use help(gromacs.tool_name) doesn't works in Gromacs 5

[pslacerda]

gromacs.tool_name.help() works but help(gromacs.tool_name) doesn't

[orbeckst]

Funnily enough, in ipython

gromacs.tool_name?

works and shows the doc string:

In [6]: gromacs.grompp?

Type:            Grompp
String form:     <gromacs.tools.Grompp object at 0x105c60910>
File:            /Volumes/Data/oliver/Biop/Projects/Methods/GromacsWrapper/gromacs/tools.py
Signature:       gromacs.grompp(self, *args, **kwargs)
Docstring:
DESCRIPTION

gmx grompp (the gromacs preprocessor) reads a molecular topology file, checks
the validity of the file, expands the topology from a molecular description to
...

whereas

In [8]: help(gromacs.grompp)

Help on Grompp in module gromacs.tools object:

class Grompp(gromacs.core.GromacsCommand)
 |  Gromacs tool '%(name)r'.
 |
 |  Method resolution order:
 |      Grompp
 |      gromacs.core.GromacsCommand
 |      gromacs.core.Command
 |      __builtin__.object
 |
 |  Data and other attributes defined here:
 |
 |  command_name = 'grompp'
 |
 |  driver = 'gmx'
 |
 |  ----------------------------------------------------------------------
 |  Methods inherited from gromacs.core.GromacsCommand:
 |
 |  __init__(self, *args, **kwargs)
 |      Set up the command with gromacs flags as keyword arguments.
 |
 |      The following  are generic instructions; refer  to the Gromacs

[pslacerda]

Funny that getdoc works but help doesn't.

import pydoc, gromacs
pydoc.getdoc(gromacs.trjconv)
pydoc.help(gromacs.trjconv)

Is related to the fact that properties are being used as C has the same problem:

class C:
    @property
    def __doc__(self):
       return "c"

[orbeckst]

I looked at https://bfroehle.com/2012/11/08/property-for-doc-attribute/ (see https://gist.github.com/bfroehle/4041015) which proposes a custom docstring_property but when I tried it, it didn't not solve our problem, it just makes a class-level doc string available when there's no generated property doc string.

I also looked on StackOverflow but couldn't find an answer.

Given that you have a minimum working example do you want to ask on S/O?

[pslacerda]

Nice read, I never heard about the descriptor protocol and just learned a bit about how Python resolve member attributes of an object.

Also very funny, I tried dostring_property than set up some breakpoints inside pydoc.py to realize that help works on the object's class instead of the object itself (see https://hg.python.org/cpython/file/v2.7.12/Lib/pydoc.py#l1571). It means that help(1) invokes the int class help instead of print the __doc__. Maybe shows the doc string is a IPython feature?

So much work and we simply need to remove this line https://github.com/Becksteinlab/GromacsWrapper/blob/develop/gromacs/__init__.py#L77

[pslacerda]

Just committed =)

[orbeckst]

Yes, I agree – changing the docs was the easiest route.

(It is slightly strange behavior that help() only shows the class-level doc string. We could perhaps do something very hackish with class methods but I didn't find a useable solution and it does not seem worthwhile.... more important things to do.)