Start of 0.16.2

point to new conda-forge release version

Removed TestCase usage

Fixes issue #1395

Issue 1395 gro resid truncate

This fixes ERRORs and FAILs in the testsuite on 32bit:

TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe'

and

assert_(out[0].dtype == np.int64)
  File "/usr/lib/python2.7/site-packages/numpy/testing/utils.py", line 92, in assert_
    raise AssertionError(smsg)
AssertionError

- Added tests for 32 bit index support
- added @rathann to AUTHORS

Issue #1362 : use np.intp types for indexing instead of np.int64

- According to numpy/numpy#4384 (comment), `np.intp` is the recommended dtype for indexing:
   "... use np.intp as dtype whenever things have to do with indexing or are logically related to 
   indexing/array sizes. This is the natural dtype for it and it will normally also be the fastest one.
- see https://docs.scipy.org/doc/numpy/user/basics.types.html
- see also PR #1391 for discussion
- This change should go some way towards increasing compatibility with i386/i696 (32 bit) platforms.

NOTE: No dedicated testing on 32 bit yet (see WIP PR #1392 )

Groups (AtomGroup, ResidueGroup, SegmentGroup) cannot be stored in sets
or used as dict key if they are not hashable. In python 3, the __hash__
method is not defined implicitly anymore when a class has a __eq__ method.

Fixes #1397

- Explicitly define __hash__ for groups:
   Groups (AtomGroup, ResidueGroup, SegmentGroup) cannot be stored in sets
   or used as dict key if they are not hashable. In python 3, the hash
   method is not defined implicitly anymore when a class has a eq method.
- fixes #1397

Fixes #1362

this was missed in eed7761

Merge into single command

Fix for root dir files

Move files in root dir to utils folder

Drop plugins directory

Merge coverage files

Fix covage run command

Fix test list env variable

Fix output coverage file

Fix covegae file

Fix case

Commnet out test__set_verbose

Fix minimal build

Fix merge command

Undo minial build change

Fix multiline command

Fix lint build

Remove plugins from the minimal build

Try to fix the doc build

Adds the test flags to the minimal build

Reactivate tests that pass in test_log.py

Remove if-else logic from "script" phase

Adds missing call to evail in "script" phase

Filip test flags and test directories

Adds cover package argument

Split command into constituent variables

Fix MAIN_CMD in full build

Have the same order of execution for all builds

Add lib folder to the testing command

Make the lib folder a python package

* Adds __init__.py file to the lib folder

Adds __future__ import

- closes #1383
- included deprecations:
  - #1373 Timeseries (targeted for 0.17)
    Note that the deprecation for core.Timeseries will always show up;
    this is deliberate so that users WILL see it as it will be gone in
    the next release!
  - #1377 Quick selectors (target 1.0)
  - #782 flags (target 1.0)
- updated CHANGELOG

- improved installation instructions (minimal/full install for pip, always full
  install for conda; also added entry on installation of tests)
- analysis landing page: better explained optional packages, removed scipy as example
  and replaced with sklearn and HOLE.

- removed imports in core and MDAnalysis
- replaced MDAnalysis.collection with a mock object that issues
  warnings and raises NotImplementedError
- added a test for MDAnalysis.collection

- instant selectors AtomGroup['<name>'], AtomGroup.<name>, ResidueGroup.<name>,
  Segment.<segid>, Segment.r<resid>, SegmentGroup.<segid>  emit warnings
- added tests
- updated docs with detailed deprecation and alternatives

Thanks to @richardjgowers for insights #1403 (comment)

See comment #1403 (comment)

It turns out that with this warning in place we raise two deprecation warnings because we also
have a warning on _get_named_atom(item).

Example output:

 >>> w.atoms['AAA']
 .../mdanalysis/package/MDAnalysis/core/groups.py:1520: DeprecationWarning: Using the [] operator with strings is deprecated and will be removed in 1.0. Please use `select_atoms('name AAA')` instead.
   category=DeprecationWarning)
 .../mdanalysis/package/MDAnalysis/core/groups.py:1522: DeprecationWarning: `_get_named_atom` is deprecated!
 Instant selector AtomGroup['<name>'] or AtomGroup.<name> is deprecated and will be removed in 1.0. Use AtomGroup.select_atoms('name <name>') instead.
   return self._get_named_atom(item)
 <Atom 1: AAA of resname RsA, resid 1 and segid SegA>

This allows code to use the `getattr` function and only throw
an error if the requested attribute is an atom name.

- updated all modules
- removed any code that guards against scipy or matplotlib import
- conforms to style guide https://github.com/MDAnalysis/mdanalysis/wiki/Style-Guide#module-imports-in-mdanalysisanalysis
- fixes #1159
- fixes #1361

…ssing

Conflicts:
	package/CHANGELOG