Towards sphinx >= 3 #3438
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Towards sphinx >= 3 #3438
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Codecov Report
@@ Coverage Diff @@
## develop #3438 +/- ##
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Coverage 93.77% 93.77%
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Files 176 176
Lines 23219 23219
Branches 3308 3308
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Hits 21773 21773
Misses 1395 1395
Partials 51 51
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This is 100% duplicate object stuff... I started working on it but it's incredibly tedious work. Best thing we can do here is have folks contribute a few changes at a time until we clear all the warnings. |
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I am adding micro-commits that need to be squashed. This should make it easier to resolve issues when multiple people contribute. |
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Hello @IAlibay! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:
Comment last updated at 2021-11-03 00:33:54 UTC |
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This is what's currently left to do (with sphinx 4.0.2)
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- only explicitly include TRZReader and TRZWriter - explicitly reference base.Timestep as type
Hide the property doc with :meta private:, see https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#directives available since sphinx 3.0
- fix sphinx duplicate indexing complaints by using the explicit attribute docs and using :meta private: for property docs - update return types for methods - reorganized main Universe doc string to conform to numpydoc
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Note that one common problem is that we document a managed attribute (
I chose the explicit attr description because these tend to be important attributes that should be listed together instead of spread across. By keeping the explicit docs, the interactive doc string is also more readable. |
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Locally with sphinx 4.2 I have no more warnings and the build succeeds without erroring. |
lilyminium
approved these changes
Nov 3, 2021
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Thanks for doing the work to fix the errors, @IAlibay @richardjgowers @orbeckst. Docs are building (https://mdanalysis--3438.org.readthedocs.build/en/3438/documentation_pages/core/universe.html#MDAnalysis.core.universe.Universe.angles) and look good so I'll approve -- just curious about the use of meta private and whether it's needed.
orbeckst
reviewed
Nov 3, 2021
Co-authored-by: Lily Wang <[email protected]>
richardjgowers
approved these changes
Nov 3, 2021
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Fixes #3224 #2667
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