MDAnalysis · richardjgowers · Jun 10, 2020 · Jun 9, 2020 · Jun 10, 2020 · Jun 10, 2020
diff --git a/.travis.yml b/.travis.yml
@@ -19,7 +19,7 @@ env:
     - GIT_CI_EMAIL=TravisCI@mdanalysis.org
     - MDA_DOCDIR=${TRAVIS_BUILD_DIR}/package/doc/html/html
     # Set default python version to avoid repetition later
-    - PYTHON_VERSION=3.5
+    - PYTHON_VERSION=3.6
     - BUILD_DOCS=false
     - CODECOV=false
     - PYTEST_FLAGS="--disable-pytest-warnings --durations=50"
@@ -41,7 +41,6 @@ env:
     - CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
     - PYTHON_VERSION=3.8 CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
     - PYTHON_VERSION=3.7 CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
-    - PYTHON_VERSION=3.6 CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
     - NUMPY_VERSION=1.13.3
     - NUMPY_VERSION=dev  EVENT_TYPE="cron"
 
@@ -65,13 +64,6 @@ matrix:
            CONDA_DEPENDENCIES=""
            INSTALL_HOLE="false"
 
-    - env: NAME="python 2.7"
-           PYTHON_VERSION=2.7
-           CODECOV="true"
-           NUMPY_VERSION=1.16
-           SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
-           PIP_DEPENDENCIES="${PIP_DEPENDENCIES} setuptools<45.0.0"
-
     - env: NAME="asv check"
            PYTHON_VERSION=2.7
            CODECOV="false"
@@ -85,14 +77,6 @@ matrix:
       env: PYTHON_VERSION=3.6
            NUMPY_VERSION=1.17.3
 
-# macOS Python 2.7 works in principle but times out on Travis CI:
-# Disabled so that the tests can pass.
-#    - os: osx
-#      env: PYTHON_VERSION=2.7
-#           NUMPY_VERSION=1.16
-#           CODECOV="true"
-#           SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
-
     - env: NAME='minimal'
            PIP_DEPENDENCIES=""
            CONDA_DEPENDENCIES=${CONDA_MIN_DEPENDENCIES}

diff --git a/package/CHANGELOG b/package/CHANGELOG
@@ -13,14 +13,26 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-mm/dd/yy richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira,
+??/??/?? richardjgowers
+
+  * 2.0.0
+
+Fixes
+
+Enhancements
+
+Deprecations
+* Dropped Python 2 support
+
+
+06/09/20 richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira,
          PicoCentauri, davidercruz, jbarnoud, RMeli, IAlibay, mtiberti, CCook96,
          Yuan-Yu, xiki-tempula, HTian1997, Iv-Hristov, hmacdope, AnshulAngaria,
          ss62171, Luthaf, yuxuanzhuang, abhishandy, mlnance, shfrz, orbeckst,
          wvandertoorn, cbouy, AmeyaHarmalkar, Oscuro-Phoenix, andrrizzi, WG150,
          tylerjereddy, Marcello-Sega
 
-  * 0.21.0
+  * 1.0.0
 
 Fixes
   * MOL2Writer now accepts both Universes and AtomgGroups (Issue #2717)

diff --git a/package/MDAnalysis/analysis/align.py b/package/MDAnalysis/analysis/align.py
@@ -458,7 +458,7 @@ def alignto(mobile, reference, select=None, weights=None,
     .. _ClustalW: http://www.clustal.org/
     .. _STAMP: http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/
 
-    .. versionchanged:: 0.21.0
+    .. versionchanged:: 1.0.0
        Added *match_atoms* keyword to toggle atom matching.
 
     .. versionchanged:: 0.8
@@ -803,7 +803,7 @@ def __init__(self, mobile, reference=None, select='all', filename=None,
           already a :class:`MemoryReader` then it is *always* treated as if
           ``in_memory`` had been set to ``True``.
 
-        .. versionadded:: 0.21.0
+        .. versionadded:: 1.0.0
 
         .. versionchanged:: 1.0.0
            Support for the ``start``, ``stop``, and ``step`` keywords has been

diff --git a/package/MDAnalysis/analysis/gnm.py b/package/MDAnalysis/analysis/gnm.py
@@ -395,10 +395,8 @@ class closeContactGNMAnalysis(GNMAnalysis):
     .. deprecated:: 0.16.0
        Instead of ``MassWeight=True`` use ``weights="size"``.
 
-    .. versionchanged:: 0.21.0
-       MassWeight option (see above deprecation entry).
-
     .. versionchanged:: 1.0.0
+       MassWeight option (see above deprecation entry).
        Changed `selection` keyword to `select`
     """
 

diff --git a/package/MDAnalysis/analysis/hbonds/hbond_analysis.py b/package/MDAnalysis/analysis/hbonds/hbond_analysis.py
@@ -383,10 +383,8 @@ class HydrogenBondAnalysis(base.AnalysisBase):
        DEFAULT_DONORS/ACCEPTORS is now embedded in a dict to switch between
        default values for different force fields.
 
-    .. versionchanged:: 0.21.0
-        Added autocorrelation (MDAnalysis.lib.correlations.py) for calculating hydrogen bond lifetime
-
     .. versionchanged:: 1.0.0
+        Added autocorrelation (MDAnalysis.lib.correlations.py) for calculating hydrogen bond lifetime
        ``save_table()`` method has been removed. You can use ``np.save()`` or
        ``cPickle.dump()`` on :attr:`HydrogenBondAnalysis.table` instead.
     """

diff --git a/package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py b/package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py
@@ -28,7 +28,7 @@
 :Year: 2019
 :Copyright: GNU Public License v3
 
-.. versionadded:: 0.21.0
+.. versionadded:: 1.0.0
 
 This module provides methods to find and analyse hydrogen bonds in a Universe.
 

diff --git a/package/MDAnalysis/analysis/psa.py b/package/MDAnalysis/analysis/psa.py
@@ -1680,7 +1680,7 @@ def plot(self, filename=None, linkage='ward', count_sort=False,
         dist_matrix_clus
           clustered distance matrix (reordered)
 
-        .. versionchanged:: 0.21.0
+        .. versionchanged:: 1.0.0
             :attr:`tick1On`, :attr:`tick2On`, :attr:`label1On` and :attr:`label2On`
             changed to :attr:`tick1line`, :attr:`tick2line`, :attr:`label1` and
             :attr:`label2` due to upstream deprecation (see #2493)
@@ -1807,7 +1807,7 @@ def plot_annotated_heatmap(self, filename=None, linkage='ward',             \
 
         .. _seaborn: https://seaborn.pydata.org/
 
-        .. versionchanged:: 0.21.0
+        .. versionchanged:: 1.0.0
             :attr:`tick1On`, :attr:`tick2On`, :attr:`label1On` and :attr:`label2On`
             changed to :attr:`tick1line`, :attr:`tick2line`, :attr:`label1` and
             :attr:`label2` due to upstream deprecation (see #2493)

diff --git a/package/MDAnalysis/coordinates/XDR.py b/package/MDAnalysis/coordinates/XDR.py
@@ -113,7 +113,7 @@ class XDRBaseReader(base.ReaderBase):
     Reader. However, the  next time the trajectory is opened,  the offsets will
     have to be rebuilt again.
 
-    .. versionchanged:: 0.21.0
+    .. versionchanged:: 1.0.0
        XDR offsets read from trajectory if offsets file read-in fails
 
     """

diff --git a/package/MDAnalysis/coordinates/XYZ.py b/package/MDAnalysis/coordinates/XYZ.py
@@ -109,7 +109,7 @@ class XYZWriter(base.WriterBase):
     .. _xyzplugin:
        http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html
 
-    .. versionchanged: 0.21.0
+    .. versionchanged: 1.0.0
        Use elements attribute instead of names attribute, if present
     """
 

diff --git a/package/MDAnalysis/core/_get_readers.py b/package/MDAnalysis/core/_get_readers.py
@@ -276,7 +276,7 @@ def get_converter_for(format):
         If no appropriate parser could be found.
 
 
-    .. versionadded:: 0.21.0
+    .. versionadded:: 1.0.0
     """
     try:
         writer = _CONVERTERS[format]

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
@@ -802,7 +802,7 @@ def center(self, weights, pbc=False, compound='group', unwrap=False):
         .. versionchanged:: 0.20.0 Added ``'molecules'`` and ``'fragments'``
             compounds
         .. versionchanged:: 0.20.0 Added `unwrap` parameter
-        .. versionchanged:: 0.21.0 Removed flags affecting default behaviour
+        .. versionchanged:: 1.0.0 Removed flags affecting default behaviour
         """
         atoms = self.atoms
 
@@ -933,7 +933,7 @@ def center_of_geometry(self, pbc=False, compound='group', unwrap=False):
         .. versionchanged:: 0.20.0 Added ``'molecules'`` and ``'fragments'``
             compounds
         .. versionchanged:: 0.20.0 Added `unwrap` parameter
-        .. versionchanged:: 0.21.0 Removed flags affecting default behaviour
+        .. versionchanged:: 1.0.0 Removed flags affecting default behaviour
         """
         return self.center(None, pbc=pbc, compound=compound, unwrap=unwrap)
 
@@ -1107,7 +1107,7 @@ def bbox(self, pbc=False):
 
         .. versionadded:: 0.7.2
         .. versionchanged:: 0.8 Added *pbc* keyword
-        .. versionchanged:: 0.21.0 Removed flags affecting default behaviour
+        .. versionchanged:: 1.0.0 Removed flags affecting default behaviour
         """
         atomgroup = self.atoms
 
@@ -3043,7 +3043,7 @@ def ureybradley(self):
             If the :class:`AtomGroup` is not length 2
 
 
-        .. versionadded:: 0.21.0
+        .. versionadded:: 1.0.0
         """
         if len(self) != 2:
             raise ValueError(
@@ -3061,7 +3061,7 @@ def cmap(self):
             If the :class:`AtomGroup` is not length 5
 
 
-        .. versionadded:: 0.21.0
+        .. versionadded:: 1.0.0
         """
         if len(self) != 5:
             raise ValueError(
@@ -3104,7 +3104,7 @@ def convert_to(self, package):
             No converter was found for the required package
 
 
-        .. versionadded:: 0.21.0
+        .. versionadded:: 1.0.0
         """
         converter = get_converter_for(package)
         return converter().convert(self.atoms)

diff --git a/package/MDAnalysis/core/topologyattrs.py b/package/MDAnalysis/core/topologyattrs.py
@@ -1931,7 +1931,7 @@ def _check_connection_values(func):
      - coerces them to tuples of ints (for hashing)
      - ensures that first value is less than last (reversibility & hashing)
 
-    .. versionadded:: 0.21.0
+    .. versionadded:: 1.0.0
 
     """
     @functools.wraps(func)
@@ -1955,7 +1955,7 @@ def wrapper(self, values, *args, **kwargs):
 class _Connection(AtomAttr):
     """Base class for connectivity between atoms
 
-    .. versionchanged:: 0.21.0
+    .. versionchanged:: 1.0.0
         Added type checking to atom index values.
     """
 
@@ -2044,7 +2044,7 @@ def _add_bonds(self, values, types=None, guessed=True, order=None):
     @_check_connection_values
     def _delete_bonds(self, values):
         """
-        .. versionadded:: 0.21.0
+        .. versionadded:: 1.0.0
         """
 
         to_check = set(values)
@@ -2231,7 +2231,7 @@ class UreyBradleys(_Connection):
 
     These indices refer to the atom indices.
 
-    .. versionadded:: 0.21.0
+    .. versionadded:: 1.0.0
     """
     attrname = 'ureybradleys'
     singular = 'ureybradleys'
@@ -2272,7 +2272,7 @@ class Impropers(_Connection):
 class CMaps(_Connection):
     """
     A connection between five atoms
-    .. versionadded:: 0.21.0
+    .. versionadded:: 1.0.0
     """
     attrname = 'cmaps'
     singular = 'cmaps'

diff --git a/package/MDAnalysis/core/topologyobjects.py b/package/MDAnalysis/core/topologyobjects.py
@@ -337,7 +337,7 @@ class UreyBradley(TopologyObject):
     ``!=`` operators. A UreyBradley angle is equal to another if the same atom
     numbers are involved.
 
-    .. versionadded:: 0.21.0
+    .. versionadded:: 1.0.0
     """
     btype = 'ureybradley'
 
@@ -369,7 +369,7 @@ class CMap(TopologyObject):
     Coupled-torsion correction map term between five 
     :class:`~MDAnalysis.core.groups.Atom` instances.
 
-    .. versionadded:: 0.21.0
+    .. versionadded:: 1.0.0
     """
     btype = 'cmap'
 
@@ -568,7 +568,7 @@ class TopologyGroup(object):
     .. versionchanged:: 0.19.0
        Empty TopologyGroup now returns correctly shaped empty array via
        indices property and to_indices()
-    .. versionchanged::0.21.0
+    .. versionchanged::1.0.0
        ``type``, ``guessed``, and ``order`` are no longer reshaped to arrays
        with an extra dimension
     """

diff --git a/package/MDAnalysis/core/universe.py b/package/MDAnalysis/core/universe.py
@@ -456,7 +456,7 @@ def empty(cls, n_atoms, n_residues=1, n_segments=1,
         .. versionadded:: 0.17.0
         .. versionchanged:: 0.19.0
            The attached Reader when trajectory=True is now a MemoryReader
-        .. versionchanged:: 0.21.0
+        .. versionchanged:: 1.0.0
            Universes can now be created with 0 atoms
         """
         if not n_atoms:
@@ -981,7 +981,7 @@ def _add_topology_objects(self, object_type, values, types=None, guessed=False,
             None, or an iterable of hashable values with the same length as ``values``
 
 
-        .. versionadded:: 0.21.0
+        .. versionadded:: 1.0.0
         """
         if all(isinstance(x, TopologyObject) for x in values):
             try:
@@ -1061,7 +1061,7 @@ def add_bonds(self, values, types=None, guessed=False, order=None):
             u2.add_bonds(u.bonds.to_indices())
 
 
-        .. versionadded:: 0.21.0
+        .. versionadded:: 1.0.0
         """
         self._add_topology_objects('bonds', values, types=types,
                                  guessed=guessed, order=order)
@@ -1083,7 +1083,7 @@ def add_angles(self, values, types=None, guessed=False):
         guessed : bool or iterable (optional, default False)
             bool, or an iterable of hashable values with the same length as ``values``
 
-        .. versionadded:: 0.21.0
+        .. versionadded:: 1.0.0
         """
         self._add_topology_objects('angles', values, types=types,
                                  guessed=guessed)
@@ -1105,7 +1105,7 @@ def add_dihedrals(self, values, types=None, guessed=False):
             bool, or an iterable of hashable values with the same length as ``values``
 
 
-        .. versionadded:: 0.21.0
+        .. versionadded:: 1.0.0
         """
         self._add_topology_objects('dihedrals', values, types=types,
                                  guessed=guessed)
@@ -1127,7 +1127,7 @@ def add_impropers(self, values, types=None, guessed=False):
             bool, or an iterable of hashable values with the same length as ``values``
 
 
-        .. versionadded:: 0.21.0
+        .. versionadded:: 1.0.0
         """
         self._add_topology_objects('impropers', values, types=types,
                                  guessed=guessed)
@@ -1145,7 +1145,7 @@ def _delete_topology_objects(self, object_type, values):
             If AtomGroups, TopologyObjects, or a TopologyGroup are passed,
             they *must* be from the same Universe.
 
-        .. versionadded:: 0.21.0
+        .. versionadded:: 1.0.0
         """
         indices = []
         for x in values:
@@ -1199,7 +1199,7 @@ def delete_bonds(self, values):
             u.delete_bonds(u2.bonds.to_indices())
 
 
-        .. versionadded:: 0.21.0
+        .. versionadded:: 1.0.0
         """
         self._delete_topology_objects('bonds', values)
         self._cache.pop('fragments', None)
@@ -1216,7 +1216,7 @@ def delete_angles(self, values):
             they *must* be from the same Universe.
 
 
-        .. versionadded:: 0.21.0
+        .. versionadded:: 1.0.0
         """
         self._delete_topology_objects('angles', values)
 
@@ -1232,7 +1232,7 @@ def delete_dihedrals(self, values):
             they *must* be from the same Universe.
 
 
-        .. versionadded:: 0.21.0
+        .. versionadded:: 1.0.0
         """
         self._delete_topology_objects('dihedrals', values)
 
@@ -1248,7 +1248,7 @@ def delete_impropers(self, values):
             they *must* be from the same Universe.
 
 
-        .. versionadded:: 0.21.0
+        .. versionadded:: 1.0.0
         """
         self._delete_topology_objects('impropers', values)