From 7a751eec86aed7f484e71e1971a7d1dc47d563d2 Mon Sep 17 00:00:00 2001
From: Irfan Alibay <IAlibay@users.noreply.github.com>
Date: Sat, 29 Feb 2020 22:06:51 +0000
Subject: [PATCH] Atomgroup removal (#2562)

* Completes #1070 and moves us towards v1.0 #2443
* Removed AtomGroup stubs.
* Removed unnecessary import from groups.py
* Removes deprecation test
* Update CHANGELOG
---
 package/CHANGELOG                             |  1 +
 package/MDAnalysis/core/AtomGroup.py          | 67 -------------------
 package/MDAnalysis/core/__init__.py           |  1 -
 package/MDAnalysis/core/groups.py             |  2 -
 .../MDAnalysisTests/core/test_atomgroup.py    |  6 --
 5 files changed, 1 insertion(+), 76 deletions(-)
 delete mode 100644 package/MDAnalysis/core/AtomGroup.py

diff --git a/package/CHANGELOG b/package/CHANGELOG
index b315d06017a..9ab0f957240 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -86,6 +86,7 @@ Enhancements
   * Improve the distance search in water bridge analysis with capped_distance (PR #2480)
 
 Changes
+  * Removed AtomGroup stubs (PR #1070, Issue #2443).
   * encore.hes() doesn't accept the details keyword anymore, it always returns
     the relevant details instead, consistently with ces() and dres(), in the
     form of a dictionary (Issue #2465)
diff --git a/package/MDAnalysis/core/AtomGroup.py b/package/MDAnalysis/core/AtomGroup.py
deleted file mode 100644
index 3967fe7a9ec..00000000000
--- a/package/MDAnalysis/core/AtomGroup.py
+++ /dev/null
@@ -1,67 +0,0 @@
-# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
-# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
-#
-# MDAnalysis --- https://www.mdanalysis.org
-# Copyright (c) 2006-2017 The MDAnalysis Development 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.
-# doi: 10.25080/majora-629e541a-00e
-#
-# 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
-#
-from __future__ import absolute_import
-import warnings
-
-from .groups import (Atom, AtomGroup, Residue, ResidueGroup, Segment,
-                     SegmentGroup)
-from . import universe
-
-
-def deprecate_class(class_new, message):
-    """utility to deprecate a class"""
-
-    class new_class(class_new):
-        def __init__(self, *args, **kwargs):
-            super(new_class, self).__init__(*args, **kwargs)
-            warnings.warn(message, DeprecationWarning)
-
-    return new_class
-
-
-Universe = deprecate_class(
-    universe.Universe,
-    "MDAnalysis.core.AtomGroup.Universe has been removed."
-    "Please use MDAnalysis.Universe."
-    "This stub will be removed in 1.0")
-
-_group_message = ("MDAnalysis.core.AtomGroup.{0} has been removed."
-                  "Please use MDAnalysis.groups.{0}"
-                  "This stub will be removed in 1.0")
-
-Atom = deprecate_class(Atom, message=_group_message.format('Atom'))
-AtomGroup = deprecate_class(
-    AtomGroup, message=_group_message.format('AtomGroup'))
-
-Residue = deprecate_class(Residue, message=_group_message.format('Residue'))
-ResidueGroup = deprecate_class(
-    ResidueGroup, message=_group_message.format('ResidueGroup'))
-
-Segment = deprecate_class(Segment, message=_group_message.format('Segment'))
-SegmentGroup = deprecate_class(
-    SegmentGroup, message=_group_message.format('SegmentGroup'))
-
-__all__ = [
-    'Universe', 'Atom', 'AtomGroup', 'Residue', 'ResidueGroup', 'Segment',
-    'SegmentGroup'
-]
diff --git a/package/MDAnalysis/core/__init__.py b/package/MDAnalysis/core/__init__.py
index ee659fc524f..35ed5b0031e 100644
--- a/package/MDAnalysis/core/__init__.py
+++ b/package/MDAnalysis/core/__init__.py
@@ -55,4 +55,3 @@
 
 from . import groups
 from . import selection
-from . import AtomGroup
diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 952ce6534be..0d6ad9d07ba 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -100,8 +100,6 @@
 import os
 import warnings
 
-from numpy.lib.utils import deprecate
-
 from .. import _ANCHOR_UNIVERSES, _CONVERTERS
 from ..lib import util
 from ..lib.util import cached, warn_if_not_unique, unique_int_1d
diff --git a/testsuite/MDAnalysisTests/core/test_atomgroup.py b/testsuite/MDAnalysisTests/core/test_atomgroup.py
index 14d3b853d15..42b0a153d34 100644
--- a/testsuite/MDAnalysisTests/core/test_atomgroup.py
+++ b/testsuite/MDAnalysisTests/core/test_atomgroup.py
@@ -56,12 +56,6 @@
 import pytest
 
 
-class TestDeprecationWarnings(object):
-    def test_AtomGroupUniverse_usage_warning(self):
-        with pytest.deprecated_call():
-            mda.core.AtomGroup.Universe(PSF, DCD)
-
-
 class TestAtomGroupToTopology(object):
     """Test the conversion of AtomGroup to TopologyObjects"""
     @pytest.fixture()