From fc9e5d3825bede8799b5cf44c1fb17dc03168e71 Mon Sep 17 00:00:00 2001 From: richardjgowers Date: Tue, 9 Oct 2018 11:10:38 -0500 Subject: [PATCH 1/3] finished version 0.19.0 --- package/CHANGELOG | 4 ++-- package/MDAnalysis/analysis/density.py | 2 +- package/MDAnalysis/analysis/dihedrals.py | 2 +- package/MDAnalysis/coordinates/LAMMPS.py | 2 +- package/MDAnalysis/coordinates/PDB.py | 2 +- package/MDAnalysis/coordinates/memory.py | 2 +- package/MDAnalysis/core/groups.py | 5 +++-- package/MDAnalysis/core/topologyobjects.py | 8 ++++---- package/MDAnalysis/topology/LAMMPSParser.py | 2 +- package/MDAnalysis/topology/TOPParser.py | 2 +- package/MDAnalysis/version.py | 2 +- package/setup.py | 2 +- testsuite/CHANGELOG | 4 ++-- testsuite/MDAnalysisTests/__init__.py | 2 +- testsuite/setup.py | 2 +- 15 files changed, 22 insertions(+), 21 deletions(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index 70691ee318b..f360f38d4c4 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -13,11 +13,11 @@ The rules for this file: * release numbers follow "Semantic Versioning" http://semver.org ------------------------------------------------------------------------------ -??/??/18 tylerjereddy, richardjgowers, palnabarun, orbeckst, kain88-de, zemanj, +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) diff --git a/package/MDAnalysis/analysis/density.py b/package/MDAnalysis/analysis/density.py index b9a71deb340..e384e6b4b38 100644 --- a/package/MDAnalysis/analysis/density.py +++ b/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 diff --git a/package/MDAnalysis/analysis/dihedrals.py b/package/MDAnalysis/analysis/dihedrals.py index 872801de604..71360709a7e 100644 --- a/package/MDAnalysis/analysis/dihedrals.py +++ b/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. diff --git a/package/MDAnalysis/coordinates/LAMMPS.py b/package/MDAnalysis/coordinates/LAMMPS.py index 0d138bf9032..ce35656c437 100644 --- a/package/MDAnalysis/coordinates/LAMMPS.py +++ b/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' diff --git a/package/MDAnalysis/coordinates/PDB.py b/package/MDAnalysis/coordinates/PDB.py index a084b403626..83f9b504f00 100644 --- a/package/MDAnalysis/coordinates/PDB.py +++ b/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. """ diff --git a/package/MDAnalysis/coordinates/memory.py b/package/MDAnalysis/coordinates/memory.py index c03421a43cb..ef11bde65d7 100644 --- a/package/MDAnalysis/coordinates/memory.py +++ b/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 """ diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py index 12c2e263fe6..18afdf0a62a 100644 --- a/package/MDAnalysis/core/groups.py +++ b/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']) diff --git a/package/MDAnalysis/core/topologyobjects.py b/package/MDAnalysis/core/topologyobjects.py index f57e3346dfe..213d1df2d80 100644 --- a/package/MDAnalysis/core/topologyobjects.py +++ b/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() """ diff --git a/package/MDAnalysis/topology/LAMMPSParser.py b/package/MDAnalysis/topology/LAMMPSParser.py index caa8a9ab73c..b2a9bd1f435 100644 --- a/package/MDAnalysis/topology/LAMMPSParser.py +++ b/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' diff --git a/package/MDAnalysis/topology/TOPParser.py b/package/MDAnalysis/topology/TOPParser.py index 4c985427155..a5c5926fb56 100644 --- a/package/MDAnalysis/topology/TOPParser.py +++ b/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'] diff --git a/package/MDAnalysis/version.py b/package/MDAnalysis/version.py index c12981b3c5d..9efaa6bff50 100644 --- a/package/MDAnalysis/version.py +++ b/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__ = "0.19.0" # NOTE: keep in sync with RELEASE in setup.py diff --git a/package/setup.py b/package/setup.py index b67280bf552..dfda3260718 100755 --- a/package/setup.py +++ b/package/setup.py @@ -67,7 +67,7 @@ # NOTE: keep in sync with MDAnalysis.__version__ in version.py -RELEASE = "0.18.1-dev" +RELEASE = "0.19.0" is_release = 'dev' not in RELEASE diff --git a/testsuite/CHANGELOG b/testsuite/CHANGELOG index 2005a6397b7..da86b840aa7 100644 --- a/testsuite/CHANGELOG +++ b/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 diff --git a/testsuite/MDAnalysisTests/__init__.py b/testsuite/MDAnalysisTests/__init__.py index 4ad9d92fdf2..24b83c1ac42 100644 --- a/testsuite/MDAnalysisTests/__init__.py +++ b/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__ = "0.19.0" try: from MDAnalysisTests.authors import __authors__ except ImportError: diff --git a/testsuite/setup.py b/testsuite/setup.py index 15912d67843..14a594c4626 100755 --- a/testsuite/setup.py +++ b/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 = "0.19.0" with open("README") as summary: LONG_DESCRIPTION = summary.read() From 251f377101f55af9bc9fbc9c154ffeb4dfb298ce Mon Sep 17 00:00:00 2001 From: richardjgowers Date: Tue, 9 Oct 2018 12:17:21 -0500 Subject: [PATCH 2/3] fixed compilation of cpp sources --- package/setup.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/package/setup.py b/package/setup.py index dfda3260718..108445f9d0e 100755 --- a/package/setup.py +++ b/package/setup.py @@ -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, From 54f5ce54ea704c2b5af35404ca596de43047b125 Mon Sep 17 00:00:00 2001 From: richardjgowers Date: Tue, 9 Oct 2018 12:25:30 -0500 Subject: [PATCH 3/3] started version 0.19.1 --- maintainer/conda/MDAnalysis/meta.yaml | 2 +- package/CHANGELOG | 12 ++++++++++++ package/MDAnalysis/version.py | 2 +- package/setup.py | 2 +- testsuite/MDAnalysisTests/__init__.py | 2 +- testsuite/setup.py | 2 +- 6 files changed, 17 insertions(+), 5 deletions(-) diff --git a/maintainer/conda/MDAnalysis/meta.yaml b/maintainer/conda/MDAnalysis/meta.yaml index 4e708dde41b..577e4893f63 100644 --- a/maintainer/conda/MDAnalysis/meta.yaml +++ b/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 diff --git a/package/CHANGELOG b/package/CHANGELOG index f360f38d4c4..c27020dc097 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -13,6 +13,18 @@ The rules for this file: * release numbers follow "Semantic Versioning" http://semver.org ------------------------------------------------------------------------------ +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 diff --git a/package/MDAnalysis/version.py b/package/MDAnalysis/version.py index 9efaa6bff50..6044279e0b5 100644 --- a/package/MDAnalysis/version.py +++ b/package/MDAnalysis/version.py @@ -66,4 +66,4 @@ # e.g. with lib.log #: Release of MDAnalysis as a string, using `semantic versioning`_. -__version__ = "0.19.0" # NOTE: keep in sync with RELEASE in setup.py +__version__ = "0.19.1-dev" # NOTE: keep in sync with RELEASE in setup.py diff --git a/package/setup.py b/package/setup.py index 108445f9d0e..51594a3d481 100755 --- a/package/setup.py +++ b/package/setup.py @@ -67,7 +67,7 @@ # NOTE: keep in sync with MDAnalysis.__version__ in version.py -RELEASE = "0.19.0" +RELEASE = "0.19.1-dev" is_release = 'dev' not in RELEASE diff --git a/testsuite/MDAnalysisTests/__init__.py b/testsuite/MDAnalysisTests/__init__.py index 24b83c1ac42..7b6819499fe 100644 --- a/testsuite/MDAnalysisTests/__init__.py +++ b/testsuite/MDAnalysisTests/__init__.py @@ -97,7 +97,7 @@ logger = logging.getLogger("MDAnalysisTests.__init__") # keep in sync with RELEASE in setup.py -__version__ = "0.19.0" +__version__ = "0.19.1-dev" try: from MDAnalysisTests.authors import __authors__ except ImportError: diff --git a/testsuite/setup.py b/testsuite/setup.py index 14a594c4626..8b765857ed4 100755 --- a/testsuite/setup.py +++ b/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 = "0.19.0" + RELEASE = "0.19.1-dev" with open("README") as summary: LONG_DESCRIPTION = summary.read()