Remove deprecated hole, and completes py2 removal

.appveyor.yml

@@ -10,7 +10,7 @@ cache:
 environment:
     global:
         CONDA_CHANNELS: conda-forge
-        CONDA_DEPENDENCIES: pip setuptools wheel cython six biopython networkx joblib matplotlib scipy vs2015_runtime pytest mmtf-python GridDataFormats hypothesis pytest-cov codecov chemfiles tqdm tidynamics>=1.0.0 rdkit
+        CONDA_DEPENDENCIES: pip setuptools wheel cython biopython networkx joblib matplotlib scipy vs2015_runtime pytest mmtf-python GridDataFormats hypothesis pytest-cov codecov chemfiles tqdm tidynamics>=1.0.0 rdkit
         PIP_DEPENDENCIES: gsd==1.9.3 duecredit parmed
         DEBUG: "False"
         MINGW_64: C:\mingw-w64\x86_64-6.3.0-posix-seh-rt_v5-rev1\mingw64\bin

.travis.yml

@@ -28,7 +28,7 @@ env:
     - MAIN_CMD="pytest ${PYTEST_LIST}"
     - SETUP_CMD="${PYTEST_FLAGS}"
     - BUILD_CMD="pip install -e package/ && (cd testsuite/ && python setup.py build)"
-    - CONDA_MIN_DEPENDENCIES="mmtf-python six biopython networkx cython matplotlib scipy griddataformats hypothesis gsd codecov"
+    - CONDA_MIN_DEPENDENCIES="mmtf-python biopython networkx cython matplotlib scipy griddataformats hypothesis gsd codecov"
     - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12 chemfiles tqdm>=4.43.0 tidynamics>=1.0.0 rdkit"
     - CONDA_CHANNELS='biobuilds conda-forge'
     - CONDA_CHANNEL_PRIORITY=True

package/.pylintrc

@@ -323,7 +323,7 @@ callbacks=cb_,_cb
 
 # List of qualified module names which can have objects that can redefine
 # builtins.
-redefining-builtins-modules=six.moves,future.builtins
+redefining-builtins-modules=
 
 
 [SIMILARITIES]

package/CHANGELOG

@@ -13,11 +13,13 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-??/??/?? richardjgowers, IAlibay, hmacdope, orbeckst, cbouy
+??/??/?? richardjgowers, IAlibay, hmacdope, orbeckst, cbouy, lilyminium
 
   * 2.0.0
 
 Fixes
+  * Selections on emtpy AtomGroups now return an empty AtomGroup instead of an
+    error (Issue #2765)
   * TOPParser no longer guesses elements when missing atomic number records
     (Issues #2449, #2651)
   * Testsuite does not any more matplotlib.use('agg') (#2191)
@@ -32,6 +34,9 @@ Enhancements
   * Added computation of Mean Squared Displacements (#2438, PR #2619)
 
 Changes
+  * Changes development status from Beta to Mature (Issue #2773)
+  * Removes deprecated MDAnalysis.analysis.hole, please use
+    MDAnalysis.analysis.hole2.hole instead (Issue #2739)
   * Replaces use of mock in favour of unittest.mock (Issue #2777)
   * Removes support for passing `atoms` to XYZWriter. (Issue #2739, PR #2754)
   * Removes; deprecated support for using Writer.write(Timestep), deprecated

package/MDAnalysis/analysis/__init__.py

@@ -59,7 +59,7 @@
 :mod:`~MDAnalysis.analysis.helanal`
     Analysis of helices with the HELANAL_ algorithm.
 
-:mod:`~MDAnalysis.analysis.hole`
+:mod:`~MDAnalysis.analysis.hole2`
     Run and process output from the :program:`HOLE` program
     to analyze pores, tunnels and cavities in proteins.
 
@@ -72,6 +72,10 @@
     a bilayer; the algorithm can deal with any deformations as long as
     the two leaflets are topologically distinct.
 
+:mod:`~MDAnalysis.analysis.msd`
+    Implements the calculation of Mean Squared Displacements (MSDs) by the
+    Einstein relation.
+
 :mod:`~MDAnalysis.analysis.nuclinfo`
     Analyse the nucleic acid for the backbone dihedrals, chi, sugar
     pucker, and Watson-Crick distance (minor and major groove
@@ -108,6 +112,9 @@
    :mod:`~MDAnalysis.analysis.legacy.x3dna` was moved to the
    :mod:`MDAnalysis.analysis.legacy` package
 
+.. versionchanged:: 2.0.0
+   Adds MSD, and changes hole for hole2.hole.
+
 """
 
 __all__ = [
@@ -120,8 +127,9 @@
     'hbonds',
     'hydrogenbonds',
     'helanal',
-    'hole',
+    'hole2',
     'leaflet',
+    'msd',
     'nuclinfo',
     'polymer',
     'psa',

package/MDAnalysis/analysis/hbonds/hbond_analysis.py

@@ -319,10 +319,6 @@ class HydrogenBondAnalysis_OtherFF(HydrogenBondAnalysis):
    .. automethod:: _get_bonded_hydrogens_list
 
 """
-from __future__ import division, absolute_import
-import six
-from six.moves import range, zip
-
 import warnings
 import logging
 from collections import defaultdict
@@ -1252,7 +1248,7 @@ def count_by_type(self):
 
         # float because of division later
         tsteps = float(len(self.timesteps))
-        for cursor, (key, count) in enumerate(six.iteritems(hbonds)):
+        for cursor, (key, count) in enumerate(hbonds.items()):
             out[cursor] = key + (count / tsteps,)
 
         # return array as recarray
@@ -1310,7 +1306,7 @@ def timesteps_by_type(self):
 
         out_nrows = 0
         # count number of timesteps per key to get length of output table
-        for ts_list in six.itervalues(hbonds):
+        for ts_list in hbonds.values():
             out_nrows += len(ts_list)
 
         # build empty output table
@@ -1322,7 +1318,7 @@ def timesteps_by_type(self):
         out = np.empty((out_nrows,), dtype=dtype)
 
         out_row = 0
-        for (key, times) in six.iteritems(hbonds):
+        for (key, times) in hbonds.items():
             for tstep in times:
                 out[out_row] = key + (tstep,)
                 out_row += 1