new topology docs

[orbeckst]

Expected behaviour

The philosophy behind the new topology system #363 should be outlined.

• docs
• CHANGELOG

Actual behaviour

At the moment, PR #1077 only removed obviously outdated comments in the docs in topology/__init__.py.

See also TODO in core/topology.py and the structure doc/sphinx/documentation_pages/core_module.rst.

Perhaps it would be worthwhile making this a proper rst file under doc/sphinx instead of cramming all the docs into a __init__.py etc (?).

[orbeckst]

git grep TODO shows a few more

• package/MDAnalysis/core/topologyattrs.py:# TODO: update docs to property doc
• package/MDAnalysis/core/topology.py:# TODO Notes:
• package/doc/sphinx/source/documentation_pages/overview.rst:.. TODO: more about philosophy etc... copy and paste from paper (more than just topology)

[richardjgowers]

So this definitely needs doing. I wouldn't want to put it in a rst directly as many people might not even know they exist when they start hacking MDA, I'd rather have all the docs in the .py source (which gets slurped into the rst automatically.

[orbeckst]

If you prefer in the py then that's totally fine with me – as long as it is somewhere ;-).

[orbeckst]

Note: #363 is not even mentioned in CHANGELOG!! Please add as part of fixing this issue (and don't forget to add @dotsdl to the 0.16.0 changes).

[kain88-de]

Related #1108 to explain what we mean with a unique segment/residue