Merge pull request #2096 from MDAnalysis/start_0.19.1

Start 0.19.1

maintainer/conda/MDAnalysis/meta.yaml

@@ -1,7 +1,7 @@
 package:
   name: mdanalysis
   # This has to be changed after a release
-  version: "0.18.1dev"
+  version: "0.19.1dev"
 
 source:
    git_url: https://github.com/MDAnalysis/mdanalysis

package/CHANGELOG

@@ -13,11 +13,23 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-??/??/18 tylerjereddy, richardjgowers, palnabarun, orbeckst, kain88-de, zemanj,
+mm/dd/18
+  * 0.19.1
+
+Enhancements
+
+Fixes
+
+Changes
+
+Deprecations
+
+
+10/09/18 tylerjereddy, richardjgowers, palnabarun, orbeckst, kain88-de, zemanj,
          VOD555, davidercruz, jbarnoud, ayushsuhane, hfmull, micaela-matta,
          sebastien.buchoux, arm61, p-j-smith, IAlibay
 
-  * 0.18.1
+  * 0.19.0
 
 Enhancements
   * Added bond/angle/dihedral reading in PARM7 TOPParser (PR #2052)

package/MDAnalysis/analysis/density.py

@@ -682,7 +682,7 @@ def density_from_Universe(universe, delta=1.0, atomselection='name OH2',
       (It should be noted that the `padding` keyword is not used when a user
       defined grid is assigned).
 
-    .. versionchanged:: 0.18.1
+    .. versionchanged:: 0.19.0
        *gridcenter*, *xdim*, *ydim* and *zdim* keywords added to allow for user
        defined boxes
     .. versionchanged:: 0.13.0

package/MDAnalysis/analysis/dihedrals.py

@@ -26,7 +26,7 @@
 :Year: 2018
 :Copyright: GNU Public License v2
 
-.. versionadded:: 0.18.1
+.. versionadded:: 0.19.0
 
 This module contains classes for calculating dihedral angles for a given set of
 atoms or residues. This can be done for selected frames or whole trajectories.

package/MDAnalysis/coordinates/LAMMPS.py

@@ -462,7 +462,7 @@ class DumpReader(base.ReaderBase):
     Will automatically convert positions from their scaled/fractional
     representation to their real values.
 
-    .. versionadded:: 0.18.1
+    .. versionadded:: 0.19.0
     """
     format = 'LAMMPSDUMP'
 

package/MDAnalysis/coordinates/PDB.py

@@ -1002,7 +1002,7 @@ def MODEL(self, modelnumber):
         .. _MODEL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#MODEL
 
 
-        .. versionchanged:: 0.18.1
+        .. versionchanged:: 0.19.0
            Maximum model number is enforced.
 
         """

package/MDAnalysis/coordinates/memory.py

@@ -299,7 +299,7 @@ def __init__(self, coordinate_array, order='fac',
 
         .. _`#1041`: https://github.com/MDAnalysis/mdanalysis/issues/1041
 
-        .. versionchanged:: 0.18.1
+        .. versionchanged:: 0.19.0
             The input to the MemoryReader now must be a np.ndarray
             Added optional velocities and forces
         """

package/MDAnalysis/core/groups.py

@@ -2361,8 +2361,9 @@ def select_atoms(self, sel, *othersel, **selgroups):
         .. versionchanged:: 0.16.0 Updating selections now possible by setting
             the `updating` argument.
         .. versionchanged:: 0.17.0 Added *moltype* and *molnum* selections.
-        .. versionchanged:: 0.18.1 Added strict type checking for passed groups.
-        .. versionchanged:: 0.19.0 Added periodic kwarg (default True)
+        .. versionchanged:: 0.19.0
+           Added strict type checking for passed groups.
+           Added periodic kwarg (default True)
         """
         # once flags removed, replace with default=True
         periodic = selgroups.pop('periodic', flags['use_periodic_selections'])

package/MDAnalysis/core/topologyobjects.py

@@ -196,7 +196,7 @@ def length(self, pbc=True):
 
         .. versionchanged:: 0.11.0
            Added pbc keyword
-        .. versionchanged:: 0.18.1
+        .. versionchanged:: 0.19.0
            Changed default of pbc to True
         """
         box = self.universe.dimensions if pbc else None
@@ -236,7 +236,7 @@ def angle(self, pbc=True):
         .. versionadded:: 0.9.0
         .. versionchanged:: 0.17.0
            Fixed angles close to 180 giving NaN
-        .. versionchanged:: 0.18.1
+        .. versionchanged:: 0.19.0
            Added pbc keyword, default True
         """
         box = self.universe.dimensions if pbc else None
@@ -285,7 +285,7 @@ def dihedral(self, pbc=True):
         4 decimals (and is only tested to 3 decimals).
 
         .. versionadded:: 0.9.0
-        .. versionchanged:: 0.18.1
+        .. versionchanged:: 0.19.0
            Added pbc keyword, default True
         """
         box = self.universe.dimensions if pbc else None
@@ -518,7 +518,7 @@ class TopologyGroup(object):
     .. versionchanged:: 0.11.0
        Added `values` method to return the size of each object in this group
        Deprecated selectBonds method in favour of select_bonds
-    .. versionchanged:: 0.18.1
+    .. versionchanged:: 0.19.0
        Empty TopologyGroup now returns correctly shaped empty array via
        indices property and to_indices()
     """

package/MDAnalysis/topology/LAMMPSParser.py

@@ -585,7 +585,7 @@ class LammpsDumpParser(TopologyReaderBase):
 
     Only reads atom ids.  Sets all masses to 1.0.
 
-    .. versionadded:: 0.18.1
+    .. versionadded:: 0.19.0
     """
     format = 'LAMMPSDUMP'
 

package/MDAnalysis/topology/TOPParser.py

@@ -143,7 +143,7 @@ class TOPParser(TopologyReaderBase):
 
     .. versionchanged:: 0.7.6
       parses both amber10 and amber12 formats
-    .. versionchanged:: 0.18.1
+    .. versionchanged:: 0.19.0
       parses bonds, angles, dihedrals, and impropers
     """
     format = ['TOP', 'PRMTOP', 'PARM7']

package/MDAnalysis/version.py

@@ -66,4 +66,4 @@
 # e.g. with lib.log
 
 #: Release of MDAnalysis as a string, using `semantic versioning`_.
-__version__ = "0.18.1-dev"  # NOTE: keep in sync with RELEASE in setup.py
+__version__ = "0.19.1-dev"  # NOTE: keep in sync with RELEASE in setup.py

package/setup.py

@@ -67,7 +67,7 @@
 
 
 # NOTE: keep in sync with MDAnalysis.__version__ in version.py
-RELEASE = "0.18.1-dev"
+RELEASE = "0.19.1-dev"
 
 is_release = 'dev' not in RELEASE
 
@@ -289,6 +289,7 @@ def extensions(config):
         print('Will not attempt to use Cython.')
 
     source_suffix = '.pyx' if use_cython else '.c'
+    cpp_source_suffix = '.pyx' if use_cython else '.cpp'
 
     # The callable is passed so that it is only evaluated at install time.
 
@@ -347,14 +348,14 @@ def extensions(config):
                         define_macros=define_macros,
                         extra_compile_args=extra_compile_args)
     cutil = MDAExtension('MDAnalysis.lib._cutil',
-                         sources=['MDAnalysis/lib/_cutil' + source_suffix],
+                         sources=['MDAnalysis/lib/_cutil' + cpp_source_suffix],
                          language='c++',
                          libraries=mathlib,
                          include_dirs=include_dirs + ['MDAnalysis/lib/include'],
                          define_macros=define_macros,
                          extra_compile_args=cpp_extra_compile_args)
     augment = MDAExtension('MDAnalysis.lib._augment',
-                         sources=['MDAnalysis/lib/_augment' + source_suffix],
+                         sources=['MDAnalysis/lib/_augment' + cpp_source_suffix],
                          language='c++',
                          include_dirs=include_dirs,
                          define_macros=define_macros,
@@ -381,7 +382,7 @@ def extensions(config):
                               define_macros=define_macros,
                               extra_compile_args=extra_compile_args)
     nsgrid = MDAExtension('MDAnalysis.lib.nsgrid',
-                             ['MDAnalysis/lib/nsgrid' + source_suffix],
+                             ['MDAnalysis/lib/nsgrid' + cpp_source_suffix],
                              include_dirs=include_dirs,
                              language='c++',
                              define_macros=define_macros,

testsuite/CHANGELOG

@@ -13,8 +13,8 @@ Also see https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysisTests
 and https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests
 
 ------------------------------------------------------------------------------
-mm/dd/18 orbeckst, arm61
-  * 0.18.1
+10/09/18 orbeckst, arm61
+  * 0.19.0
     - skip tests for duecredit when duecredit is not installed (#1906)
     - updated meta data for PyPi and updated README and INSTALL
     - added test for fix to issue #1897

testsuite/MDAnalysisTests/__init__.py

@@ -97,7 +97,7 @@
 logger = logging.getLogger("MDAnalysisTests.__init__")
 
 # keep in sync with RELEASE in setup.py
-__version__ = "0.18.1-dev"
+__version__ = "0.19.1-dev"
 try:
     from MDAnalysisTests.authors import __authors__
 except ImportError:

testsuite/setup.py

@@ -132,7 +132,7 @@ def dynamic_author_list():
         warnings.warn('Cannot write the list of authors.')
 
     # this must be in-sync with MDAnalysis
-    RELEASE = "0.18.1-dev"
+    RELEASE = "0.19.1-dev"
     with open("README") as summary:
         LONG_DESCRIPTION = summary.read()