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convert all docs to numpy style #1277

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orbeckst opened this issue Apr 1, 2017 · 5 comments
Closed
3 tasks done

convert all docs to numpy style #1277

orbeckst opened this issue Apr 1, 2017 · 5 comments
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@orbeckst @jbarnoud @tylerjereddy
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@orbeckst
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orbeckst commented Apr 1, 2017 •
edited by kain88-de
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According to our Style Guide, all doc strings should be in written with the numpy doc formatting. All new docs are being written according to this style (and for an example see the numpy doc/example.py).

Old docs need to be manually converted:
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orbeckst commented Apr 1, 2017

@tylerjereddy could you have a look at your code in visualization to update the docs to numpy style when you have a moment? Thanks.

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orbeckst commented Apr 1, 2017

@tylerjereddy ... or if you can find someone willing to do it (new contributors, anyone?) feel free to delegate. But all in visualization is your code so I think you should at least review any changes there.

@orbeckst orbeckst mentioned this issue Apr 17, 2017
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orbeckst added a commit that referenced this issue May 13, 2017
@orbeckst
numpy-docs for visualization module
5293abf 
closes #1277
@orbeckst orbeckst mentioned this issue May 13, 2017
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orbeckst added a commit that referenced this issue May 15, 2017
@orbeckst
numpy-docs for visualization module
72c1d81 
- closes #1277
- updated citation for Chavent2014
- shortened module headings
orbeckst added a commit that referenced this issue May 16, 2017
@orbeckst
numpy-docs for visualization module
2de183e 
- closes #1277
- updated citation for Chavent2014
- shortened module headings
- better formatting for return values
- added more parameter/return sections to the undocumented helper functions
  (possibly refactor into underscore-hidden functions)
- made clear that "coordinate files" are really "topology
  files" in MDAnalysis parlance: changed variable names and docs accordingly
kain88-de pushed a commit that referenced this issue May 16, 2017
@orbeckst @kain88-de
numpy-docs for visualization module (#1346)
26149a1 
- closes #1277
- updated citation for Chavent2014
- shortened module headings
- better formatting for return values
- added more parameter/return sections to the undocumented helper functions
  (possibly refactor into underscore-hidden functions)
- made clear that "coordinate files" are really "topology
  files" in MDAnalysis parlance: changed variable names and docs accordingly
@kain88-de
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Are all docs now really numpy style?

@orbeckst
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I think so... always possible that we missed something, of course.

Just did a

git grep :Keywords:

and got

MDAnalysis/analysis/contacts.py:        :Keywords:
MDAnalysis/coordinates/PDB.py:        :Keywords:
MDAnalysis/core/topologyobjects.py:        :Keywords:
MDAnalysis/core/topologyobjects.py:        :Keywords:

so probably a few stragglers that need to be mopped up.

@kain88-de
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Contacts is deprecated classes that will be removed soon.

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