moved analysis.x3dna to analysis.legacy.x3dna (#987)

* moved analysis.x3dna to analysis.legacy.x3dna

- created new MDAnalysis.analysis.legacy package
  - directory
  - docs
- x3dna is now considered legacy code (no/minimal testing, no maintenance)
- see #906 for reasons (mainly because the x3dna license does not allow us
  to just install it for testing on travis, or rather, licensing and access
  to x3dna is unknown/too complicated)
- closes #906
- see #743 on background for legacy code and also https://github.com/MDAnalysis/mdanalysis/wiki/Style-Guide#tests-for-mdanalysisanalysis
- added stub with deprecation warning: until release 1.0, MDAnalysis.analysis.x3dna is still accessible
- added test case that the stub is there

* updated CHANGELOG

- legacy module (#743)
- x3dna is now legacy code (#906)
- updated upcoming release number to 0.16.0

[skip ci]

* Removed legacy submodule from coverage

.coveragerc

@@ -5,7 +5,7 @@ omit =
     */migration/*
     */visualization/*
     */MDAnalysis/tests/*
-
+    */legacy/*
 
 [report]
 exclude_lines =

package/CHANGELOG

@@ -16,10 +16,9 @@ The rules for this file:
 ??/??/16 kain88-de, fiona-naughton, richardjgowers, tyler.je.reddy, jdetle
          euhruska, orbeckst, rbrtdlg, jbarnoud
 
-  * 0.15.1
+  * 0.16.0
 
 Enhancements
-
   * Added regression tests for MDAnalysis.analysis.nuclinfo (Issue #790)
   * All classes derived from 'AnalysisBase' now display a ProgressMeter
   with 'quiet=False'
@@ -32,6 +31,9 @@ Enhancements
   * Added Auxiliary module for reading additional timeseries data alongside
     trajectories (Issue #785)
   * Added AnalysisFromFunction & analysis_class, see (Issue #946 and PR #950)
+  * Established the MDAnalysis.analysis.legacy module for unmaintained
+    analysis code (Issue #743)
+
 Fixes
   * GROWriter resids now truncated properly (Issue #886)
   * reading/writing lambda value in trr files (Issue #859)
@@ -66,7 +68,8 @@ Changes
 
 Deprecations (Issue #599)
   * Use of rms_fit_trj deprecated in favor of AlignTraj class (Issue #845)
-
+  * Moved analysis.x3dna to the analysis.legacy module (Issue #906)
+
 05/15/16 jandom, abhinavgupta94, orbeckst, kain88-de, hainm, jbarnoud,
          dotsdl, richardjgowers, BartBruininks, jdetle
 

package/MDAnalysis/analysis/legacy/__init__.py

@@ -0,0 +1,42 @@
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
+#
+# MDAnalysis --- http://www.MDAnalysis.org
+# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein
+# and contributors (see AUTHORS for the full list)
+#
+# Released under the GNU Public Licence, v2 or any higher version
+#
+# Please cite your use of MDAnalysis in published work:
+#
+# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
+# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
+# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
+#
+
+""":mod:`MDAnalysis.analysis.legacy` --- Legacy analysis code
+==========================================================
+
+.. versionadded:: 0.16.0
+
+The :mod:`MDAnalysis.analysis.legacy` package contains analysis
+modules that are not or only incompletely tested and not regularly
+maintained. They nevertheless still provide useful and sometimes
+unique analysis capabilities and are therefore provided **as is**.
+
+.. warning::
+
+   Code in this module is not regularly maintained. Please use it very
+   carefully.
+
+If you want to use code from this module then you will have to import
+it explicitly. For example, ::
+
+   from MDAnalysis.analysis.legacy import x3dna
+
+(For further discussion, see `Issue 743`_.)
+
+
+.. _Issue 743: https://github.com/MDAnalysis/mdanalysis/issues/743
+
+"""