Update density.py

[Balasubra]

To update atoms selection inside density_from_Universe function: a new parameter has been added ("sel_update"). When user set sel_update=True, then atomselection is updated for each frame. Accordingly lines 515 to 520 have been modified to consider/not to consider updates for each frame.

[kain88-de]

The syntax is not correct here. To check for equality one would use ==. But since sel_update contains a boolean that is not even necessary. Just writinge if sel_update is enough.

if sel_update:
    # do stuff

[orbeckst]

sel_update --> update_selection

[orbeckst]

Your tests failed. Follow the link Details for continuous-integration/travis-ci/pr — The Travis CI build failed and fix whatever made the test fail (probably the syntax error that @kain88-de pointed out but you need to check for yourself – that's the usual development pattern: submit PR, check tests, fix, repeat).

[orbeckst]

sel_update --> update_selection

[Balasubra]

Sorry for the delayed response. Now i corrected code taking your suggestion. I am presently checking it.

[orbeckst]

at the bottom of the doc string add

.. versionchanged:: 0.13.0
   *update_selection* keyword added

[orbeckst]

Looking good, only a few things to do:

1. address my comment regarding the docs
2. (optional) reqrite your history and squish the five "Update density.py" commits into one (see below)
3. add entry to CHANGELOG (see below)
4. add yourself as an author to MDAnalysis

History rewriting

Do you know how squish all five commits into a single one (using e.g. git rebase -i)? If not then that's ok (it's a dangerous operation...) and then let us know and one of us can do it.

The commit history in the develop branch should be reasonable clean, along the lines of "one commit, one feature" (and as little as work in progress).

Also, if you rewrite your history with rebase, make the commit title and text more expressive, along the lines of

add option to update selection every frame for density calculations

To update atoms selection inside density_from_Universe function: a new keyword
has been added ("update_selection"). When user set sel_update=True, then 
the atomselection is updated for each frame. 

Then make another commit with CHANGELOG and authorship:

CHANGELOG

• add an entry to the 0.13.0 entry in package/CHANGELOG under Enhancements, briefly describing the change
• add you git handle balasubra to the contributor list for 0.13.0

Authorship

This is your first contribution to MDAnalysis --- welcome and thank you!

• add your real name to package/AUTHORS under a 2016 heading
• add your real name to the authors list in package/doc/sphinx/source/conf.py (see comment in the file where to put your name)

I am adding you as a contributor to the project on github and you should get a notification soon.

[Balasubra]

Hi,
No 1. Done
2. Merging commits and History rewriting : Could nt figure out how to do it.
3, 4 Changes in CHANGELOG, package/AUTHOURS, conf.py : All these have been inserted in Balasubra-Issue584 branch.

[orbeckst]

I'll do the clean-up.

[orbeckst]

Note: This PR belongs to #584 .

[orbeckst]

This is now on PR #614