MDAnalysis · richardjgowers · Jun 27, 2017 · Jun 3, 2017 · Jun 4, 2017 · Jun 4, 2017
diff --git a/.travis.yml b/.travis.yml
@@ -21,23 +21,32 @@ 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"
-    # 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"
     - 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
+           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"
            MAIN_CMD="cd package && python setup.py"
@@ -55,7 +64,8 @@ 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'
 
@@ -76,7 +86,7 @@ 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 \
@@ -92,8 +102,13 @@ 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/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
diff --git 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
@@ -13,6 +13,25 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
+
+06/27/17 richardjgowers, rathann, jbarnoud, orbeckst, utkbansal
+
+  * 0.16.2
+
+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
+  * scipy and matplotlib are now required dependencies (Issue #1159)
+
+
 06/03/17 utkbansal, kain88-de, xiki-tempula, kaplajon, wouterboomsma,
          richardjgowers, Shtkddud123, QuantumEntangledAndy, orbeckst,
          kaceyreidy

diff --git 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
@@ -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/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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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/__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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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