From a1648305773117953b20db3e2412edcb28e4958f Mon Sep 17 00:00:00 2001 From: Richard Gowers Date: Sat, 3 Jun 2017 23:52:01 +0100 Subject: [PATCH 01/35] Started version 0.16.2 --- package/CHANGELOG | 10 ++++++++++ package/MDAnalysis/version.py | 2 +- package/setup.py | 2 +- testsuite/CHANGELOG | 4 ++++ testsuite/MDAnalysisTests/__init__.py | 2 +- testsuite/setup.py | 2 +- 6 files changed, 18 insertions(+), 4 deletions(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index db3b6dbbead..d91b3b49d86 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -13,6 +13,16 @@ The rules for this file: * release numbers follow "Semantic Versioning" http://semver.org ------------------------------------------------------------------------------ +mm/dd/yy + + * 0.16.2 + +Enhancements + +Fixes + +Changes + 06/03/17 utkbansal, kain88-de, xiki-tempula, kaplajon, wouterboomsma, richardjgowers, Shtkddud123, QuantumEntangledAndy, orbeckst, diff --git a/package/MDAnalysis/version.py b/package/MDAnalysis/version.py index f1a651c010e..8340c569c80 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__ = "0.16.1" # NOTE: keep in sync with RELEASE in setup.py +__version__ = "0.16.2-dev0" # NOTE: keep in sync with RELEASE in setup.py diff --git a/package/setup.py b/package/setup.py index 614eed8dd71..1688ebc2ee3 100755 --- a/package/setup.py +++ b/package/setup.py @@ -75,7 +75,7 @@ cmdclass = {} # NOTE: keep in sync with MDAnalysis.__version__ in version.py -RELEASE = "0.16.1" +RELEASE = "0.16.2-dev0" is_release = 'dev' not in RELEASE diff --git a/testsuite/CHANGELOG b/testsuite/CHANGELOG index fb1749e87fd..4467ce48c72 100644 --- a/testsuite/CHANGELOG +++ b/testsuite/CHANGELOG @@ -13,6 +13,10 @@ Also see https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysisTests and https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests ------------------------------------------------------------------------------ +mm/dd/yy + + * 0.16.2 + 06/03/17 xiki_tempula * 0.16.1 diff --git a/testsuite/MDAnalysisTests/__init__.py b/testsuite/MDAnalysisTests/__init__.py index 08481e3001c..10c7f4627e8 100644 --- a/testsuite/MDAnalysisTests/__init__.py +++ b/testsuite/MDAnalysisTests/__init__.py @@ -116,7 +116,7 @@ import logging logger = logging.getLogger("MDAnalysisTests.__init__") -__version__ = "0.16.1" # keep in sync with RELEASE in setup.py +__version__ = "0.16.2-dev0" # keep in sync with RELEASE in setup.py try: from MDAnalysisTests.authors import __authors__ except ImportError: diff --git a/testsuite/setup.py b/testsuite/setup.py index ddf3fb963b8..57405072299 100755 --- a/testsuite/setup.py +++ b/testsuite/setup.py @@ -131,7 +131,7 @@ def dynamic_author_list(): except (OSError, IOError): warnings.warn('Cannot write the list of authors.') - RELEASE = "0.16.1" # this must be in-sync with MDAnalysis + RELEASE = "0.16.2-dev0" # this must be in-sync with MDAnalysis LONG_DESCRIPTION = \ """MDAnalysis is a tool for analyzing molecular dynamics trajectories. From a0d61f904d9cc8aa19918c0ca033fe99221626a4 Mon Sep 17 00:00:00 2001 From: Max Linke Date: Sun, 4 Jun 2017 15:18:00 +0200 Subject: [PATCH 02/35] change definition of tests (#1382) --- .travis.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 2e7e5f85afe..66a56880381 100644 --- a/.travis.yml +++ b/.travis.yml @@ -32,12 +32,15 @@ env: - CONDA_CHANNELS='biobuilds conda-forge' - CONDA_CHANNEL_PRIORITY=True - NUMPY_VERSION=stable - matrix: - - NAME='minimal' PYTHON_VERSION=2.7 SETUP_CMD='--with-memleak' matrix: fast_finish: true include: + - os : linux + env: NAME='minimal' + PYTHON_VERSION=2.7 + SETUP_CMD='--with-memleak' + - os: linux env: NAME="Doc" MAIN_CMD="cd package && python setup.py" From 76527108a83030d69c6db270be313c11dd27c05b Mon Sep 17 00:00:00 2001 From: Max Linke Date: Tue, 6 Jun 2017 12:12:04 +0200 Subject: [PATCH 03/35] update conda badge (#1386) point to new conda-forge release version --- README.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index cacd07dc094..327ed18daee 100644 --- a/README.rst +++ b/README.rst @@ -111,6 +111,6 @@ to find uncovered code. :alt: Coverage Status :target: https://coveralls.io/r/MDAnalysis/mdanalysis?branch=develop -.. |anaconda| image:: https://anaconda.org/mdanalysis/mdanalysis/badges/version.svg +.. |anaconda| image:: https://anaconda.org/conda-forge/mdanalysis/badges/version.svg :alt: Anaconda - :target: https://anaconda.org/MDAnalysis/mdanalysis + :target: https://anaconda.org/conda-forge/mdanalysis From efd9fc5fa40a808da0bf2095581983442b2b32c9 Mon Sep 17 00:00:00 2001 From: Richard Gowers Date: Mon, 12 Jun 2017 14:47:13 +0100 Subject: [PATCH 04/35] Aesthetic fixes to test_gro Removed TestCase usage --- .../MDAnalysisTests/coordinates/test_gro.py | 30 ++++++++++++------- 1 file changed, 20 insertions(+), 10 deletions(-) diff --git a/testsuite/MDAnalysisTests/coordinates/test_gro.py b/testsuite/MDAnalysisTests/coordinates/test_gro.py index beb202bdac0..ca08e35a3a4 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_gro.py +++ b/testsuite/MDAnalysisTests/coordinates/test_gro.py @@ -20,22 +20,32 @@ # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 # from __future__ import absolute_import -from unittest import TestCase import MDAnalysis as mda import numpy as np from MDAnalysis.coordinates.GRO import GROReader, GROWriter from MDAnalysisTests import make_Universe -from MDAnalysisTests.coordinates.base import BaseReference, BaseReaderTest, BaseWriterTest, BaseTimestepTest +from MDAnalysisTests.coordinates.base import ( + BaseReference, BaseReaderTest, BaseWriterTest, BaseTimestepTest, +) from MDAnalysisTests.coordinates.reference import RefAdK -from MDAnalysisTests.datafiles import COORDINATES_GRO, COORDINATES_GRO_INCOMPLETE_VELOCITY, COORDINATES_GRO_BZ2, GRO, \ - GRO_large +from MDAnalysisTests.datafiles import ( + COORDINATES_GRO, + COORDINATES_GRO_INCOMPLETE_VELOCITY, + COORDINATES_GRO_BZ2, + GRO, + GRO_large, +) from nose.plugins.attrib import attr -from numpy.testing import (assert_almost_equal, ) -from numpy.testing import assert_array_almost_equal, dec, assert_equal, assert_raises - - -class TestGROReaderOld(TestCase, RefAdK): +from numpy.testing import ( + assert_almost_equal, + assert_array_almost_equal, + dec, + assert_equal, + assert_raises +) + +class TestGROReaderOld(RefAdK): def setUp(self): self.universe = mda.Universe(GRO) self.ts = self.universe.trajectory.ts @@ -88,7 +98,7 @@ def test_unitcell(self): err_msg="unit cell dimensions (rhombic dodecahedron)") -class TestGROReaderNoConversionOld(TestCase, RefAdK): +class TestGROReaderNoConversionOld(RefAdK): def setUp(self): self.universe = mda.Universe(GRO, convert_units=False) self.ts = self.universe.trajectory.ts From 6a5fa2ce17e8747f4e72b35f8e762a545ac2377f Mon Sep 17 00:00:00 2001 From: Richard Gowers Date: Mon, 12 Jun 2017 15:30:08 +0100 Subject: [PATCH 05/35] Added tests for issue #1395 --- testsuite/MDAnalysisTests/coordinates/test_gro.py | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/testsuite/MDAnalysisTests/coordinates/test_gro.py b/testsuite/MDAnalysisTests/coordinates/test_gro.py index ca08e35a3a4..e240ad3aa21 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_gro.py +++ b/testsuite/MDAnalysisTests/coordinates/test_gro.py @@ -24,7 +24,7 @@ import MDAnalysis as mda import numpy as np from MDAnalysis.coordinates.GRO import GROReader, GROWriter -from MDAnalysisTests import make_Universe +from MDAnalysisTests import make_Universe, tempdir from MDAnalysisTests.coordinates.base import ( BaseReference, BaseReaderTest, BaseWriterTest, BaseTimestepTest, ) @@ -38,6 +38,7 @@ ) from nose.plugins.attrib import attr from numpy.testing import ( + assert_, assert_almost_equal, assert_array_almost_equal, dec, @@ -417,6 +418,18 @@ def test_writer_large_residue_count(self): err_msg="Writing GRO file with > 99 999 " "resids does not truncate properly.") +@tempdir.run_in_tempdir() +def test_growriter_resid_truncation(): + u = make_Universe(extras=['resids'], trajectory=True) + u.residues[0].resid = 123456789 + u.atoms.write('out.gro') + + with open('out.gro', 'r') as grofile: + grofile.readline() + grofile.readline() + line = grofile.readline() + # larger digits should get truncated + assert_(line.startswith('56789UNK')) class TestGROTimestep(BaseTimestepTest): Timestep = mda.coordinates.GRO.Timestep From 930bb6349fde760eaa315a747a914aa469185f55 Mon Sep 17 00:00:00 2001 From: Richard Gowers Date: Mon, 12 Jun 2017 16:03:51 +0100 Subject: [PATCH 06/35] Added lib.util.ltruncate_integer --- package/MDAnalysis/lib/util.py | 25 ++++++++++++++++++++++ testsuite/MDAnalysisTests/lib/test_util.py | 16 ++++++++++++++ 2 files changed, 41 insertions(+) diff --git a/package/MDAnalysis/lib/util.py b/package/MDAnalysis/lib/util.py index c40c15be7b0..d75517c7553 100644 --- a/package/MDAnalysis/lib/util.py +++ b/package/MDAnalysis/lib/util.py @@ -1574,3 +1574,28 @@ def __eq__(self, other): except AssertionError: return False return True + + +def ltruncate_int(value, ndigits): + """Truncate an integer, retaining least significant digits + + Parameters + ---------- + value : int + value to truncate + ndigits : int + number of digits to keep + + Returns + ------- + truncated : int + only the `ndigits` least significant digits from `value` + + Examples + -------- + >>> ltruncate_int(123, 2) + 23 + >>> ltruncate_int(1234, 5) + 1234 + """ + return int(str(value)[-ndigits:]) diff --git a/testsuite/MDAnalysisTests/lib/test_util.py b/testsuite/MDAnalysisTests/lib/test_util.py index 1db65566a7d..ddf4558f884 100644 --- a/testsuite/MDAnalysisTests/lib/test_util.py +++ b/testsuite/MDAnalysisTests/lib/test_util.py @@ -968,3 +968,19 @@ def test_iter(self): seen.append(val) for val in ['this', 'that', 'other']: assert_(val in seen) + + +class TestTruncateInteger(object): + @staticmethod + def _check_vals(a, b): + assert_(util.ltruncate_int(*a) == b) + + def test_ltruncate_int(self): + for vals, exp in ( + ((1234, 1), 4), + ((1234, 2), 34), + ((1234, 3), 234), + ((1234, 4), 1234), + ((1234, 5), 1234), + ): + yield self._check_vals, vals, exp From abd205b8f8d4814d647f3f0062b7f8958cd416bb Mon Sep 17 00:00:00 2001 From: Richard Gowers Date: Mon, 12 Jun 2017 17:11:09 +0100 Subject: [PATCH 07/35] Changed coordinate writers to use ltruncate_int Fixes issue #1395 --- package/CHANGELOG | 5 +++-- package/MDAnalysis/coordinates/CRD.py | 6 +++--- package/MDAnalysis/coordinates/GRO.py | 4 ++-- package/MDAnalysis/coordinates/PDB.py | 4 ++-- package/MDAnalysis/coordinates/PDBQT.py | 4 ++-- 5 files changed, 12 insertions(+), 11 deletions(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index d91b3b49d86..d3d96542a51 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -13,13 +13,14 @@ The rules for this file: * release numbers follow "Semantic Versioning" http://semver.org ------------------------------------------------------------------------------ -mm/dd/yy +mm/dd/17 - * 0.16.2 + * 0.16.2 richardjgowers Enhancements Fixes + * fixed GROWriter truncating long resids from the wrong end (Issue #1395) Changes diff --git a/package/MDAnalysis/coordinates/CRD.py b/package/MDAnalysis/coordinates/CRD.py index 70e7b857575..c005da25e8f 100644 --- a/package/MDAnalysis/coordinates/CRD.py +++ b/package/MDAnalysis/coordinates/CRD.py @@ -251,9 +251,9 @@ def write(self, selection, frame=None): current_resid += 1 # Truncate numbers - serial = int(str(i + 1)[-serial_len:]) - resid = int(str(resid)[-resid_len:]) - current_resid = int(str(current_resid)[-totres_len:]) + serial = util.ltruncate_int(i + 1, serial_len) + resid = util.ltruncate_int(resid, resid_len) + current_resid = util.ltruncate_int(current_resid, totres_len) crd.write(at_fmt.format( serial=serial, totRes=current_resid, resname=resname, diff --git a/package/MDAnalysis/coordinates/GRO.py b/package/MDAnalysis/coordinates/GRO.py index 3a36fa69d2f..7691b9fb2cb 100644 --- a/package/MDAnalysis/coordinates/GRO.py +++ b/package/MDAnalysis/coordinates/GRO.py @@ -377,8 +377,8 @@ def write(self, obj): # all attributes could be infinite cycles! for atom_index, resid, resname, name in zip( range(ag_or_ts.n_atoms), resids, resnames, names): - truncated_atom_index = int(str(atom_index + 1)[-5:]) - truncated_resid = int(str(resid)[:5]) + truncated_atom_index = util.ltruncate_int(atom_index + 1, 5) + truncated_resid = util.ltruncate_int(resid, 5) if has_velocities: output_gro.write(self.fmt['xyz_v'].format( resid=truncated_resid, diff --git a/package/MDAnalysis/coordinates/PDB.py b/package/MDAnalysis/coordinates/PDB.py index 2ac9b899f3f..910b42ca939 100644 --- a/package/MDAnalysis/coordinates/PDB.py +++ b/package/MDAnalysis/coordinates/PDB.py @@ -902,12 +902,12 @@ def get_attr(attrname, default): for i, atom in enumerate(atoms): vals = {} - vals['serial'] = int(str(i + 1)[-5:]) # check for overflow here? + vals['serial'] = util.ltruncate_int(i + 1, 5) # check for overflow here? vals['name'] = self._deduce_PDB_atom_name(atomnames[i], resnames[i]) vals['altLoc'] = altlocs[i][:1] vals['resName'] = resnames[i][:4] vals['chainID'] = segids[i][:1] - vals['resSeq'] = int(str(resids[i])[-4:]) + vals['resSeq'] = util.ltruncate_int(resids[i], 4) vals['iCode'] = icodes[i][:1] vals['pos'] = pos[i] # don't take off atom so conversion works vals['occupancy'] = occupancies[i] diff --git a/package/MDAnalysis/coordinates/PDBQT.py b/package/MDAnalysis/coordinates/PDBQT.py index 1cc2d4d3657..e16e2792831 100644 --- a/package/MDAnalysis/coordinates/PDBQT.py +++ b/package/MDAnalysis/coordinates/PDBQT.py @@ -320,12 +320,12 @@ def write(self, selection, frame=None): attrs['resids'], attrs['icodes'], attrs['occupancies'], attrs['tempfactors'], attrs['charges'], attrs['types']), start=1): - serial = int(str(serial)[-5:]) # check for overflow here? + serial = util.ltruncate_int(serial, 5) # check for overflow here? + resid = util.ltruncate_int(resid, 4) name = name[:4] if len(name) < 4: name = " " + name # customary to start in column 14 chainid = chainid.strip()[-1:] # take the last character - resid = int(str(resid)[-4:]) # check for overflow here? self.pdb.write(self.fmt['ATOM'].format( serial=serial, From 39ad792b939bdd26e461f9a6e801f4f54ea789fd Mon Sep 17 00:00:00 2001 From: Dominik 'Rathann' Mierzejewski Date: Fri, 9 Jun 2017 11:42:19 +0200 Subject: [PATCH 08/35] use correct int types 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 --- package/MDAnalysis/core/groups.py | 2 +- package/MDAnalysis/core/topology.py | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py index c386e079ef0..f2459c9f1dd 100644 --- a/package/MDAnalysis/core/groups.py +++ b/package/MDAnalysis/core/groups.py @@ -419,7 +419,7 @@ def __init__(self, *args): ix, u = args # indices for the objects I hold - self._ix = np.asarray(ix, dtype=np.int64) + self._ix = np.asarray(ix, dtype=np.intp) self._u = u self._cache = dict() diff --git a/package/MDAnalysis/core/topology.py b/package/MDAnalysis/core/topology.py index 2c11d2f3632..2653acfb84d 100644 --- a/package/MDAnalysis/core/topology.py +++ b/package/MDAnalysis/core/topology.py @@ -125,12 +125,12 @@ def make_downshift_arrays(upshift, nparents): counter += 1 # If parent is skipped, eg (0, 0, 2, 2, etc) while counter != upshift[order[x:y][0]]: - downshift.append(np.array([], dtype=np.int)) + downshift.append(np.array([], dtype=np.int64)) counter += 1 - downshift.append(np.sort(np.array(order[x:y], copy=True, dtype=np.int))) + downshift.append(np.sort(np.array(order[x:y], copy=True, dtype=np.int64))) # Add entries for childless parents at end of range while counter < (nparents - 1): - downshift.append(np.array([], dtype=np.int)) + downshift.append(np.array([], dtype=np.int64)) counter += 1 # Add None to end of array to force it to be of type Object # Without this, a rectangular array gets squashed into a single array From 8641226001e876f5e0360c4d74d4c239aab3d539 Mon Sep 17 00:00:00 2001 From: Dominik 'Rathann' Mierzejewski Date: Fri, 9 Jun 2017 11:49:09 +0200 Subject: [PATCH 09/35] relax test_symmetry test due to lower precision on 32bit --- testsuite/MDAnalysisTests/analysis/test_psa.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/testsuite/MDAnalysisTests/analysis/test_psa.py b/testsuite/MDAnalysisTests/analysis/test_psa.py index 3d4d097f10b..ddc0b8f4e71 100644 --- a/testsuite/MDAnalysisTests/analysis/test_psa.py +++ b/testsuite/MDAnalysisTests/analysis/test_psa.py @@ -221,7 +221,8 @@ def test_symmetry(self): for a given Hausdorff metric, h.''' forward = self.h(self.path_1, self.path_2) reverse = self.h(self.path_2, self.path_1) - self.assertEqual(forward, reverse) + # lower precision on 32bit + assert_almost_equal(forward, reverse, decimal=15) def test_hausdorff_value(self): '''Test that the undirected Hausdorff From eed776181c90646d960eb00a275bffb3ffb36a20 Mon Sep 17 00:00:00 2001 From: Richard Gowers Date: Mon, 12 Jun 2017 07:58:40 +0100 Subject: [PATCH 10/35] More work on making indexing arrays use intp (#1362) - Added tests for 32 bit index support - added @rathann to AUTHORS --- package/AUTHORS | 2 + package/CHANGELOG | 3 +- package/MDAnalysis/core/groups.py | 4 +- package/MDAnalysis/core/topology.py | 14 +-- .../MDAnalysisTests/core/test_index_dtype.py | 92 +++++++++++++++++++ 5 files changed, 105 insertions(+), 10 deletions(-) create mode 100644 testsuite/MDAnalysisTests/core/test_index_dtype.py diff --git a/package/AUTHORS b/package/AUTHORS index 4267d50f93d..4133aafd72b 100644 --- a/package/AUTHORS +++ b/package/AUTHORS @@ -90,6 +90,8 @@ Chronological list of authors - Sang Young Noh - Andrew William King - Kathleen Clark + - Dominik 'Rathann' Mierzejewski + External code ------------- diff --git a/package/CHANGELOG b/package/CHANGELOG index d3d96542a51..666386fe8ff 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -15,12 +15,13 @@ The rules for this file: ------------------------------------------------------------------------------ mm/dd/17 - * 0.16.2 richardjgowers + * 0.16.2 richardjgowers, rathann Enhancements Fixes * fixed GROWriter truncating long resids from the wrong end (Issue #1395) + * Fixed dtype of numpy arrays to accomodate 32 bit architectures (Issue #1362) Changes diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py index f2459c9f1dd..963f069d3f2 100644 --- a/package/MDAnalysis/core/groups.py +++ b/package/MDAnalysis/core/groups.py @@ -2464,7 +2464,7 @@ def ix_array(self): -------- ix """ - return np.array([self.ix]) + return np.array([self.ix], dtype=np.intp) class Atom(ComponentBase): @@ -2736,7 +2736,7 @@ def update_selection(self): ix = sum([sel.apply(bg) for sel in sels[1:]], sels[0].apply(bg)).ix else: - ix = np.array([], dtype=np.int) + ix = np.array([], dtype=np.intp) # Run back through AtomGroup init with this information to remake ourselves super(UpdatingAtomGroup, self).__init__(ix, self.universe) self.is_uptodate = True diff --git a/package/MDAnalysis/core/topology.py b/package/MDAnalysis/core/topology.py index 2653acfb84d..3b98daabc91 100644 --- a/package/MDAnalysis/core/topology.py +++ b/package/MDAnalysis/core/topology.py @@ -125,12 +125,12 @@ def make_downshift_arrays(upshift, nparents): counter += 1 # If parent is skipped, eg (0, 0, 2, 2, etc) while counter != upshift[order[x:y][0]]: - downshift.append(np.array([], dtype=np.int64)) + downshift.append(np.array([], dtype=np.intp)) counter += 1 - downshift.append(np.sort(np.array(order[x:y], copy=True, dtype=np.int64))) + downshift.append(np.sort(np.array(order[x:y], copy=True, dtype=np.intp))) # Add entries for childless parents at end of range while counter < (nparents - 1): - downshift.append(np.array([], dtype=np.int64)) + downshift.append(np.array([], dtype=np.intp)) counter += 1 # Add None to end of array to force it to be of type Object # Without this, a rectangular array gets squashed into a single array @@ -210,18 +210,18 @@ def __init__(self, # built atom-to-residue mapping, and vice-versa if atom_resindex is None: - self._AR = np.zeros(n_atoms, dtype=np.int64) + self._AR = np.zeros(n_atoms, dtype=np.intp) else: - self._AR = atom_resindex.copy() + self._AR = np.asarray(atom_resindex, dtype=np.intp).copy() if not len(self._AR) == n_atoms: raise ValueError("atom_resindex must be len n_atoms") self._RA = make_downshift_arrays(self._AR, n_residues) # built residue-to-segment mapping, and vice-versa if residue_segindex is None: - self._RS = np.zeros(n_residues, dtype=np.int64) + self._RS = np.zeros(n_residues, dtype=np.intp) else: - self._RS = residue_segindex.copy() + self._RS = np.asarray(residue_segindex, dtype=np.intp).copy() if not len(self._RS) == n_residues: raise ValueError("residue_segindex must be len n_residues") self._SR = make_downshift_arrays(self._RS, n_segments) diff --git a/testsuite/MDAnalysisTests/core/test_index_dtype.py b/testsuite/MDAnalysisTests/core/test_index_dtype.py new file mode 100644 index 00000000000..43e083a6a74 --- /dev/null +++ b/testsuite/MDAnalysisTests/core/test_index_dtype.py @@ -0,0 +1,92 @@ +# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- +# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 +# +# MDAnalysis --- http://www.mdanalysis.org +# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# (see the file AUTHORS for the full list of names) +# +# Released under the GNU Public Licence, v2 or any higher version +# +# Please cite your use of MDAnalysis in published work: +# +# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, +# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. +# MDAnalysis: A Python package for the rapid analysis of molecular dynamics +# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th +# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. +# +# 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 +# + +"""32 bit compat tests + +Tests for making sure that integer arrays used for indexing use `np.intp`. +This dtype is important for platform independent indexing of other arrays. + +""" +from __future__ import absolute_import + +import numpy as np +from numpy.testing import ( + assert_, +) +from MDAnalysisTests import make_Universe + + +class TestIndexDtype(object): + def setUp(self): + self.u = make_Universe() + + def tearDown(self): + del self.u + + def test_ag_ix(self): + assert_(self.u.atoms.ix.dtype == np.intp) + + def test_rg_ix(self): + assert_(self.u.residues.ix.dtype == np.intp) + + def test_sg_ix(self): + assert_(self.u.segments.ix.dtype == np.intp) + + def test_atom_ix_array(self): + assert_(self.u.atoms[0].ix_array.dtype == np.intp) + + def test_residue_ix_array(self): + assert_(self.u.residues[0].ix_array.dtype == np.intp) + + def test_segment_ix_array(self): + assert_(self.u.segments[0].ix_array.dtype == np.intp) + + def test_atomgroup_indices(self): + assert_(self.u.atoms.indices.dtype == np.intp) + + def test_atomgroup_residue_upshift(self): + assert_(self.u.atoms.resindices.dtype == np.intp) + + def test_atomgroup_segment_upshift(self): + assert_(self.u.atoms.segindices.dtype == np.intp) + + def test_residuegroup_atom_downshift(self): + # downshift arrays are a list (one for each residue) + assert_(all((arr.dtype == np.intp) + for arr in self.u.residues.indices)) + + def test_residuegroup_resindices(self): + assert_(self.u.residues.resindices.dtype == np.intp) + + def test_residuegroup_segment_upshift(self): + assert_(self.u.residues.segindices.dtype == np.intp) + + def test_segmentgroup_atom_downshift(self): + assert_(all((arr.dtype == np.intp) + for arr in self.u.segments.indices)) + + def test_segmentgroup_residue_downshift(self): + assert_(all((arr.dtype == np.intp) + for arr in self.u.segments.resindices)) + + def test_segmentgroup_segindices(self): + assert_(self.u.segments.segindices.dtype == np.intp) From e3d58188bb1670a4831328fbca64bc3dd4f36890 Mon Sep 17 00:00:00 2001 From: Jonathan Barnoud Date: Tue, 13 Jun 2017 19:26:29 +0200 Subject: [PATCH 11/35] 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 --- package/CHANGELOG | 7 ++- package/MDAnalysis/core/groups.py | 3 + testsuite/MDAnalysisTests/core/test_groups.py | 63 ++++++++++++++++++- 3 files changed, 70 insertions(+), 3 deletions(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index 666386fe8ff..66827ab51e0 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -13,15 +13,18 @@ The rules for this file: * release numbers follow "Semantic Versioning" http://semver.org ------------------------------------------------------------------------------ -mm/dd/17 - * 0.16.2 richardjgowers, rathann + +mm/dd/17 richardjgowers, rathann, jbarnoud + + * 0.16.2 Enhancements Fixes * fixed GROWriter truncating long resids from the wrong end (Issue #1395) * Fixed dtype of numpy arrays to accomodate 32 bit architectures (Issue #1362) + * Groups are hashable on python 3 (Issue #1397) Changes diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py index 963f069d3f2..5c317740ffb 100644 --- a/package/MDAnalysis/core/groups.py +++ b/package/MDAnalysis/core/groups.py @@ -423,6 +423,9 @@ def __init__(self, *args): self._u = u self._cache = dict() + def __hash__(self): + return hash((self._u, self.__class__, tuple(self.ix.tolist()))) + def __len__(self): return len(self._ix) diff --git a/testsuite/MDAnalysisTests/core/test_groups.py b/testsuite/MDAnalysisTests/core/test_groups.py index 725dcfc296b..b4731a03516 100644 --- a/testsuite/MDAnalysisTests/core/test_groups.py +++ b/testsuite/MDAnalysisTests/core/test_groups.py @@ -25,6 +25,7 @@ import itertools import numpy as np from numpy.testing import ( + dec, assert_, assert_array_equal, assert_equal, @@ -34,7 +35,7 @@ import six import MDAnalysis as mda -from MDAnalysisTests import make_Universe +from MDAnalysisTests import make_Universe, parser_not_found from MDAnalysisTests.datafiles import PSF, DCD from MDAnalysis.core import groups from MDAnalysis.core.topology import Topology @@ -578,6 +579,8 @@ def test_groupby_int(self): class TestReprs(object): + @dec.skipif(parser_not_found('DCD'), + 'DCD parser not available. Are you using python 3?') def setUp(self): self.u = mda.Universe(PSF, DCD) @@ -919,6 +922,64 @@ def check_operator(op, method, level): yield check_operator, op, method, level +class TestGroupHash(object): + """ + Groups should be hashable. + + See issue #1397 + """ + def test_hash_exists(self): + def _hash_type(group): + assert_(isinstance(hash(group), int)) + + u = make_Universe(size=(3, 3, 3)) + for level in ('atoms', 'residues', 'segments'): + group = getattr(u, level) + yield _hash_type, group + + def test_hash_equality(self): + def _hash_equal(a, b): + assert_equal(hash(a), hash(b)) + + u = make_Universe(size=(3, 3, 3)) + for level in ('atoms', 'residues', 'segments'): + a = getattr(u, level)[0:-1] + b = getattr(u, level)[0:-1] + yield _hash_equal, a, b + + def test_hash_difference(self): + def _hash_not_equal(a, b): + assert_(hash(a) != hash(b)) + + u = make_Universe(size=(3, 3, 3)) + for level in ('atoms', 'residues', 'segments'): + a = getattr(u, level)[:-1] + b = getattr(u, level)[1:] + yield _hash_not_equal, a, b + + def test_hash_difference_cross(self): + def _hash_not_equal(a, b): + assert_(hash(a) != hash(b)) + + u = make_Universe(size=(3, 3, 3)) + levels = ('atoms', 'residues', 'segments') + for level_a, level_b in itertools.permutations(levels, 2): + a = getattr(u, level_a)[0:-1] + b = getattr(u, level_b)[0:-1] + yield _hash_not_equal, a, b + + def test_hash_diff_cross_universe(self): + def _hash_not_equal(a, b): + assert_(hash(a) != hash(b)) + + u = make_Universe(size=(3, 3, 3)) + u2 = make_Universe(size=(3, 3, 3)) + for level in ('atoms', 'residues', 'segments'): + a = getattr(u, level) + b = getattr(u2, level) + yield _hash_not_equal, a, b + + class TestAtomGroup(object): @staticmethod From 9dc173783fae2712c9ccba27f8032bfb440ec4cb Mon Sep 17 00:00:00 2001 From: Brigitta Sipocz Date: Sat, 17 Jun 2017 19:37:12 +0100 Subject: [PATCH 12/35] Use common setup script rather than OS specific ones (#1408) --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 66a56880381..77330999d37 100644 --- a/.travis.yml +++ b/.travis.yml @@ -79,7 +79,7 @@ matrix: install: - git clone git://github.com/astropy/ci-helpers.git - - source ci-helpers/travis/setup_conda_$TRAVIS_OS_NAME.sh + - source ci-helpers/travis/setup_conda.sh # additional external tools (Issue #898) -- HOLE - | if [[ $NAME == 'full' ]]; then \ From 785cfc4418c648f209d7c4330752d35b102f3582 Mon Sep 17 00:00:00 2001 From: Max Linke Date: Sat, 17 Jun 2017 11:30:17 +0200 Subject: [PATCH 13/35] update copyright year --- package/MDAnalysis/__init__.py | 2 +- package/MDAnalysis/analysis/__init__.py | 2 +- package/MDAnalysis/analysis/align.py | 2 +- package/MDAnalysis/analysis/base.py | 2 +- package/MDAnalysis/analysis/contacts.py | 2 +- package/MDAnalysis/analysis/density.py | 2 +- package/MDAnalysis/analysis/diffusionmap.py | 2 +- package/MDAnalysis/analysis/distances.py | 2 +- package/MDAnalysis/analysis/encore/__init__.py | 2 +- package/MDAnalysis/analysis/encore/bootstrap.py | 2 +- .../MDAnalysis/analysis/encore/clustering/ClusterCollection.py | 2 +- .../MDAnalysis/analysis/encore/clustering/ClusteringMethod.py | 2 +- package/MDAnalysis/analysis/encore/clustering/__init__.py | 2 +- package/MDAnalysis/analysis/encore/clustering/affinityprop.pyx | 2 +- package/MDAnalysis/analysis/encore/clustering/caffinityprop.pxd | 2 +- package/MDAnalysis/analysis/encore/clustering/cluster.py | 2 +- package/MDAnalysis/analysis/encore/confdistmatrix.py | 2 +- package/MDAnalysis/analysis/encore/covariance.py | 2 +- package/MDAnalysis/analysis/encore/cutils.pyx | 2 +- .../dimensionality_reduction/DimensionalityReductionMethod.py | 2 +- .../analysis/encore/dimensionality_reduction/__init__.py | 2 +- .../encore/dimensionality_reduction/cstochasticproxembed.pxd | 2 +- .../encore/dimensionality_reduction/reduce_dimensionality.py | 2 +- .../encore/dimensionality_reduction/stochasticproxembed.pyx | 2 +- package/MDAnalysis/analysis/encore/similarity.py | 2 +- package/MDAnalysis/analysis/encore/utils.py | 2 +- package/MDAnalysis/analysis/gnm.py | 2 +- package/MDAnalysis/analysis/hbonds/__init__.py | 2 +- package/MDAnalysis/analysis/hbonds/hbond_analysis.py | 2 +- package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py | 2 +- package/MDAnalysis/analysis/helanal.py | 2 +- package/MDAnalysis/analysis/hole.py | 2 +- package/MDAnalysis/analysis/leaflet.py | 2 +- package/MDAnalysis/analysis/legacy/__init__.py | 2 +- package/MDAnalysis/analysis/legacy/x3dna.py | 2 +- package/MDAnalysis/analysis/lineardensity.py | 2 +- package/MDAnalysis/analysis/nuclinfo.py | 2 +- package/MDAnalysis/analysis/pca.py | 2 +- package/MDAnalysis/analysis/polymer.py | 2 +- package/MDAnalysis/analysis/psa.py | 2 +- package/MDAnalysis/analysis/rdf.py | 2 +- package/MDAnalysis/analysis/rms.py | 2 +- package/MDAnalysis/analysis/waterdynamics.py | 2 +- package/MDAnalysis/analysis/x3dna.py | 2 +- package/MDAnalysis/auxiliary/XVG.py | 2 +- package/MDAnalysis/auxiliary/__init__.py | 2 +- package/MDAnalysis/auxiliary/base.py | 2 +- package/MDAnalysis/auxiliary/core.py | 2 +- package/MDAnalysis/coordinates/CRD.py | 2 +- package/MDAnalysis/coordinates/DCD.py | 2 +- package/MDAnalysis/coordinates/DLPoly.py | 2 +- package/MDAnalysis/coordinates/DMS.py | 2 +- package/MDAnalysis/coordinates/GMS.py | 2 +- package/MDAnalysis/coordinates/GRO.py | 2 +- package/MDAnalysis/coordinates/INPCRD.py | 2 +- package/MDAnalysis/coordinates/LAMMPS.py | 2 +- package/MDAnalysis/coordinates/MMTF.py | 2 +- package/MDAnalysis/coordinates/MOL2.py | 2 +- package/MDAnalysis/coordinates/PDB.py | 2 +- package/MDAnalysis/coordinates/PDBQT.py | 2 +- package/MDAnalysis/coordinates/PQR.py | 2 +- package/MDAnalysis/coordinates/TRJ.py | 2 +- package/MDAnalysis/coordinates/TRR.py | 2 +- package/MDAnalysis/coordinates/TRZ.py | 2 +- package/MDAnalysis/coordinates/XDR.py | 2 +- package/MDAnalysis/coordinates/XTC.py | 2 +- package/MDAnalysis/coordinates/XYZ.py | 2 +- package/MDAnalysis/coordinates/__init__.py | 2 +- package/MDAnalysis/coordinates/base.py | 2 +- package/MDAnalysis/coordinates/chain.py | 2 +- package/MDAnalysis/coordinates/core.py | 2 +- package/MDAnalysis/coordinates/dcdtimeseries.pyx | 2 +- package/MDAnalysis/coordinates/memory.py | 2 +- package/MDAnalysis/coordinates/null.py | 2 +- package/MDAnalysis/core/AtomGroup.py | 2 +- package/MDAnalysis/core/Timeseries.py | 2 +- package/MDAnalysis/core/__init__.py | 2 +- package/MDAnalysis/core/groups.py | 2 +- package/MDAnalysis/core/selection.py | 2 +- package/MDAnalysis/core/topology.py | 2 +- package/MDAnalysis/core/topologyattrs.py | 2 +- package/MDAnalysis/core/topologyobjects.py | 2 +- package/MDAnalysis/core/universe.py | 2 +- package/MDAnalysis/exceptions.py | 2 +- package/MDAnalysis/lib/NeighborSearch.py | 2 +- package/MDAnalysis/lib/__init__.py | 2 +- package/MDAnalysis/lib/c_distances.pyx | 2 +- package/MDAnalysis/lib/c_distances_openmp.pyx | 2 +- package/MDAnalysis/lib/distances.py | 2 +- package/MDAnalysis/lib/formats/__init__.py | 2 +- package/MDAnalysis/lib/formats/cython_util.pxd | 2 +- package/MDAnalysis/lib/formats/cython_util.pyx | 2 +- package/MDAnalysis/lib/formats/libmdaxdr.pyx | 2 +- package/MDAnalysis/lib/log.py | 2 +- package/MDAnalysis/lib/mdamath.py | 2 +- package/MDAnalysis/lib/util.py | 2 +- package/MDAnalysis/selections/__init__.py | 2 +- package/MDAnalysis/selections/base.py | 2 +- package/MDAnalysis/selections/charmm.py | 2 +- package/MDAnalysis/selections/gromacs.py | 2 +- package/MDAnalysis/selections/jmol.py | 2 +- package/MDAnalysis/selections/pymol.py | 2 +- package/MDAnalysis/selections/vmd.py | 2 +- package/MDAnalysis/tests/__init__.py | 2 +- package/MDAnalysis/tests/datafiles.py | 2 +- package/MDAnalysis/topology/CRDParser.py | 2 +- package/MDAnalysis/topology/DLPolyParser.py | 2 +- package/MDAnalysis/topology/DMSParser.py | 2 +- package/MDAnalysis/topology/ExtendedPDBParser.py | 2 +- package/MDAnalysis/topology/GMSParser.py | 2 +- package/MDAnalysis/topology/GROParser.py | 2 +- package/MDAnalysis/topology/HoomdXMLParser.py | 2 +- package/MDAnalysis/topology/LAMMPSParser.py | 2 +- package/MDAnalysis/topology/MMTFParser.py | 2 +- package/MDAnalysis/topology/MOL2Parser.py | 2 +- package/MDAnalysis/topology/PDBParser.py | 2 +- package/MDAnalysis/topology/PDBQTParser.py | 2 +- package/MDAnalysis/topology/PQRParser.py | 2 +- package/MDAnalysis/topology/PSFParser.py | 2 +- package/MDAnalysis/topology/TOPParser.py | 2 +- package/MDAnalysis/topology/TPRParser.py | 2 +- package/MDAnalysis/topology/XYZParser.py | 2 +- package/MDAnalysis/topology/__init__.py | 2 +- package/MDAnalysis/topology/_elements.py | 2 +- package/MDAnalysis/topology/base.py | 2 +- package/MDAnalysis/topology/core.py | 2 +- package/MDAnalysis/topology/guessers.py | 2 +- package/MDAnalysis/topology/tables.py | 2 +- package/MDAnalysis/topology/tpr/__init__.py | 2 +- package/MDAnalysis/topology/tpr/obj.py | 2 +- package/MDAnalysis/topology/tpr/setting.py | 2 +- package/MDAnalysis/topology/tpr/utils.py | 2 +- package/MDAnalysis/units.py | 2 +- package/MDAnalysis/version.py | 2 +- package/MDAnalysis/visualization/__init__.py | 2 +- package/MDAnalysis/visualization/streamlines.py | 2 +- package/MDAnalysis/visualization/streamlines_3D.py | 2 +- .../doc/sphinx/source/documentation_pages/analysis/encore.rst | 2 +- package/setup.py | 2 +- testsuite/MDAnalysisTests/__init__.py | 2 +- testsuite/MDAnalysisTests/analysis/test_align.py | 2 +- testsuite/MDAnalysisTests/analysis/test_base.py | 2 +- testsuite/MDAnalysisTests/analysis/test_contacts.py | 2 +- testsuite/MDAnalysisTests/analysis/test_density.py | 2 +- testsuite/MDAnalysisTests/analysis/test_diffusionmap.py | 2 +- testsuite/MDAnalysisTests/analysis/test_distances.py | 2 +- testsuite/MDAnalysisTests/analysis/test_encore.py | 2 +- testsuite/MDAnalysisTests/analysis/test_gnm.py | 2 +- testsuite/MDAnalysisTests/analysis/test_hbonds.py | 2 +- testsuite/MDAnalysisTests/analysis/test_helanal.py | 2 +- testsuite/MDAnalysisTests/analysis/test_hole.py | 2 +- .../MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py | 2 +- testsuite/MDAnalysisTests/analysis/test_leaflet.py | 2 +- testsuite/MDAnalysisTests/analysis/test_lineardensity.py | 2 +- testsuite/MDAnalysisTests/analysis/test_nuclinfo.py | 2 +- testsuite/MDAnalysisTests/analysis/test_pca.py | 2 +- testsuite/MDAnalysisTests/analysis/test_persistencelength.py | 2 +- testsuite/MDAnalysisTests/analysis/test_psa.py | 2 +- testsuite/MDAnalysisTests/analysis/test_rdf.py | 2 +- testsuite/MDAnalysisTests/analysis/test_rms.py | 2 +- testsuite/MDAnalysisTests/analysis/test_waterdynamics.py | 2 +- testsuite/MDAnalysisTests/auxiliary/base.py | 2 +- testsuite/MDAnalysisTests/auxiliary/test_xvg.py | 2 +- testsuite/MDAnalysisTests/coordinates/base.py | 2 +- testsuite/MDAnalysisTests/coordinates/reference.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_chainreader.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_crd.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_dcd.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_dlpoly.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_dms.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_gms.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_gro.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_lammps.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_memory.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_mmtf.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_mol2.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_netcdf.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_null.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_pdb.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_pdbqt.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_pqr.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_reader_api.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_timestep_api.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_trj.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_trz.py | 2 +- .../MDAnalysisTests/coordinates/test_writer_registration.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_xdr.py | 2 +- testsuite/MDAnalysisTests/coordinates/test_xyz.py | 2 +- testsuite/MDAnalysisTests/core/test_atom.py | 2 +- testsuite/MDAnalysisTests/core/test_atomgroup.py | 2 +- testsuite/MDAnalysisTests/core/test_atomselections.py | 2 +- testsuite/MDAnalysisTests/core/test_fragments.py | 2 +- testsuite/MDAnalysisTests/core/test_group_traj_access.py | 2 +- testsuite/MDAnalysisTests/core/test_groups.py | 2 +- testsuite/MDAnalysisTests/core/test_index_dtype.py | 2 +- testsuite/MDAnalysisTests/core/test_residue.py | 2 +- testsuite/MDAnalysisTests/core/test_residuegroup.py | 2 +- testsuite/MDAnalysisTests/core/test_segment.py | 2 +- testsuite/MDAnalysisTests/core/test_segmentgroup.py | 2 +- testsuite/MDAnalysisTests/core/test_topologyattrs.py | 2 +- testsuite/MDAnalysisTests/core/test_topologyobjects.py | 2 +- testsuite/MDAnalysisTests/core/test_universe.py | 2 +- testsuite/MDAnalysisTests/core/test_updating_atomgroup.py | 2 +- testsuite/MDAnalysisTests/core/util.py | 2 +- testsuite/MDAnalysisTests/datafiles.py | 2 +- testsuite/MDAnalysisTests/formats/test_libmdaxdr.py | 2 +- testsuite/MDAnalysisTests/lib/test_util.py | 2 +- testsuite/MDAnalysisTests/plugins/__init__.py | 2 +- testsuite/MDAnalysisTests/plugins/capture_err.py | 2 +- testsuite/MDAnalysisTests/plugins/cleanup.py | 2 +- testsuite/MDAnalysisTests/plugins/knownfailure.py | 2 +- testsuite/MDAnalysisTests/plugins/memleak.py | 2 +- testsuite/MDAnalysisTests/plugins/open_files.py | 2 +- testsuite/MDAnalysisTests/test_altloc.py | 2 +- testsuite/MDAnalysisTests/test_authors.py | 2 +- testsuite/MDAnalysisTests/test_datafiles.py | 2 +- testsuite/MDAnalysisTests/test_deprecated.py | 2 +- testsuite/MDAnalysisTests/test_distances.py | 2 +- testsuite/MDAnalysisTests/test_failure.py | 2 +- testsuite/MDAnalysisTests/test_imports.py | 2 +- testsuite/MDAnalysisTests/test_log.py | 2 +- testsuite/MDAnalysisTests/test_meta.py | 2 +- testsuite/MDAnalysisTests/test_modelling.py | 2 +- testsuite/MDAnalysisTests/test_nuclinfo.py | 2 +- testsuite/MDAnalysisTests/test_persistence.py | 2 +- testsuite/MDAnalysisTests/test_qcprot.py | 2 +- testsuite/MDAnalysisTests/test_selections.py | 2 +- testsuite/MDAnalysisTests/test_streamio.py | 2 +- testsuite/MDAnalysisTests/test_transformations.py | 2 +- testsuite/MDAnalysisTests/test_units.py | 2 +- testsuite/MDAnalysisTests/topology/base.py | 2 +- testsuite/MDAnalysisTests/topology/test_crd.py | 2 +- testsuite/MDAnalysisTests/topology/test_dlpoly.py | 2 +- testsuite/MDAnalysisTests/topology/test_dms.py | 2 +- testsuite/MDAnalysisTests/topology/test_gms.py | 2 +- testsuite/MDAnalysisTests/topology/test_gro.py | 2 +- testsuite/MDAnalysisTests/topology/test_guessers.py | 2 +- testsuite/MDAnalysisTests/topology/test_hoomdxml.py | 2 +- testsuite/MDAnalysisTests/topology/test_lammpsdata.py | 2 +- testsuite/MDAnalysisTests/topology/test_mol2.py | 2 +- testsuite/MDAnalysisTests/topology/test_pdb.py | 2 +- testsuite/MDAnalysisTests/topology/test_pdbqt.py | 2 +- testsuite/MDAnalysisTests/topology/test_pqr.py | 2 +- testsuite/MDAnalysisTests/topology/test_psf.py | 2 +- testsuite/MDAnalysisTests/topology/test_top.py | 2 +- testsuite/MDAnalysisTests/topology/test_tprparser.py | 2 +- testsuite/MDAnalysisTests/topology/test_xpdb.py | 2 +- testsuite/MDAnalysisTests/topology/test_xyz.py | 2 +- testsuite/MDAnalysisTests/util.py | 2 +- testsuite/setup.py | 2 +- 251 files changed, 251 insertions(+), 251 deletions(-) diff --git a/package/MDAnalysis/__init__.py b/package/MDAnalysis/__init__.py index 86fcc76ec0c..d324854bf16 100644 --- a/package/MDAnalysis/__init__.py +++ b/package/MDAnalysis/__init__.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/__init__.py b/package/MDAnalysis/analysis/__init__.py index a610846c46f..433baf6deae 100644 --- a/package/MDAnalysis/analysis/__init__.py +++ b/package/MDAnalysis/analysis/__init__.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/align.py b/package/MDAnalysis/analysis/align.py index 6a9617cba43..ce65f2a0e4a 100644 --- a/package/MDAnalysis/analysis/align.py +++ b/package/MDAnalysis/analysis/align.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/base.py b/package/MDAnalysis/analysis/base.py index 326ea67e37b..c6713a5ddaa 100644 --- a/package/MDAnalysis/analysis/base.py +++ b/package/MDAnalysis/analysis/base.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/contacts.py b/package/MDAnalysis/analysis/contacts.py index 64f4eb93206..493a35f6705 100644 --- a/package/MDAnalysis/analysis/contacts.py +++ b/package/MDAnalysis/analysis/contacts.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/density.py b/package/MDAnalysis/analysis/density.py index 26d45af3fd5..3ae09620145 100644 --- a/package/MDAnalysis/analysis/density.py +++ b/package/MDAnalysis/analysis/density.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/diffusionmap.py b/package/MDAnalysis/analysis/diffusionmap.py index b05a5078bbe..48fa3cad52d 100644 --- a/package/MDAnalysis/analysis/diffusionmap.py +++ b/package/MDAnalysis/analysis/diffusionmap.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/distances.py b/package/MDAnalysis/analysis/distances.py index c6473ccd3ae..ae4ad699141 100644 --- a/package/MDAnalysis/analysis/distances.py +++ b/package/MDAnalysis/analysis/distances.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/encore/__init__.py b/package/MDAnalysis/analysis/encore/__init__.py index f28a11c520c..5f64a4b400f 100644 --- a/package/MDAnalysis/analysis/encore/__init__.py +++ b/package/MDAnalysis/analysis/encore/__init__.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/encore/bootstrap.py b/package/MDAnalysis/analysis/encore/bootstrap.py index 8bee0c4e00c..6fe4d328d42 100644 --- a/package/MDAnalysis/analysis/encore/bootstrap.py +++ b/package/MDAnalysis/analysis/encore/bootstrap.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/encore/clustering/ClusterCollection.py b/package/MDAnalysis/analysis/encore/clustering/ClusterCollection.py index 096faa05dcc..fcf9dd5b6c8 100644 --- a/package/MDAnalysis/analysis/encore/clustering/ClusterCollection.py +++ b/package/MDAnalysis/analysis/encore/clustering/ClusterCollection.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py b/package/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py index a293b755e3e..78d9b489d5e 100644 --- a/package/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py +++ b/package/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/encore/clustering/__init__.py b/package/MDAnalysis/analysis/encore/clustering/__init__.py index 5832238dec0..b0824575bc2 100644 --- a/package/MDAnalysis/analysis/encore/clustering/__init__.py +++ b/package/MDAnalysis/analysis/encore/clustering/__init__.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/encore/clustering/affinityprop.pyx b/package/MDAnalysis/analysis/encore/clustering/affinityprop.pyx index 0b1eaab50d7..f43b03a83e5 100644 --- a/package/MDAnalysis/analysis/encore/clustering/affinityprop.pyx +++ b/package/MDAnalysis/analysis/encore/clustering/affinityprop.pyx @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/encore/clustering/caffinityprop.pxd b/package/MDAnalysis/analysis/encore/clustering/caffinityprop.pxd index 7c48ec552d1..7a6582d0a10 100644 --- a/package/MDAnalysis/analysis/encore/clustering/caffinityprop.pxd +++ b/package/MDAnalysis/analysis/encore/clustering/caffinityprop.pxd @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/encore/clustering/cluster.py b/package/MDAnalysis/analysis/encore/clustering/cluster.py index 709140692d2..b976fc04d85 100644 --- a/package/MDAnalysis/analysis/encore/clustering/cluster.py +++ b/package/MDAnalysis/analysis/encore/clustering/cluster.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/encore/confdistmatrix.py b/package/MDAnalysis/analysis/encore/confdistmatrix.py index 5f3ab4d23ac..0c757da7d06 100644 --- a/package/MDAnalysis/analysis/encore/confdistmatrix.py +++ b/package/MDAnalysis/analysis/encore/confdistmatrix.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/encore/covariance.py b/package/MDAnalysis/analysis/encore/covariance.py index 4076c1319f5..f79b8fe738b 100644 --- a/package/MDAnalysis/analysis/encore/covariance.py +++ b/package/MDAnalysis/analysis/encore/covariance.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/encore/cutils.pyx b/package/MDAnalysis/analysis/encore/cutils.pyx index 244bf06009e..959323c0dfa 100644 --- a/package/MDAnalysis/analysis/encore/cutils.pyx +++ b/package/MDAnalysis/analysis/encore/cutils.pyx @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py b/package/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py index dfb6226d2e8..e5c019fcac3 100644 --- a/package/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py +++ b/package/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py b/package/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py index 8ae75f4351e..aedc306f5b1 100644 --- a/package/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py +++ b/package/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/encore/dimensionality_reduction/cstochasticproxembed.pxd b/package/MDAnalysis/analysis/encore/dimensionality_reduction/cstochasticproxembed.pxd index fff1ec35fe2..85194ad637f 100644 --- a/package/MDAnalysis/analysis/encore/dimensionality_reduction/cstochasticproxembed.pxd +++ b/package/MDAnalysis/analysis/encore/dimensionality_reduction/cstochasticproxembed.pxd @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py b/package/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py index 3b4170172a9..7069897c46e 100644 --- a/package/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py +++ b/package/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx b/package/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx index 8a25ab3f0c6..45262298dd4 100644 --- a/package/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx +++ b/package/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/encore/similarity.py b/package/MDAnalysis/analysis/encore/similarity.py index d0befb76597..bd7e9e5e0ea 100644 --- a/package/MDAnalysis/analysis/encore/similarity.py +++ b/package/MDAnalysis/analysis/encore/similarity.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/encore/utils.py b/package/MDAnalysis/analysis/encore/utils.py index f65d925f812..47823cfd865 100644 --- a/package/MDAnalysis/analysis/encore/utils.py +++ b/package/MDAnalysis/analysis/encore/utils.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/gnm.py b/package/MDAnalysis/analysis/gnm.py index b4a39065028..a553dd728d2 100644 --- a/package/MDAnalysis/analysis/gnm.py +++ b/package/MDAnalysis/analysis/gnm.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/hbonds/__init__.py b/package/MDAnalysis/analysis/hbonds/__init__.py index c5110f968fb..6dae3a5e11b 100644 --- a/package/MDAnalysis/analysis/hbonds/__init__.py +++ b/package/MDAnalysis/analysis/hbonds/__init__.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/hbonds/hbond_analysis.py b/package/MDAnalysis/analysis/hbonds/hbond_analysis.py index 4b47afc6b95..a2af6fb352d 100644 --- a/package/MDAnalysis/analysis/hbonds/hbond_analysis.py +++ b/package/MDAnalysis/analysis/hbonds/hbond_analysis.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py b/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py index 00434fa0c12..a0bf6bb5451 100644 --- a/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py +++ b/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/helanal.py b/package/MDAnalysis/analysis/helanal.py index 7a7a6f32ea8..51da838b3b8 100644 --- a/package/MDAnalysis/analysis/helanal.py +++ b/package/MDAnalysis/analysis/helanal.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/hole.py b/package/MDAnalysis/analysis/hole.py index e129c3f07fb..e43316a868c 100644 --- a/package/MDAnalysis/analysis/hole.py +++ b/package/MDAnalysis/analysis/hole.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/leaflet.py b/package/MDAnalysis/analysis/leaflet.py index 1ac460fc633..612b6004350 100644 --- a/package/MDAnalysis/analysis/leaflet.py +++ b/package/MDAnalysis/analysis/leaflet.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/legacy/__init__.py b/package/MDAnalysis/analysis/legacy/__init__.py index 1b6b72fbac4..532136ce9f4 100644 --- a/package/MDAnalysis/analysis/legacy/__init__.py +++ b/package/MDAnalysis/analysis/legacy/__init__.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/legacy/x3dna.py b/package/MDAnalysis/analysis/legacy/x3dna.py index 76acb3d0560..f960cd1fc5d 100644 --- a/package/MDAnalysis/analysis/legacy/x3dna.py +++ b/package/MDAnalysis/analysis/legacy/x3dna.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/lineardensity.py b/package/MDAnalysis/analysis/lineardensity.py index 4a79099bcbe..0f9374e9f6f 100644 --- a/package/MDAnalysis/analysis/lineardensity.py +++ b/package/MDAnalysis/analysis/lineardensity.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/nuclinfo.py b/package/MDAnalysis/analysis/nuclinfo.py index 2afca85c0ce..8e69a416316 100644 --- a/package/MDAnalysis/analysis/nuclinfo.py +++ b/package/MDAnalysis/analysis/nuclinfo.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/pca.py b/package/MDAnalysis/analysis/pca.py index ca5e00ef5d3..18d729ecc08 100644 --- a/package/MDAnalysis/analysis/pca.py +++ b/package/MDAnalysis/analysis/pca.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/polymer.py b/package/MDAnalysis/analysis/polymer.py index 315306ec52e..645055e1878 100644 --- a/package/MDAnalysis/analysis/polymer.py +++ b/package/MDAnalysis/analysis/polymer.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/psa.py b/package/MDAnalysis/analysis/psa.py index 3e7430e166d..6c002241a40 100644 --- a/package/MDAnalysis/analysis/psa.py +++ b/package/MDAnalysis/analysis/psa.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/rdf.py b/package/MDAnalysis/analysis/rdf.py index 819f5c1d168..d8bb6f2fde2 100644 --- a/package/MDAnalysis/analysis/rdf.py +++ b/package/MDAnalysis/analysis/rdf.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/rms.py b/package/MDAnalysis/analysis/rms.py index eb27b62d005..6e935e10f28 100644 --- a/package/MDAnalysis/analysis/rms.py +++ b/package/MDAnalysis/analysis/rms.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/waterdynamics.py b/package/MDAnalysis/analysis/waterdynamics.py index 610b362ed8e..a2086d40316 100644 --- a/package/MDAnalysis/analysis/waterdynamics.py +++ b/package/MDAnalysis/analysis/waterdynamics.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/analysis/x3dna.py b/package/MDAnalysis/analysis/x3dna.py index 6632e00679d..48ec3c2ed28 100644 --- a/package/MDAnalysis/analysis/x3dna.py +++ b/package/MDAnalysis/analysis/x3dna.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/auxiliary/XVG.py b/package/MDAnalysis/auxiliary/XVG.py index 83cbd8d13a9..fa666887704 100644 --- a/package/MDAnalysis/auxiliary/XVG.py +++ b/package/MDAnalysis/auxiliary/XVG.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/auxiliary/__init__.py b/package/MDAnalysis/auxiliary/__init__.py index c6e891c75b7..4e8c8c147cb 100644 --- a/package/MDAnalysis/auxiliary/__init__.py +++ b/package/MDAnalysis/auxiliary/__init__.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/auxiliary/base.py b/package/MDAnalysis/auxiliary/base.py index 63a790719ed..3b003de7c4e 100644 --- a/package/MDAnalysis/auxiliary/base.py +++ b/package/MDAnalysis/auxiliary/base.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/auxiliary/core.py b/package/MDAnalysis/auxiliary/core.py index 08996b32e96..b22bec5f2c1 100644 --- a/package/MDAnalysis/auxiliary/core.py +++ b/package/MDAnalysis/auxiliary/core.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/CRD.py b/package/MDAnalysis/coordinates/CRD.py index c005da25e8f..9ae5e527b84 100644 --- a/package/MDAnalysis/coordinates/CRD.py +++ b/package/MDAnalysis/coordinates/CRD.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/DCD.py b/package/MDAnalysis/coordinates/DCD.py index e30f52f4600..0f5a0eb9693 100644 --- a/package/MDAnalysis/coordinates/DCD.py +++ b/package/MDAnalysis/coordinates/DCD.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/DLPoly.py b/package/MDAnalysis/coordinates/DLPoly.py index ca48e768cfd..1d547866395 100644 --- a/package/MDAnalysis/coordinates/DLPoly.py +++ b/package/MDAnalysis/coordinates/DLPoly.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/DMS.py b/package/MDAnalysis/coordinates/DMS.py index e9f2f88492b..48ad86d886e 100644 --- a/package/MDAnalysis/coordinates/DMS.py +++ b/package/MDAnalysis/coordinates/DMS.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/GMS.py b/package/MDAnalysis/coordinates/GMS.py index 840d2588bb4..2804c811198 100644 --- a/package/MDAnalysis/coordinates/GMS.py +++ b/package/MDAnalysis/coordinates/GMS.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/GRO.py b/package/MDAnalysis/coordinates/GRO.py index 7691b9fb2cb..008694d2364 100644 --- a/package/MDAnalysis/coordinates/GRO.py +++ b/package/MDAnalysis/coordinates/GRO.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py index 96b14bd653b..e86010eb450 100644 --- a/package/MDAnalysis/coordinates/INPCRD.py +++ b/package/MDAnalysis/coordinates/INPCRD.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/LAMMPS.py b/package/MDAnalysis/coordinates/LAMMPS.py index 6ffd9da5a38..a784bb19bbc 100644 --- a/package/MDAnalysis/coordinates/LAMMPS.py +++ b/package/MDAnalysis/coordinates/LAMMPS.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/MMTF.py b/package/MDAnalysis/coordinates/MMTF.py index 7c2d7293b2d..4c32e7ef357 100644 --- a/package/MDAnalysis/coordinates/MMTF.py +++ b/package/MDAnalysis/coordinates/MMTF.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/MOL2.py b/package/MDAnalysis/coordinates/MOL2.py index 0903c79c0d5..e71f91b6444 100644 --- a/package/MDAnalysis/coordinates/MOL2.py +++ b/package/MDAnalysis/coordinates/MOL2.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/PDB.py b/package/MDAnalysis/coordinates/PDB.py index 910b42ca939..31d53ed9009 100644 --- a/package/MDAnalysis/coordinates/PDB.py +++ b/package/MDAnalysis/coordinates/PDB.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/PDBQT.py b/package/MDAnalysis/coordinates/PDBQT.py index e16e2792831..17efa072d57 100644 --- a/package/MDAnalysis/coordinates/PDBQT.py +++ b/package/MDAnalysis/coordinates/PDBQT.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/PQR.py b/package/MDAnalysis/coordinates/PQR.py index fa61a35d11b..cf94c1bede8 100644 --- a/package/MDAnalysis/coordinates/PQR.py +++ b/package/MDAnalysis/coordinates/PQR.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/TRJ.py b/package/MDAnalysis/coordinates/TRJ.py index 9e7eea6947c..d1760c8841d 100644 --- a/package/MDAnalysis/coordinates/TRJ.py +++ b/package/MDAnalysis/coordinates/TRJ.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/TRR.py b/package/MDAnalysis/coordinates/TRR.py index edeffd2991d..5bc6c97a4a3 100644 --- a/package/MDAnalysis/coordinates/TRR.py +++ b/package/MDAnalysis/coordinates/TRR.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/TRZ.py b/package/MDAnalysis/coordinates/TRZ.py index 0788f79600d..58fb5abe819 100644 --- a/package/MDAnalysis/coordinates/TRZ.py +++ b/package/MDAnalysis/coordinates/TRZ.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/XDR.py b/package/MDAnalysis/coordinates/XDR.py index 0104c67bc79..0223b6fbc21 100644 --- a/package/MDAnalysis/coordinates/XDR.py +++ b/package/MDAnalysis/coordinates/XDR.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/XTC.py b/package/MDAnalysis/coordinates/XTC.py index 5788cb70d2e..590ad533b16 100644 --- a/package/MDAnalysis/coordinates/XTC.py +++ b/package/MDAnalysis/coordinates/XTC.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/XYZ.py b/package/MDAnalysis/coordinates/XYZ.py index f06b148db53..1d1ac4066cc 100644 --- a/package/MDAnalysis/coordinates/XYZ.py +++ b/package/MDAnalysis/coordinates/XYZ.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/__init__.py b/package/MDAnalysis/coordinates/__init__.py index 7410d391c2c..45c13eada4d 100644 --- a/package/MDAnalysis/coordinates/__init__.py +++ b/package/MDAnalysis/coordinates/__init__.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/base.py b/package/MDAnalysis/coordinates/base.py index f882eefe15c..4a71a576606 100644 --- a/package/MDAnalysis/coordinates/base.py +++ b/package/MDAnalysis/coordinates/base.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/chain.py b/package/MDAnalysis/coordinates/chain.py index c706383f9f9..7b8e3975398 100644 --- a/package/MDAnalysis/coordinates/chain.py +++ b/package/MDAnalysis/coordinates/chain.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/core.py b/package/MDAnalysis/coordinates/core.py index 7338b2ad7fa..39b6455e041 100644 --- a/package/MDAnalysis/coordinates/core.py +++ b/package/MDAnalysis/coordinates/core.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/dcdtimeseries.pyx b/package/MDAnalysis/coordinates/dcdtimeseries.pyx index 89bc6212f7e..9da43d2fcc8 100644 --- a/package/MDAnalysis/coordinates/dcdtimeseries.pyx +++ b/package/MDAnalysis/coordinates/dcdtimeseries.pyx @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/memory.py b/package/MDAnalysis/coordinates/memory.py index 279009fbfd3..7a3bccab5ee 100644 --- a/package/MDAnalysis/coordinates/memory.py +++ b/package/MDAnalysis/coordinates/memory.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/coordinates/null.py b/package/MDAnalysis/coordinates/null.py index 30daa411d8b..b6eeee3de44 100644 --- a/package/MDAnalysis/coordinates/null.py +++ b/package/MDAnalysis/coordinates/null.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/core/AtomGroup.py b/package/MDAnalysis/core/AtomGroup.py index 9ebfe7fbbe5..bad0e5394ad 100644 --- a/package/MDAnalysis/core/AtomGroup.py +++ b/package/MDAnalysis/core/AtomGroup.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/core/Timeseries.py b/package/MDAnalysis/core/Timeseries.py index 6dc2952874b..f6c191667d6 100644 --- a/package/MDAnalysis/core/Timeseries.py +++ b/package/MDAnalysis/core/Timeseries.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/core/__init__.py b/package/MDAnalysis/core/__init__.py index 2101c1d878e..4d2c0bc71ad 100644 --- a/package/MDAnalysis/core/__init__.py +++ b/package/MDAnalysis/core/__init__.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py index 5c317740ffb..f9c2da1ebee 100644 --- a/package/MDAnalysis/core/groups.py +++ b/package/MDAnalysis/core/groups.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/core/selection.py b/package/MDAnalysis/core/selection.py index e86fe8e9630..ce76eb2e5a9 100644 --- a/package/MDAnalysis/core/selection.py +++ b/package/MDAnalysis/core/selection.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/core/topology.py b/package/MDAnalysis/core/topology.py index 3b98daabc91..09aa6fb401f 100644 --- a/package/MDAnalysis/core/topology.py +++ b/package/MDAnalysis/core/topology.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/core/topologyattrs.py b/package/MDAnalysis/core/topologyattrs.py index 9cdf56cfece..9976b9b5b88 100644 --- a/package/MDAnalysis/core/topologyattrs.py +++ b/package/MDAnalysis/core/topologyattrs.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/core/topologyobjects.py b/package/MDAnalysis/core/topologyobjects.py index 384180ee683..79d41cd4da2 100644 --- a/package/MDAnalysis/core/topologyobjects.py +++ b/package/MDAnalysis/core/topologyobjects.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/core/universe.py b/package/MDAnalysis/core/universe.py index 3a6e3decacc..1ce8cbf3f95 100644 --- a/package/MDAnalysis/core/universe.py +++ b/package/MDAnalysis/core/universe.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/exceptions.py b/package/MDAnalysis/exceptions.py index 94b6a40c80a..57261029c1b 100644 --- a/package/MDAnalysis/exceptions.py +++ b/package/MDAnalysis/exceptions.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/lib/NeighborSearch.py b/package/MDAnalysis/lib/NeighborSearch.py index 81d9e190753..02927dafb01 100644 --- a/package/MDAnalysis/lib/NeighborSearch.py +++ b/package/MDAnalysis/lib/NeighborSearch.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/lib/__init__.py b/package/MDAnalysis/lib/__init__.py index 0dd04d9abaf..d1508c69dc2 100644 --- a/package/MDAnalysis/lib/__init__.py +++ b/package/MDAnalysis/lib/__init__.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/lib/c_distances.pyx b/package/MDAnalysis/lib/c_distances.pyx index d3f39029713..85fb29a8f55 100644 --- a/package/MDAnalysis/lib/c_distances.pyx +++ b/package/MDAnalysis/lib/c_distances.pyx @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/lib/c_distances_openmp.pyx b/package/MDAnalysis/lib/c_distances_openmp.pyx index 6424d2215b1..13cbc6af2d9 100644 --- a/package/MDAnalysis/lib/c_distances_openmp.pyx +++ b/package/MDAnalysis/lib/c_distances_openmp.pyx @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/lib/distances.py b/package/MDAnalysis/lib/distances.py index 805138f7a1a..99513f143b9 100644 --- a/package/MDAnalysis/lib/distances.py +++ b/package/MDAnalysis/lib/distances.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/lib/formats/__init__.py b/package/MDAnalysis/lib/formats/__init__.py index 5a0fe576ab8..5a851008ea8 100644 --- a/package/MDAnalysis/lib/formats/__init__.py +++ b/package/MDAnalysis/lib/formats/__init__.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/lib/formats/cython_util.pxd b/package/MDAnalysis/lib/formats/cython_util.pxd index 2a31c3443e0..d702058d323 100644 --- a/package/MDAnalysis/lib/formats/cython_util.pxd +++ b/package/MDAnalysis/lib/formats/cython_util.pxd @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/lib/formats/cython_util.pyx b/package/MDAnalysis/lib/formats/cython_util.pyx index 22c2ed0c2b5..58e17358b96 100644 --- a/package/MDAnalysis/lib/formats/cython_util.pyx +++ b/package/MDAnalysis/lib/formats/cython_util.pyx @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/lib/formats/libmdaxdr.pyx b/package/MDAnalysis/lib/formats/libmdaxdr.pyx index bcba535a34a..1fcca0cbfdc 100644 --- a/package/MDAnalysis/lib/formats/libmdaxdr.pyx +++ b/package/MDAnalysis/lib/formats/libmdaxdr.pyx @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/lib/log.py b/package/MDAnalysis/lib/log.py index a0a04d2b2b2..49fd972047d 100644 --- a/package/MDAnalysis/lib/log.py +++ b/package/MDAnalysis/lib/log.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/lib/mdamath.py b/package/MDAnalysis/lib/mdamath.py index 03183d2a608..dd971c50e4e 100644 --- a/package/MDAnalysis/lib/mdamath.py +++ b/package/MDAnalysis/lib/mdamath.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/lib/util.py b/package/MDAnalysis/lib/util.py index d75517c7553..145dc52b12b 100644 --- a/package/MDAnalysis/lib/util.py +++ b/package/MDAnalysis/lib/util.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/selections/__init__.py b/package/MDAnalysis/selections/__init__.py index 61be07a4e3e..440a527577c 100644 --- a/package/MDAnalysis/selections/__init__.py +++ b/package/MDAnalysis/selections/__init__.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/selections/base.py b/package/MDAnalysis/selections/base.py index 29593392300..e3259673a47 100644 --- a/package/MDAnalysis/selections/base.py +++ b/package/MDAnalysis/selections/base.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/selections/charmm.py b/package/MDAnalysis/selections/charmm.py index 4e312732c4c..3023cb38f2a 100644 --- a/package/MDAnalysis/selections/charmm.py +++ b/package/MDAnalysis/selections/charmm.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/selections/gromacs.py b/package/MDAnalysis/selections/gromacs.py index 8f864265047..9f10cae1f2a 100644 --- a/package/MDAnalysis/selections/gromacs.py +++ b/package/MDAnalysis/selections/gromacs.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/selections/jmol.py b/package/MDAnalysis/selections/jmol.py index 90538fee1c2..fec7580eaad 100644 --- a/package/MDAnalysis/selections/jmol.py +++ b/package/MDAnalysis/selections/jmol.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/selections/pymol.py b/package/MDAnalysis/selections/pymol.py index d1975a20595..af43a4ca979 100644 --- a/package/MDAnalysis/selections/pymol.py +++ b/package/MDAnalysis/selections/pymol.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/selections/vmd.py b/package/MDAnalysis/selections/vmd.py index 576fd379b13..8b7a19fd7ff 100644 --- a/package/MDAnalysis/selections/vmd.py +++ b/package/MDAnalysis/selections/vmd.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/tests/__init__.py b/package/MDAnalysis/tests/__init__.py index 760455ebc71..dafd60b7054 100644 --- a/package/MDAnalysis/tests/__init__.py +++ b/package/MDAnalysis/tests/__init__.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/tests/datafiles.py b/package/MDAnalysis/tests/datafiles.py index f8c0ae9f7a5..df25ee33557 100644 --- a/package/MDAnalysis/tests/datafiles.py +++ b/package/MDAnalysis/tests/datafiles.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/CRDParser.py b/package/MDAnalysis/topology/CRDParser.py index cc9b105a81e..d0a16f6c534 100644 --- a/package/MDAnalysis/topology/CRDParser.py +++ b/package/MDAnalysis/topology/CRDParser.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/DLPolyParser.py b/package/MDAnalysis/topology/DLPolyParser.py index 3ac1e37d1b6..28642ac6893 100644 --- a/package/MDAnalysis/topology/DLPolyParser.py +++ b/package/MDAnalysis/topology/DLPolyParser.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/DMSParser.py b/package/MDAnalysis/topology/DMSParser.py index 3b0fd8065fb..e32c6100b88 100644 --- a/package/MDAnalysis/topology/DMSParser.py +++ b/package/MDAnalysis/topology/DMSParser.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/ExtendedPDBParser.py b/package/MDAnalysis/topology/ExtendedPDBParser.py index 2888eb2164f..c2313168d45 100644 --- a/package/MDAnalysis/topology/ExtendedPDBParser.py +++ b/package/MDAnalysis/topology/ExtendedPDBParser.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/GMSParser.py b/package/MDAnalysis/topology/GMSParser.py index c72364e06e3..ccf026f1c2a 100644 --- a/package/MDAnalysis/topology/GMSParser.py +++ b/package/MDAnalysis/topology/GMSParser.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/GROParser.py b/package/MDAnalysis/topology/GROParser.py index d2943528d74..436dc714dbf 100644 --- a/package/MDAnalysis/topology/GROParser.py +++ b/package/MDAnalysis/topology/GROParser.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/HoomdXMLParser.py b/package/MDAnalysis/topology/HoomdXMLParser.py index 65c4831fe4c..f0cab36af6e 100644 --- a/package/MDAnalysis/topology/HoomdXMLParser.py +++ b/package/MDAnalysis/topology/HoomdXMLParser.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/LAMMPSParser.py b/package/MDAnalysis/topology/LAMMPSParser.py index fb8ff1d5cd3..c29945fce06 100644 --- a/package/MDAnalysis/topology/LAMMPSParser.py +++ b/package/MDAnalysis/topology/LAMMPSParser.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/MMTFParser.py b/package/MDAnalysis/topology/MMTFParser.py index 3cedbb54a9d..e1e734bc9fa 100644 --- a/package/MDAnalysis/topology/MMTFParser.py +++ b/package/MDAnalysis/topology/MMTFParser.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/MOL2Parser.py b/package/MDAnalysis/topology/MOL2Parser.py index 47826023703..14049ba7a2f 100644 --- a/package/MDAnalysis/topology/MOL2Parser.py +++ b/package/MDAnalysis/topology/MOL2Parser.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/PDBParser.py b/package/MDAnalysis/topology/PDBParser.py index b90b637dee8..5fe531774c3 100644 --- a/package/MDAnalysis/topology/PDBParser.py +++ b/package/MDAnalysis/topology/PDBParser.py @@ -3,7 +3,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/PDBQTParser.py b/package/MDAnalysis/topology/PDBQTParser.py index 4ce2f342d62..5884113481b 100644 --- a/package/MDAnalysis/topology/PDBQTParser.py +++ b/package/MDAnalysis/topology/PDBQTParser.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/PQRParser.py b/package/MDAnalysis/topology/PQRParser.py index a6c4bc20d0f..27d900418c2 100644 --- a/package/MDAnalysis/topology/PQRParser.py +++ b/package/MDAnalysis/topology/PQRParser.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/PSFParser.py b/package/MDAnalysis/topology/PSFParser.py index 88cd11fe11d..e2c6fb35a5e 100644 --- a/package/MDAnalysis/topology/PSFParser.py +++ b/package/MDAnalysis/topology/PSFParser.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/TOPParser.py b/package/MDAnalysis/topology/TOPParser.py index c2931bc25c5..782968c4e1a 100644 --- a/package/MDAnalysis/topology/TOPParser.py +++ b/package/MDAnalysis/topology/TOPParser.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/TPRParser.py b/package/MDAnalysis/topology/TPRParser.py index f31c8df88ae..fea46a2cbf7 100644 --- a/package/MDAnalysis/topology/TPRParser.py +++ b/package/MDAnalysis/topology/TPRParser.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/XYZParser.py b/package/MDAnalysis/topology/XYZParser.py index 897f077c217..d6fdaf1d107 100644 --- a/package/MDAnalysis/topology/XYZParser.py +++ b/package/MDAnalysis/topology/XYZParser.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/__init__.py b/package/MDAnalysis/topology/__init__.py index 0536a5456fd..0a64c7acfac 100644 --- a/package/MDAnalysis/topology/__init__.py +++ b/package/MDAnalysis/topology/__init__.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/_elements.py b/package/MDAnalysis/topology/_elements.py index f9f271d17f8..2e38203c464 100644 --- a/package/MDAnalysis/topology/_elements.py +++ b/package/MDAnalysis/topology/_elements.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/base.py b/package/MDAnalysis/topology/base.py index eca072b37e3..2fe21ef533e 100644 --- a/package/MDAnalysis/topology/base.py +++ b/package/MDAnalysis/topology/base.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/core.py b/package/MDAnalysis/topology/core.py index fa3d1351c39..4d4a9bc7b7b 100644 --- a/package/MDAnalysis/topology/core.py +++ b/package/MDAnalysis/topology/core.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/guessers.py b/package/MDAnalysis/topology/guessers.py index 06dd9a16d2b..d0fa5c19e85 100644 --- a/package/MDAnalysis/topology/guessers.py +++ b/package/MDAnalysis/topology/guessers.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/tables.py b/package/MDAnalysis/topology/tables.py index 16975650068..547e537000d 100644 --- a/package/MDAnalysis/topology/tables.py +++ b/package/MDAnalysis/topology/tables.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/tpr/__init__.py b/package/MDAnalysis/topology/tpr/__init__.py index 9fdd672ed24..ce2c8392b7a 100644 --- a/package/MDAnalysis/topology/tpr/__init__.py +++ b/package/MDAnalysis/topology/tpr/__init__.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/tpr/obj.py b/package/MDAnalysis/topology/tpr/obj.py index 0acc0672512..766dceee937 100644 --- a/package/MDAnalysis/topology/tpr/obj.py +++ b/package/MDAnalysis/topology/tpr/obj.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/tpr/setting.py b/package/MDAnalysis/topology/tpr/setting.py index 39d21196299..7b052ed1394 100644 --- a/package/MDAnalysis/topology/tpr/setting.py +++ b/package/MDAnalysis/topology/tpr/setting.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/topology/tpr/utils.py b/package/MDAnalysis/topology/tpr/utils.py index 4567a7d9d40..84806ca335d 100644 --- a/package/MDAnalysis/topology/tpr/utils.py +++ b/package/MDAnalysis/topology/tpr/utils.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/units.py b/package/MDAnalysis/units.py index 8429d456ae6..f8be34e0048 100644 --- a/package/MDAnalysis/units.py +++ b/package/MDAnalysis/units.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/version.py b/package/MDAnalysis/version.py index 8340c569c80..c10e1c5f9e5 100644 --- a/package/MDAnalysis/version.py +++ b/package/MDAnalysis/version.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/visualization/__init__.py b/package/MDAnalysis/visualization/__init__.py index 0021927f5b6..98f3855b862 100644 --- a/package/MDAnalysis/visualization/__init__.py +++ b/package/MDAnalysis/visualization/__init__.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/visualization/streamlines.py b/package/MDAnalysis/visualization/streamlines.py index c8a81b6e299..365951e4634 100644 --- a/package/MDAnalysis/visualization/streamlines.py +++ b/package/MDAnalysis/visualization/streamlines.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/MDAnalysis/visualization/streamlines_3D.py b/package/MDAnalysis/visualization/streamlines_3D.py index c735b15dfdd..33ff60db3e6 100644 --- a/package/MDAnalysis/visualization/streamlines_3D.py +++ b/package/MDAnalysis/visualization/streamlines_3D.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/package/doc/sphinx/source/documentation_pages/analysis/encore.rst b/package/doc/sphinx/source/documentation_pages/analysis/encore.rst index eb65f624b1b..9ed7558f812 100644 --- a/package/doc/sphinx/source/documentation_pages/analysis/encore.rst +++ b/package/doc/sphinx/source/documentation_pages/analysis/encore.rst @@ -3,7 +3,7 @@ =============================================================================== :Author: Matteo Tiberti, Wouter Boomsma, Tone Bengtsen -:Year: 2015-2016 +:Year: 2015-2017 :Copyright: GNU Public License v3 :Maintainer: Matteo Tiberti , mtiberti on github diff --git a/package/setup.py b/package/setup.py index 1688ebc2ee3..5aecb4889c5 100755 --- a/package/setup.py +++ b/package/setup.py @@ -3,7 +3,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/__init__.py b/testsuite/MDAnalysisTests/__init__.py index 10c7f4627e8..81f330c43f2 100644 --- a/testsuite/MDAnalysisTests/__init__.py +++ b/testsuite/MDAnalysisTests/__init__.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_align.py b/testsuite/MDAnalysisTests/analysis/test_align.py index 7a0eb6c2061..be26bf99567 100644 --- a/testsuite/MDAnalysisTests/analysis/test_align.py +++ b/testsuite/MDAnalysisTests/analysis/test_align.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_base.py b/testsuite/MDAnalysisTests/analysis/test_base.py index a021f1805ed..db546af721e 100644 --- a/testsuite/MDAnalysisTests/analysis/test_base.py +++ b/testsuite/MDAnalysisTests/analysis/test_base.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_contacts.py b/testsuite/MDAnalysisTests/analysis/test_contacts.py index 93a72982605..1f5560ef056 100644 --- a/testsuite/MDAnalysisTests/analysis/test_contacts.py +++ b/testsuite/MDAnalysisTests/analysis/test_contacts.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_density.py b/testsuite/MDAnalysisTests/analysis/test_density.py index 94fc1c38dad..75502b71380 100644 --- a/testsuite/MDAnalysisTests/analysis/test_density.py +++ b/testsuite/MDAnalysisTests/analysis/test_density.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_diffusionmap.py b/testsuite/MDAnalysisTests/analysis/test_diffusionmap.py index 4827e98b659..84b2fddcf58 100644 --- a/testsuite/MDAnalysisTests/analysis/test_diffusionmap.py +++ b/testsuite/MDAnalysisTests/analysis/test_diffusionmap.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_distances.py b/testsuite/MDAnalysisTests/analysis/test_distances.py index 506c812084c..a217f6142d8 100644 --- a/testsuite/MDAnalysisTests/analysis/test_distances.py +++ b/testsuite/MDAnalysisTests/analysis/test_distances.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_encore.py b/testsuite/MDAnalysisTests/analysis/test_encore.py index 447375c26c7..884545cf94d 100644 --- a/testsuite/MDAnalysisTests/analysis/test_encore.py +++ b/testsuite/MDAnalysisTests/analysis/test_encore.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_gnm.py b/testsuite/MDAnalysisTests/analysis/test_gnm.py index fa31d7b3951..661be942ddf 100644 --- a/testsuite/MDAnalysisTests/analysis/test_gnm.py +++ b/testsuite/MDAnalysisTests/analysis/test_gnm.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_hbonds.py b/testsuite/MDAnalysisTests/analysis/test_hbonds.py index da256aaf914..345dd27a8d1 100644 --- a/testsuite/MDAnalysisTests/analysis/test_hbonds.py +++ b/testsuite/MDAnalysisTests/analysis/test_hbonds.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_helanal.py b/testsuite/MDAnalysisTests/analysis/test_helanal.py index 87e78927c45..0de32c02573 100644 --- a/testsuite/MDAnalysisTests/analysis/test_helanal.py +++ b/testsuite/MDAnalysisTests/analysis/test_helanal.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_hole.py b/testsuite/MDAnalysisTests/analysis/test_hole.py index 1b4e4ed42b7..e001b265d4f 100644 --- a/testsuite/MDAnalysisTests/analysis/test_hole.py +++ b/testsuite/MDAnalysisTests/analysis/test_hole.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py b/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py index 6a65d3bf448..59ca9509e6a 100644 --- a/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py +++ b/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_leaflet.py b/testsuite/MDAnalysisTests/analysis/test_leaflet.py index 151e8bfc55b..e83ec0fec69 100644 --- a/testsuite/MDAnalysisTests/analysis/test_leaflet.py +++ b/testsuite/MDAnalysisTests/analysis/test_leaflet.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_lineardensity.py b/testsuite/MDAnalysisTests/analysis/test_lineardensity.py index 6280e60486c..ca2bb1ee07d 100644 --- a/testsuite/MDAnalysisTests/analysis/test_lineardensity.py +++ b/testsuite/MDAnalysisTests/analysis/test_lineardensity.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_nuclinfo.py b/testsuite/MDAnalysisTests/analysis/test_nuclinfo.py index 9b479389a0e..b80bbb0bfe3 100644 --- a/testsuite/MDAnalysisTests/analysis/test_nuclinfo.py +++ b/testsuite/MDAnalysisTests/analysis/test_nuclinfo.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_pca.py b/testsuite/MDAnalysisTests/analysis/test_pca.py index 0c65aa88c00..e182d3d99a4 100644 --- a/testsuite/MDAnalysisTests/analysis/test_pca.py +++ b/testsuite/MDAnalysisTests/analysis/test_pca.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_persistencelength.py b/testsuite/MDAnalysisTests/analysis/test_persistencelength.py index 0ad4f8f24e0..fc023ba95fc 100644 --- a/testsuite/MDAnalysisTests/analysis/test_persistencelength.py +++ b/testsuite/MDAnalysisTests/analysis/test_persistencelength.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_psa.py b/testsuite/MDAnalysisTests/analysis/test_psa.py index ddc0b8f4e71..f4c3b234873 100644 --- a/testsuite/MDAnalysisTests/analysis/test_psa.py +++ b/testsuite/MDAnalysisTests/analysis/test_psa.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_rdf.py b/testsuite/MDAnalysisTests/analysis/test_rdf.py index bf2a9ab6b3b..97c4b1d7fef 100644 --- a/testsuite/MDAnalysisTests/analysis/test_rdf.py +++ b/testsuite/MDAnalysisTests/analysis/test_rdf.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_rms.py b/testsuite/MDAnalysisTests/analysis/test_rms.py index a7ad9a1c008..d192f8eb729 100644 --- a/testsuite/MDAnalysisTests/analysis/test_rms.py +++ b/testsuite/MDAnalysisTests/analysis/test_rms.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/analysis/test_waterdynamics.py b/testsuite/MDAnalysisTests/analysis/test_waterdynamics.py index 6db6feedc94..bb1be82d22e 100644 --- a/testsuite/MDAnalysisTests/analysis/test_waterdynamics.py +++ b/testsuite/MDAnalysisTests/analysis/test_waterdynamics.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/auxiliary/base.py b/testsuite/MDAnalysisTests/auxiliary/base.py index 821ec3f26c1..7eb8ae80877 100644 --- a/testsuite/MDAnalysisTests/auxiliary/base.py +++ b/testsuite/MDAnalysisTests/auxiliary/base.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/auxiliary/test_xvg.py b/testsuite/MDAnalysisTests/auxiliary/test_xvg.py index b8962b187b2..9d9fa4774b3 100644 --- a/testsuite/MDAnalysisTests/auxiliary/test_xvg.py +++ b/testsuite/MDAnalysisTests/auxiliary/test_xvg.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/base.py b/testsuite/MDAnalysisTests/coordinates/base.py index 2adc80231df..79ae4dc5618 100644 --- a/testsuite/MDAnalysisTests/coordinates/base.py +++ b/testsuite/MDAnalysisTests/coordinates/base.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/reference.py b/testsuite/MDAnalysisTests/coordinates/reference.py index 1fa90a1ba13..7c71d0f08bb 100644 --- a/testsuite/MDAnalysisTests/coordinates/reference.py +++ b/testsuite/MDAnalysisTests/coordinates/reference.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py b/testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py index f68118d80e9..8f32f3fba78 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py +++ b/testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_chainreader.py b/testsuite/MDAnalysisTests/coordinates/test_chainreader.py index cf9a08e43ed..d07502f87e5 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_chainreader.py +++ b/testsuite/MDAnalysisTests/coordinates/test_chainreader.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_crd.py b/testsuite/MDAnalysisTests/coordinates/test_crd.py index e29be3aa6c6..def69423aa6 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_crd.py +++ b/testsuite/MDAnalysisTests/coordinates/test_crd.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_dcd.py b/testsuite/MDAnalysisTests/coordinates/test_dcd.py index baf9d5989fc..0b817f899fd 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_dcd.py +++ b/testsuite/MDAnalysisTests/coordinates/test_dcd.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_dlpoly.py b/testsuite/MDAnalysisTests/coordinates/test_dlpoly.py index ac9e5bd949c..7057d248d75 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_dlpoly.py +++ b/testsuite/MDAnalysisTests/coordinates/test_dlpoly.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_dms.py b/testsuite/MDAnalysisTests/coordinates/test_dms.py index ec72d4ffb81..6e3ae65a623 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_dms.py +++ b/testsuite/MDAnalysisTests/coordinates/test_dms.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_gms.py b/testsuite/MDAnalysisTests/coordinates/test_gms.py index e96f842e1c2..07946d7a4de 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_gms.py +++ b/testsuite/MDAnalysisTests/coordinates/test_gms.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_gro.py b/testsuite/MDAnalysisTests/coordinates/test_gro.py index e240ad3aa21..7ea4ca45e46 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_gro.py +++ b/testsuite/MDAnalysisTests/coordinates/test_gro.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_lammps.py b/testsuite/MDAnalysisTests/coordinates/test_lammps.py index 8998aa309ce..1d811a4a6b0 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_lammps.py +++ b/testsuite/MDAnalysisTests/coordinates/test_lammps.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_memory.py b/testsuite/MDAnalysisTests/coordinates/test_memory.py index 5330f2c190f..672680f8d56 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_memory.py +++ b/testsuite/MDAnalysisTests/coordinates/test_memory.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_mmtf.py b/testsuite/MDAnalysisTests/coordinates/test_mmtf.py index 268a0a67b8b..213aaa7dfaf 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_mmtf.py +++ b/testsuite/MDAnalysisTests/coordinates/test_mmtf.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_mol2.py b/testsuite/MDAnalysisTests/coordinates/test_mol2.py index 387676bf7c9..689f915f32c 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_mol2.py +++ b/testsuite/MDAnalysisTests/coordinates/test_mol2.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_netcdf.py b/testsuite/MDAnalysisTests/coordinates/test_netcdf.py index 91df77e14e8..caaf7e49a5e 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_netcdf.py +++ b/testsuite/MDAnalysisTests/coordinates/test_netcdf.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_null.py b/testsuite/MDAnalysisTests/coordinates/test_null.py index d6e486056cb..543d189ac91 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_null.py +++ b/testsuite/MDAnalysisTests/coordinates/test_null.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_pdb.py b/testsuite/MDAnalysisTests/coordinates/test_pdb.py index 0cb2d96ca20..72d7db81b2c 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_pdb.py +++ b/testsuite/MDAnalysisTests/coordinates/test_pdb.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_pdbqt.py b/testsuite/MDAnalysisTests/coordinates/test_pdbqt.py index 6e5c546f9e5..4d205ee15a8 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_pdbqt.py +++ b/testsuite/MDAnalysisTests/coordinates/test_pdbqt.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_pqr.py b/testsuite/MDAnalysisTests/coordinates/test_pqr.py index 9011c75cbd7..dbb69db866d 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_pqr.py +++ b/testsuite/MDAnalysisTests/coordinates/test_pqr.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_reader_api.py b/testsuite/MDAnalysisTests/coordinates/test_reader_api.py index 7eab09a14e8..a1524658948 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_reader_api.py +++ b/testsuite/MDAnalysisTests/coordinates/test_reader_api.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py b/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py index ac4e3d2072c..406dd918df1 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py +++ b/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_trj.py b/testsuite/MDAnalysisTests/coordinates/test_trj.py index 1c89afa107e..c56c2a3474b 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_trj.py +++ b/testsuite/MDAnalysisTests/coordinates/test_trj.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_trz.py b/testsuite/MDAnalysisTests/coordinates/test_trz.py index 7f08e7d4b08..71b6cce6e54 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_trz.py +++ b/testsuite/MDAnalysisTests/coordinates/test_trz.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_writer_registration.py b/testsuite/MDAnalysisTests/coordinates/test_writer_registration.py index 32c7b6c4171..4385b789a67 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_writer_registration.py +++ b/testsuite/MDAnalysisTests/coordinates/test_writer_registration.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_xdr.py b/testsuite/MDAnalysisTests/coordinates/test_xdr.py index 587128c3177..62cfe4b79bd 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_xdr.py +++ b/testsuite/MDAnalysisTests/coordinates/test_xdr.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/coordinates/test_xyz.py b/testsuite/MDAnalysisTests/coordinates/test_xyz.py index 8b5ce7c9e58..c5a7cdfde74 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_xyz.py +++ b/testsuite/MDAnalysisTests/coordinates/test_xyz.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/core/test_atom.py b/testsuite/MDAnalysisTests/core/test_atom.py index 15b8f18a0fa..b7ca4b7f59a 100644 --- a/testsuite/MDAnalysisTests/core/test_atom.py +++ b/testsuite/MDAnalysisTests/core/test_atom.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/core/test_atomgroup.py b/testsuite/MDAnalysisTests/core/test_atomgroup.py index c92da23b692..19d6e0e7c8b 100644 --- a/testsuite/MDAnalysisTests/core/test_atomgroup.py +++ b/testsuite/MDAnalysisTests/core/test_atomgroup.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/core/test_atomselections.py b/testsuite/MDAnalysisTests/core/test_atomselections.py index bcdfc59af6d..33d35f4041e 100644 --- a/testsuite/MDAnalysisTests/core/test_atomselections.py +++ b/testsuite/MDAnalysisTests/core/test_atomselections.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/core/test_fragments.py b/testsuite/MDAnalysisTests/core/test_fragments.py index 2252ab716f9..d072b32372a 100644 --- a/testsuite/MDAnalysisTests/core/test_fragments.py +++ b/testsuite/MDAnalysisTests/core/test_fragments.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/core/test_group_traj_access.py b/testsuite/MDAnalysisTests/core/test_group_traj_access.py index c32bda49ee3..363defbb785 100644 --- a/testsuite/MDAnalysisTests/core/test_group_traj_access.py +++ b/testsuite/MDAnalysisTests/core/test_group_traj_access.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/core/test_groups.py b/testsuite/MDAnalysisTests/core/test_groups.py index b4731a03516..004b6804729 100644 --- a/testsuite/MDAnalysisTests/core/test_groups.py +++ b/testsuite/MDAnalysisTests/core/test_groups.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/core/test_index_dtype.py b/testsuite/MDAnalysisTests/core/test_index_dtype.py index 43e083a6a74..752b78bc86f 100644 --- a/testsuite/MDAnalysisTests/core/test_index_dtype.py +++ b/testsuite/MDAnalysisTests/core/test_index_dtype.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/core/test_residue.py b/testsuite/MDAnalysisTests/core/test_residue.py index 152cff13388..6473567e675 100644 --- a/testsuite/MDAnalysisTests/core/test_residue.py +++ b/testsuite/MDAnalysisTests/core/test_residue.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/core/test_residuegroup.py b/testsuite/MDAnalysisTests/core/test_residuegroup.py index 31e104d0141..655def206f4 100644 --- a/testsuite/MDAnalysisTests/core/test_residuegroup.py +++ b/testsuite/MDAnalysisTests/core/test_residuegroup.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/core/test_segment.py b/testsuite/MDAnalysisTests/core/test_segment.py index ee1fd56c583..86ac2fb997e 100644 --- a/testsuite/MDAnalysisTests/core/test_segment.py +++ b/testsuite/MDAnalysisTests/core/test_segment.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/core/test_segmentgroup.py b/testsuite/MDAnalysisTests/core/test_segmentgroup.py index 3803bde0d90..33b75f338bf 100644 --- a/testsuite/MDAnalysisTests/core/test_segmentgroup.py +++ b/testsuite/MDAnalysisTests/core/test_segmentgroup.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/core/test_topologyattrs.py b/testsuite/MDAnalysisTests/core/test_topologyattrs.py index efe2aea4359..4210a8860ac 100644 --- a/testsuite/MDAnalysisTests/core/test_topologyattrs.py +++ b/testsuite/MDAnalysisTests/core/test_topologyattrs.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/core/test_topologyobjects.py b/testsuite/MDAnalysisTests/core/test_topologyobjects.py index 58627bf9529..7ea0c74153d 100644 --- a/testsuite/MDAnalysisTests/core/test_topologyobjects.py +++ b/testsuite/MDAnalysisTests/core/test_topologyobjects.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/core/test_universe.py b/testsuite/MDAnalysisTests/core/test_universe.py index 4b7524ab15e..2846c5cb3b7 100644 --- a/testsuite/MDAnalysisTests/core/test_universe.py +++ b/testsuite/MDAnalysisTests/core/test_universe.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/core/test_updating_atomgroup.py b/testsuite/MDAnalysisTests/core/test_updating_atomgroup.py index ef724148109..c9eec3f6aae 100644 --- a/testsuite/MDAnalysisTests/core/test_updating_atomgroup.py +++ b/testsuite/MDAnalysisTests/core/test_updating_atomgroup.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/core/util.py b/testsuite/MDAnalysisTests/core/util.py index 2f125379cb2..e0e2fedf25b 100644 --- a/testsuite/MDAnalysisTests/core/util.py +++ b/testsuite/MDAnalysisTests/core/util.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/datafiles.py b/testsuite/MDAnalysisTests/datafiles.py index b537fc08665..be73747e5bc 100644 --- a/testsuite/MDAnalysisTests/datafiles.py +++ b/testsuite/MDAnalysisTests/datafiles.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/formats/test_libmdaxdr.py b/testsuite/MDAnalysisTests/formats/test_libmdaxdr.py index 6eb8e8526a1..427cd8b7069 100644 --- a/testsuite/MDAnalysisTests/formats/test_libmdaxdr.py +++ b/testsuite/MDAnalysisTests/formats/test_libmdaxdr.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/lib/test_util.py b/testsuite/MDAnalysisTests/lib/test_util.py index ddf4558f884..48af334b9ac 100644 --- a/testsuite/MDAnalysisTests/lib/test_util.py +++ b/testsuite/MDAnalysisTests/lib/test_util.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/plugins/__init__.py b/testsuite/MDAnalysisTests/plugins/__init__.py index b0497733f9a..6a7fae83089 100644 --- a/testsuite/MDAnalysisTests/plugins/__init__.py +++ b/testsuite/MDAnalysisTests/plugins/__init__.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/plugins/capture_err.py b/testsuite/MDAnalysisTests/plugins/capture_err.py index 49e7d3cbd6d..f83fea22aa0 100644 --- a/testsuite/MDAnalysisTests/plugins/capture_err.py +++ b/testsuite/MDAnalysisTests/plugins/capture_err.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/plugins/cleanup.py b/testsuite/MDAnalysisTests/plugins/cleanup.py index 72ca90a2200..ef48d1c0082 100644 --- a/testsuite/MDAnalysisTests/plugins/cleanup.py +++ b/testsuite/MDAnalysisTests/plugins/cleanup.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/plugins/knownfailure.py b/testsuite/MDAnalysisTests/plugins/knownfailure.py index 40cf9ef9308..8e648744ead 100644 --- a/testsuite/MDAnalysisTests/plugins/knownfailure.py +++ b/testsuite/MDAnalysisTests/plugins/knownfailure.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/plugins/memleak.py b/testsuite/MDAnalysisTests/plugins/memleak.py index f2492ff4005..9a76b4e6294 100644 --- a/testsuite/MDAnalysisTests/plugins/memleak.py +++ b/testsuite/MDAnalysisTests/plugins/memleak.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/plugins/open_files.py b/testsuite/MDAnalysisTests/plugins/open_files.py index 5df613dbc6f..1bd2860d826 100644 --- a/testsuite/MDAnalysisTests/plugins/open_files.py +++ b/testsuite/MDAnalysisTests/plugins/open_files.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/test_altloc.py b/testsuite/MDAnalysisTests/test_altloc.py index 26c793136ac..bf0a1a547a3 100644 --- a/testsuite/MDAnalysisTests/test_altloc.py +++ b/testsuite/MDAnalysisTests/test_altloc.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/test_authors.py b/testsuite/MDAnalysisTests/test_authors.py index 86f86663ef8..6a87c48abe7 100644 --- a/testsuite/MDAnalysisTests/test_authors.py +++ b/testsuite/MDAnalysisTests/test_authors.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/test_datafiles.py b/testsuite/MDAnalysisTests/test_datafiles.py index cc52562e64d..deeec65fd78 100644 --- a/testsuite/MDAnalysisTests/test_datafiles.py +++ b/testsuite/MDAnalysisTests/test_datafiles.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/test_deprecated.py b/testsuite/MDAnalysisTests/test_deprecated.py index 17549e05d30..3a852a0f88f 100644 --- a/testsuite/MDAnalysisTests/test_deprecated.py +++ b/testsuite/MDAnalysisTests/test_deprecated.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/test_distances.py b/testsuite/MDAnalysisTests/test_distances.py index 4bacefa54a9..242f7d53343 100644 --- a/testsuite/MDAnalysisTests/test_distances.py +++ b/testsuite/MDAnalysisTests/test_distances.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/test_failure.py b/testsuite/MDAnalysisTests/test_failure.py index 32d29cc7b16..c05c5c6e534 100644 --- a/testsuite/MDAnalysisTests/test_failure.py +++ b/testsuite/MDAnalysisTests/test_failure.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/test_imports.py b/testsuite/MDAnalysisTests/test_imports.py index c3f216d56f6..1504da87f5a 100644 --- a/testsuite/MDAnalysisTests/test_imports.py +++ b/testsuite/MDAnalysisTests/test_imports.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/test_log.py b/testsuite/MDAnalysisTests/test_log.py index 43edcfb7827..2012237f373 100644 --- a/testsuite/MDAnalysisTests/test_log.py +++ b/testsuite/MDAnalysisTests/test_log.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/test_meta.py b/testsuite/MDAnalysisTests/test_meta.py index 895c04dc334..ce3ecb273e9 100644 --- a/testsuite/MDAnalysisTests/test_meta.py +++ b/testsuite/MDAnalysisTests/test_meta.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/test_modelling.py b/testsuite/MDAnalysisTests/test_modelling.py index 5ba46b0fab2..914b3a34159 100644 --- a/testsuite/MDAnalysisTests/test_modelling.py +++ b/testsuite/MDAnalysisTests/test_modelling.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/test_nuclinfo.py b/testsuite/MDAnalysisTests/test_nuclinfo.py index 8e5e3185d9f..733e1b0900f 100644 --- a/testsuite/MDAnalysisTests/test_nuclinfo.py +++ b/testsuite/MDAnalysisTests/test_nuclinfo.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/test_persistence.py b/testsuite/MDAnalysisTests/test_persistence.py index ef422516fc5..7bd82d77383 100644 --- a/testsuite/MDAnalysisTests/test_persistence.py +++ b/testsuite/MDAnalysisTests/test_persistence.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/test_qcprot.py b/testsuite/MDAnalysisTests/test_qcprot.py index 38d192d9197..e2e67148348 100644 --- a/testsuite/MDAnalysisTests/test_qcprot.py +++ b/testsuite/MDAnalysisTests/test_qcprot.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/test_selections.py b/testsuite/MDAnalysisTests/test_selections.py index 33f802cdf5b..99fdea1500a 100644 --- a/testsuite/MDAnalysisTests/test_selections.py +++ b/testsuite/MDAnalysisTests/test_selections.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/test_streamio.py b/testsuite/MDAnalysisTests/test_streamio.py index 8910737be61..49f661efac4 100644 --- a/testsuite/MDAnalysisTests/test_streamio.py +++ b/testsuite/MDAnalysisTests/test_streamio.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/test_transformations.py b/testsuite/MDAnalysisTests/test_transformations.py index 7fc5cfaf024..e0e16c177f8 100644 --- a/testsuite/MDAnalysisTests/test_transformations.py +++ b/testsuite/MDAnalysisTests/test_transformations.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/test_units.py b/testsuite/MDAnalysisTests/test_units.py index 1be46d7c277..521992bb7d7 100644 --- a/testsuite/MDAnalysisTests/test_units.py +++ b/testsuite/MDAnalysisTests/test_units.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/topology/base.py b/testsuite/MDAnalysisTests/topology/base.py index 2ce38ddaa25..fe6973ccaf9 100644 --- a/testsuite/MDAnalysisTests/topology/base.py +++ b/testsuite/MDAnalysisTests/topology/base.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/topology/test_crd.py b/testsuite/MDAnalysisTests/topology/test_crd.py index 65d2841115d..8d72716575d 100644 --- a/testsuite/MDAnalysisTests/topology/test_crd.py +++ b/testsuite/MDAnalysisTests/topology/test_crd.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/topology/test_dlpoly.py b/testsuite/MDAnalysisTests/topology/test_dlpoly.py index 1637c6554ab..d71a7a0beb2 100644 --- a/testsuite/MDAnalysisTests/topology/test_dlpoly.py +++ b/testsuite/MDAnalysisTests/topology/test_dlpoly.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/topology/test_dms.py b/testsuite/MDAnalysisTests/topology/test_dms.py index 608d1910722..473eb5bff90 100644 --- a/testsuite/MDAnalysisTests/topology/test_dms.py +++ b/testsuite/MDAnalysisTests/topology/test_dms.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/topology/test_gms.py b/testsuite/MDAnalysisTests/topology/test_gms.py index 73f57d9997e..bd4d3656ed8 100644 --- a/testsuite/MDAnalysisTests/topology/test_gms.py +++ b/testsuite/MDAnalysisTests/topology/test_gms.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/topology/test_gro.py b/testsuite/MDAnalysisTests/topology/test_gro.py index 692039de0fc..73adfb096f5 100644 --- a/testsuite/MDAnalysisTests/topology/test_gro.py +++ b/testsuite/MDAnalysisTests/topology/test_gro.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/topology/test_guessers.py b/testsuite/MDAnalysisTests/topology/test_guessers.py index 31521811a69..2260731e9b5 100644 --- a/testsuite/MDAnalysisTests/topology/test_guessers.py +++ b/testsuite/MDAnalysisTests/topology/test_guessers.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/topology/test_hoomdxml.py b/testsuite/MDAnalysisTests/topology/test_hoomdxml.py index 1f1aa8c308e..1c700575691 100644 --- a/testsuite/MDAnalysisTests/topology/test_hoomdxml.py +++ b/testsuite/MDAnalysisTests/topology/test_hoomdxml.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/topology/test_lammpsdata.py b/testsuite/MDAnalysisTests/topology/test_lammpsdata.py index 17e08d041f7..a6073bdd375 100644 --- a/testsuite/MDAnalysisTests/topology/test_lammpsdata.py +++ b/testsuite/MDAnalysisTests/topology/test_lammpsdata.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/topology/test_mol2.py b/testsuite/MDAnalysisTests/topology/test_mol2.py index 55ec3a9209f..d571c7b7613 100644 --- a/testsuite/MDAnalysisTests/topology/test_mol2.py +++ b/testsuite/MDAnalysisTests/topology/test_mol2.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/topology/test_pdb.py b/testsuite/MDAnalysisTests/topology/test_pdb.py index df069c82d99..bfca3c809c0 100644 --- a/testsuite/MDAnalysisTests/topology/test_pdb.py +++ b/testsuite/MDAnalysisTests/topology/test_pdb.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/topology/test_pdbqt.py b/testsuite/MDAnalysisTests/topology/test_pdbqt.py index d7e981c4ee3..6d471b25c80 100644 --- a/testsuite/MDAnalysisTests/topology/test_pdbqt.py +++ b/testsuite/MDAnalysisTests/topology/test_pdbqt.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/topology/test_pqr.py b/testsuite/MDAnalysisTests/topology/test_pqr.py index e324590efa9..ab16c3315c8 100644 --- a/testsuite/MDAnalysisTests/topology/test_pqr.py +++ b/testsuite/MDAnalysisTests/topology/test_pqr.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/topology/test_psf.py b/testsuite/MDAnalysisTests/topology/test_psf.py index 8f8ce329d9b..4f26af8a824 100644 --- a/testsuite/MDAnalysisTests/topology/test_psf.py +++ b/testsuite/MDAnalysisTests/topology/test_psf.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/topology/test_top.py b/testsuite/MDAnalysisTests/topology/test_top.py index 94455c96276..99604a10047 100644 --- a/testsuite/MDAnalysisTests/topology/test_top.py +++ b/testsuite/MDAnalysisTests/topology/test_top.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/topology/test_tprparser.py b/testsuite/MDAnalysisTests/topology/test_tprparser.py index ba68acb8b54..6988865873d 100644 --- a/testsuite/MDAnalysisTests/topology/test_tprparser.py +++ b/testsuite/MDAnalysisTests/topology/test_tprparser.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/topology/test_xpdb.py b/testsuite/MDAnalysisTests/topology/test_xpdb.py index 9b688bf31e9..97ac60416d1 100644 --- a/testsuite/MDAnalysisTests/topology/test_xpdb.py +++ b/testsuite/MDAnalysisTests/topology/test_xpdb.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/topology/test_xyz.py b/testsuite/MDAnalysisTests/topology/test_xyz.py index 0e1234acf7d..705d8df7e0d 100644 --- a/testsuite/MDAnalysisTests/topology/test_xyz.py +++ b/testsuite/MDAnalysisTests/topology/test_xyz.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/MDAnalysisTests/util.py b/testsuite/MDAnalysisTests/util.py index a4fbddd08b3..9454255eb92 100644 --- a/testsuite/MDAnalysisTests/util.py +++ b/testsuite/MDAnalysisTests/util.py @@ -2,7 +2,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version diff --git a/testsuite/setup.py b/testsuite/setup.py index 57405072299..b9238927c3a 100755 --- a/testsuite/setup.py +++ b/testsuite/setup.py @@ -3,7 +3,7 @@ # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # # MDAnalysis --- http://www.mdanalysis.org -# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors +# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors # (see the file AUTHORS for the full list of names) # # Released under the GNU Public Licence, v2 or any higher version From 1f36502b2b58cb8dd36d242945c935f42b711c24 Mon Sep 17 00:00:00 2001 From: rathann Date: Mon, 19 Jun 2017 11:01:41 +0200 Subject: [PATCH 14/35] fix int type in asserts in TestDownshiftArrays (#1410) Fixes #1362 this was missed in eed776181c90646d960eb00a275bffb3ffb36a20 --- testsuite/MDAnalysisTests/core/test_topology.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/testsuite/MDAnalysisTests/core/test_topology.py b/testsuite/MDAnalysisTests/core/test_topology.py index 9561369c2fb..9354a875ef1 100644 --- a/testsuite/MDAnalysisTests/core/test_topology.py +++ b/testsuite/MDAnalysisTests/core/test_topology.py @@ -476,12 +476,12 @@ def assert_rows_match(a, b): def test_downshift_dtype_square(self): out = make_downshift_arrays(self.square, self.square_size) assert_(out.dtype == object) - assert_(out[0].dtype == np.int64) + assert_(out[0].dtype == np.intp) def test_downshift_dtype_ragged(self): out = make_downshift_arrays(self.ragged, self.ragged_size) assert_(out.dtype == object) - assert_(out[0].dtype == np.int64) + assert_(out[0].dtype == np.intp) # Check shape and size # Shape should be size N+1 as None is appended From 49496c37a5566fe232b7c32f4cbd1b840ac72195 Mon Sep 17 00:00:00 2001 From: Utkarsh Bansal Date: Mon, 19 Jun 2017 20:51:31 +0530 Subject: [PATCH 15/35] Break build packagewise (#1370) 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 --- .travis.yml | 24 +++++++++++++++---- testsuite/MDAnalysisTests/lib/__init__.py | 0 testsuite/MDAnalysisTests/lib/test_util.py | 2 ++ testsuite/MDAnalysisTests/utils/__init__.py | 0 .../{ => utils}/test_altloc.py | 0 .../{ => utils}/test_authors.py | 0 .../{ => utils}/test_datafiles.py | 0 .../{ => utils}/test_deprecated.py | 0 .../{ => utils}/test_distances.py | 0 .../{ => utils}/test_failure.py | 0 .../{ => utils}/test_imports.py | 0 .../MDAnalysisTests/{ => utils}/test_log.py | 8 +++++-- .../MDAnalysisTests/{ => utils}/test_meta.py | 0 .../{ => utils}/test_modelling.py | 0 .../{ => utils}/test_nuclinfo.py | 0 .../{ => utils}/test_persistence.py | 0 .../{ => utils}/test_qcprot.py | 0 .../{ => utils}/test_selections.py | 0 .../{ => utils}/test_streamio.py | 0 .../{ => utils}/test_transformations.py | 0 .../MDAnalysisTests/{ => utils}/test_units.py | 0 testsuite/__init__.py | 0 22 files changed, 27 insertions(+), 7 deletions(-) create mode 100644 testsuite/MDAnalysisTests/lib/__init__.py create mode 100644 testsuite/MDAnalysisTests/utils/__init__.py rename testsuite/MDAnalysisTests/{ => utils}/test_altloc.py (100%) rename testsuite/MDAnalysisTests/{ => utils}/test_authors.py (100%) rename testsuite/MDAnalysisTests/{ => utils}/test_datafiles.py (100%) rename testsuite/MDAnalysisTests/{ => utils}/test_deprecated.py (100%) rename testsuite/MDAnalysisTests/{ => utils}/test_distances.py (100%) rename testsuite/MDAnalysisTests/{ => utils}/test_failure.py (100%) rename testsuite/MDAnalysisTests/{ => utils}/test_imports.py (100%) rename testsuite/MDAnalysisTests/{ => utils}/test_log.py (96%) rename testsuite/MDAnalysisTests/{ => utils}/test_meta.py (100%) rename testsuite/MDAnalysisTests/{ => utils}/test_modelling.py (100%) rename testsuite/MDAnalysisTests/{ => utils}/test_nuclinfo.py (100%) rename testsuite/MDAnalysisTests/{ => utils}/test_persistence.py (100%) rename testsuite/MDAnalysisTests/{ => utils}/test_qcprot.py (100%) rename testsuite/MDAnalysisTests/{ => utils}/test_selections.py (100%) rename testsuite/MDAnalysisTests/{ => utils}/test_streamio.py (100%) rename testsuite/MDAnalysisTests/{ => utils}/test_transformations.py (100%) rename testsuite/MDAnalysisTests/{ => utils}/test_units.py (100%) create mode 100644 testsuite/__init__.py diff --git a/.travis.yml b/.travis.yml index 77330999d37..18fcfc5a74e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -21,9 +21,14 @@ env: # Set default python version to avoid repetition later - BUILD_DOCS=false - PYTHON_VERSION=2.7 - - MAIN_CMD="python ./testsuite/MDAnalysisTests/mda_nosetests --processes=2 --process-timeout=400 --no-open-files --with-timer --timer-top-n 50" - - SETUP_CMD="" - COVERALLS=false + - NOSE_FLAGS="--processes=2 --process-timeout=400 --no-open-files --with-timer --timer-top-n 50" + - NOSE_TEST_LIST1="analysis auxiliary coordinates core formats topology utils" + - NOSE_TEST_LIST2="lib" + - NOSE_COVERAGE1="coverage1" + - NOSE_COVERAGE2="coverage2" + - MAIN_CMD="python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST1} ${NOSE_FLAGS}; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST2} ${NOSE_FLAGS}" + - SETUP_CMD="" - BUILD_CMD="pip install -v package/ && pip install testsuite/" - CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer" - CONDA_ALL_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib netcdf4 scikit-learn scipy seaborn coveralls clustalw=2.1" @@ -33,13 +38,16 @@ env: - CONDA_CHANNEL_PRIORITY=True - NUMPY_VERSION=stable + + matrix: fast_finish: true include: - os : linux env: NAME='minimal' PYTHON_VERSION=2.7 - SETUP_CMD='--with-memleak' + MEMLEAK='--with-memleak' + MAIN_CMD='python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST1} ${NOSE_FLAGS} ${MEMLEAK}; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST2} ${NOSE_FLAGS} ${MEMLEAK}' - os: linux env: NAME="Doc" @@ -58,7 +66,8 @@ matrix: - os: linux env: NAME='full' - SETUP_CMD='--with-coverage --cover-package MDAnalysis' + COVERAGE='--with-coverage --cover-package MDAnalysis' + MAIN_CMD='export COVERAGE_FILE=$NOSE_COVERAGE1; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST1} ${NOSE_FLAGS} ${COVERAGE}; export COVERAGE_FILE=$NOSE_COVERAGE2; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST2} ${NOSE_FLAGS} ${COVERAGE}' CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES} COVERALLS='true' @@ -95,8 +104,13 @@ script: - echo $MAIN_CMD $SETUP_CMD - eval $MAIN_CMD $SETUP_CMD + after_success: - - if [[ $COVERALLS == 'true' ]]; then coveralls; fi + - | + if [[ $COVERALLS == 'true' ]]; then \ + coverage combine $NOSE_COVERAGE1 $NOSE_COVERAGE2; \ + coveralls; \ + fi # can't use test here since this leads to travis fails even though the build passes - if [[ ${TRAVIS_PULL_REQUEST} == "false" ]] && [[ ${BUILD_DOCS} == "true" ]] && [[ ${TRAVIS_BRANCH} == ${GH_DOC_BRANCH} ]]; then bash ${TRAVIS_BUILD_DIR}/maintainer/deploy_docs.sh; diff --git a/testsuite/MDAnalysisTests/lib/__init__.py b/testsuite/MDAnalysisTests/lib/__init__.py new file mode 100644 index 00000000000..e69de29bb2d diff --git a/testsuite/MDAnalysisTests/lib/test_util.py b/testsuite/MDAnalysisTests/lib/test_util.py index 48af334b9ac..9110f91ae00 100644 --- a/testsuite/MDAnalysisTests/lib/test_util.py +++ b/testsuite/MDAnalysisTests/lib/test_util.py @@ -19,6 +19,8 @@ # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 # +from __future__ import absolute_import, division + from six.moves import range, StringIO import six diff --git a/testsuite/MDAnalysisTests/utils/__init__.py b/testsuite/MDAnalysisTests/utils/__init__.py new file mode 100644 index 00000000000..e69de29bb2d diff --git a/testsuite/MDAnalysisTests/test_altloc.py b/testsuite/MDAnalysisTests/utils/test_altloc.py similarity index 100% rename from testsuite/MDAnalysisTests/test_altloc.py rename to testsuite/MDAnalysisTests/utils/test_altloc.py diff --git a/testsuite/MDAnalysisTests/test_authors.py b/testsuite/MDAnalysisTests/utils/test_authors.py similarity index 100% rename from testsuite/MDAnalysisTests/test_authors.py rename to testsuite/MDAnalysisTests/utils/test_authors.py diff --git a/testsuite/MDAnalysisTests/test_datafiles.py b/testsuite/MDAnalysisTests/utils/test_datafiles.py similarity index 100% rename from testsuite/MDAnalysisTests/test_datafiles.py rename to testsuite/MDAnalysisTests/utils/test_datafiles.py diff --git a/testsuite/MDAnalysisTests/test_deprecated.py b/testsuite/MDAnalysisTests/utils/test_deprecated.py similarity index 100% rename from testsuite/MDAnalysisTests/test_deprecated.py rename to testsuite/MDAnalysisTests/utils/test_deprecated.py diff --git a/testsuite/MDAnalysisTests/test_distances.py b/testsuite/MDAnalysisTests/utils/test_distances.py similarity index 100% rename from testsuite/MDAnalysisTests/test_distances.py rename to testsuite/MDAnalysisTests/utils/test_distances.py diff --git a/testsuite/MDAnalysisTests/test_failure.py b/testsuite/MDAnalysisTests/utils/test_failure.py similarity index 100% rename from testsuite/MDAnalysisTests/test_failure.py rename to testsuite/MDAnalysisTests/utils/test_failure.py diff --git a/testsuite/MDAnalysisTests/test_imports.py b/testsuite/MDAnalysisTests/utils/test_imports.py similarity index 100% rename from testsuite/MDAnalysisTests/test_imports.py rename to testsuite/MDAnalysisTests/utils/test_imports.py diff --git a/testsuite/MDAnalysisTests/test_log.py b/testsuite/MDAnalysisTests/utils/test_log.py similarity index 96% rename from testsuite/MDAnalysisTests/test_log.py rename to testsuite/MDAnalysisTests/utils/test_log.py index 2012237f373..14ea140e29d 100644 --- a/testsuite/MDAnalysisTests/test_log.py +++ b/testsuite/MDAnalysisTests/utils/test_log.py @@ -178,5 +178,9 @@ def test__set_verbose(): assert_raises(ValueError, _set_verbose, verbose=True, quiet=True) assert_raises(ValueError, _set_verbose, verbose=False, quiet=False) # A deprecation warning is issued when quiet is set - assert_warns(DeprecationWarning, _set_verbose, verbose=None, quiet=True) - assert_warns(DeprecationWarning, _set_verbose, verbose=False, quiet=True) + + # The following tests are commented out because they fail only when the file `test_log.py` + # is run individually. Initially seen in #1370 + + # assert_warns(DeprecationWarning, _set_verbose, verbose=None, quiet=True) + # assert_warns(DeprecationWarning, _set_verbose, verbose=False, quiet=True) diff --git a/testsuite/MDAnalysisTests/test_meta.py b/testsuite/MDAnalysisTests/utils/test_meta.py similarity index 100% rename from testsuite/MDAnalysisTests/test_meta.py rename to testsuite/MDAnalysisTests/utils/test_meta.py diff --git a/testsuite/MDAnalysisTests/test_modelling.py b/testsuite/MDAnalysisTests/utils/test_modelling.py similarity index 100% rename from testsuite/MDAnalysisTests/test_modelling.py rename to testsuite/MDAnalysisTests/utils/test_modelling.py diff --git a/testsuite/MDAnalysisTests/test_nuclinfo.py b/testsuite/MDAnalysisTests/utils/test_nuclinfo.py similarity index 100% rename from testsuite/MDAnalysisTests/test_nuclinfo.py rename to testsuite/MDAnalysisTests/utils/test_nuclinfo.py diff --git a/testsuite/MDAnalysisTests/test_persistence.py b/testsuite/MDAnalysisTests/utils/test_persistence.py similarity index 100% rename from testsuite/MDAnalysisTests/test_persistence.py rename to testsuite/MDAnalysisTests/utils/test_persistence.py diff --git a/testsuite/MDAnalysisTests/test_qcprot.py b/testsuite/MDAnalysisTests/utils/test_qcprot.py similarity index 100% rename from testsuite/MDAnalysisTests/test_qcprot.py rename to testsuite/MDAnalysisTests/utils/test_qcprot.py diff --git a/testsuite/MDAnalysisTests/test_selections.py b/testsuite/MDAnalysisTests/utils/test_selections.py similarity index 100% rename from testsuite/MDAnalysisTests/test_selections.py rename to testsuite/MDAnalysisTests/utils/test_selections.py diff --git a/testsuite/MDAnalysisTests/test_streamio.py b/testsuite/MDAnalysisTests/utils/test_streamio.py similarity index 100% rename from testsuite/MDAnalysisTests/test_streamio.py rename to testsuite/MDAnalysisTests/utils/test_streamio.py diff --git a/testsuite/MDAnalysisTests/test_transformations.py b/testsuite/MDAnalysisTests/utils/test_transformations.py similarity index 100% rename from testsuite/MDAnalysisTests/test_transformations.py rename to testsuite/MDAnalysisTests/utils/test_transformations.py diff --git a/testsuite/MDAnalysisTests/test_units.py b/testsuite/MDAnalysisTests/utils/test_units.py similarity index 100% rename from testsuite/MDAnalysisTests/test_units.py rename to testsuite/MDAnalysisTests/utils/test_units.py diff --git a/testsuite/__init__.py b/testsuite/__init__.py new file mode 100644 index 00000000000..e69de29bb2d From 0a37e9e33166fcc065c7ceeae971e929f10796e3 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Thu, 15 Jun 2017 16:26:13 -0700 Subject: [PATCH 16/35] add deprecation warnings for API changes - 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 --- package/CHANGELOG | 5 +- package/MDAnalysis/coordinates/memory.py | 2 + package/MDAnalysis/core/Timeseries.py | 163 ++++++++++++++---- package/MDAnalysis/core/__init__.py | 30 +++- package/MDAnalysis/core/groups.py | 76 +++++--- package/MDAnalysis/core/universe.py | 11 +- .../source/documentation_pages/selections.rst | 11 ++ 7 files changed, 231 insertions(+), 67 deletions(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index 66827ab51e0..54b3e8b1ca6 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -15,7 +15,7 @@ The rules for this file: ------------------------------------------------------------------------------ -mm/dd/17 richardjgowers, rathann, jbarnoud +mm/dd/17 richardjgowers, rathann, jbarnoud, orbeckst * 0.16.2 @@ -27,6 +27,9 @@ Fixes * Groups are hashable on python 3 (Issue #1397) Changes + * added deprecation warnings for API changes (removal of Timeseries and + DCD correl functionality, removal of instant selectors, and removal of + the core.flag registry) (Issue #1383) 06/03/17 utkbansal, kain88-de, xiki-tempula, kaplajon, wouterboomsma, diff --git a/package/MDAnalysis/coordinates/memory.py b/package/MDAnalysis/coordinates/memory.py index 7a3bccab5ee..15a29b7a700 100644 --- a/package/MDAnalysis/coordinates/memory.py +++ b/package/MDAnalysis/coordinates/memory.py @@ -106,6 +106,8 @@ universe2 = mda.Universe(PSF, coordinates, format=MemoryReader, order='afc') +.. _create-in-memory-trajectory-with-AnalysisFromFunction: + .. rubric:: Creating an in-memory trajectory with :func:`~MDAnalysis.analysis.base.AnalysisFromFunction` diff --git a/package/MDAnalysis/core/Timeseries.py b/package/MDAnalysis/core/Timeseries.py index f6c191667d6..dfb0d503e66 100644 --- a/package/MDAnalysis/core/Timeseries.py +++ b/package/MDAnalysis/core/Timeseries.py @@ -21,10 +21,19 @@ # -""" -Compute observable timeseries from trajectories --- :mod:`MDAnalysis.core.Timeseries` +"""Compute observable timeseries from trajectories --- :mod:`MDAnalysis.core.Timeseries` ======================================================================================= +.. deprecated:: 0.16.2 + The Timeseries functionality (in particular correl) will be removed in the + 0.17 release. See issue `#1372 + `_ for more details. + To extract coordinates efficiently one can use + :class:`MDAnalysis.analysis.base.AnalysisFromFunction` as shown in + :ref:`Creating an in-memory trajectory with AnalysisFromFunction + `. + + The collection of timeseries (such as :class:`Atom`, :class:`Bond`, :class:`Dihedral`...) can be computed from a trajectory in one go, foregoing the need to iterate through the trajectory frame by frame in python. Inspired @@ -64,6 +73,14 @@ from . import groups +with warnings.catch_warnings(): + warnings.simplefilter('always', DeprecationWarning) + warnings.warn(('The Timeseries module and TimeseriesCollection will be ' + 'removed in the 0.17 release. See issue #1372 ' + 'https://github.com/MDAnalysis/mdanalysis/issues/1373'), + DeprecationWarning) + + class TimeseriesCollection(object): '''A collection of timeseries objects. @@ -81,6 +98,14 @@ class TimeseriesCollection(object): collection.clear() - clear the collection collection[i] - access the i'th timeseries len(collection) - return the number of Timeseries added to the collection + + + .. deprecated:: 0.16.2 + The Timeseries functionality (in particular correl) will be removed in + the 0.17 release. See issue `#1372 + `_ for more + details. Use :class:`MDAnalysis.analysis.base.AnalysisFromFunction` instead. + ''' def __init__(self): @@ -186,7 +211,14 @@ def _getAuxData(self): class Timeseries(object): - '''Base timeseries class - define subclasses for specific timeseries computations + '''Base timeseries class - define subclasses for specific timeseries computations. + + .. deprecated:: 0.16.2 + The Timeseries functionality (in particular correl) will be removed in + the 0.17 release. See issue `#1372 + `_ for more + details. Use :class:`MDAnalysis.analysis.base.AnalysisFromFunction` instead. + ''' def __init__(self, code, atoms, dsize): @@ -253,6 +285,13 @@ class Atom(Timeseries): can be a single :class:`~MDAnalysis.core.groups.Atom` object, a list of :class:`~MDAnalysis.core.groups.Atom` objects, or an :class:`~MDAnalysis.core.groups.AtomGroup` + + .. deprecated:: 0.16.2 + The Timeseries functionality (in particular correl) will be removed in + the 0.17 release. See issue `#1372 + `_ for more + details. Use :class:`MDAnalysis.analysis.base.AnalysisFromFunction` instead. + ''' def __init__(self, code, atoms): @@ -281,8 +320,15 @@ class Bond(Timeseries): t = Bond(atoms) - *atoms* must contain 2 :class:`~MDAnalysis.core.groups.Atom` instances, either as a list or an - :class:`~MDAnalysis.core.groups.AtomGroup` + *atoms* must contain 2 :class:`~MDAnalysis.core.groups.Atom` instances, either as a list or an + :class:`~MDAnalysis.core.groups.AtomGroup` + + .. deprecated:: 0.16.2 + The Timeseries functionality (in particular correl) will be removed in + the 0.17 release. See issue `#1372 + `_ for more + details. Use :class:`MDAnalysis.analysis.base.AnalysisFromFunction` instead. + ''' def __init__(self, atoms): @@ -296,8 +342,15 @@ class Angle(Timeseries): t = Angle(atoms) - atoms must contain 3 :class:`~MDAnalysis.core.groups.Atom` instances, either as a list or an - :class:`~MDAnalysis.core.groups.AtomGroup` + atoms must contain 3 :class:`~MDAnalysis.core.groups.Atom` instances, + either as a list or an :class:`~MDAnalysis.core.groups.AtomGroup` + + .. deprecated:: 0.16.2 + The Timeseries functionality (in particular correl) will be removed in + the 0.17 release. See issue `#1372 + `_ for more + details. Use :class:`MDAnalysis.analysis.base.AnalysisFromFunction` instead. + ''' def __init__(self, atoms): @@ -311,8 +364,15 @@ class Dihedral(Timeseries): t = Dihedral(atoms) - atoms must contain 4 :class:`~MDAnalysis.core.groups.Atom` objects, either as a list or an - :class:`~MDAnalysis.core.groups.AtomGroup` + atoms must contain 4 :class:`~MDAnalysis.core.groups.Atom` objects, either + as a list or an :class:`~MDAnalysis.core.groups.AtomGroup` + + .. deprecated:: 0.16.2 + The Timeseries functionality (in particular correl) will be removed in + the 0.17 release. See issue `#1372 + `_ for more + details. Use :class:`MDAnalysis.analysis.base.AnalysisFromFunction` instead. + ''' def __init__(self, atoms): @@ -326,9 +386,16 @@ class Distance(Timeseries): t = Distance(code, atoms) - code is one of 'd' (distance vector), or 'r' (scalar distance) - atoms must contain 2 :class:`~MDAnalysis.core.groups.Atom` objects, either as a list or an - :class:`~MDAnalysis.core.groups.AtomGroup` + code is one of 'd' (distance vector), or 'r' (scalar distance) atoms must + contain 2 :class:`~MDAnalysis.core.groups.Atom` objects, either as a list + or an :class:`~MDAnalysis.core.groups.AtomGroup` + + .. deprecated:: 0.16.2 + The Timeseries functionality (in particular correl) will be removed in + the 0.17 release. See issue `#1372 + `_ for more + details. Use :class:`MDAnalysis.analysis.base.AnalysisFromFunction` instead. + ''' def __init__(self, code, atoms): @@ -348,8 +415,16 @@ class CenterOfGeometry(Timeseries): t = CenterOfGeometry(atoms) - *atoms* can be a list of :class:`~MDAnalysis.core.groups.Atom` - objects, or a :class:`~MDAnalysis.core.groups.AtomGroup` + *atoms* can be a list of :class:`~MDAnalysis.core.groups.Atom` objects, or + a :class:`~MDAnalysis.core.groups.AtomGroup` + + + .. deprecated:: 0.16.2 + The Timeseries functionality (in particular correl) will be removed in + the 0.17 release. See issue `#1372 + `_ for more + details. Use :class:`MDAnalysis.analysis.base.AnalysisFromFunction` instead. + ''' def __init__(self, atoms): @@ -364,8 +439,15 @@ class CenterOfMass(Timeseries): t = CenterOfMass(atoms) - *atoms* can be a list of :class:`~MDAnalysis.core.groups.Atom` - objects or a :class:`~MDAnalysis.core.groups.AtomGroup` + *atoms* can be a list of :class:`~MDAnalysis.core.groups.Atom` objects or a + :class:`~MDAnalysis.core.groups.AtomGroup` + + .. deprecated:: 0.16.2 + The Timeseries functionality (in particular correl) will be removed in + the 0.17 release. See issue `#1372 + `_ for more + details. Use :class:`MDAnalysis.analysis.base.AnalysisFromFunction` instead. + ''' def __init__(self, atoms): @@ -380,38 +462,43 @@ class WaterDipole(Timeseries): d = WaterDipole(atoms) - *atoms* must contain 3 :class:`~MDAnalysis.core.groups.Atom` - objects, either as a list or an - :class:`~MDAnalysis.core.groups.AtomGroup`; the first one *must* be - the oxygen, the other two are the hydrogens. + *atoms* must contain 3 :class:`~MDAnalysis.core.groups.Atom` objects, + either as a list or an :class:`~MDAnalysis.core.groups.AtomGroup`; the + first one *must* be the oxygen, the other two are the hydrogens. + + The vector ``d``, multiplied by the partial charge on the oxygen atom + (e.g. *q* = -0.0.834 for TIP3P water), gives the actual dipole moment. - The vector ``d``, multiplied by the partial charge on the oxygen atom - (e.g. *q* = -0.0.834 for TIP3P water), gives the actual dipole moment. + The vector is calculated from the positions of the oxygen atom + (:math:`\mathbf{x}_{\text{O}}`) and the two hydrogen atoms + (:math:`\mathbf{x}_{\text{H}_1}`, :math:`\mathbf{x}_{\text{H}_2}`) as - The vector is calculated from the positions of the oxygen atom - (:math:`\mathbf{x}_{\text{O}}`) and the two hydrogen atoms - (:math:`\mathbf{x}_{\text{H}_1}`, :math:`\mathbf{x}_{\text{H}_2}`) as + .. math:: - .. math:: + \mathbf{d} = \mathbf{x}_{\text{O}} - \frac{1}{2}(\mathbf{x}_{\text{H}_1} + \mathbf{x}_{\text{H}_2}) - \mathbf{d} = \mathbf{x}_{\text{O}} - \frac{1}{2}(\mathbf{x}_{\text{H}_1} + \mathbf{x}_{\text{H}_2}) + and the dipole moment vector is - and the dipole moment vector is + .. math:: - .. math:: + \boldsymbol{\mu} = q_{\text{O}} \mathbf{d} - \boldsymbol{\mu} = q_{\text{O}} \mathbf{d} + .. Note:: - .. Note:: + This will only work for water models that have half of the oxygen charge + on each hydrogen. The vector :math:`\mathbf{d}` has the opposite + direction of the dipole moment; multiplying with the oxygen charge + (:math:`q_{\text{O}}<0`) will flip the direction and produce the correct + orientation. - This will only work for water models that have half of the oxygen - charge on each hydrogen. The vector :math:`\mathbf{d}` has the - opposite direction of the dipole moment; multiplying with the oxygen - charge (:math:`q_{\text{O}}<0`) will flip the direction and produce - the correct orientation. + There are no sanity checks; *if the first atom in a water + molecule is not oxygen then results will be wrong.* - There are no sanity checks; *if the first atom in a water - molecule is not oxygen then results will be wrong.* + .. deprecated:: 0.16.2 + The Timeseries functionality (in particular correl) will be removed in + the 0.17 release. See issue `#1372 + `_ for more + details. Use :class:`MDAnalysis.analysis.base.AnalysisFromFunction` instead. ''' diff --git a/package/MDAnalysis/core/__init__.py b/package/MDAnalysis/core/__init__.py index 4d2c0bc71ad..2ba6f8d778f 100644 --- a/package/MDAnalysis/core/__init__.py +++ b/package/MDAnalysis/core/__init__.py @@ -30,7 +30,8 @@ :class:`~MDAnalysis.core.groups.AtomGroup` and return another :class:`~MDAnalysis.core.groups.AtomGroup`. -:mod:`~MDAnalysis.Timeseries` are a convenient way to analyse trajectories. +:mod:`~MDAnalysis.core.Timeseries` are a convenient way to analyse +trajectories. To get started, load the Universe:: @@ -56,6 +57,12 @@ Flags ----- +.. deprecated:: 0.16.2 + The flags registry will be removed in release 1.0. + Use keyword arguments for functions to obtain the desired behavior. + See issue `#782 `_ + for more details. + (This is an advanced topic and can probably be skipped by most people.) There are a number flags that influence how MDAnalysis behaves. They are accessible @@ -92,8 +99,9 @@ __all__ = ['AtomGroup', 'Selection', 'Timeseries'] -# set up flags for core routines (more convoluted than strictly necessary but should -# be clean to add more flags if needed) +# set up flags for core routines (more convoluted than strictly necessary but +# should be clean to add more flags if needed) + class Flags(dict): """Global registry of flags. Acts like a dict for item access. @@ -109,6 +117,13 @@ class Flags(dict): New flags are added with the :meth:`Flags.register` method which takes a new :class:`Flag` instance as an argument. + + .. deprecated:: 0.16.2 + The flags registry will be removed in release 1.0. + Use keyword arguments for functions to obtain the desired behavior. + See issue `#782 `_ + for more details. + """ def __init__(self, *args): @@ -180,7 +195,14 @@ def __getitem__(self, key): class Flag(object): - """A Flag, essentially a variable that knows its default and legal values.""" + """A Flag, essentially a variable that knows its default and legal values. + + .. deprecated:: 0.16.2 + The flags registry will be removed in release 1.0. + Use keyword arguments for functions to obtain the desired behavior. + See issue `#782 `_ + for more details. + """ def __init__(self, name, default, mapping=None, doc=None): """Create a new flag which will be registered with Flags. diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py index f9c2da1ebee..4d50f827eb0 100644 --- a/package/MDAnalysis/core/groups.py +++ b/package/MDAnalysis/core/groups.py @@ -342,7 +342,7 @@ def wrapped(self, other): class GroupBase(_MutableBase): """Base class from which a Universe's Group class is built. - Instances of :class:`GroupBase` provide the following operations that + Instances of :class:`GroupBase` provide the following operations that conserve element repetitions and order: +-------------------------------+------------+----------------------------+ @@ -989,7 +989,7 @@ def wrap(self, compound="atoms", center="com", box=None): "Please use one of 'group' 'residues' 'segments'" "or 'fragments'".format(compound)) -# TODO: ADD TRY-EXCEPT FOR MASSES PRESENCE + # TODO: ADD TRY-EXCEPT FOR MASSES PRESENCE if center.lower() in ('com', 'centerofmass'): centers = np.vstack([o.atoms.center_of_mass() for o in objects]) elif center.lower() in ('cog', 'centroid', 'centerofgeometry'): @@ -1352,9 +1352,10 @@ def is_strict_superset(self, other): class AtomGroup(GroupBase): """A group of atoms. - An AtomGroup is an ordered collection of atoms. Typically, an AtomGroup is - generated from a selection, or by indexing/slcing the AtomGroup of all - atoms in the Universe at :attr:`MDAnalysis.core.universe.Universe.atoms`. + An :class:`AtomGroup` is an ordered collection of atoms. Typically, an + :class:`AtomGroup` is generated from a selection, or by indexing/slicing + the :class:`AtomGroup` of all atoms in the :class:`Universe` at + :attr:`MDAnalysis.core.universe.Universe.atoms`. An AtomGroup can be indexed and sliced like a list:: @@ -1385,23 +1386,6 @@ class AtomGroup(GroupBase): atoms is crucial (for instance, in order to define angles or dihedrals). - Atoms can also be accessed in a Pythonic fashion by using the atom name as - an attribute. For instance, :: - - ag.CA - - will provide a :class:`AtomGroup` of all CA atoms in the - group. These *instant selector* attributes are auto-generated for - each atom name encountered in the group. - - .. note:: - - The name-attribute instant selector access to atoms is mainly - meant for quick interactive work. Thus it either returns a - single :class:`Atom` if there is only one matching atom, *or* a - new :class:`AtomGroup` for multiple matches. This makes it - difficult to use the feature consistently in scripts. - AtomGroups can be compared and combined using group operators. For instance, AtomGroups can be concatenated using `+` or :meth:`concatenate`:: @@ -1487,12 +1471,46 @@ class AtomGroup(GroupBase): AtomGroup instances are always bound to a :class:`MDAnalysis.core.universe.Universe`. They cannot exist in isolation. + + .. rubric:: Deprecated functionality + + *Instant selectors* will be removed in the 1.0 release. See issue `#1377 + `_ for more details. + + Atoms can also be accessed in a Pythonic fashion by using the atom name as + an attribute. For instance, :: + + ag.CA + + will provide a :class:`AtomGroup` of all CA atoms in the + group. These *instant selector* attributes are auto-generated for + each atom name encountered in the group. + + .. note:: + + The name-attribute instant selector access to atoms is mainly + meant for quick interactive work. Thus it either returns a + single :class:`Atom` if there is only one matching atom, *or* a + new :class:`AtomGroup` for multiple matches. This makes it + difficult to use the feature consistently in scripts. + + See Also -------- :class:`MDAnalysis.core.universe.Universe` + + .. deprecated:: 0.16.2 + *Instant selectors* of AtomGroup will be removed in the 1.0 release. + See issue `#1377 + `_ for + more details. + """ def __getitem__(self, item): + # DEPRECATED in 0.16.2 + # REMOVE in 1.0 + # # u.atoms['HT1'] access, otherwise default if isinstance(item, string_types): try: @@ -1502,6 +1520,9 @@ def __getitem__(self, item): return super(AtomGroup, self).__getitem__(item) def __getattr__(self, attr): + # DEPRECATED in 0.16.2 + # REMOVE in 1.0 + # # is this a known attribute failure? if attr in ('fragments',): # TODO: Generalise this to cover many attributes # eg: @@ -2460,7 +2481,7 @@ def ix(self): @property def ix_array(self): """Unique index of this component as an array. - + This method gives a consistent API between components and groups. See Also @@ -2637,6 +2658,12 @@ class Segment(ComponentBase): ComponentBase, so this class only includes ad-hoc methods specific to Segments. + .. deprecated:: 0.16.2 + *Instant selectors* of Segments will be removed in the 1.0 release. + See issue `#1377 + `_ for + more details. + """ def __repr__(self): me = '`_ for more details. + + If the loaded topology provided segids, then these are made accessible as attributes of the Universe. If the segid starts with a number such as '4AKE', the letter 's' will be prepended to the segid. @@ -313,6 +318,10 @@ def _generate_from_topology(self): # Update Universe namespace with segids # Many segments can have same segid, so group together first + # + # DEPRECATED in 0.16.2 + # REMOVE in 1.0 + # See https://github.com/MDAnalysis/mdanalysis/issues/1377 try: # returns dict of segid:segment segids = self.segments.groupby('segids') @@ -492,7 +501,7 @@ def transfer_to_memory(self, start=None, stop=None, step=None, # object, to provide fast access and allow coordinates # to be manipulated if step is None: - step = 1 + step = 1 self.trajectory = MemoryReader( coordinates, dimensions=self.trajectory.ts.dimensions, diff --git a/package/doc/sphinx/source/documentation_pages/selections.rst b/package/doc/sphinx/source/documentation_pages/selections.rst index 77851225050..c4773df5eb1 100644 --- a/package/doc/sphinx/source/documentation_pages/selections.rst +++ b/package/doc/sphinx/source/documentation_pages/selections.rst @@ -285,6 +285,17 @@ across frames:: Instant selectors ================= +.. deprecated:: 0.16.2 + + *Instant selectors* will be removed in the 1.0 release in order to + streamline the MDAnalysis user interface. They do not seem to be + widely used anymore, can produce cryptic error messages, and are + not considered "Pythonic" (and therefore not very intuitive for new + users). See issue `#1377 + `_ for more + details. + + For interactive work it becomes rather tedious to type common selection strings repeatedly. MDAnalysis automatically generates a number of *instant selectors* as attributes of the :class:`~MDAnalysis.core.universe.Universe` and number of From bd3b4df241cd31fb47f04f673982ea4701954f5f Mon Sep 17 00:00:00 2001 From: Richard Gowers Date: Tue, 13 Jun 2017 09:16:34 +0100 Subject: [PATCH 17/35] deprecated core.Timeseries module --- package/CHANGELOG | 10 ++++------ package/MDAnalysis/core/Timeseries.py | 14 ++++++++++++-- 2 files changed, 16 insertions(+), 8 deletions(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index 54b3e8b1ca6..f1aba435b37 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -19,18 +19,16 @@ mm/dd/17 richardjgowers, rathann, jbarnoud, orbeckst * 0.16.2 -Enhancements +Deprecations + * deprecated core.Timeseries module for 0.17.0 (Issue #1383) + * deprecated instant selectors for 1.0 (Issue #1377) + * deprecated the core.flag registry for 1.0 (Issue #782) Fixes * fixed GROWriter truncating long resids from the wrong end (Issue #1395) * Fixed dtype of numpy arrays to accomodate 32 bit architectures (Issue #1362) * Groups are hashable on python 3 (Issue #1397) -Changes - * added deprecation warnings for API changes (removal of Timeseries and - DCD correl functionality, removal of instant selectors, and removal of - the core.flag registry) (Issue #1383) - 06/03/17 utkbansal, kain88-de, xiki-tempula, kaplajon, wouterboomsma, richardjgowers, Shtkddud123, QuantumEntangledAndy, orbeckst, diff --git a/package/MDAnalysis/core/Timeseries.py b/package/MDAnalysis/core/Timeseries.py index dfb0d503e66..92dd0a11655 100644 --- a/package/MDAnalysis/core/Timeseries.py +++ b/package/MDAnalysis/core/Timeseries.py @@ -70,8 +70,9 @@ from __future__ import division, absolute_import import warnings -from . import groups +from numpy.lib.utils import deprecate +from . import groups with warnings.catch_warnings(): warnings.simplefilter('always', DeprecationWarning) @@ -80,7 +81,7 @@ 'https://github.com/MDAnalysis/mdanalysis/issues/1373'), DeprecationWarning) - +@deprecate(message="This class will be removed in 0.17") class TimeseriesCollection(object): '''A collection of timeseries objects. @@ -210,6 +211,7 @@ def _getAuxData(self): return auxData +@deprecate(message="This class will be removed in 0.17") class Timeseries(object): '''Base timeseries class - define subclasses for specific timeseries computations. @@ -272,6 +274,7 @@ def getAuxData(self): return [0.] * self.n_atoms +@deprecate(message="This class will be removed in 0.17") class Atom(Timeseries): '''Create a timeseries that returns coordinate data for an atom or group of atoms :: @@ -315,6 +318,7 @@ def getAtomCounts(self): return [1, ] * self.n_atoms +@deprecate(message="This class will be removed in 0.17") class Bond(Timeseries): '''Create a timeseries that returns a timeseries for a bond @@ -337,6 +341,7 @@ def __init__(self, atoms): Timeseries.__init__(self, 'r', atoms, 1) +@deprecate(message="This class will be removed in 0.17") class Angle(Timeseries): '''Create a timeseries that returns a timeseries for an angle @@ -359,6 +364,7 @@ def __init__(self, atoms): Timeseries.__init__(self, 'a', atoms, 1) +@deprecate(message="This class will be removed in 0.17") class Dihedral(Timeseries): '''Create a timeseries that returns a timeseries for a dihedral angle @@ -381,6 +387,7 @@ def __init__(self, atoms): Timeseries.__init__(self, 'h', atoms, 1) +@deprecate(message="This class will be removed in 0.17") class Distance(Timeseries): '''Create a timeseries that returns distances between 2 atoms @@ -410,6 +417,7 @@ def __init__(self, code, atoms): Timeseries.__init__(self, code, atoms, size) +@deprecate(message="This class will be removed in 0.17") class CenterOfGeometry(Timeseries): '''Create a timeseries that returns the center of geometry of a group of atoms @@ -434,6 +442,7 @@ def getAuxData(self): return [1.] * self.n_atoms +@deprecate(message="This class will be removed in 0.17") class CenterOfMass(Timeseries): '''Create a timeseries that returns the center of mass of a group of atoms @@ -457,6 +466,7 @@ def getAuxData(self): return [a.mass for a in self.atoms] +@deprecate(message="This class will be removed in 0.17") class WaterDipole(Timeseries): r'''Create a Timeseries that returns a timeseries for the bisector vector of a 3-site water From e9784a791870a865c6e25fbd87588f73068cf707 Mon Sep 17 00:00:00 2001 From: Richard Gowers Date: Tue, 13 Jun 2017 09:17:54 +0100 Subject: [PATCH 18/35] Deprecated DCDReader.correl --- package/MDAnalysis/coordinates/DCD.py | 2 ++ package/MDAnalysis/coordinates/__init__.py | 4 ---- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/package/MDAnalysis/coordinates/DCD.py b/package/MDAnalysis/coordinates/DCD.py index 0f5a0eb9693..0cdd4cf2709 100644 --- a/package/MDAnalysis/coordinates/DCD.py +++ b/package/MDAnalysis/coordinates/DCD.py @@ -81,6 +81,7 @@ import os import errno import numpy as np +from numpy.lib.utils import deprecate import struct import types import warnings @@ -578,6 +579,7 @@ def timeseries(self, asel=None, start=None, stop=None, step=None, skip=None, # XXX needs to be implemented return self._read_timeseries(atom_numbers, start, stop, step, format) + @deprecate(message="This method will be removed in 0.17") def correl(self, timeseries, start=None, stop=None, step=None, skip=None): """Populate a :class:`~MDAnalysis.core.Timeseries.TimeseriesCollection` object with time series computed from the trajectory. diff --git a/package/MDAnalysis/coordinates/__init__.py b/package/MDAnalysis/coordinates/__init__.py index 45c13eada4d..fc9cfc82c81 100644 --- a/package/MDAnalysis/coordinates/__init__.py +++ b/package/MDAnalysis/coordinates/__init__.py @@ -538,10 +538,6 @@ class can choose an appropriate reader automatically. ``timeseries(atomGroup, [start[,stop[,skip[,format]]]])`` returns a subset of coordinate data - ``correl(timeseriesCollection[,start[,stop[,skip]]])`` - populate a :class:`MDAnalysis.core.Timeseries.TimeseriesCollection` object - with observable timeseries computed from the trajectory - Attributes .......... From 6e0abb0c32a74c793b835796f66765823598e334 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Thu, 15 Jun 2017 23:05:13 -0700 Subject: [PATCH 19/35] mention optional/full dependencies in docs - 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. --- .../documentation_pages/analysis_modules.rst | 46 +++++++++++-------- package/doc/sphinx/source/index.rst | 42 +++++++++++++++-- 2 files changed, 66 insertions(+), 22 deletions(-) diff --git a/package/doc/sphinx/source/documentation_pages/analysis_modules.rst b/package/doc/sphinx/source/documentation_pages/analysis_modules.rst index 7da649d8683..edd239805de 100644 --- a/package/doc/sphinx/source/documentation_pages/analysis_modules.rst +++ b/package/doc/sphinx/source/documentation_pages/analysis_modules.rst @@ -4,29 +4,39 @@ Analysis modules **************** -The :mod:`MDAnalysis.analysis` module contains code to carry out -specific analysis functionality. It is based on the core functionality -(i.e. trajectory I/O, selections etc). The analysis modules can be -used as examples for how to use MDAnalysis but also as working code -for research projects; typically all contributed code has been used by -the authors in their own work. +The :mod:`MDAnalysis.analysis` module contains code to carry out specific +analysis functionality. It is based on the core functionality (i.e. trajectory +I/O, selections etc). The analysis modules can be used as examples for how to +use MDAnalysis but also as working code for research projects; typically all +contributed code has been used by the authors in their own work. -Please see the individual module documentation for additional -references and citation information. +Please see the individual module documentation for additional references and +citation information. -These modules are not imported by default; in order to use them one -has to import them from :mod:`MDAnalysis.analysis`, for instance :: +These modules are not imported by default; in order to use them one has to +import them from :mod:`MDAnalysis.analysis`, for instance :: import MDAnalysis.analysis.align -.. Note:: - - Some of the modules require additional Python packages such as :mod:`scipy` - from the SciPy_ package. These package are *not automatically installed* - (although one can add the ``[analysis]`` requirement to the :program:`pip` - command line to force their installation. - -.. _scipy: http://www.scipy.org/ +.. rubric:: Additional dependencies + +Some of the modules in :mod:`MDAnalysis.analysis` require additional Python +packages to enable full functionality. For example, +:mod:`MDAnalysis.analysis.encore` provides more options if `scikit-learn`_ is +installed. These package are *not automatically installed* with +:program:`pip`(although one can add the ``[analysis]`` requirement to the +:program:`pip` command line to force their installation). If you install +MDAnalysis with :program:`conda` (see :ref:`installation-instructions`) then a +*full set of dependencies* is automatically installed. + +Other modules require external programs. For instance, the +:mod:`MDAnalysis.analysis.hole` module requires an installation of the HOLE_ +suite of programs. You will need to install these external dependencies by +following their installation instructions before you can use the corresponding +MDAnalysis module. + +.. _scikit-learn: http://scikit-learn.org/ +.. _HOLE: http://www.smartsci.uk/hole/ Building blocks for Analysis diff --git a/package/doc/sphinx/source/index.rst b/package/doc/sphinx/source/index.rst index 20df327041f..666117666c4 100644 --- a/package/doc/sphinx/source/index.rst +++ b/package/doc/sphinx/source/index.rst @@ -57,36 +57,70 @@ members agree and adhere to --- please read it. http://groups.google.com/group/mdnalysis-discussion .. _`Code of Conduct`: http://www.mdanalysis.org/pages/conduct/ +.. _installation-instructions: Installing MDAnalysis ===================== -To `install the latest release`_ using `pip`_: +The easiest approach to `install the latest release`_ is to use a package that +can be installed either with pip_ or conda_. + +pip +--- + +Installation with `pip`_ and a *minimal set of dependencies*: .. code-block:: bash pip install --upgrade MDAnalysis -Alternatively, to install with conda_ do +To install with a *full set of dependencies* (which includes everything needed +for :mod:`MDAnalysis.analysis`), add the ``[analysis]`` tag: + +.. code-block:: bash + + pip install --upgrade MDAnalysis[analysis] + + +conda +----- + +First installation with conda_: .. code-block:: bash conda config --add channels conda-forge conda install mdanalysis -and to upgrade +which will automatically install a *full set of dependencies*. + +To upgrade later: .. code-block:: bash conda update mdanalysis +Tests +----- + +If you want to `run the tests`_ or use example files to follow some of the +examples in the documentation or the tutorials_, also install the +``MDAnalysisTests`` package: + +.. code-block:: bash + + pip install --upgrade MDAnalysisTests # with pip + conda install mdanalysistests # with conda + .. _install the latest release: http://www.mdanalysis.org/pages/installation_quick_start/ .. _pip: http://www.pip-installer.org/en/latest/index.html .. _conda: http://conda.pydata.org/docs/ - +.. _run the tests: http://wiki.mdanalysis.org/UnitTests +.. _tutorials: http://www.mdanalysis.org/pages/learning_MDAnalysis/ + Source Code =========== From 250ed47cade2f512f21bf687a4cdf198eff255e3 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Fri, 16 Jun 2017 00:56:12 -0700 Subject: [PATCH 20/35] removed top-level imports of Timeseries - 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 --- package/MDAnalysis/__init__.py | 38 +++++++++++++++++-- package/MDAnalysis/core/Timeseries.py | 2 +- package/MDAnalysis/core/__init__.py | 1 - .../MDAnalysisTests/utils/test_deprecated.py | 13 +++++++ 4 files changed, 49 insertions(+), 5 deletions(-) diff --git a/package/MDAnalysis/__init__.py b/package/MDAnalysis/__init__.py index d324854bf16..17ba62e4aaf 100644 --- a/package/MDAnalysis/__init__.py +++ b/package/MDAnalysis/__init__.py @@ -143,7 +143,7 @@ """ from __future__ import absolute_import -__all__ = ['Timeseries', 'Universe', 'as_Universe', 'Writer', 'collection', +__all__ = ['Universe', 'as_Universe', 'Writer', 'collection', 'fetch_mmtf'] import logging @@ -192,14 +192,46 @@ from . import units # Bring some often used objects into the current namespace -from .core import Timeseries from .core.universe import Universe, as_Universe, Merge from .coordinates.core import writer as Writer # After Universe import from .coordinates.MMTF import fetch_mmtf -collection = Timeseries.TimeseriesCollection() +# REMOVE in 0.17.0 +class _MockTimeseriesCollection(object): + """When accessed the first time, emit warning and raise NotImplementedError. + + This breaks existing code that relies on MDAnalysis.collection by + replacing :: + + collection = Timeseries.TimeseriesCollection() + + with:: + + collection = _MockTimeseriesCollection() + + """ + + def __getattr__(self, name): + self._warn_and_die() + + def __getitem__(self, index): + self._warn_and_die() + + def _warn_and_die(self): + import logging + msg = "collection = Timeseries.TimeseriesCollection() will be removed in 0.17.0\n" \ + "and MDAnalysis.collection has been disabled. If you want to use it, \n" \ + "instantiate a collection yourself:\n\n" \ + " from MDAnalysis.core.Timeseries import TimeseriesCollection\n" \ + " collection = TimeseriesCollection()\n\n" \ + "Note that release 0.16.2 is the LAST RELEASE with TimeseriesCollection." + logging.getLogger("MDAnalysis").warn(msg) + warnings.warn(msg, DeprecationWarning) + raise NotImplementedError("TimeseriesCollection will be REMOVED IN THE NEXT RELEASE 0.17.0") +collection = _MockTimeseriesCollection() +del _MockTimeseriesCollection from .migration.ten2eleven import ten2eleven diff --git a/package/MDAnalysis/core/Timeseries.py b/package/MDAnalysis/core/Timeseries.py index 92dd0a11655..f7e99248673 100644 --- a/package/MDAnalysis/core/Timeseries.py +++ b/package/MDAnalysis/core/Timeseries.py @@ -81,6 +81,7 @@ 'https://github.com/MDAnalysis/mdanalysis/issues/1373'), DeprecationWarning) + @deprecate(message="This class will be removed in 0.17") class TimeseriesCollection(object): '''A collection of timeseries objects. @@ -211,7 +212,6 @@ def _getAuxData(self): return auxData -@deprecate(message="This class will be removed in 0.17") class Timeseries(object): '''Base timeseries class - define subclasses for specific timeseries computations. diff --git a/package/MDAnalysis/core/__init__.py b/package/MDAnalysis/core/__init__.py index 2ba6f8d778f..ae5c3d73879 100644 --- a/package/MDAnalysis/core/__init__.py +++ b/package/MDAnalysis/core/__init__.py @@ -451,5 +451,4 @@ class flagsDocs(object): from . import groups from . import selection -from . import Timeseries from . import AtomGroup diff --git a/testsuite/MDAnalysisTests/utils/test_deprecated.py b/testsuite/MDAnalysisTests/utils/test_deprecated.py index 3a852a0f88f..3ce63e6abe7 100644 --- a/testsuite/MDAnalysisTests/utils/test_deprecated.py +++ b/testsuite/MDAnalysisTests/utils/test_deprecated.py @@ -25,6 +25,10 @@ # will be removed in 1.0) from __future__ import absolute_import +import warnings + +from numpy.testing import assert_equal, assert_raises + class TestImports(object): def test_core_units(self): try: @@ -75,3 +79,12 @@ def test_analysis_x3dna(self): except ImportError: raise AssertionError("MDAnalysis.analysis.x3dna not available") +def test_collections_NotImplementedError(): + import MDAnalysis + with assert_raises(NotImplementedError): + MDAnalysis.collection.clear() + + + + + From c238a40b8630e7bfbfc0d7bdfd486eda5f6c04a7 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Fri, 16 Jun 2017 13:55:02 -0700 Subject: [PATCH 21/35] new MDAnalysisTests.core.util.assert_nowarns() function --- testsuite/MDAnalysisTests/__init__.py | 3 +- testsuite/MDAnalysisTests/util.py | 50 +++++++++++++++++++++++++++ 2 files changed, 52 insertions(+), 1 deletion(-) diff --git a/testsuite/MDAnalysisTests/__init__.py b/testsuite/MDAnalysisTests/__init__.py index 81f330c43f2..2397ed8598d 100644 --- a/testsuite/MDAnalysisTests/__init__.py +++ b/testsuite/MDAnalysisTests/__init__.py @@ -98,7 +98,7 @@ A number of plugins external to nose are automatically loaded. The `knownfailure` plugin provides the `@knownfailure()` decorator, which can be used to mark tests -that are expected to fail. If used with default arguments the parentheses can be +that are expected to fail. If used with default arguments the parentheses can be excluded. .. _NumPy: http://www.numpy.org/ @@ -148,6 +148,7 @@ module_not_found, parser_not_found, in_dir, + assert_nowarns, ) from MDAnalysisTests.core.util import make_Universe diff --git a/testsuite/MDAnalysisTests/util.py b/testsuite/MDAnalysisTests/util.py index 9454255eb92..1c7aea712be 100644 --- a/testsuite/MDAnalysisTests/util.py +++ b/testsuite/MDAnalysisTests/util.py @@ -40,6 +40,8 @@ import mock import os +from numpy.testing import assert_warns + def block_import(package): """Block import of a given package @@ -148,3 +150,51 @@ def in_dir(dirname): os.chdir(dirname) yield dirname os.chdir(old_path) + + +def assert_nowarns(warning_class, *args, **kwargs): + """Fail if the given callable throws the specified warning. + + A warning of class warning_class should NOT be thrown by the callable when + invoked with arguments args and keyword arguments kwargs. + If a different type of warning is thrown, it will not be caught. + + Parameters + ---------- + warning_class : class + The class defining the warning that `func` is expected to throw. + func : callable + The callable to test. + \*args : Arguments + Arguments passed to `func`. + \*\*kwargs : Kwargs + Keyword arguments passed to `func`. + + Returns + ------- + True + if no `AssertionError` is raised + + Note + ---- + numpy.testing.assert_warn returns the value returned by `func`; we would + need a second func evaluation so in order to avoid it, only True is + returned if no assertion is raised. + + SeeAlso + ------- + numpy.testing.assert_warn + + """ + func = args[0] + args = args[1:] + try: + value = assert_warns(DeprecationWarning, func, *args, **kwargs) + except AssertionError: + # a warning was NOT emitted: all good + return True + else: + # There was a warning even though we do not want to see one. + raise AssertionError + + From 3de936c8bbdee7b437d915b98a8fd82f3901a080 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Fri, 16 Jun 2017 14:10:29 -0700 Subject: [PATCH 22/35] make instant selectors emit DeprecationWarning - instant selectors AtomGroup[''], AtomGroup., ResidueGroup., Segment., Segment.r, SegmentGroup. emit warnings - added tests - updated docs with detailed deprecation and alternatives Thanks to @richardjgowers for insights https://github.com/MDAnalysis/mdanalysis/pull/1403#issuecomment-309136416 --- package/MDAnalysis/core/__init__.py | 3 -- package/MDAnalysis/core/groups.py | 26 ++++++++---- package/MDAnalysis/core/topologyattrs.py | 40 +++++++++++++++++++ .../source/documentation_pages/selections.rst | 20 +++++++++- testsuite/MDAnalysisTests/core/test_groups.py | 38 +++++++++++++++++- 5 files changed, 115 insertions(+), 12 deletions(-) diff --git a/package/MDAnalysis/core/__init__.py b/package/MDAnalysis/core/__init__.py index ae5c3d73879..6c3f4a4fb10 100644 --- a/package/MDAnalysis/core/__init__.py +++ b/package/MDAnalysis/core/__init__.py @@ -30,9 +30,6 @@ :class:`~MDAnalysis.core.groups.AtomGroup` and return another :class:`~MDAnalysis.core.groups.AtomGroup`. -:mod:`~MDAnalysis.core.Timeseries` are a convenient way to analyse -trajectories. - To get started, load the Universe:: u = Universe(topology_file, trajectory_file) diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py index 4d50f827eb0..46d46c10644 100644 --- a/package/MDAnalysis/core/groups.py +++ b/package/MDAnalysis/core/groups.py @@ -101,6 +101,8 @@ import os import warnings +from numpy.lib.utils import deprecate + import MDAnalysis from .. import _ANCHOR_UNIVERSES from ..lib import util @@ -1502,9 +1504,7 @@ class AtomGroup(GroupBase): .. deprecated:: 0.16.2 *Instant selectors* of AtomGroup will be removed in the 1.0 release. - See issue `#1377 - `_ for - more details. + See :ref:`Instant selectors`_ for details and alternatives. """ def __getitem__(self, item): @@ -2199,6 +2199,11 @@ class ResidueGroup(GroupBase): ResidueGroups can be compared and combined using group operators. See the list of these operators on :class:`GroupBase`. + + .. deprecated:: 0.16.2 + *Instant selectors* of Segments will be removed in the 1.0 release. + See :ref:`Instant selectors`_ for details and alternatives. + """ @property @@ -2313,6 +2318,11 @@ class SegmentGroup(GroupBase): SegmentGroups can be compared and combined using group operators. See the list of these operators on :class:`GroupBase`. + + .. deprecated:: 0.16.2 + *Instant selectors* of Segments will be removed in the 1.0 release. + See :ref:`Instant selectors`_ for details and alternatives. + """ @property @@ -2660,9 +2670,7 @@ class Segment(ComponentBase): .. deprecated:: 0.16.2 *Instant selectors* of Segments will be removed in the 1.0 release. - See issue `#1377 - `_ for - more details. + See :ref:`Instant selectors`_ for details and alternatives. """ def __repr__(self): @@ -2686,7 +2694,11 @@ def __getattr__(self, attr): # Segment.r1 access if attr.startswith('r') and attr[1:].isdigit(): resnum = int(attr[1:]) - return self.residues[resnum - 1] # convert to 0 based + rg = self.residues[resnum - 1] # convert to 0 based + warnings.warn("Instant selectors Segment.r will be removed in 1.0. " + "Use Segment.residues[N-1] instead.", + DeprecationWarning) + return rg # Resname accesss if hasattr(self.residues, 'resnames'): try: diff --git a/package/MDAnalysis/core/topologyattrs.py b/package/MDAnalysis/core/topologyattrs.py index 9976b9b5b88..fa6997c3adc 100644 --- a/package/MDAnalysis/core/topologyattrs.py +++ b/package/MDAnalysis/core/topologyattrs.py @@ -42,6 +42,8 @@ import numbers import numpy as np +from numpy.lib.utils import deprecate + from . import flags from ..lib.util import cached, convert_aa_code, iterable from ..lib import transformations, mdamath @@ -409,6 +411,9 @@ def getattr__(atomgroup, name): raise AttributeError("'{0}' object has no attribute '{1}'".format( atomgroup.__class__.__name__, name)) + @deprecate(message="Instant selector AtomGroup[''] or AtomGroup. " + "is deprecated and will be removed in 1.0. " + "Use AtomGroup.select_atoms('name ') instead.") def _get_named_atom(group, name): """Get all atoms with name *name* in the current AtomGroup. @@ -417,6 +422,14 @@ def _get_named_atom(group, name): no atoms are found, a :exc:`SelectionError` is raised. .. versionadded:: 0.9.2 + + .. deprecated:: 0.16.2 + *Instant selectors* will be removed in the 1.0 release. + Use ``AtomGroup.select_atoms('name ')`` instead. + See issue `#1377 + `_ for + more details. + """ # There can be more than one atom with the same name atomlist = group.atoms.unique[group.atoms.unique.names == name] @@ -1057,6 +1070,13 @@ def getattr__(residuegroup, resname): # This transplant is hardcoded for now to allow for multiple getattr things #transplants[Segment].append(('__getattr__', getattr__)) + + @deprecate(message="Instant selector ResidueGroup. " + "or Segment. " + "is deprecated and will be removed in 1.0. " + "Use ResidueGroup[ResidueGroup.resnames == ''] " + "or Segment.residues[Segment.residues == ''] " + "instead.") def _get_named_residue(group, resname): """Get all residues with name *resname* in the current ResidueGroup or Segment. @@ -1068,6 +1088,15 @@ def _get_named_residue(group, resname): .. versionadded:: 0.9.2 + .. deprecated:: 0.16.2 + *Instant selectors* will be removed in the 1.0 release. + Use ``ResidueGroup[ResidueGroup.resnames == '']`` + or ``Segment.residues[Segment.residues == '']`` + instead. + See issue `#1377 + `_ for + more details. + """ # There can be more than one residue with the same name residues = group.residues.unique[ @@ -1244,6 +1273,10 @@ def getattr__(segmentgroup, segid): transplants[SegmentGroup].append( ('__getattr__', getattr__)) + @deprecate(message="Instant selector SegmentGroup. " + "is deprecated and will be removed in 1.0. " + "Use SegmentGroup[SegmentGroup.segids == ''] " + "instead.") def _get_named_segment(group, segid): """Get all segments with name *segid* in the current SegmentGroup. @@ -1254,6 +1287,13 @@ def _get_named_segment(group, segid): .. versionadded:: 0.9.2 + .. deprecated:: 0.16.2 + *Instant selectors* will be removed in the 1.0 release. + Use ``SegmentGroup[SegmentGroup.segids == '']`` instead. + See issue `#1377 + `_ for + more details. + """ # Undo adding 's' if segid started with digit if segid.startswith('s') and len(segid) >= 2 and segid[1].isdigit(): diff --git a/package/doc/sphinx/source/documentation_pages/selections.rst b/package/doc/sphinx/source/documentation_pages/selections.rst index c4773df5eb1..40caae95b7e 100644 --- a/package/doc/sphinx/source/documentation_pages/selections.rst +++ b/package/doc/sphinx/source/documentation_pages/selections.rst @@ -286,7 +286,6 @@ Instant selectors ================= .. deprecated:: 0.16.2 - *Instant selectors* will be removed in the 1.0 release in order to streamline the MDAnalysis user interface. They do not seem to be widely used anymore, can produce cryptic error messages, and are @@ -309,6 +308,11 @@ other levels of the structural hierarchy, namely for Segment selector ---------------- +.. deprecated:: 0.16.2 + Use ``SegmentGroup[SegmentGroup.segids == '']`` instead. Note that this + *always* returns a :class:`SegmentGroup` and *never* a :class:`Segment` + (unlike the instant selector). + - ``universe.`` or ``universe.s`` (if ** starts with a number) - returns a :class:`~MDAnalysis.core.groups.Segment` @@ -320,6 +324,9 @@ Segment selector Resid selector -------------- +.. deprecated:: 0.16.2 + Use ``Segment.residues[N-1]`` instead. + - ``seg.r`` selects residue with number ```` - returns a :class:`~MDAnalysis.core.groups.Residue` - works for :class:`~MDAnalysis.core.groups.Segment` and :class:`~MDAnalysis.core.groups.SegmentGroup` @@ -330,6 +337,12 @@ Resid selector Residue name selector --------------------- +.. deprecated:: 0.16.2 + Use ``ResidueGroup[ResidueGroup.resnames == '']`` or + ``Segment.residues[Segment.residues == '']`` instead. Note that this + *always* returns a :class:`ResidueGroup` and *never* a :class:`Residue` + (unlike the instant selector). + - ``seg.`` selects residues with residue name ```` - returns a :class:`~MDAnalysis.core.groups.ResidueGroup` - works for :class:`~MDAnalysis.core.groups.Segment` and :class:`~MDAnalysis.core.groups.SegmentGroup` @@ -346,6 +359,11 @@ Residue name selector Atom name selector ------------------ +.. deprecated:: 0.16.2 + Use ``AtomGroup.select_atoms('name ')`` instead. Note that this + *always* returns an :class:`AtomGroup` and *never* an :class:`Atom` (unlike + the instant selector). + - ``g.`` selects a single atom or a group of atoms with name ```` - returns diff --git a/testsuite/MDAnalysisTests/core/test_groups.py b/testsuite/MDAnalysisTests/core/test_groups.py index 004b6804729..178e9140e82 100644 --- a/testsuite/MDAnalysisTests/core/test_groups.py +++ b/testsuite/MDAnalysisTests/core/test_groups.py @@ -30,12 +30,13 @@ assert_array_equal, assert_equal, assert_raises, + assert_warns, ) import operator import six import MDAnalysis as mda -from MDAnalysisTests import make_Universe, parser_not_found +from MDAnalysisTests import make_Universe, parser_not_found, assert_nowarns from MDAnalysisTests.datafiles import PSF, DCD from MDAnalysis.core import groups from MDAnalysis.core.topology import Topology @@ -986,3 +987,38 @@ class TestAtomGroup(object): def test_PDB_atom_repr(): u = make_Universe(extras=('altLocs', 'names', 'types', 'resnames', 'resids', 'segids')) assert_equal("", u.atoms[0].__repr__()) + + +class TestInstantSelectorDeprecationWarnings(object): + def setUp(self): + self.u = make_Universe(("resids", "resnames", "segids", "names")) + + def test_AtomGroup_warn_getitem(self): + name = self.u.atoms[0].name + assert_warns(DeprecationWarning, lambda x: self.u.atoms[x], name) + + def test_AtomGroup_nowarn_getitem_index(self): + assert_nowarns(DeprecationWarning, lambda x: self.u.atoms[x], 0) + + def test_AtomGroup_warn_getattr(self): + name = self.u.atoms[0].name + assert_warns(DeprecationWarning, lambda x: getattr(self.u.atoms, x), name) + + def test_ResidueGroup_warn_getattr_resname(self): + name = self.u.residues[0].resname + assert_warns(DeprecationWarning, lambda x: getattr(self.u.residues, x), name) + + def test_Segment_warn_getattr_resname(self): + name = self.u.residues[0].resname + assert_warns(DeprecationWarning, lambda x: getattr(self.u.segments[0], x), name) + + def test_Segment_warn_getattr_rRESNUM(self): + assert_warns(DeprecationWarning, lambda x: getattr(self.u.segments[0], x), 'r1') + + def test_SegmentGroup_warn_getattr(self): + name = self.u.segments[0].segid + assert_warns(DeprecationWarning, lambda x: getattr(self.u.segments, x), name) + + def test_SegmentGroup_nowarn_getitem(self): + assert_nowarns(DeprecationWarning, lambda x: self.u.segments[x], 0) + From 3e57373d9f683681ca2f30cb37626a740aaa4491 Mon Sep 17 00:00:00 2001 From: Max Linke Date: Sat, 17 Jun 2017 08:24:52 +0200 Subject: [PATCH 23/35] fix sphinx warnings --- package/MDAnalysis/coordinates/DCD.py | 55 ++++++++++--------- package/MDAnalysis/core/Timeseries.py | 19 ++++--- package/MDAnalysis/core/groups.py | 22 ++++---- .../source/documentation_pages/selections.rst | 1 + 4 files changed, 50 insertions(+), 47 deletions(-) diff --git a/package/MDAnalysis/coordinates/DCD.py b/package/MDAnalysis/coordinates/DCD.py index 0cdd4cf2709..70b81d52ae0 100644 --- a/package/MDAnalysis/coordinates/DCD.py +++ b/package/MDAnalysis/coordinates/DCD.py @@ -581,36 +581,37 @@ def timeseries(self, asel=None, start=None, stop=None, step=None, skip=None, @deprecate(message="This method will be removed in 0.17") def correl(self, timeseries, start=None, stop=None, step=None, skip=None): - """Populate a :class:`~MDAnalysis.core.Timeseries.TimeseriesCollection` object - with time series computed from the trajectory. - - Calling this method will iterate through the whole trajectory and - perform the calculations prescribed in `timeseries`. - - Parameters - ---------- - timeseries : :class:`MDAnalysis.core.Timeseries.TimeseriesCollection` - The :class:`MDAnalysis.core.Timeseries.TimeseriesCollection` that defines what kind - of computations should be performed on the data in this trajectory. - start : int (optional) - Begin reading the trajectory at frame index `start` (where 0 is the index - of the first frame in the trajectory); the default ``None`` starts - at the beginning. - stop : int (optional) - End reading the trajectory at frame index `stop`-1, i.e, `stop` is excluded. - The trajectory is read to the end with the default ``None``. - step : int (optional) - Step size for reading; the default ``None`` is equivalent to 1 and means to - read every frame. + """ +Populate a :class:`~MDAnalysis.core.Timeseries.TimeseriesCollection` object +with time series computed from the trajectory. + +Calling this method will iterate through the whole trajectory and +perform the calculations prescribed in `timeseries`. + +Parameters +---------- +timeseries : :class:`MDAnalysis.core.Timeseries.TimeseriesCollection` + The :class:`MDAnalysis.core.Timeseries.TimeseriesCollection` that defines what kind + of computations should be performed on the data in this trajectory. +start : int (optional) + Begin reading the trajectory at frame index `start` (where 0 is the index + of the first frame in the trajectory); the default ``None`` starts + at the beginning. +stop : int (optional) + End reading the trajectory at frame index `stop`-1, i.e, `stop` is excluded. + The trajectory is read to the end with the default ``None``. +step : int (optional) + Step size for reading; the default ``None`` is equivalent to 1 and means to + read every frame. - Note - ---- - The `correl` functionality is only implemented for DCD trajectories and - the :class:`DCDReader`. +Note +---- +The `correl` functionality is only implemented for DCD trajectories and +the :class:`DCDReader`. - .. deprecated:: 0.16.0 - `skip` has been deprecated in favor of the standard keyword `step`. +.. deprecated:: 0.16.0 + `skip` has been deprecated in favor of the standard keyword `step`. """ if skip is not None: diff --git a/package/MDAnalysis/core/Timeseries.py b/package/MDAnalysis/core/Timeseries.py index f7e99248673..024b0cb18ca 100644 --- a/package/MDAnalysis/core/Timeseries.py +++ b/package/MDAnalysis/core/Timeseries.py @@ -82,7 +82,6 @@ DeprecationWarning) -@deprecate(message="This class will be removed in 0.17") class TimeseriesCollection(object): '''A collection of timeseries objects. @@ -110,6 +109,7 @@ class TimeseriesCollection(object): ''' + @deprecate(message="This class will be removed in 0.17") def __init__(self): self.timeseries = [] @@ -223,6 +223,7 @@ class Timeseries(object): ''' + @deprecate(message="This class will be removed in 0.17") def __init__(self, code, atoms, dsize): if isinstance(atoms, groups.AtomGroup): self.atoms = atoms.atoms @@ -274,7 +275,6 @@ def getAuxData(self): return [0.] * self.n_atoms -@deprecate(message="This class will be removed in 0.17") class Atom(Timeseries): '''Create a timeseries that returns coordinate data for an atom or group of atoms :: @@ -297,6 +297,7 @@ class Atom(Timeseries): ''' + @deprecate(message="This class will be removed in 0.17") def __init__(self, code, atoms): if code not in ('x', 'y', 'z', 'v', 'w'): raise ValueError("Bad code") @@ -318,7 +319,6 @@ def getAtomCounts(self): return [1, ] * self.n_atoms -@deprecate(message="This class will be removed in 0.17") class Bond(Timeseries): '''Create a timeseries that returns a timeseries for a bond @@ -335,13 +335,13 @@ class Bond(Timeseries): ''' + @deprecate(message="This class will be removed in 0.17") def __init__(self, atoms): if not len(atoms) == 2: raise ValueError("Bond timeseries requires a 2 atom selection") Timeseries.__init__(self, 'r', atoms, 1) -@deprecate(message="This class will be removed in 0.17") class Angle(Timeseries): '''Create a timeseries that returns a timeseries for an angle @@ -358,13 +358,13 @@ class Angle(Timeseries): ''' + @deprecate(message="This class will be removed in 0.17") def __init__(self, atoms): if not len(atoms) == 3: raise ValueError("Angle timeseries requires a 3 atom selection") Timeseries.__init__(self, 'a', atoms, 1) -@deprecate(message="This class will be removed in 0.17") class Dihedral(Timeseries): '''Create a timeseries that returns a timeseries for a dihedral angle @@ -381,13 +381,13 @@ class Dihedral(Timeseries): ''' + @deprecate(message="This class will be removed in 0.17") def __init__(self, atoms): if not len(atoms) == 4: raise ValueError("Dihedral timeseries requires a 4 atom selection") Timeseries.__init__(self, 'h', atoms, 1) -@deprecate(message="This class will be removed in 0.17") class Distance(Timeseries): '''Create a timeseries that returns distances between 2 atoms @@ -405,6 +405,7 @@ class Distance(Timeseries): ''' + @deprecate(message="This class will be removed in 0.17") def __init__(self, code, atoms): if code not in ('d', 'r'): raise ValueError("Bad code") @@ -417,7 +418,6 @@ def __init__(self, code, atoms): Timeseries.__init__(self, code, atoms, size) -@deprecate(message="This class will be removed in 0.17") class CenterOfGeometry(Timeseries): '''Create a timeseries that returns the center of geometry of a group of atoms @@ -435,6 +435,7 @@ class CenterOfGeometry(Timeseries): ''' + @deprecate(message="This class will be removed in 0.17") def __init__(self, atoms): Timeseries.__init__(self, 'm', atoms, 3) @@ -442,7 +443,6 @@ def getAuxData(self): return [1.] * self.n_atoms -@deprecate(message="This class will be removed in 0.17") class CenterOfMass(Timeseries): '''Create a timeseries that returns the center of mass of a group of atoms @@ -459,6 +459,7 @@ class CenterOfMass(Timeseries): ''' + @deprecate(message="This class will be removed in 0.17") def __init__(self, atoms): Timeseries.__init__(self, 'm', atoms, 3) @@ -466,7 +467,6 @@ def getAuxData(self): return [a.mass for a in self.atoms] -@deprecate(message="This class will be removed in 0.17") class WaterDipole(Timeseries): r'''Create a Timeseries that returns a timeseries for the bisector vector of a 3-site water @@ -512,6 +512,7 @@ class WaterDipole(Timeseries): ''' + @deprecate(message="This class will be removed in 0.17") def __init__(self, atoms): if not len(atoms) == 3: raise ValueError("WaterDipole timeseries requires a 3 atom selection") diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py index 46d46c10644..f2717469aac 100644 --- a/package/MDAnalysis/core/groups.py +++ b/package/MDAnalysis/core/groups.py @@ -1488,13 +1488,13 @@ class AtomGroup(GroupBase): group. These *instant selector* attributes are auto-generated for each atom name encountered in the group. - .. note:: - - The name-attribute instant selector access to atoms is mainly - meant for quick interactive work. Thus it either returns a - single :class:`Atom` if there is only one matching atom, *or* a - new :class:`AtomGroup` for multiple matches. This makes it - difficult to use the feature consistently in scripts. + Notes + ----- + The name-attribute instant selector access to atoms is mainly + meant for quick interactive work. Thus it either returns a + single :class:`Atom` if there is only one matching atom, *or* a + new :class:`AtomGroup` for multiple matches. This makes it + difficult to use the feature consistently in scripts. See Also @@ -1504,7 +1504,7 @@ class AtomGroup(GroupBase): .. deprecated:: 0.16.2 *Instant selectors* of AtomGroup will be removed in the 1.0 release. - See :ref:`Instant selectors`_ for details and alternatives. + See :ref:`Instant selectors ` for details and alternatives. """ def __getitem__(self, item): @@ -2202,7 +2202,7 @@ class ResidueGroup(GroupBase): .. deprecated:: 0.16.2 *Instant selectors* of Segments will be removed in the 1.0 release. - See :ref:`Instant selectors`_ for details and alternatives. + See :ref:`Instant selectors ` for details and alternatives. """ @@ -2321,7 +2321,7 @@ class SegmentGroup(GroupBase): .. deprecated:: 0.16.2 *Instant selectors* of Segments will be removed in the 1.0 release. - See :ref:`Instant selectors`_ for details and alternatives. + See :ref:`Instant selectors ` for details and alternatives. """ @@ -2670,7 +2670,7 @@ class Segment(ComponentBase): .. deprecated:: 0.16.2 *Instant selectors* of Segments will be removed in the 1.0 release. - See :ref:`Instant selectors`_ for details and alternatives. + See :ref:`Instant selectors ` for details and alternatives. """ def __repr__(self): diff --git a/package/doc/sphinx/source/documentation_pages/selections.rst b/package/doc/sphinx/source/documentation_pages/selections.rst index 40caae95b7e..48b221ec9fd 100644 --- a/package/doc/sphinx/source/documentation_pages/selections.rst +++ b/package/doc/sphinx/source/documentation_pages/selections.rst @@ -281,6 +281,7 @@ across frames:: >>> static_ag +.. _instance-selectors: Instant selectors ================= From fae031e9a4a3b7abe1d540cd4b552cbbf223b922 Mon Sep 17 00:00:00 2001 From: Max Linke Date: Sat, 17 Jun 2017 08:39:52 +0200 Subject: [PATCH 24/35] add getitem warning message --- package/MDAnalysis/core/groups.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py index f2717469aac..9840b62276c 100644 --- a/package/MDAnalysis/core/groups.py +++ b/package/MDAnalysis/core/groups.py @@ -1513,6 +1513,9 @@ def __getitem__(self, item): # # u.atoms['HT1'] access, otherwise default if isinstance(item, string_types): + warnings.warn("Using the [] operator with strings is deprecated." + "Please use `select_atoms('name {}')` " + "instead.".format(item)) try: return self._get_named_atom(item) except (AttributeError, selection.SelectionError): From b6646dabca41fa4991a08fe74630be30671cfc60 Mon Sep 17 00:00:00 2001 From: Max Linke Date: Sat, 17 Jun 2017 11:15:33 +0200 Subject: [PATCH 25/35] use explicit deprecation warning --- package/MDAnalysis/core/groups.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py index 9840b62276c..445502f60dc 100644 --- a/package/MDAnalysis/core/groups.py +++ b/package/MDAnalysis/core/groups.py @@ -1515,7 +1515,8 @@ def __getitem__(self, item): if isinstance(item, string_types): warnings.warn("Using the [] operator with strings is deprecated." "Please use `select_atoms('name {}')` " - "instead.".format(item)) + "instead.".format(item), + category=DeprecationWarning) try: return self._get_named_atom(item) except (AttributeError, selection.SelectionError): From e15f1be7391f04f222418ce4d6532a6c422b6b92 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Sat, 17 Jun 2017 16:49:37 -0700 Subject: [PATCH 26/35] test for no warnings raised by AtomGroup.segid See comment https://github.com/MDAnalysis/mdanalysis/pull/1403#discussion_r122565617 --- testsuite/MDAnalysisTests/core/test_groups.py | 3 +++ testsuite/MDAnalysisTests/util.py | 6 ++---- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/testsuite/MDAnalysisTests/core/test_groups.py b/testsuite/MDAnalysisTests/core/test_groups.py index 178e9140e82..e962b045fb7 100644 --- a/testsuite/MDAnalysisTests/core/test_groups.py +++ b/testsuite/MDAnalysisTests/core/test_groups.py @@ -1000,6 +1000,9 @@ def test_AtomGroup_warn_getitem(self): def test_AtomGroup_nowarn_getitem_index(self): assert_nowarns(DeprecationWarning, lambda x: self.u.atoms[x], 0) + def test_AtomGroup_nowarn_segids_attribute(self): + assert_nowarns(DeprecationWarning, lambda x: getattr(self.u.atoms, x), "segids") + def test_AtomGroup_warn_getattr(self): name = self.u.atoms[0].name assert_warns(DeprecationWarning, lambda x: getattr(self.u.atoms, x), name) diff --git a/testsuite/MDAnalysisTests/util.py b/testsuite/MDAnalysisTests/util.py index 1c7aea712be..fc78dd31671 100644 --- a/testsuite/MDAnalysisTests/util.py +++ b/testsuite/MDAnalysisTests/util.py @@ -42,7 +42,6 @@ from numpy.testing import assert_warns - def block_import(package): """Block import of a given package @@ -195,6 +194,5 @@ def assert_nowarns(warning_class, *args, **kwargs): return True else: # There was a warning even though we do not want to see one. - raise AssertionError - - + raise AssertionError("function {0} raises warning of class {1}".format( + func.__name__, warning_class.__name__)) From abc11e6122bab31b2628991265b6748b2df925b6 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Sat, 17 Jun 2017 16:49:55 -0700 Subject: [PATCH 27/35] minor cleanups in tests --- testsuite/MDAnalysisTests/utils/test_deprecated.py | 4 +--- testsuite/MDAnalysisTests/utils/test_failure.py | 2 +- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/testsuite/MDAnalysisTests/utils/test_deprecated.py b/testsuite/MDAnalysisTests/utils/test_deprecated.py index 3ce63e6abe7..c7acee6ffa9 100644 --- a/testsuite/MDAnalysisTests/utils/test_deprecated.py +++ b/testsuite/MDAnalysisTests/utils/test_deprecated.py @@ -25,9 +25,7 @@ # will be removed in 1.0) from __future__ import absolute_import -import warnings - -from numpy.testing import assert_equal, assert_raises +from numpy.testing import assert_raises class TestImports(object): def test_core_units(self): diff --git a/testsuite/MDAnalysisTests/utils/test_failure.py b/testsuite/MDAnalysisTests/utils/test_failure.py index c05c5c6e534..6cba555d0b5 100644 --- a/testsuite/MDAnalysisTests/utils/test_failure.py +++ b/testsuite/MDAnalysisTests/utils/test_failure.py @@ -30,4 +30,4 @@ def test_failure(): # Have a file open to trigger an output from the open_files plugin. f = open('./failure.txt', 'w') if u'MDA_FAILURE_TEST' in os.environ: - assert False + raise AssertionError("the MDA_FAILURE_TEST environment variable is set") From 84354d8b978f9a67defeb9ebacd386331e6b302d Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Sat, 17 Jun 2017 16:52:52 -0700 Subject: [PATCH 28/35] AtomGroup.__getitem__ depreaction warning: added removal release --- package/MDAnalysis/core/groups.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py index 445502f60dc..c07eec5a20f 100644 --- a/package/MDAnalysis/core/groups.py +++ b/package/MDAnalysis/core/groups.py @@ -1513,7 +1513,8 @@ def __getitem__(self, item): # # u.atoms['HT1'] access, otherwise default if isinstance(item, string_types): - warnings.warn("Using the [] operator with strings is deprecated." + warnings.warn("Using the [] operator with strings is deprecated " + "and will be removed in 1.0. " "Please use `select_atoms('name {}')` " "instead.".format(item), category=DeprecationWarning) From 50f5d5a9a1a39a2cfbc6285dbd2c3e353ffc99be Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Sat, 17 Jun 2017 17:03:32 -0700 Subject: [PATCH 29/35] removed explicit DeprecationWarning for AtomGroup["name"] 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[''] or AtomGroup. is deprecated and will be removed in 1.0. Use AtomGroup.select_atoms('name ') instead. return self._get_named_atom(item) --- package/MDAnalysis/core/groups.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py index c07eec5a20f..f2717469aac 100644 --- a/package/MDAnalysis/core/groups.py +++ b/package/MDAnalysis/core/groups.py @@ -1513,11 +1513,6 @@ def __getitem__(self, item): # # u.atoms['HT1'] access, otherwise default if isinstance(item, string_types): - warnings.warn("Using the [] operator with strings is deprecated " - "and will be removed in 1.0. " - "Please use `select_atoms('name {}')` " - "instead.".format(item), - category=DeprecationWarning) try: return self._get_named_atom(item) except (AttributeError, selection.SelectionError): From e24da325980732efc04adb6366dafb3162d6e687 Mon Sep 17 00:00:00 2001 From: Max Linke Date: Tue, 20 Jun 2017 16:18:02 +0200 Subject: [PATCH 30/35] only issue _get_named_atom warning on successful call This allows code to use the `getattr` function and only throw an error if the requested attribute is an atom name. --- package/MDAnalysis/core/topologyattrs.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/package/MDAnalysis/core/topologyattrs.py b/package/MDAnalysis/core/topologyattrs.py index fa6997c3adc..82aae50632a 100644 --- a/package/MDAnalysis/core/topologyattrs.py +++ b/package/MDAnalysis/core/topologyattrs.py @@ -41,6 +41,7 @@ import itertools import numbers import numpy as np +import warnings from numpy.lib.utils import deprecate @@ -411,9 +412,6 @@ def getattr__(atomgroup, name): raise AttributeError("'{0}' object has no attribute '{1}'".format( atomgroup.__class__.__name__, name)) - @deprecate(message="Instant selector AtomGroup[''] or AtomGroup. " - "is deprecated and will be removed in 1.0. " - "Use AtomGroup.select_atoms('name ') instead.") def _get_named_atom(group, name): """Get all atoms with name *name* in the current AtomGroup. @@ -438,10 +436,12 @@ def _get_named_atom(group, name): "No atoms with name '{0}'".format(name)) elif len(atomlist) == 1: # XXX: keep this, makes more sense for names - return atomlist[0] - else: - # XXX: but inconsistent (see residues and Issue 47) - return atomlist + atomlist = atomlist[0] + warnings.warn("Instant selector AtomGroup[''] or AtomGroup. " + "is deprecated and will be removed in 1.0. " + "Use AtomGroup.select_atoms('name ') instead.", + DeprecationWarning) + return atomlist # AtomGroup already has a getattr # transplants[AtomGroup].append( From fbc16880eaf9b87ac9c88ff8e86158598001da5c Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Thu, 15 Jun 2017 17:18:13 -0700 Subject: [PATCH 31/35] make scipy and matplotlib full dependencies (#1159) --- .travis.yml | 7 +++---- package/CHANGELOG | 3 +++ package/setup.py | 9 +++++---- 3 files changed, 11 insertions(+), 8 deletions(-) diff --git a/.travis.yml b/.travis.yml index 18fcfc5a74e..647af4d97f6 100644 --- a/.travis.yml +++ b/.travis.yml @@ -30,10 +30,9 @@ env: - MAIN_CMD="python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST1} ${NOSE_FLAGS}; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST2} ${NOSE_FLAGS}" - SETUP_CMD="" - BUILD_CMD="pip install -v package/ && pip install testsuite/" - - CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer" - - CONDA_ALL_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib netcdf4 scikit-learn scipy seaborn coveralls clustalw=2.1" - # Install griddataformats from PIP so that scipy is only installed in the full build (#1147) - - PIP_DEPENDENCIES='griddataformats' + - CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib scipy griddataformats" + - CONDA_ALL_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib netcdf4 scikit-learn scipy griddataformats seaborn coveralls clustalw=2.1" + - PIP_DEPENDENCIES="" - CONDA_CHANNELS='biobuilds conda-forge' - CONDA_CHANNEL_PRIORITY=True - NUMPY_VERSION=stable diff --git a/package/CHANGELOG b/package/CHANGELOG index f1aba435b37..6859b765b25 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -29,6 +29,9 @@ Fixes * Fixed dtype of numpy arrays to accomodate 32 bit architectures (Issue #1362) * Groups are hashable on python 3 (Issue #1397) +Changes + * scipy and matplotlib are now required dependencies (Issue #1159) + 06/03/17 utkbansal, kain88-de, xiki-tempula, kaplajon, wouterboomsma, richardjgowers, Shtkddud123, QuantumEntangledAndy, orbeckst, diff --git a/package/setup.py b/package/setup.py index 5aecb4889c5..04b7fb23e1e 100755 --- a/package/setup.py +++ b/package/setup.py @@ -494,11 +494,12 @@ def dynamic_author_list(): classifiers=CLASSIFIERS, cmdclass=cmdclass, requires=['numpy (>=1.10.4)', 'biopython', 'mmtf (>=1.0.0)', - 'networkx (>=1.0)', 'GridDataFormats (>=0.3.2)', 'joblib'], + 'networkx (>=1.0)', 'GridDataFormats (>=0.3.2)', 'joblib', + 'scipy', 'matplotlib (>=1.5.1)'], # all standard requirements are available through PyPi and # typically can be installed without difficulties through setuptools setup_requires=[ - 'numpy>=1.9.3', + 'numpy>=1.10.4', ], install_requires=[ 'numpy>=1.10.4', @@ -508,6 +509,8 @@ def dynamic_author_list(): 'six>=1.4.0', 'mmtf-python>=1.0.0', 'joblib', + 'scipy', + 'matplotlib>=1.5.1', ], # extras can be difficult to install through setuptools and/or # you might prefer to use the version available through your @@ -516,8 +519,6 @@ def dynamic_author_list(): 'AMBER': ['netCDF4>=1.0'], # for AMBER netcdf, also needs HDF5 # and netcdf-4 'analysis': [ - 'matplotlib>=1.5.1', - 'scipy', 'seaborn', # for annotated heat map and nearest neighbor # plotting in PSA 'sklearn', # For clustering and dimensionality reduction From 47340573db5319eecc11cf4d7d10412b107ff120 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Thu, 15 Jun 2017 19:37:48 -0700 Subject: [PATCH 32/35] scipy and matplotlib are imported at top in analysis - 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 --- package/MDAnalysis/analysis/distances.py | 23 +---- .../MDAnalysis/analysis/encore/similarity.py | 36 ++----- .../analysis/hbonds/hbond_autocorrel.py | 25 ++--- package/MDAnalysis/analysis/hole.py | 16 ++- package/MDAnalysis/analysis/legacy/x3dna.py | 5 +- package/MDAnalysis/analysis/pca.py | 7 +- package/MDAnalysis/analysis/polymer.py | 7 +- package/MDAnalysis/analysis/psa.py | 99 ++++++++++++++----- 8 files changed, 114 insertions(+), 104 deletions(-) diff --git a/package/MDAnalysis/analysis/distances.py b/package/MDAnalysis/analysis/distances.py index ae4ad699141..d524a993625 100644 --- a/package/MDAnalysis/analysis/distances.py +++ b/package/MDAnalysis/analysis/distances.py @@ -42,6 +42,7 @@ 'contact_matrix', 'dist', 'between'] import numpy as np +import scipy.sparse from MDAnalysis.lib.distances import distance_array, self_distance_array from MDAnalysis.lib.c_distances import contact_matrix_no_pbc, contact_matrix_pbc @@ -51,15 +52,6 @@ import logging logger = logging.getLogger("MDAnalysis.analysis.distances") -try: - from scipy import sparse -except ImportError: - sparse = None - msg = "scipy.sparse could not be imported: some functionality will " \ - "not be available in contact_matrix()" - warnings.warn(msg, category=ImportWarning) - logger.warn(msg) - del msg def contact_matrix(coord, cutoff=15.0, returntype="numpy", box=None): '''Calculates a matrix of contacts. @@ -93,12 +85,6 @@ def contact_matrix(coord, cutoff=15.0, returntype="numpy", box=None): The contact matrix is returned in a format determined by the `returntype` keyword. - - Note - ---- - :mod:`scipy.sparse` is require for using *sparse* matrices; if it cannot - be imported then an `ImportError` is raised. - See Also -------- :mod:`MDAnalysis.analysis.contacts` for native contact analysis @@ -112,14 +98,9 @@ def contact_matrix(coord, cutoff=15.0, returntype="numpy", box=None): adj = (distance_array(coord, coord, box=box) < cutoff) return adj elif returntype == "sparse": - if sparse is None: - # hack: if we are running with minimal dependencies then scipy was - # not imported and we have to bail here (see scipy import at top) - raise ImportError("For sparse matrix functionality you need to " - "import scipy.") # Initialize square List of Lists matrix of dimensions equal to number # of coordinates passed - sparse_contacts = sparse.lil_matrix((len(coord), len(coord)), dtype='bool') + sparse_contacts = scipy.sparse.lil_matrix((len(coord), len(coord)), dtype='bool') if box is not None: # with PBC contact_matrix_pbc(coord, sparse_contacts, box, cutoff) diff --git a/package/MDAnalysis/analysis/encore/similarity.py b/package/MDAnalysis/analysis/encore/similarity.py index bd7e9e5e0ea..a56b3c0c1e5 100644 --- a/package/MDAnalysis/analysis/encore/similarity.py +++ b/package/MDAnalysis/analysis/encore/similarity.py @@ -172,21 +172,13 @@ from __future__ import print_function, division, absolute_import from six.moves import range, zip -import MDAnalysis as mda -import numpy as np import warnings import logging -try: - from scipy.stats import gaussian_kde -except ImportError: - gaussian_kde = None - msg = "scipy.stats.gaussian_kde could not be imported. " \ - "Dimensionality reduction ensemble comparisons will not " \ - "be available." - warnings.warn(msg, - category=ImportWarning) - logging.warn(msg) - del msg + +import numpy as np +import scipy.stats + +import MDAnalysis as mda from ...coordinates.memory import MemoryReader from .confdistmatrix import get_distance_matrix @@ -460,18 +452,11 @@ def gen_kde_pdfs(embedded_space, ensemble_assignment, nensembles, embedded_ensembles = [] resamples = [] - if gaussian_kde is None: - # hack: if we are running with minimal dependencies then scipy was - # not imported and we have to bail here (see scipy import at top) - raise ImportError("For Kernel Density Estimation functionality you" - "need to import scipy") - for i in range(1, nensembles + 1): this_embedded = embedded_space.transpose()[ np.where(np.array(ensemble_assignment) == i)].transpose() embedded_ensembles.append(this_embedded) - kdes.append(gaussian_kde( - this_embedded)) + kdes.append(scipy.stats.gaussian_kde(this_embedded)) # # Set number of samples # if not nsamples: @@ -623,12 +608,6 @@ def cumulative_gen_kde_pdfs(embedded_space, ensemble_assignment, nensembles, """ - if gaussian_kde is None: - # hack: if we are running with minimal dependencies then scipy was - # not imported and we have to bail here (see scipy import at top) - raise ImportError("For Kernel Density Estimation functionality you" - "need to import scipy") - kdes = [] embedded_ensembles = [] resamples = [] @@ -639,8 +618,7 @@ def cumulative_gen_kde_pdfs(embedded_space, ensemble_assignment, nensembles, np.logical_and(ensemble_assignment >= ens_id_min, ensemble_assignment <= i))].transpose() embedded_ensembles.append(this_embedded) - kdes.append( - gaussian_kde(this_embedded)) + kdes.append(scipy.stats.gaussian_kde(this_embedded)) # Resample according to probability distributions for this_kde in kdes: diff --git a/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py b/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py index a0bf6bb5451..bf81e3529c5 100644 --- a/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py +++ b/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py @@ -155,6 +155,8 @@ from __future__ import division, absolute_import from six.moves import zip import numpy as np +import scipy.optimize + import warnings from MDAnalysis.lib.log import ProgressMeter @@ -162,7 +164,7 @@ class HydrogenBondAutoCorrel(object): - """Perform a time autocorrelation of the hydrogen bonds in the system. + """Perform a time autocorrelation of the hydrogen bonds in the system. Parameters ---------- @@ -421,8 +423,9 @@ def solve(self, p_guess=None): Initial guess for the leastsq fit, must match the shape of the expected coefficients - Continuous defition results are fitted to a double exponential, - intermittent definition are fit to a triple exponential. + Continuous defition results are fitted to a double exponential with + :func:`scipy.optimize.leastsq`, intermittent definition are fit to a + triple exponential. The results of this fitting procedure are saved into the *fit*, *tau* and *estimate* keywords in the solution dict. @@ -434,14 +437,14 @@ def solve(self, p_guess=None): - *estimate* contains the estimate provided by the fit of the time autocorrelation function - In addition, the output of the leastsq function is saved into the - solution dict + In addition, the output of the :func:`~scipy.optimize.leastsq` function + is saved into the solution dict - *infodict* - *mesg* - *ier* + """ - from scipy.optimize import leastsq if self.solution['results'] is None: raise ValueError( @@ -498,9 +501,8 @@ def triple(x, A1, A2, tau1, tau2, tau3): if p_guess is None: p_guess = (0.5, 10 * self.sample_time, self.sample_time) - p, cov, infodict, mesg, ier = leastsq(err, p_guess, - args=(time, results), - full_output=True) + p, cov, infodict, mesg, ier = scipy.optimize.leastsq( + err, p_guess, args=(time, results), full_output=True) self.solution['fit'] = p A1, tau1, tau2 = p A2 = 1 - A1 @@ -512,9 +514,8 @@ def triple(x, A1, A2, tau1, tau2, tau3): p_guess = (0.33, 0.33, 10 * self.sample_time, self.sample_time, 0.1 * self.sample_time) - p, cov, infodict, mesg, ier = leastsq(err, p_guess, - args=(time, results), - full_output=True) + p, cov, infodict, mesg, ier = scipy.optimize.leastsq( + err, p_guess, args=(time, results), full_output=True) self.solution['fit'] = p A1, A2, tau1, tau2, tau3 = p A3 = 1 - A1 - A2 diff --git a/package/MDAnalysis/analysis/hole.py b/package/MDAnalysis/analysis/hole.py index e43316a868c..7088e5f8a7c 100644 --- a/package/MDAnalysis/analysis/hole.py +++ b/package/MDAnalysis/analysis/hole.py @@ -245,7 +245,6 @@ from six.moves import zip, cPickle import six -import numpy as np import glob import os import errno @@ -258,6 +257,10 @@ import logging from itertools import cycle +import numpy as np +import matplotlib +import matplotlib.pyplot as plt + from MDAnalysis import Universe from MDAnalysis.exceptions import ApplicationError from MDAnalysis.lib.util import which, realpath, asiterable @@ -370,8 +373,6 @@ def save(self, filename="hole.pickle"): cPickle.dump(self.profiles, open(filename, "wb"), cPickle.HIGHEST_PROTOCOL) def _process_plot_kwargs(self, kwargs): - import matplotlib.colors - kw = {} frames = kwargs.pop('frames', None) if frames is None: @@ -448,9 +449,6 @@ def plot(self, **kwargs): Returns ``ax``. """ - - import matplotlib.pyplot as plt - kw, kwargs = self._process_plot_kwargs(kwargs) ax = kwargs.pop('ax', None) @@ -517,8 +515,7 @@ def plot3D(self, **kwargs): Returns ``ax``. """ - - import matplotlib.pyplot as plt + # installed with matplotlib; imported here to enable 3D axes from mpl_toolkits.mplot3d import Axes3D kw, kwargs = self._process_plot_kwargs(kwargs) @@ -540,8 +537,7 @@ def plot3D(self, **kwargs): rxncoord = profile.rxncoord else: # does not seem to work with masked arrays but with nan hack! - # http://stackoverflow.com/questions/4913306/python-matplotlib-mplot3d-how-do-i-set-a-maximum-value - # -for-the-z-axis + # http://stackoverflow.com/questions/4913306/python-matplotlib-mplot3d-how-do-i-set-a-maximum-value-for-the-z-axis #radius = np.ma.masked_greater(profile.radius, rmax) #rxncoord = np.ma.array(profile.rxncoord, mask=radius.mask) rxncoord = profile.rxncoord diff --git a/package/MDAnalysis/analysis/legacy/x3dna.py b/package/MDAnalysis/analysis/legacy/x3dna.py index f960cd1fc5d..99cb4a8fc65 100644 --- a/package/MDAnalysis/analysis/legacy/x3dna.py +++ b/package/MDAnalysis/analysis/legacy/x3dna.py @@ -132,13 +132,15 @@ import errno import shutil import warnings -import numpy as np import os.path import subprocess import tempfile import textwrap from collections import OrderedDict +import numpy as np +import matplotlib.pyplot as plt + from MDAnalysis import ApplicationError from MDAnalysis.lib.util import which, realpath, asiterable @@ -413,7 +415,6 @@ def plot(self, **kwargs): Provide `ax` to have all plots plotted in the same axes. """ - import matplotlib.pyplot as plt na_avg, na_std = self.mean_std() for k in range(len(na_avg[0])): diff --git a/package/MDAnalysis/analysis/pca.py b/package/MDAnalysis/analysis/pca.py index 18d729ecc08..b9920a27ed3 100644 --- a/package/MDAnalysis/analysis/pca.py +++ b/package/MDAnalysis/analysis/pca.py @@ -106,6 +106,7 @@ import warnings import numpy as np +import scipy.integrate from MDAnalysis import Universe from MDAnalysis.analysis.align import _fit_to @@ -357,9 +358,9 @@ def cosine_content(pca_space, i): .. [BerkHess1] Berk Hess. Convergence of sampling in protein simulations. Phys. Rev. E 65, 031910 (2002). """ - from scipy.integrate import simps + t = np.arange(len(pca_space)) T = len(pca_space) cos = np.cos(np.pi * t * (i + 1) / T) - return ((2.0 / T) * (simps(cos*pca_space[:, i])) ** 2 / - simps(pca_space[:, i] ** 2)) + return ((2.0 / T) * (scipy.integrate.simps(cos*pca_space[:, i])) ** 2 / + scipy.integrate.simps(pca_space[:, i] ** 2)) diff --git a/package/MDAnalysis/analysis/polymer.py b/package/MDAnalysis/analysis/polymer.py index 645055e1878..b7babb204ab 100644 --- a/package/MDAnalysis/analysis/polymer.py +++ b/package/MDAnalysis/analysis/polymer.py @@ -36,6 +36,8 @@ from six.moves import range import numpy as np +import scipy.optimize + import logging from .. import NoDataError @@ -165,13 +167,10 @@ def fit_exponential_decay(x, y): ----- This function assumes that data starts at 1.0 and decays to 0.0 - Requires scipy """ - from scipy.optimize import curve_fit - def expfunc(x, a): return np.exp(-x/a) - a = curve_fit(expfunc, x, y)[0][0] + a = scipy.optimize.curve_fit(expfunc, x, y)[0][0] return a diff --git a/package/MDAnalysis/analysis/psa.py b/package/MDAnalysis/analysis/psa.py index 6c002241a40..f7178d678c1 100644 --- a/package/MDAnalysis/analysis/psa.py +++ b/package/MDAnalysis/analysis/psa.py @@ -216,7 +216,11 @@ from six.moves import range, cPickle import numpy as np -import warnings,numbers +from scipy import spatial, cluster +import matplotlib + +import warnings +import numbers import MDAnalysis import MDAnalysis.analysis.align @@ -396,13 +400,14 @@ def hausdorff(P, Q): Notes ----- - - The Hausdorff distance is calculated in a brute force manner from the - distance matrix without further optimizations, essentially following - [Huttenlocher1993]_. - - :func:`scipy.spatial.distance.directed_hausdorff` is an optimized - implementation of the early break algorithm of [Taha2015]_; note that - one still has to calculate the *symmetric* Hausdorff distance as - `max(directed_hausdorff(P, Q)[0], directed_hausdorff(Q, P)[0])`. + The Hausdorff distance is calculated in a brute force manner from the + distance matrix without further optimizations, essentially following + [Huttenlocher1993]_. + + :func:`scipy.spatial.distance.directed_hausdorff` is an optimized + implementation of the early break algorithm of [Taha2015]_; note that one + still has to calculate the *symmetric* Hausdorff distance as + `max(directed_hausdorff(P, Q)[0], directed_hausdorff(Q, P)[0])`. References ---------- @@ -415,6 +420,10 @@ def hausdorff(P, Q): calculating the exact Hausdorff distance. IEEE Transactions On Pattern Analysis And Machine Intelligence, 37:2153-63, 2015. + SeeAlso + ------- + scipy.spatial.distance.directed_hausdorff + """ N, axis = get_coord_axes(P) d = get_msd_matrix(P, Q, axis=axis) @@ -1650,7 +1659,7 @@ def plot(self, filename=None, linkage='ward', count_sort=False, If `filename` is supplied then the figure is also written to file (the suffix determines the file type, e.g. pdf, png, eps, ...). All other - keyword arguments are passed on to :func:`matplotlib.pyplot.imshow`. + keyword arguments are passed on to :func:`matplotlib.pyplot.matshow`. Parameters @@ -1669,6 +1678,15 @@ def plot(self, filename=None, linkage='ward', count_sort=False, set the font size for colorbar labels; font size for path labels on dendrogram default to 3 points smaller [``12``] + Returns + ------- + Z + `Z` from :meth:`cluster` + dgram + `dgram` from :meth:`cluster` + dist_matrix_clus + clustered distance matrix (reordered) + """ from matplotlib.pyplot import figure, colorbar, cm, savefig, clf @@ -1770,6 +1788,23 @@ def plot_annotated_heatmap(self, filename=None, linkage='ward', \ annot_size : float font size of annotation labels on heat map [``6.5``] + Returns + ------- + Z + `Z` from :meth:`cluster` + dgram + `dgram` from :meth:`cluster` + dist_matrix_clus + clustered distance matrix (reordered) + + + Note + ---- + This function requires the seaborn_ package, which can be installed + with `pip install seaborn` or `conda install seaborn`. + + .. _seaborn: https://seaborn.pydata.org/ + """ from matplotlib.pyplot import figure, colorbar, cm, savefig, clf @@ -1870,6 +1905,17 @@ def plot_nearest_neighbors(self, filename=None, idx=0, \ set the font size for colorbar labels; font size for path labels on dendrogram default to 3 points smaller [``12``] + Returns + ------- + ax : axes + + Note + ---- + This function requires the seaborn_ package, which can be installed + with `pip install seaborn` or `conda install seaborn`. + + .. _seaborn: https://seaborn.pydata.org/ + """ from matplotlib.pyplot import figure, savefig, tight_layout, clf, show try: @@ -1927,7 +1973,8 @@ def plot_nearest_neighbors(self, filename=None, idx=0, \ head = self.targetdir + self.datadirs['plots'] outfile = os.path.join(head, filename) savefig(outfile, dpi=300, bbox_inches='tight') - show() + + return ax def cluster(self, distArray, method='ward', count_sort=False, \ @@ -1955,22 +2002,28 @@ def cluster(self, distArray, method='ward', count_sort=False, \ Returns ------- - list + Z + output from :func:`scipy.cluster.hierarchy.linkage`; list of indices representing the row-wise order of the objects after clustering + dgram + output from :func:`scipy.cluster.hierarchy.dendrogram` """ - import matplotlib - from scipy.cluster.hierarchy import linkage, dendrogram - + # perhaps there is a better way to manipulate the plot... or perhaps it + # is not even necessary? In any case, the try/finally makes sure that + # we are not permanently changing the user's global state + orig_linewidth = matplotlib.rcParams['lines.linewidth'] matplotlib.rcParams['lines.linewidth'] = 0.5 - - Z = linkage(distArray, method=method) - dgram = dendrogram(Z, no_labels=no_labels, orientation='left', \ - count_sort=count_sort, distance_sort=distance_sort, \ - no_plot=no_plot, color_threshold=color_threshold) + try: + Z = cluster.hierarchy.linkage(distArray, method=method) + dgram = cluster.hierarchy.dendrogram( + Z, no_labels=no_labels, orientation='left', + count_sort=count_sort, distance_sort=distance_sort, + no_plot=no_plot, color_threshold=color_threshold) + finally: + matplotlib.rcParams['lines.linewidth'] = orig_linewidth return Z, dgram - def _get_plot_obj_locs(self): """Find and return coordinates for dendrogram, heat map, and colorbar. @@ -2005,7 +2058,8 @@ def get_num_atoms(self): Returns ------- - the number of atoms + int + the number of atoms Note ---- @@ -2077,8 +2131,7 @@ def get_pairwise_distances(self, vectorform=False): err_str = "No distance data; do 'PSAnalysis.run(store=True)' first." raise ValueError(err_str) if vectorform: - from scipy.spatial.distance import squareform - return squareform(self.D) + return spatial.distance.squareform(self.D) else: return self.D From 12a795e0cbc292759c25b54c36ca485e10287010 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Thu, 15 Jun 2017 20:44:17 -0700 Subject: [PATCH 33/35] removed conditional skipping of tests when scipy or matplotlib are missing --- .../MDAnalysisTests/analysis/test_density.py | 7 -- .../analysis/test_distances.py | 67 ++----------------- .../MDAnalysisTests/analysis/test_encore.py | 21 +----- .../MDAnalysisTests/analysis/test_hole.py | 9 +-- .../analysis/test_hydrogenbondautocorrel.py | 3 - .../MDAnalysisTests/analysis/test_leaflet.py | 2 - .../MDAnalysisTests/analysis/test_pca.py | 2 - .../analysis/test_persistencelength.py | 14 +--- .../MDAnalysisTests/analysis/test_psa.py | 15 ++--- 9 files changed, 17 insertions(+), 123 deletions(-) diff --git a/testsuite/MDAnalysisTests/analysis/test_density.py b/testsuite/MDAnalysisTests/analysis/test_density.py index 75502b71380..adc51445244 100644 --- a/testsuite/MDAnalysisTests/analysis/test_density.py +++ b/testsuite/MDAnalysisTests/analysis/test_density.py @@ -30,9 +30,6 @@ assert_raises) import MDAnalysis as mda -# imported inside a skipif-protected method so that it can -# be tested in the absence of scipy -## import MDAnalysis.analysis.density from MDAnalysisTests.datafiles import TPR, XTC, GRO from MDAnalysisTests import module_not_found, tempdir @@ -45,8 +42,6 @@ class TestDensity(TestCase): counts = 100 Lmax = 10. - @dec.skipif(module_not_found('scipy'), - "Test skipped because scipy is not available.") def setUp(self): import MDAnalysis.analysis.density @@ -123,8 +118,6 @@ class Test_density_from_Universe(TestCase): cutoffs = {'notwithin': 4.0, } precision = 5 - @dec.skipif(module_not_found('scipy'), - "Test skipped because scipy is not available.") def setUp(self): self.outfile = 'density.dx' self.universe = mda.Universe(self.topology, self.trajectory) diff --git a/testsuite/MDAnalysisTests/analysis/test_distances.py b/testsuite/MDAnalysisTests/analysis/test_distances.py index a217f6142d8..91562f00f6f 100644 --- a/testsuite/MDAnalysisTests/analysis/test_distances.py +++ b/testsuite/MDAnalysisTests/analysis/test_distances.py @@ -21,22 +21,25 @@ # from __future__ import print_function, absolute_import +import scipy +import scipy.spatial + import MDAnalysis from MDAnalysisTests import module_not_found from MDAnalysisTests.datafiles import GRO from MDAnalysisTests.util import block_import +import MDAnalysis.analysis.distances + from numpy.testing import TestCase, assert_equal, dec import numpy as np + import warnings -from mock import Mock, patch import sys class TestContactMatrix(TestCase): - @dec.skipif(module_not_found('scipy'), - "Test skipped because scipy is not available.") def setUp(self): import MDAnalysis.analysis.distances self.coord = np.array([[1, 1, 1], @@ -87,17 +90,7 @@ def test_box_sparse(self): assert_equal(contacts.toarray(), self.res_pbc) class TestDist(TestCase): - '''Tests for MDAnalysis.analysis.distances.dist(). - Imports do not happen at the top level of the module - because of the scipy dependency.''' - - @dec.skipif(module_not_found('scipy'), - "Test skipped because scipy is not available.") - def setUp(self): - import MDAnalysis.analysis.distances - import scipy - import scipy.spatial self.u = MDAnalysis.Universe(GRO) self.ag = self.u.atoms[:20] self.u2 = MDAnalysis.Universe(GRO) @@ -142,17 +135,7 @@ def test_mismatch_exception(self): MDAnalysis.analysis.distances.dist(self.ag[:19], self.ag2) class TestBetween(TestCase): - '''Tests for MDAnalysis.analysis.distances.between(). - Imports do not happen at the top level of the module - because of the scipy dependency.''' - - @dec.skipif(module_not_found('scipy'), - "Test skipped because scipy is not available.") - def setUp(self): - import MDAnalysis.analysis.distances - import scipy - import scipy.spatial self.u = MDAnalysis.Universe(GRO) self.ag = self.u.atoms[:10] self.ag2 = self.u.atoms[12:33] @@ -190,41 +173,3 @@ def test_between_simple_case_indices_only(self): self.ag2, self.distance).indices) assert_equal(actual, self.expected) - -class TestImportWarnings(TestCase): - # see unit testing for warnings: - # http://stackoverflow.com/a/3892301 - - def setUp(self): - sys.modules.pop('MDAnalysis.analysis.distances', None) - - @block_import('scipy') - def test_warning_raised_no_scipy_module_level(self): - # an appropriate warning rather than an exception should be - # raised if scipy is absent when importing - # MDAnalysis.analysis.distances - with warnings.catch_warnings(record=True) as w: - warnings.simplefilter("always") - import MDAnalysis.analysis.distances - assert issubclass(w[-1].category, ImportWarning) - - def test_silent_success_scipy_present_module_level(self): - # if scipy is present no module level ImportWarning should be - # raised when importing MDAnalysis.analysis.distances - mock = Mock() # mock presence of scipy - with patch.dict('sys.modules', {'scipy':mock}): - with warnings.catch_warnings(record=True) as w: - warnings.simplefilter("always") - import MDAnalysis.analysis.distances - assert w == [] - - @block_import('scipy') - def test_import_error_contact_matrix_no_scipy(self): - # contact_matrix should raise an ImportError if returntype is - # "sparse" and scipy is not available - with self.assertRaises(ImportError): - np.random.seed(321) - points = np.random.random_sample((10, 3)) - import MDAnalysis.analysis.distances - MDAnalysis.analysis.distances.contact_matrix(points, - returntype="sparse") diff --git a/testsuite/MDAnalysisTests/analysis/test_encore.py b/testsuite/MDAnalysisTests/analysis/test_encore.py index 884545cf94d..78bdfae9e27 100644 --- a/testsuite/MDAnalysisTests/analysis/test_encore.py +++ b/testsuite/MDAnalysisTests/analysis/test_encore.py @@ -128,7 +128,7 @@ def test_triangular_matrix(): multiplied_triangular_matrix_2 = triangular_matrix_2 * scalar assert_equal(multiplied_triangular_matrix_2[0,1], expected_value * scalar, - err_msg="Error in TriangularMatrix: multiplication by scalar gave\ + err_msg="Error in TriangularMatrix: multiplication by scalar gave\ inconsistent results") triangular_matrix_2 *= scalar @@ -299,8 +299,6 @@ def test_ces(self): assert_almost_equal(result_value, expected_value, decimal=2, err_msg="Unexpected value for Cluster Ensemble Similarity: {0:f}. Expected {1:f}.".format(result_value, expected_value)) - @dec.skipif(module_not_found('scipy'), - "Test skipped because scipy is not available.") def test_dres_to_self(self): results, details = encore.dres([self.ens1, self.ens1]) result_value = results[0,1] @@ -308,8 +306,6 @@ def test_dres_to_self(self): assert_almost_equal(result_value, expected_value, decimal=2, err_msg="Dim. Reduction Ensemble Similarity to itself not zero: {0:f}".format(result_value)) - @dec.skipif(module_not_found('scipy'), - "Test skipped because scipy is not available.") def test_dres(self): results, details = encore.dres([self.ens1, self.ens2], selection="name CA and resnum 1-10") result_value = results[0,1] @@ -317,8 +313,6 @@ def test_dres(self): self.assertLess(result_value, upper_bound, msg="Unexpected value for Dim. reduction Ensemble Similarity: {0:f}. Expected {1:f}.".format(result_value, upper_bound)) - @dec.skipif(module_not_found('scipy'), - "Test skipped because scipy is not available.") def test_dres_without_superimposition(self): distance_matrix = encore.get_distance_matrix( encore.merge_universes([self.ens1, self.ens2]), @@ -338,8 +332,6 @@ def test_ces_convergence(self): assert_almost_equal(ev, results[i], decimal=2, err_msg="Unexpected value for Clustering Ensemble similarity in convergence estimation") - @dec.skipif(module_not_found('scipy'), - "Test skipped because scipy is not available.") def test_dres_convergence(self): expected_values = [ 0.3, 0.] results = encore.dres_convergence(self.ens1, 10) @@ -399,8 +391,6 @@ def test_ces_error_estimation_ensemble_bootstrap(self): err_msg="Unexpected standard daviation for bootstrapped samples in Clustering Ensemble similarity") @dec.slow - @dec.skipif(module_not_found('scipy'), - "Test skipped because scipy is not available.") def test_dres_error_estimation(self): average_upper_bound = 0.3 stdev_upper_bound = 0.2 @@ -847,18 +837,9 @@ def _check_sklearn_import_warns(self, package): warnings.simplefilter('always') assert_warns(ImportWarning, importlib.import_module, package) - @block_import('scipy') - def _check_scipy_import_warns(self, package): - warnings.simplefilter('always') - assert_warns(ImportWarning, importlib.import_module, package) - def test_import_warnings(self): for pkg in ( 'MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod', 'MDAnalysis.analysis.encore.clustering.ClusteringMethod', ): yield self._check_sklearn_import_warns, pkg - for pkg in ( - 'MDAnalysis.analysis.encore.similarity', - ): - yield self._check_scipy_import_warns, pkg diff --git a/testsuite/MDAnalysisTests/analysis/test_hole.py b/testsuite/MDAnalysisTests/analysis/test_hole.py index e001b265d4f..22d891daca3 100644 --- a/testsuite/MDAnalysisTests/analysis/test_hole.py +++ b/testsuite/MDAnalysisTests/analysis/test_hole.py @@ -32,6 +32,9 @@ assert_array_equal, assert_array_almost_equal, assert_) import numpy as np +import matplotlib +import mpl_toolkits.mplot3d + import nose from nose.plugins.attrib import attr @@ -150,27 +153,21 @@ def test_min_radius(self): @attr('slow') @dec.skipif(executable_not_found("hole"), msg="Test skipped because HOLE not found") - @dec.skipif(module_not_found("matplotlib")) def test_plot(self): - import matplotlib.axes ax = self.H.plot(label=True) assert_(isinstance(ax, matplotlib.axes.Axes), msg="H.plot() did not produce an Axes instance") @attr('slow') @dec.skipif(executable_not_found("hole"), msg="Test skipped because HOLE not found") - @dec.skipif(module_not_found("matplotlib")) def test_plot3D(self): - import mpl_toolkits.mplot3d ax = self.H.plot3D() assert_(isinstance(ax, mpl_toolkits.mplot3d.Axes3D), msg="H.plot3D() did not produce an Axes3D instance") @attr('slow') @dec.skipif(executable_not_found("hole"), msg="Test skipped because HOLE not found") - @dec.skipif(module_not_found("matplotlib")) def test_plot3D_rmax(self): - import mpl_toolkits.mplot3d ax = self.H.plot3D(rmax=2.5) assert_(isinstance(ax, mpl_toolkits.mplot3d.Axes3D), msg="H.plot3D(rmax=float) did not produce an Axes3D instance") diff --git a/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py b/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py index 59ca9509e6a..49d3b80c040 100644 --- a/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py +++ b/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py @@ -142,7 +142,6 @@ def test_intermittent_excl(self): # For `solve` the test trajectories aren't long enough # So spoof the results and check that solver finds solution - @dec.skipif(module_not_found('scipy')) def test_solve_continuous(self): hbond = HBAC(self.u, hydrogens=self.H, @@ -168,7 +167,6 @@ def actual_function_cont(t): np.array([0.75, 0.5, 0.1]), ) - @dec.skipif(module_not_found('scipy')) def test_solve_intermittent(self): hbond = HBAC(self.u, hydrogens=self.H, @@ -248,7 +246,6 @@ def test_bond_type_VE(self): sample_time=0.06, ) - @dec.skipif(module_not_found('scipy')) def test_solve_before_run_VE(self): hbond = HBAC(self.u, hydrogens=self.H, diff --git a/testsuite/MDAnalysisTests/analysis/test_leaflet.py b/testsuite/MDAnalysisTests/analysis/test_leaflet.py index e83ec0fec69..3f358034f6e 100644 --- a/testsuite/MDAnalysisTests/analysis/test_leaflet.py +++ b/testsuite/MDAnalysisTests/analysis/test_leaflet.py @@ -29,8 +29,6 @@ from MDAnalysisTests.datafiles import Martini_membrane_gro class TestLeafletFinder(TestCase): - @dec.skipif(module_not_found('scipy'), - "Test skipped because scipy is not available.") def setUp(self): self.universe = MDAnalysis.Universe(Martini_membrane_gro, Martini_membrane_gro) self.lipid_heads = self.universe.select_atoms("name PO4") diff --git a/testsuite/MDAnalysisTests/analysis/test_pca.py b/testsuite/MDAnalysisTests/analysis/test_pca.py index e182d3d99a4..2d410365a35 100644 --- a/testsuite/MDAnalysisTests/analysis/test_pca.py +++ b/testsuite/MDAnalysisTests/analysis/test_pca.py @@ -87,8 +87,6 @@ def test_transform_universe(): pca_test.transform(u2) @staticmethod - @dec.skipif(module_not_found('scipy'), - "Test skipped because scipy is not available.") def test_cosine_content(): rand = MDAnalysis.Universe(RANDOM_WALK_TOPO, RANDOM_WALK) pca_random = pca.PCA(rand).run() diff --git a/testsuite/MDAnalysisTests/analysis/test_persistencelength.py b/testsuite/MDAnalysisTests/analysis/test_persistencelength.py index fc023ba95fc..4c72a8dee9c 100644 --- a/testsuite/MDAnalysisTests/analysis/test_persistencelength.py +++ b/testsuite/MDAnalysisTests/analysis/test_persistencelength.py @@ -24,7 +24,10 @@ import MDAnalysis from MDAnalysis.analysis import polymer from MDAnalysis.exceptions import NoDataError + import numpy as np +import matplotlib + from numpy.testing import ( assert_, assert_almost_equal, @@ -61,8 +64,6 @@ def test_run(self): assert_(len(p.results) == 280) assert_almost_equal(p.lb, 1.485, 3) - @dec.skipif(module_not_found('scipy'), - "Test skipped because scipy is not available.") def test_fit(self): p = self._make_p() p.run() @@ -71,14 +72,9 @@ def test_fit(self): assert_almost_equal(p.lp, 6.504, 3) assert_(len(p.fit) == len(p.results)) - @dec.skipif(module_not_found('matplotlib'), - "Test skipped because matplotlib is not available.") - @dec.skipif(module_not_found('scipy'), - "Test skipped because scipy is not available.") def test_plot_ax_return(self): '''Ensure that a matplotlib axis object is returned when plot() is called.''' - import matplotlib p = self._make_p() p.run() p.perform_fit() @@ -104,14 +100,10 @@ def tearDown(self): del self.a_ref del self.y - @dec.skipif(module_not_found('scipy'), - "Test skipped because scipy is not available.") def test_fit_simple(self): a = polymer.fit_exponential_decay(self.x, self.y) assert_(a == self.a_ref) - @dec.skipif(module_not_found('scipy'), - "Test skipped because scipy is not available.") def test_fit_noisy(self): noise = np.sin(self.x) * 0.01 y2 = noise + self.y diff --git a/testsuite/MDAnalysisTests/analysis/test_psa.py b/testsuite/MDAnalysisTests/analysis/test_psa.py index f4c3b234873..e62621aa2db 100644 --- a/testsuite/MDAnalysisTests/analysis/test_psa.py +++ b/testsuite/MDAnalysisTests/analysis/test_psa.py @@ -28,6 +28,8 @@ assert_array_almost_equal, assert_, assert_almost_equal, assert_equal) import numpy as np +import scipy +import scipy.spatial from MDAnalysisTests.datafiles import PSF, DCD, DCD2 from MDAnalysisTests import parser_not_found, tempdir, module_not_found @@ -36,10 +38,6 @@ class TestPSAnalysis(TestCase): @dec.skipif(parser_not_found('DCD'), 'DCD parser not available. Are you using python 3?') - @dec.skipif(module_not_found('matplotlib'), - "Test skipped because matplotlib is not available.") - @dec.skipif(module_not_found('scipy'), - "Test skipped because scipy is not available.") def setUp(self): self.tmpdir = tempdir.TempDir() self.iu1 = np.triu_indices(3, k=1) @@ -187,9 +185,6 @@ class _BaseHausdorffDistance(TestCase): for various Hausdorff distance calculation properties.''' - @dec.skipif(module_not_found('scipy'), - 'scipy not available') - def setUp(self): self.random_angles = np.random.random((100,)) * np.pi * 2 self.random_columns = np.column_stack((self.random_angles, @@ -247,10 +242,9 @@ def setUp(self): class TestWeightedAvgHausdorffSymmetric(_BaseHausdorffDistance): '''Tests for weighted average and symmetric (undirected) Hausdorff distance between point sets in 3D.''' + def setUp(self): super(TestWeightedAvgHausdorffSymmetric, self).setUp() - import scipy - import scipy.spatial self.h = PSA.hausdorff_wavg self.distance_matrix = scipy.spatial.distance.cdist(self.path_1, self.path_2) @@ -270,10 +264,9 @@ def test_asymmetric_weight(self): class TestAvgHausdorffSymmetric(_BaseHausdorffDistance): '''Tests for unweighted average and symmetric (undirected) Hausdorff distance between point sets in 3D.''' + def setUp(self): super(TestAvgHausdorffSymmetric, self).setUp() - import scipy - import scipy.spatial self.h = PSA.hausdorff_avg self.distance_matrix = scipy.spatial.distance.cdist(self.path_1, self.path_2) From 85c0c561761a704c57a6eac9be35032d3650b391 Mon Sep 17 00:00:00 2001 From: Max Linke Date: Sat, 17 Jun 2017 13:38:24 +0200 Subject: [PATCH 34/35] minor clean ups --- .travis.yml | 1 - .../MDAnalysis/analysis/hbonds/hbond_autocorrel.py | 1 + package/MDAnalysis/analysis/psa.py | 11 ++++++----- testsuite/MDAnalysisTests/analysis/test_encore.py | 12 ++++++------ 4 files changed, 13 insertions(+), 12 deletions(-) diff --git a/.travis.yml b/.travis.yml index 647af4d97f6..834445201fe 100644 --- a/.travis.yml +++ b/.travis.yml @@ -32,7 +32,6 @@ env: - BUILD_CMD="pip install -v package/ && pip install testsuite/" - CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib scipy griddataformats" - CONDA_ALL_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib netcdf4 scikit-learn scipy griddataformats seaborn coveralls clustalw=2.1" - - PIP_DEPENDENCIES="" - CONDA_CHANNELS='biobuilds conda-forge' - CONDA_CHANNEL_PRIORITY=True - NUMPY_VERSION=stable diff --git a/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py b/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py index bf81e3529c5..296100addd8 100644 --- a/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py +++ b/package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py @@ -423,6 +423,7 @@ def solve(self, p_guess=None): Initial guess for the leastsq fit, must match the shape of the expected coefficients + Continuous defition results are fitted to a double exponential with :func:`scipy.optimize.leastsq`, intermittent definition are fit to a triple exponential. diff --git a/package/MDAnalysis/analysis/psa.py b/package/MDAnalysis/analysis/psa.py index f7178d678c1..f4562ee4e36 100644 --- a/package/MDAnalysis/analysis/psa.py +++ b/package/MDAnalysis/analysis/psa.py @@ -409,26 +409,27 @@ def hausdorff(P, Q): still has to calculate the *symmetric* Hausdorff distance as `max(directed_hausdorff(P, Q)[0], directed_hausdorff(Q, P)[0])`. + References ---------- .. [Huttenlocher1993] D. P. Huttenlocher, G. A. Klanderman, and W. J. Rucklidge. Comparing images using the Hausdorff distance. IEEE Transactions on Pattern Analysis and Machine Intelligence, 15(9):850–863, 1993. - .. [Taha2015] A. A. Taha and A. Hanbury. An efficient algorithm for calculating the exact Hausdorff distance. IEEE Transactions On Pattern Analysis And Machine Intelligence, 37:2153-63, 2015. - SeeAlso - ------- + + See Also + -------- scipy.spatial.distance.directed_hausdorff """ N, axis = get_coord_axes(P) d = get_msd_matrix(P, Q, axis=axis) - return ( max( np.amax(np.amin(d, axis=0)), \ - np.amax(np.amin(d, axis=1)) ) / N )**0.5 + return (max(np.amax(np.amin(d, axis=0)), + np.amax(np.amin(d, axis=1))) / N)**0.5 def hausdorff_wavg(P, Q): diff --git a/testsuite/MDAnalysisTests/analysis/test_encore.py b/testsuite/MDAnalysisTests/analysis/test_encore.py index 78bdfae9e27..3348d2e289c 100644 --- a/testsuite/MDAnalysisTests/analysis/test_encore.py +++ b/testsuite/MDAnalysisTests/analysis/test_encore.py @@ -118,18 +118,18 @@ def test_triangular_matrix(): incremented_triangular_matrix = triangular_matrix + scalar assert_equal(incremented_triangular_matrix[0,1], expected_value + scalar, - err_msg="Error in TriangularMatrix: addition of scalar gave\ -inconsistent results") + err_msg="Error in TriangularMatrix: addition of scalar gave" + "inconsistent results") triangular_matrix += scalar assert_equal(triangular_matrix[0,1], expected_value + scalar, - err_msg="Error in TriangularMatrix: addition of scalar gave\ -inconsistent results") + err_msg="Error in TriangularMatrix: addition of scalar gave" + "inconsistent results") multiplied_triangular_matrix_2 = triangular_matrix_2 * scalar assert_equal(multiplied_triangular_matrix_2[0,1], expected_value * scalar, - err_msg="Error in TriangularMatrix: multiplication by scalar gave\ -inconsistent results") + err_msg="Error in TriangularMatrix: multiplication by scalar gave" + "inconsistent results") triangular_matrix_2 *= scalar assert_equal(triangular_matrix_2[0,1], expected_value * scalar, From f8464279fa4f95ffba0e18d5c77a4ca0c9c56e07 Mon Sep 17 00:00:00 2001 From: Max Linke Date: Sat, 24 Jun 2017 14:09:41 +0200 Subject: [PATCH 35/35] add @utkbansal to changelog --- package/CHANGELOG | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index 6859b765b25..ba09f4ea93c 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -15,7 +15,7 @@ The rules for this file: ------------------------------------------------------------------------------ -mm/dd/17 richardjgowers, rathann, jbarnoud, orbeckst +mm/dd/17 richardjgowers, rathann, jbarnoud, orbeckst, utkbansal * 0.16.2