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orbeckst commented May 4, 2021

Expected behavior

WaterBridgeAnalysis https://docs.mdanalysis.org/2.0.0-dev0/documentation_pages/analysis/wbridge_analysis.html shows up as its own entry.

Actual behavior

Instead it shows up under https://docs.mdanalysis.org/2.0.0-dev0/documentation_pages/analysis_modules.html#hydrogen-bonding

Code to reproduce the behavior

See links above.

This looks like an issue with the title formatting.

Current version of MDAnalysis

  • Which version are you using? (run python -c "import MDAnalysis as mda; print(mda.__version__)") 2.0.0-dev docs
@xiki-tempula
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I think I might need some help with regard to this issue.

Previously, the title is

Water Bridge Analysis --- :mod:`MDAnalysis.analysis.hydrogenbonds.wbridge_analysis`
=================================================================================== 

However, I got PEP warning and I blindly change it to

Water Bridge Analysis --- \
:mod:`MDAnalysis.analysis.hydrogenbonds.wbridge_analysis`
=========================================================

which seems to give this problem. I wonder if there is any way of splitting the title into two lines? Thanks.

@orbeckst
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orbeckst commented May 4, 2021

Ignore the PEP8 warning.

Check the docs when they are built. They appear on RTD and I think they get linked in the test report.

@orbeckst
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orbeckst commented May 4, 2021

I don't know of a way to split the line – maybe the sphinx or reST docs have something. Or maybe @lilyminium knows of a trick?

@IAlibay IAlibay added this to the 2.0 milestone May 5, 2021
@IAlibay
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IAlibay commented May 5, 2021

I'm adding this as a 2.0 milestone, I guess if it's just a single line change it can just be done in #3120 ?

@orbeckst
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orbeckst commented May 6, 2021

This will get fixed as part of PR #3258

orbeckst added a commit to IAlibay/mdanalysis that referenced this issue May 6, 2021
- fix MDAnalysis#3259
  (title of Water Bridge Analysis docs is not correct)
- include the Gregoret 1991 reference (that was removed with the
  deprecated hbonds.hbond_analysis module)
- minor formatting fixes in the docs
orbeckst added a commit to IAlibay/mdanalysis that referenced this issue May 6, 2021
- fix MDAnalysis#3259
  (title of Water Bridge Analysis docs is not correct)
- include the Gregoret 1991 reference (that was removed with the
  deprecated hbonds.hbond_analysis module)
- minor formatting fixes in the docs
@orbeckst orbeckst changed the title Docs for WaterBridgeAnalysis incorrectlty formatted/do not show up Docs for WaterBridgeAnalysis incorrectly formatted/do not show up May 6, 2021
IAlibay added a commit that referenced this issue May 6, 2021
Fixes #2739 #3259 

## Work done in this PR
* Moves hbond_autocorrel from hbonds to hydrogenbonds, stub
  will be removed in 3.0.0.
* Removes deprecated hbonds.hbond_analysis code.
* tests (note: tests were copied and we run full tests on the deprecated
  and the moved code, mainly to make sure that they can be called as
  expected; deprecation warnings are also tested)
* make hydrogenbonds.hbond_autocorrel primary entry for docs
* add entry for deprecated module at bottom of Hydrogen bonding docs
* fixed doc in hydrogenbonds.wbridge_analysis
* include the Gregoret 1991 reference (that was removed with the
  deprecated hbonds.hbond_analysis module)

Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
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3 participants