Docs for topology and coordinate I/O are not up-to-date

[GoogleCodeExporter]

The table with topology formats 
http://pythonhosted.org/MDAnalysis/documentation_pages/topology/init.html#suppor
ted-topology-formats contains links to modules for which no documentation is in 
sphinx such as
- MOL2
- XYZ
- XPDB (broken reST)
- GMS (should be GAMESS)
- LAMMPS

The table with coordinate formats 
http://pythonhosted.org/MDAnalysis/documentation_pages/coordinates/init.html#id1
 contains links to modules for which no documentation is in sphinx such as
- MOL2
- PDB/XPDB (broken reST)
- GAMESS

Also, the section "Coordinate modules" on 
http://pythonhosted.org/MDAnalysis/documentation_pages/coordinates_modules.html 
contains a weird entry "5.4 Classes" – this shouldn't be there.

Could someone please have a look? I am initially assigning this to Tyler but if 
someone else wants to do this, by all means, speak up!

(Docs are one of the strengths of MDAnalysis so we should really try to keep up 
the high standards that we have set.)

Original issue reported on code.google.com by orbeckst on 28 Mar 2015 at 12:20

[GoogleCodeExporter]

I think this is because the .rst stubs haven't been added to /doc/sphinx/ for 
the new(er) modules.  I'll have a look..

Original comment by richardjgowers on 28 Mar 2015 at 7:58

• Changed state: Started

[GoogleCodeExporter]

This issue was closed by revision 0fce20953c1e.

Original comment by richardjgowers on 28 Mar 2015 at 8:36

• Changed state: Fixed

[GoogleCodeExporter]

Ok so I've made the changes to the code (& pushed to dev) that needs doing, 
when I generate docs locally they seem to be fixed.

However I don't know how to push the different html docs to various places 
though, so I'm leaving the issue open again.

Original comment by richardjgowers on 28 Mar 2015 at 8:40

• Changed state: Started

[GoogleCodeExporter]

Thanks Richard for quickly fixing the docs. 

I found a few more issues that I hadn't seen before, fixed those, and 
regenerated the docs. For the development docs there's no pushing to do (while 
on Google Code). As long as docs/html is committed, it will show up as the 
development docs. On GitHub, this will be a bit more awkward and hence Issue 
235.

Original comment by orbeckst on 29 Mar 2015 at 5:27

• Changed state: Fixed