MDAnalysis docstrings not parsed properly about mdacli

[PicoCentauri]

Something like doc = NumpyDocString(NumpyDocString("\n " + TestClass.__doc__) does the job. However, adding an fixed number of spaces doesn't look stable to me. 😅

Adding something like doc = NumpyDocString("\n " + callable_obj.__doc__) in L67 of the cli_main leads to a bunch of parsing errors of numpydoc

philiploche@Philips-MacBook-Air:~/repos/mda_cli$ python3 cli_main.py -h
Warning: Unknown section Example
Traceback (most recent call last):
  File "cli_main.py", line 372, in <module>
    add_to_CLIs(member, analysis_interfaces)
  File "cli_main.py", line 67, in add_to_CLIs
    doc = NumpyDocString("\n     " + callable_obj.__doc__)
  File "/usr/local/lib/python3.8/site-packages/numpydoc/docscrape.py", line 147, in __init__
    self._parse()
  File "/usr/local/lib/python3.8/site-packages/numpydoc/docscrape.py", line 402, in _parse
    self['See Also'] = self._parse_see_also(content)
  File "/usr/local/lib/python3.8/site-packages/numpydoc/docscrape.py", line 324, in _parse_see_also
    raise ParseError("%s is not a item name" % line)
numpydoc.docscrape.ParseError: pmda.density.DensityAnalysis for a parallel version is not a item name in '\n   

Seems like there is still some work todo...

[joaomcteixeira]

EDIT:

Geez.... I just reproduced your previous answer.... sorry for this lapse :-o (see history of the comment)

I guess we need to study the NumpyDoc parser in detail because it seems is all a matter of giving the proper spaces in the docstring. File here - > https://github.com/numpy/numpydoc/blob/121c327ddbb1394eccef0fc3cb51bdf66979f5c6/numpydoc/docscrape.py#L111

We will continue on this quest, but it seems that definitively we need to change docstrings upstream.
Cheers!

[joaomcteixeira]

I am trying to write a general parser we can use to read the docstrings. In the lines of Numpy doc but not so strict and focusing only on our requirements.

[joaomcteixeira]

I forgot to set PR #3 to close this issue.
It may be that we need to readdress this with minor modifications to accommodate edge cases on the documentation of the Analysis Classes. If that comes to be the case, we will revisit this issue.