From 579074037c276d76bdf0d44d07e9f3dd206a5cd5 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Wed, 24 Mar 2021 17:56:35 +0900
Subject: [PATCH 01/45] add attribute 'sort' to atomgroup

---
 package/MDAnalysis/core/groups.py | 49 +++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 0671bcef3ad..1ab23d28672 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3324,6 +3324,55 @@ def write(self, filename=None, file_format=None,
 
         raise ValueError("No writer found for format: {}".format(filename))
 
+    def sort(self, **keys):
+        """Return sorted Atomgroup.
+
+        Example
+        -------
+
+        .. code-block:: python
+
+            >>> import MDAnalysis as mda
+            >>> from MDAnalysisTests.datafiles import PDB_small
+            >>> ag = sum([u.atoms[3], u.atoms[2], u.atoms[1], u.atoms[0]])
+            >>> ag.ids
+            [4 3 2 1]
+            >>> ag.ix
+            [3 2 1 0]
+            >>> ag = ag.sort(key=lambda atom: atom.id)
+            >>> ag.ids
+            [1 2 3 4]
+            >>> ag.ix
+            [0 1 2 3]
+
+        Parameters
+        ----------
+        keys: callable object
+        A function for the parameter of each atom to use for sorting. 
+        Example: lambda atom: atom.id
+
+        Returns
+        -------
+        output:
+            Sorted atomgroup.
+
+
+        .. versionadded:: 2.0.0
+        """
+        if len(keys) == 0:
+            raise NameError("argument 'key' is not defined. ")
+        for key, value in keys.items():
+            if key == "key":
+                n = len(self.atoms)
+                idx = np.zeros(n)
+                for i in range(n):
+                    idx[i] = value(self.atoms[i])
+                order = np.argsort(idx)
+                agsorted = self.atoms[order]
+                return agsorted
+            else:
+                raise ValueError("Incorrect parameter: {}")
+
 
 class ResidueGroup(GroupBase):
     """ResidueGroup base class.

From c9326a3591be33da56ad91fbc49f73820e6eefba Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Wed, 24 Mar 2021 17:59:16 +0900
Subject: [PATCH 02/45] Edit CHANGELOG

---
 package/AUTHORS   | 1 +
 package/CHANGELOG | 3 ++-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/package/AUTHORS b/package/AUTHORS
index 00076883aa4..e85f8d33993 100644
--- a/package/AUTHORS
+++ b/package/AUTHORS
@@ -158,6 +158,7 @@ Chronological list of authors
   - Henrik Jäger
   - Jan Stevens
   - Orion Cohen
+  - Kosuke Kudo
 
 External code
 -------------
diff --git a/package/CHANGELOG b/package/CHANGELOG
index 0de5b4a35a4..fdf5bfca12c 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -17,7 +17,7 @@ The rules for this file:
          lilyminium, daveminh, jbarnoud, yuxuanzhuang, VOD555, ianmkenney,
          calcraven，xiki-tempula, mieczyslaw, manuel.nuno.melo, PicoCentauri,
          hanatok, rmeli, aditya-kamath, tirkarthi, LeonardoBarneschi, hejamu,
-         biogen98, orioncohen
+         biogen98, orioncohen, 1ut
 
   * 2.0.0
 
@@ -89,6 +89,7 @@ Fixes
   * Fix syntax warning over comparison of literals using is (Issue #3066)
 
 Enhancements
+  * Added sort method to the atomgroup (Issue #2976) 
   * Added a ValueError raised when not given a gridcenter while
     providing grid dimensions to DensityAnalysis, also added
     check for NaN in the input (Issue #3148, PR #3154)

From 99d6d701edf5684d2277ac8971c5cccc8c404a11 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Wed, 24 Mar 2021 18:29:36 +0900
Subject: [PATCH 03/45] delete white space  according to PEP8

---
 package/MDAnalysis/core/groups.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 1ab23d28672..ac04eb33b3b 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3348,7 +3348,7 @@ def sort(self, **keys):
         Parameters
         ----------
         keys: callable object
-        A function for the parameter of each atom to use for sorting. 
+        A function for the parameter of each atom to use for sorting.
         Example: lambda atom: atom.id
 
         Returns

From 315080c87b56fe4c12d372a62bd47f5f87ddd60f Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Thu, 25 Mar 2021 12:45:02 +0900
Subject: [PATCH 04/45] Edit docs

---
 package/MDAnalysis/core/groups.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index ac04eb33b3b..771713c7e25 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3334,16 +3334,17 @@ def sort(self, **keys):
 
             >>> import MDAnalysis as mda
             >>> from MDAnalysisTests.datafiles import PDB_small
+            >>> u = mda.Universe(PDB_small)
             >>> ag = sum([u.atoms[3], u.atoms[2], u.atoms[1], u.atoms[0]])
             >>> ag.ids
-            [4 3 2 1]
+            array([4 3 2 1])
             >>> ag.ix
-            [3 2 1 0]
+            array([3 2 1 0])
             >>> ag = ag.sort(key=lambda atom: atom.id)
             >>> ag.ids
-            [1 2 3 4]
+            array([1 2 3 4])
             >>> ag.ix
-            [0 1 2 3]
+            array([0 1 2 3])
 
         Parameters
         ----------

From 6ff70a0f94284317660605ffeeb538a876c9d8b3 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Thu, 25 Mar 2021 12:45:33 +0900
Subject: [PATCH 05/45] add a test for atomgroup.sort

---
 .../MDAnalysisTests/core/test_atomgroup.py    | 25 ++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

diff --git a/testsuite/MDAnalysisTests/core/test_atomgroup.py b/testsuite/MDAnalysisTests/core/test_atomgroup.py
index 1a3d401f0ee..b5ade8d413a 100644
--- a/testsuite/MDAnalysisTests/core/test_atomgroup.py
+++ b/testsuite/MDAnalysisTests/core/test_atomgroup.py
@@ -47,7 +47,8 @@
     TRZ_psf, TRZ,
     two_water_gro,
     TPR_xvf, TRR_xvf,
-    GRO
+    GRO,
+    PDB_helix
 )
 from MDAnalysisTests import make_Universe, no_deprecated_call
 from MDAnalysisTests.core.util import UnWrapUniverse
@@ -1674,3 +1675,25 @@ def test_partial_timestep(self, universe):
                                 ag.ts.velocities,
                                 self.prec,
                                 err_msg="Partial timestep coordinates wrong")
+
+
+class TestAtomGroupSort(object):
+    """Tests the AtomGroup.sort attribute"""
+
+    @pytest.fixture()
+    def u(self):
+        return mda.Universe(PDB_helix)
+
+    @pytest.fixture()
+    def ag(self, u):
+        return sum([u.atoms[3], u.atoms[2], u.atoms[1], u.atoms[0]])
+
+    @pytest.fixture()
+    def agsort(self, ag):
+        return ag.sort(key=lambda atom: atom.id)
+
+    def test_sort(self, agsort):
+        refid = np.array([1, 2, 3, 4])
+        refix = np.array([0, 1, 2, 3])
+        assert np.array_equal(refid, agsort.ids)
+        assert np.array_equal(refix, agsort.ix)
\ No newline at end of file

From dfe7027b375d18c19e37beb766b4b7dbd1f759d0 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Mon, 29 Mar 2021 10:56:53 +0900
Subject: [PATCH 06/45] add changes to atomgroup.sort

---
 package/MDAnalysis/core/groups.py | 47 ++++++++++++-------------------
 1 file changed, 18 insertions(+), 29 deletions(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 771713c7e25..bd2cfa2ea4d 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3324,8 +3324,18 @@ def write(self, filename=None, file_format=None,
 
         raise ValueError("No writer found for format: {}".format(filename))
 
-    def sort(self, **keys):
-        """Return sorted Atomgroup.
+    def sort(self, key='ix'):
+        """Return sorted Atomgroup by a key that specifies an attribute of atomgroup. The default key is "ix".
+
+        Parameters
+        ----------
+        keys: 
+            The name for attribute of Atomgroup. (e.g. "ids", "ix")
+
+        Returns
+        -------
+        output:
+            Sorted atomgroup.
 
         Example
         -------
@@ -3335,44 +3345,23 @@ def sort(self, **keys):
             >>> import MDAnalysis as mda
             >>> from MDAnalysisTests.datafiles import PDB_small
             >>> u = mda.Universe(PDB_small)
-            >>> ag = sum([u.atoms[3], u.atoms[2], u.atoms[1], u.atoms[0]])
+            >>> ag = u.atoms[[3, 2, 1, 0]]
             >>> ag.ids
             array([4 3 2 1])
             >>> ag.ix
             array([3 2 1 0])
-            >>> ag = ag.sort(key=lambda atom: atom.id)
+            >>> ag = ag.sort()
             >>> ag.ids
             array([1 2 3 4])
             >>> ag.ix
             array([0 1 2 3])
 
-        Parameters
-        ----------
-        keys: callable object
-        A function for the parameter of each atom to use for sorting.
-        Example: lambda atom: atom.id
-
-        Returns
-        -------
-        output:
-            Sorted atomgroup.
-
-
         .. versionadded:: 2.0.0
         """
-        if len(keys) == 0:
-            raise NameError("argument 'key' is not defined. ")
-        for key, value in keys.items():
-            if key == "key":
-                n = len(self.atoms)
-                idx = np.zeros(n)
-                for i in range(n):
-                    idx[i] = value(self.atoms[i])
-                order = np.argsort(idx)
-                agsorted = self.atoms[order]
-                return agsorted
-            else:
-                raise ValueError("Incorrect parameter: {}")
+        idx = getattr(self.atoms, key)
+        order = np.argsort(idx)
+        agsorted = self.atoms[order]
+        return agsorted
 
 
 class ResidueGroup(GroupBase):

From c86db7a3d59b89a5c7ef979ce0fbbfa0d182eb14 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Mon, 29 Mar 2021 10:57:19 +0900
Subject: [PATCH 07/45] add changes to test case for atomgroup.sort

---
 testsuite/MDAnalysisTests/core/test_atomgroup.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/testsuite/MDAnalysisTests/core/test_atomgroup.py b/testsuite/MDAnalysisTests/core/test_atomgroup.py
index b5ade8d413a..f6b97933a7a 100644
--- a/testsuite/MDAnalysisTests/core/test_atomgroup.py
+++ b/testsuite/MDAnalysisTests/core/test_atomgroup.py
@@ -1686,11 +1686,11 @@ def u(self):
 
     @pytest.fixture()
     def ag(self, u):
-        return sum([u.atoms[3], u.atoms[2], u.atoms[1], u.atoms[0]])
+        return u.atoms[[3, 2, 1, 0]]
 
     @pytest.fixture()
     def agsort(self, ag):
-        return ag.sort(key=lambda atom: atom.id)
+        return ag.sort("ids")
 
     def test_sort(self, agsort):
         refid = np.array([1, 2, 3, 4])

From 6db489e8477273dec0df8e47703dd07b1ddf2cb5 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Mon, 29 Mar 2021 12:12:28 +0900
Subject: [PATCH 08/45] edit CHANGELOG

---
 package/CHANGELOG | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/package/CHANGELOG b/package/CHANGELOG
index fdf5bfca12c..7b109359889 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -141,8 +141,12 @@ Enhancements
     'protein' selection (#2751 PR #2755)
   * Added an RDKit converter that works for any input with all hydrogens
     explicit in the topology (Issue #2468, PR #2775)
+<<<<<<< HEAD
 
 
+=======
+  
+>>>>>>> edit CHANGELOG
 Changes
   * TPRParser now loads TPR files with `tpr_resid_from_one=True` by default,
     which starts TPR resid indexing from 1 (instead of 0 as in 1.x) (Issue #2364, PR #3152)

From 8b465574264e76d7cda24e516eec3157b7820652 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Mon, 29 Mar 2021 21:25:03 +0900
Subject: [PATCH 09/45] made np.argsort stable

---
 package/MDAnalysis/core/groups.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index bd2cfa2ea4d..109aa92c9b8 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3325,7 +3325,7 @@ def write(self, filename=None, file_format=None,
         raise ValueError("No writer found for format: {}".format(filename))
 
     def sort(self, key='ix'):
-        """Return sorted Atomgroup by a key that specifies an attribute of atomgroup. The default key is "ix".
+        """Return stably sorted Atomgroup by a key that specifies an attribute of atomgroup. The default key is "ix".
 
         Parameters
         ----------
@@ -3359,7 +3359,7 @@ def sort(self, key='ix'):
         .. versionadded:: 2.0.0
         """
         idx = getattr(self.atoms, key)
-        order = np.argsort(idx)
+        order = np.argsort(idx, kind='stable')
         agsorted = self.atoms[order]
         return agsorted
 

From b3f045513bd36a80417649ec0be3e8acfd7f3347 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Mon, 29 Mar 2021 21:53:19 +0900
Subject: [PATCH 10/45] Add tests for TestAtomGroupSort

---
 .../MDAnalysisTests/core/test_atomgroup.py    | 62 ++++++++++++++-----
 1 file changed, 47 insertions(+), 15 deletions(-)

diff --git a/testsuite/MDAnalysisTests/core/test_atomgroup.py b/testsuite/MDAnalysisTests/core/test_atomgroup.py
index f6b97933a7a..efe136de390 100644
--- a/testsuite/MDAnalysisTests/core/test_atomgroup.py
+++ b/testsuite/MDAnalysisTests/core/test_atomgroup.py
@@ -47,8 +47,7 @@
     TRZ_psf, TRZ,
     two_water_gro,
     TPR_xvf, TRR_xvf,
-    GRO,
-    PDB_helix
+    GRO
 )
 from MDAnalysisTests import make_Universe, no_deprecated_call
 from MDAnalysisTests.core.util import UnWrapUniverse
@@ -1681,19 +1680,52 @@ class TestAtomGroupSort(object):
     """Tests the AtomGroup.sort attribute"""
 
     @pytest.fixture()
-    def u(self):
-        return mda.Universe(PDB_helix)
+    def universe(self):
+        u = mda.Universe.empty(
+            n_atoms=7,
+            n_residues=3,
+            n_segments=2,
+            atom_resindex=np.array([0, 0, 0, 1, 1, 1, 2]),
+            residue_segindex=np.array([0, 0, 1]),
+            trajectory=True,
+            velocities=True,
+            forces=True
+        )
+        attributes = ["id", "charge", "mass", "tempfactor"]
+
+        for i in (attributes):
+            u.add_TopologyAttr(i, [6, 5, 4, 3, 2, 1, 0])
+
+        u.add_TopologyAttr('resid', [2, 1, 0])
+        u.add_TopologyAttr('segid', [1, 0])
+
+        return u
 
     @pytest.fixture()
-    def ag(self, u):
-        return u.atoms[[3, 2, 1, 0]]
+    def ag(self, universe):
+        return universe.atoms
 
-    @pytest.fixture()
-    def agsort(self, ag):
-        return ag.sort("ids")
-
-    def test_sort(self, agsort):
-        refid = np.array([1, 2, 3, 4])
-        refix = np.array([0, 1, 2, 3])
-        assert np.array_equal(refid, agsort.ids)
-        assert np.array_equal(refix, agsort.ix)
\ No newline at end of file
+    test_ids = [
+       "ix",
+       "ids",
+       "resids",
+       "segids",
+       "charges",
+       "masses",
+       "tempfactors"
+    ]
+
+    test_data = [
+        ("ix", np.array([0, 1, 2, 3, 4, 5, 6])),
+        ("ids", np.array([6, 5, 4, 3, 2, 1, 0])),
+        ("resids", np.array([6, 3, 4, 5, 0, 1, 2])),
+        ("segids", np.array([6, 0, 1, 2, 3, 4, 5])),
+        ("charges", np.array([6, 5, 4, 3, 2, 1, 0])),
+        ("masses", np.array([6, 5, 4, 3, 2, 1, 0])),
+        ("tempfactors", np.array([6, 5, 4, 3, 2, 1, 0])),
+    ]
+
+    @pytest.mark.parametrize("inputs, expected", test_data, ids=test_ids)
+    def test_sort(self, ag, inputs, expected):
+        agsort = ag.sort(inputs)
+        assert np.array_equal(expected, agsort.ix)
\ No newline at end of file

From 267a1b46f8643085eb248be8a689921782493a7d Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Mon, 29 Mar 2021 22:01:44 +0900
Subject: [PATCH 11/45] add my name to author list of changelog

---
 package/CHANGELOG | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/package/CHANGELOG b/package/CHANGELOG
index 7b109359889..d8b0b495b97 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -141,12 +141,7 @@ Enhancements
     'protein' selection (#2751 PR #2755)
   * Added an RDKit converter that works for any input with all hydrogens
     explicit in the topology (Issue #2468, PR #2775)
-<<<<<<< HEAD
-
-
-=======
   
->>>>>>> edit CHANGELOG
 Changes
   * TPRParser now loads TPR files with `tpr_resid_from_one=True` by default,
     which starts TPR resid indexing from 1 (instead of 0 as in 1.x) (Issue #2364, PR #3152)

From c6d048f8728b759516de2aeba561a66c043e8492 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Wed, 31 Mar 2021 15:36:58 +0900
Subject: [PATCH 12/45] Treat with multiple dimensional array

---
 package/MDAnalysis/core/groups.py | 27 +++++++++++++++++++++++----
 1 file changed, 23 insertions(+), 4 deletions(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 109aa92c9b8..97e9eebcefb 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3324,13 +3324,17 @@ def write(self, filename=None, file_format=None,
 
         raise ValueError("No writer found for format: {}".format(filename))
 
-    def sort(self, key='ix'):
-        """Return stably sorted Atomgroup by a key that specifies an attribute of atomgroup. The default key is "ix".
+    def sort(self, key='ix', keyfunc=None):
+        """Return stably sorted Atomgroup by a key that specifies
+           an attribute of atomgroup. The default key is "ix".
 
         Parameters
         ----------
-        keys: 
+        keys: str
             The name for attribute of Atomgroup. (e.g. "ids", "ix")
+        keyfunc: function
+            A function that returns 1 dimension array, a key for sorting the
+            atomgroup from multiple dimension array that the attribute returns.
 
         Returns
         -------
@@ -3359,7 +3363,22 @@ def sort(self, key='ix'):
         .. versionadded:: 2.0.0
         """
         idx = getattr(self.atoms, key)
-        order = np.argsort(idx, kind='stable')
+        if idx.ndim == 0:
+            return self.atoms
+        elif idx.ndim == 1:
+            order = np.argsort(idx, kind='stable')
+        else:
+            if keyfunc is None:
+                raise NameError("You have to assign the argument 'keyfunc' "
+                                "a proper function that returns 1D array "
+                                "as the attribute '{}' returns multiple "
+                                "dimension array.".format(key))
+            sortkeys = keyfunc(idx)
+            if sortkeys.ndim != 1:
+                raise ValueError("The function you assigned to the argument "
+                                 "'keyfunc':{} doesn't return 1D array."
+                                 .format(keyfunc))
+            order = np.argsort(sortkeys, kind='stable')
         agsorted = self.atoms[order]
         return agsorted
 

From 044a30255398e09b0431cdf92d114d78678a8fc6 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Wed, 31 Mar 2021 15:37:08 +0900
Subject: [PATCH 13/45] Add testsa for multiple dimensional array

---
 testsuite/MDAnalysisTests/core/test_atomgroup.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/testsuite/MDAnalysisTests/core/test_atomgroup.py b/testsuite/MDAnalysisTests/core/test_atomgroup.py
index efe136de390..c79e96e204c 100644
--- a/testsuite/MDAnalysisTests/core/test_atomgroup.py
+++ b/testsuite/MDAnalysisTests/core/test_atomgroup.py
@@ -1728,4 +1728,14 @@ def ag(self, universe):
     @pytest.mark.parametrize("inputs, expected", test_data, ids=test_ids)
     def test_sort(self, ag, inputs, expected):
         agsort = ag.sort(inputs)
-        assert np.array_equal(expected, agsort.ix)
\ No newline at end of file
+        assert np.array_equal(expected, agsort.ix)
+
+    def test_sort_position(self, ag):
+        ag.positions = (-np.arange(21)).reshape(7, 3)
+        with pytest.raises(ValueError):
+            ag.sort("positions", keyfunc=lambda x: x)
+        with pytest.raises(NameError):
+            ag.sort("positions")
+        ref = [6, 5, 4, 3, 2, 1, 0]
+        agsort = ag.sort("positions", keyfunc=lambda x: x[:, 1])
+        assert np.array_equal(ref, agsort.ix)
\ No newline at end of file

From a8b10b04698e1100c4cea170f4f7a534c6072359 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Thu, 1 Apr 2021 18:27:18 +0900
Subject: [PATCH 14/45] Check if number of atoms and idx have a same size.

---
 package/MDAnalysis/core/groups.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 97e9eebcefb..fee04205c10 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3363,6 +3363,10 @@ def sort(self, key='ix', keyfunc=None):
         .. versionadded:: 2.0.0
         """
         idx = getattr(self.atoms, key)
+        if len(idx) != len(self.atoms):
+            raise ValueError("The array returned by the attribute '{}' "
+                             "must have a same length as the number of "
+                             "atoms".format(key))
         if idx.ndim == 0:
             return self.atoms
         elif idx.ndim == 1:

From b6b9ab48263bd29aa44eda52c7fb720b98e082ae Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Thu, 1 Apr 2021 18:29:50 +0900
Subject: [PATCH 15/45] Add tests for non-number of atoms sized attributes

---
 testsuite/MDAnalysisTests/core/test_atomgroup.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/testsuite/MDAnalysisTests/core/test_atomgroup.py b/testsuite/MDAnalysisTests/core/test_atomgroup.py
index c79e96e204c..ec402ad3864 100644
--- a/testsuite/MDAnalysisTests/core/test_atomgroup.py
+++ b/testsuite/MDAnalysisTests/core/test_atomgroup.py
@@ -1732,6 +1732,8 @@ def test_sort(self, ag, inputs, expected):
 
     def test_sort_position(self, ag):
         ag.positions = (-np.arange(21)).reshape(7, 3)
+        with pytest.raises(ValueError):
+            ag.sort("angles")
         with pytest.raises(ValueError):
             ag.sort("positions", keyfunc=lambda x: x)
         with pytest.raises(NameError):

From 2a64457dc49cb41f9c1ae1e1131c2328f888a860 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Thu, 1 Apr 2021 18:31:11 +0900
Subject: [PATCH 16/45] Stop checking if idx is 0 dimension array

---
 package/MDAnalysis/core/groups.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index fee04205c10..61dbecc2263 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3367,11 +3367,9 @@ def sort(self, key='ix', keyfunc=None):
             raise ValueError("The array returned by the attribute '{}' "
                              "must have a same length as the number of "
                              "atoms".format(key))
-        if idx.ndim == 0:
-            return self.atoms
-        elif idx.ndim == 1:
+        if idx.ndim == 1:
             order = np.argsort(idx, kind='stable')
-        else:
+        elif idx.ndim > 1:
             if keyfunc is None:
                 raise NameError("You have to assign the argument 'keyfunc' "
                                 "a proper function that returns 1D array "

From c2e615a3938e90e8c1167ed1343e130f63a5bd08 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Fri, 2 Apr 2021 12:50:54 +0900
Subject: [PATCH 17/45] add pr number to CHANGELOG

---
 package/CHANGELOG | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package/CHANGELOG b/package/CHANGELOG
index d8b0b495b97..023047d9a08 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -89,7 +89,7 @@ Fixes
   * Fix syntax warning over comparison of literals using is (Issue #3066)
 
 Enhancements
-  * Added sort method to the atomgroup (Issue #2976) 
+  * Added sort method to the atomgroup (Issue #2976, PR #3188) 
   * Added a ValueError raised when not given a gridcenter while
     providing grid dimensions to DensityAnalysis, also added
     check for NaN in the input (Issue #3148, PR #3154)

From 06056e83a31489c5f4d4784583491e1c7fb77673 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Sun, 4 Apr 2021 19:06:44 +0900
Subject: [PATCH 18/45] Simplify an example in the docs

---
 package/MDAnalysis/core/groups.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 61dbecc2263..eacdf42a202 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3350,13 +3350,9 @@ def sort(self, key='ix', keyfunc=None):
             >>> from MDAnalysisTests.datafiles import PDB_small
             >>> u = mda.Universe(PDB_small)
             >>> ag = u.atoms[[3, 2, 1, 0]]
-            >>> ag.ids
-            array([4 3 2 1])
             >>> ag.ix
             array([3 2 1 0])
             >>> ag = ag.sort()
-            >>> ag.ids
-            array([1 2 3 4])
             >>> ag.ix
             array([0 1 2 3])
 

From 6cf90028ada1b17c209c28318e54a02a514a8b58 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Sun, 4 Apr 2021 19:43:29 +0900
Subject: [PATCH 19/45] Add description of kind in argsort

---
 package/MDAnalysis/core/groups.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index eacdf42a202..55d677040d3 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3356,6 +3356,10 @@ def sort(self, key='ix', keyfunc=None):
             >>> ag.ix
             array([0 1 2 3])
 
+        Note
+        ----
+        This sort is stable as it is implemented by `numpy.argsort(kind='stable')`.
+
         .. versionadded:: 2.0.0
         """
         idx = getattr(self.atoms, key)

From fa89e4bc499027d20d01d18923214ca0fdbd45f2 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Sun, 4 Apr 2021 19:45:17 +0900
Subject: [PATCH 20/45] removed unnecessary variable

---
 package/MDAnalysis/core/groups.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 55d677040d3..30206b3e39e 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3381,8 +3381,7 @@ def sort(self, key='ix', keyfunc=None):
                                  "'keyfunc':{} doesn't return 1D array."
                                  .format(keyfunc))
             order = np.argsort(sortkeys, kind='stable')
-        agsorted = self.atoms[order]
-        return agsorted
+        return self.atoms[order]
 
 
 class ResidueGroup(GroupBase):

From 5dceb3e069e85402ac115fb310e9f2886bbb0068 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Sun, 4 Apr 2021 19:45:59 +0900
Subject: [PATCH 21/45] pep8

---
 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 30206b3e39e..7b6f43c0a92 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3358,7 +3358,8 @@ def sort(self, key='ix', keyfunc=None):
 
         Note
         ----
-        This sort is stable as it is implemented by `numpy.argsort(kind='stable')`.
+        This sort is stable as it is implemented by
+        `numpy.argsort(kind='stable')`.
 
         .. versionadded:: 2.0.0
         """

From 88a5953e9bc761c1b24af84979127847a69c1465 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Sun, 4 Apr 2021 22:43:10 +0900
Subject: [PATCH 22/45] Add match arguments to pytest

---
 testsuite/MDAnalysisTests/core/test_atomgroup.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/testsuite/MDAnalysisTests/core/test_atomgroup.py b/testsuite/MDAnalysisTests/core/test_atomgroup.py
index ec402ad3864..0b8951f8ce6 100644
--- a/testsuite/MDAnalysisTests/core/test_atomgroup.py
+++ b/testsuite/MDAnalysisTests/core/test_atomgroup.py
@@ -1732,11 +1732,14 @@ def test_sort(self, ag, inputs, expected):
 
     def test_sort_position(self, ag):
         ag.positions = (-np.arange(21)).reshape(7, 3)
-        with pytest.raises(ValueError):
+        with pytest.raises(ValueError, match=r"The array returned by the"
+                           "attribute.*"):
             ag.sort("angles")
-        with pytest.raises(ValueError):
+        with pytest.raises(ValueError, match=r"The function you assigned"
+                           ".*"):
             ag.sort("positions", keyfunc=lambda x: x)
-        with pytest.raises(NameError):
+        with pytest.raises(NameError, match=r"You have to assign the argument"
+                           ".*"):
             ag.sort("positions")
         ref = [6, 5, 4, 3, 2, 1, 0]
         agsort = ag.sort("positions", keyfunc=lambda x: x[:, 1])

From a72c726287a79ad9a6cdd90f8e42748080e41c99 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Mon, 5 Apr 2021 09:21:09 +0900
Subject: [PATCH 23/45] fix tests that not worked

---
 testsuite/MDAnalysisTests/core/test_atomgroup.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/testsuite/MDAnalysisTests/core/test_atomgroup.py b/testsuite/MDAnalysisTests/core/test_atomgroup.py
index 0b8951f8ce6..612aacc7530 100644
--- a/testsuite/MDAnalysisTests/core/test_atomgroup.py
+++ b/testsuite/MDAnalysisTests/core/test_atomgroup.py
@@ -1698,6 +1698,7 @@ def universe(self):
 
         u.add_TopologyAttr('resid', [2, 1, 0])
         u.add_TopologyAttr('segid', [1, 0])
+        u.add_TopologyAttr('bonds', [(0,1)])
 
         return u
 
@@ -1732,9 +1733,9 @@ def test_sort(self, ag, inputs, expected):
 
     def test_sort_position(self, ag):
         ag.positions = (-np.arange(21)).reshape(7, 3)
-        with pytest.raises(ValueError, match=r"The array returned by the"
+        with pytest.raises(ValueError, match=r"The array returned by the "
                            "attribute.*"):
-            ag.sort("angles")
+            ag.sort("bonds")
         with pytest.raises(ValueError, match=r"The function you assigned"
                            ".*"):
             ag.sort("positions", keyfunc=lambda x: x)

From 54b096551e0416bb9d0b01ac6753e4a0d786a557 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Wed, 7 Apr 2021 12:43:02 +0900
Subject: [PATCH 24/45] pep8

---
 testsuite/MDAnalysisTests/core/test_atomgroup.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/testsuite/MDAnalysisTests/core/test_atomgroup.py b/testsuite/MDAnalysisTests/core/test_atomgroup.py
index 612aacc7530..c63736d1e5c 100644
--- a/testsuite/MDAnalysisTests/core/test_atomgroup.py
+++ b/testsuite/MDAnalysisTests/core/test_atomgroup.py
@@ -1698,7 +1698,7 @@ def universe(self):
 
         u.add_TopologyAttr('resid', [2, 1, 0])
         u.add_TopologyAttr('segid', [1, 0])
-        u.add_TopologyAttr('bonds', [(0,1)])
+        u.add_TopologyAttr('bonds', [(0, 1)])
 
         return u
 
@@ -1744,4 +1744,4 @@ def test_sort_position(self, ag):
             ag.sort("positions")
         ref = [6, 5, 4, 3, 2, 1, 0]
         agsort = ag.sort("positions", keyfunc=lambda x: x[:, 1])
-        assert np.array_equal(ref, agsort.ix)
\ No newline at end of file
+        assert np.array_equal(ref, agsort.ix)

From cc981ad14e5e50fc2a17a60249c9a59da2bfe6c6 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Wed, 7 Apr 2021 18:53:43 +0900
Subject: [PATCH 25/45] improve docs

---
 package/MDAnalysis/core/groups.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 7b6f43c0a92..c47230f3913 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3326,12 +3326,12 @@ def write(self, filename=None, file_format=None,
 
     def sort(self, key='ix', keyfunc=None):
         """Return stably sorted Atomgroup by a key that specifies
-           an attribute of atomgroup. The default key is "ix".
+           an attribute of atomgroup.
 
         Parameters
         ----------
         keys: str
-            The name for attribute of Atomgroup. (e.g. "ids", "ix")
+            The name for attribute of Atomgroup. (e.g. "ids", "ix". default="ix".)
         keyfunc: function
             A function that returns 1 dimension array, a key for sorting the
             atomgroup from multiple dimension array that the attribute returns.

From cf100fd7d14e6476805da659c8796eb9b08c14b8 Mon Sep 17 00:00:00 2001
From: 1ut <69892398+1ut@users.noreply.github.com>
Date: Thu, 8 Apr 2021 11:14:02 +0900
Subject: [PATCH 26/45] Update package/MDAnalysis/core/groups.py

Fix docs

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
---
 package/MDAnalysis/core/groups.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index c47230f3913..456fc19b08a 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3330,7 +3330,7 @@ def sort(self, key='ix', keyfunc=None):
 
         Parameters
         ----------
-        keys: str
+        key: str
             The name for attribute of Atomgroup. (e.g. "ids", "ix". default="ix".)
         keyfunc: function
             A function that returns 1 dimension array, a key for sorting the

From 53da2135042fb56fdcc77ef2c5cf5c0c6650feec Mon Sep 17 00:00:00 2001
From: 1ut <69892398+1ut@users.noreply.github.com>
Date: Thu, 8 Apr 2021 11:14:38 +0900
Subject: [PATCH 27/45] Update package/MDAnalysis/core/groups.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
---
 package/MDAnalysis/core/groups.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 456fc19b08a..a1122f7b0c3 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3331,7 +3331,7 @@ def sort(self, key='ix', keyfunc=None):
         Parameters
         ----------
         key: str
-            The name for attribute of Atomgroup. (e.g. "ids", "ix". default="ix".)
+            The name of the ``AtomGroup`` attribute to sort by (e.g. ``ids``, ``ix``. default=``ix``).
         keyfunc: function
             A function that returns 1 dimension array, a key for sorting the
             atomgroup from multiple dimension array that the attribute returns.

From baed6185d92e6d95618c007ac15d28a883a6ef26 Mon Sep 17 00:00:00 2001
From: 1ut <69892398+1ut@users.noreply.github.com>
Date: Thu, 8 Apr 2021 11:14:57 +0900
Subject: [PATCH 28/45] Update package/MDAnalysis/core/groups.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
---
 package/MDAnalysis/core/groups.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index a1122f7b0c3..6a93d1b4283 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3339,7 +3339,7 @@ def sort(self, key='ix', keyfunc=None):
         Returns
         -------
         output:
-            Sorted atomgroup.
+            Sorted ``AtomGroup``.
 
         Example
         -------

From b726fcc9299fc3b102eb95c071160aea8108ed23 Mon Sep 17 00:00:00 2001
From: 1ut <69892398+1ut@users.noreply.github.com>
Date: Thu, 8 Apr 2021 11:15:06 +0900
Subject: [PATCH 29/45] Update package/MDAnalysis/core/groups.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
---
 package/MDAnalysis/core/groups.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 6a93d1b4283..9e81ad7f394 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3358,7 +3358,7 @@ def sort(self, key='ix', keyfunc=None):
 
         Note
         ----
-        This sort is stable as it is implemented by
+        This uses a stable sort as implemented by
         `numpy.argsort(kind='stable')`.
 
         .. versionadded:: 2.0.0

From 65171187b4ee4f7152aa8cda2c24156f774fc706 Mon Sep 17 00:00:00 2001
From: 1ut <69892398+1ut@users.noreply.github.com>
Date: Thu, 8 Apr 2021 11:16:05 +0900
Subject: [PATCH 30/45] Update package/MDAnalysis/core/groups.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
---
 package/MDAnalysis/core/groups.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 9e81ad7f394..b434d041c45 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3325,8 +3325,8 @@ def write(self, filename=None, file_format=None,
         raise ValueError("No writer found for format: {}".format(filename))
 
     def sort(self, key='ix', keyfunc=None):
-        """Return stably sorted Atomgroup by a key that specifies
-           an attribute of atomgroup.
+        """Returns a sorted ``AtomGroup`` using a specified attribute as
+           the key.
 
         Parameters
         ----------

From 6925454bbb873d20b8e19cb39b85817f92014ec6 Mon Sep 17 00:00:00 2001
From: 1ut <69892398+1ut@users.noreply.github.com>
Date: Thu, 8 Apr 2021 11:16:47 +0900
Subject: [PATCH 31/45] Update package/MDAnalysis/core/groups.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
---
 package/MDAnalysis/core/groups.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index b434d041c45..050a0fa7d1a 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3333,8 +3333,11 @@ def sort(self, key='ix', keyfunc=None):
         key: str
             The name of the ``AtomGroup`` attribute to sort by (e.g. ``ids``, ``ix``. default=``ix``).
         keyfunc: function
-            A function that returns 1 dimension array, a key for sorting the
-            atomgroup from multiple dimension array that the attribute returns.
+            A function to convert multidimensional arrays to a single
+            dimension. This 1D array will be used as the sort key and
+            is required when sorting with an ``AtomGroup`` attribute
+            key which has multiple dimensions. Note: this argument
+            is ignored when the attribute is one dimensional.
 
         Returns
         -------

From d367b5c5d928b9b11e2d728aeffbeb00f8ae9879 Mon Sep 17 00:00:00 2001
From: 1ut <69892398+1ut@users.noreply.github.com>
Date: Thu, 8 Apr 2021 11:18:08 +0900
Subject: [PATCH 32/45] Update package/MDAnalysis/core/groups.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
---
 package/MDAnalysis/core/groups.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 050a0fa7d1a..d82a3f7caa8 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3369,8 +3369,8 @@ def sort(self, key='ix', keyfunc=None):
         idx = getattr(self.atoms, key)
         if len(idx) != len(self.atoms):
             raise ValueError("The array returned by the attribute '{}' "
-                             "must have a same length as the number of "
-                             "atoms".format(key))
+                             "must have the same length as the number of "
+                             "atoms in the input AtomGroup".format(key))
         if idx.ndim == 1:
             order = np.argsort(idx, kind='stable')
         elif idx.ndim > 1:

From bdd391c384e45bc0ac1afb29bb1ee5831d67e0c4 Mon Sep 17 00:00:00 2001
From: 1ut <69892398+1ut@users.noreply.github.com>
Date: Thu, 8 Apr 2021 11:18:20 +0900
Subject: [PATCH 33/45] Update package/MDAnalysis/core/groups.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
---
 package/MDAnalysis/core/groups.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index d82a3f7caa8..d28e246bc2b 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3381,7 +3381,7 @@ def sort(self, key='ix', keyfunc=None):
                                 "dimension array.".format(key))
             sortkeys = keyfunc(idx)
             if sortkeys.ndim != 1:
-                raise ValueError("The function you assigned to the argument "
+                raise ValueError("The function assigned to the argument "
                                  "'keyfunc':{} doesn't return 1D array."
                                  .format(keyfunc))
             order = np.argsort(sortkeys, kind='stable')

From e0bef58681c2fba19490ceb1d964740f60518e2d Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Thu, 8 Apr 2021 11:22:41 +0900
Subject: [PATCH 34/45] Fix error message

---
 package/MDAnalysis/core/groups.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 9e81ad7f394..51e87b5696f 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3372,10 +3372,11 @@ def sort(self, key='ix', keyfunc=None):
             order = np.argsort(idx, kind='stable')
         elif idx.ndim > 1:
             if keyfunc is None:
-                raise NameError("You have to assign the argument 'keyfunc' "
-                                "a proper function that returns 1D array "
-                                "as the attribute '{}' returns multiple "
-                                "dimension array.".format(key))
+                raise NameError("The {} attribute returns a multidimensional "
+                                "array. In order to sort it, a function "
+                                "returning a 1D array (to be used as the sort "
+                                "key) must be passed to the keyfunc argument"
+                                .format(key))
             sortkeys = keyfunc(idx)
             if sortkeys.ndim != 1:
                 raise ValueError("The function you assigned to the argument "

From 52b677a50c2977a0df07f40ba462c230f01974fb Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Thu, 8 Apr 2021 11:41:40 +0900
Subject: [PATCH 35/45] separate tests

---
 testsuite/MDAnalysisTests/core/test_atomgroup.py | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/testsuite/MDAnalysisTests/core/test_atomgroup.py b/testsuite/MDAnalysisTests/core/test_atomgroup.py
index c63736d1e5c..6356687a35c 100644
--- a/testsuite/MDAnalysisTests/core/test_atomgroup.py
+++ b/testsuite/MDAnalysisTests/core/test_atomgroup.py
@@ -1704,7 +1704,9 @@ def universe(self):
 
     @pytest.fixture()
     def ag(self, universe):
-        return universe.atoms
+        ag = universe.atoms
+        ag.positions = (-np.arange(21)).reshape(7, 3)
+        return ag
 
     test_ids = [
        "ix",
@@ -1731,17 +1733,22 @@ def test_sort(self, ag, inputs, expected):
         agsort = ag.sort(inputs)
         assert np.array_equal(expected, agsort.ix)
 
-    def test_sort_position(self, ag):
-        ag.positions = (-np.arange(21)).reshape(7, 3)
+    def test_sort_bonds(self, ag):
         with pytest.raises(ValueError, match=r"The array returned by the "
                            "attribute.*"):
             ag.sort("bonds")
+
+    def test_sort_positions_2D(self, ag):
         with pytest.raises(ValueError, match=r"The function you assigned"
                            ".*"):
             ag.sort("positions", keyfunc=lambda x: x)
+
+    def test_sort_position_no_keyfunc(self, ag):
         with pytest.raises(NameError, match=r"You have to assign the argument"
                            ".*"):
             ag.sort("positions")
+
+    def test_sort_position(self, ag):
         ref = [6, 5, 4, 3, 2, 1, 0]
         agsort = ag.sort("positions", keyfunc=lambda x: x[:, 1])
         assert np.array_equal(ref, agsort.ix)

From 338417e2ea1c71d908d22037412a8d7d5c014b72 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Thu, 8 Apr 2021 11:49:30 +0900
Subject: [PATCH 36/45] FIx error messages

---
 testsuite/MDAnalysisTests/core/test_atomgroup.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/testsuite/MDAnalysisTests/core/test_atomgroup.py b/testsuite/MDAnalysisTests/core/test_atomgroup.py
index 6356687a35c..eabb89ad9b7 100644
--- a/testsuite/MDAnalysisTests/core/test_atomgroup.py
+++ b/testsuite/MDAnalysisTests/core/test_atomgroup.py
@@ -1739,12 +1739,13 @@ def test_sort_bonds(self, ag):
             ag.sort("bonds")
 
     def test_sort_positions_2D(self, ag):
-        with pytest.raises(ValueError, match=r"The function you assigned"
+        with pytest.raises(ValueError, match=r"The function assigned to"
                            ".*"):
             ag.sort("positions", keyfunc=lambda x: x)
 
     def test_sort_position_no_keyfunc(self, ag):
-        with pytest.raises(NameError, match=r"You have to assign the argument"
+        with pytest.raises(NameError, match=r"The .* attribute returns a "
+                           "multidimensional array. In order to sort it, "
                            ".*"):
             ag.sort("positions")
 

From 170ce403a5a5eceed97e1d2086c3ed7b338126ac Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Thu, 8 Apr 2021 13:30:39 +0900
Subject: [PATCH 37/45] pep8

---
 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 9934d15ef70..f479e91d712 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3331,7 +3331,8 @@ def sort(self, key='ix', keyfunc=None):
         Parameters
         ----------
         key: str
-            The name of the ``AtomGroup`` attribute to sort by (e.g. ``ids``, ``ix``. default=``ix``).
+            The name of the ``AtomGroup`` attribute to sort by (e.g. ``ids``,
+            ``ix``. default=``ix``).
         keyfunc: function
             A function to convert multidimensional arrays to a single
             dimension. This 1D array will be used as the sort key and

From 072b15908a9537766f77c630b5357a24c8c32730 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Thu, 8 Apr 2021 13:53:01 +0900
Subject: [PATCH 38/45] Add example in the docs

---
 package/MDAnalysis/core/groups.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index f479e91d712..05c3c40a256 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3359,6 +3359,17 @@ def sort(self, key='ix', keyfunc=None):
             >>> ag = ag.sort()
             >>> ag.ix
             array([0 1 2 3])
+            >>> ag.positions
+            array([[-11.921,  26.307,  10.41 ],
+                   [-11.447,  26.741,   9.595],
+                   [-12.44 ,  27.042,  10.926],
+                   [-12.632,  25.619,  10.046]], dtype=float32)
+            >>> ag = ag.sort("positions", lambda x: x[:, 1])
+            >>> ag.positions
+            array([[-12.632,  25.619,  10.046],
+                   [-11.921,  26.307,  10.41 ],
+                   [-11.447,  26.741,   9.595],
+                   [-12.44 ,  27.042,  10.926]], dtype=float32)
 
         Note
         ----

From 18d36eedeaf8fe62f70ce494009138953b5aa004 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Thu, 8 Apr 2021 15:53:35 +0900
Subject: [PATCH 39/45] edit docs

---
 package/MDAnalysis/core/groups.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 05c3c40a256..18667058889 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3325,15 +3325,15 @@ def write(self, filename=None, file_format=None,
         raise ValueError("No writer found for format: {}".format(filename))
 
     def sort(self, key='ix', keyfunc=None):
-        """Returns a sorted ``AtomGroup`` using a specified attribute as
+        """Returns a sorted ``AtomGroup`` using a specified attribute as \
            the key.
 
         Parameters
         ----------
-        key: str
+        key: str, optional
             The name of the ``AtomGroup`` attribute to sort by (e.g. ``ids``,
-            ``ix``. default=``ix``).
-        keyfunc: function
+            ``ix``. default= ``ix`` ).
+        keyfunc: callable, optional
             A function to convert multidimensional arrays to a single
             dimension. This 1D array will be used as the sort key and
             is required when sorting with an ``AtomGroup`` attribute

From 1e9d9e4c52debf4087193b182cff99bf163793a3 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Thu, 8 Apr 2021 16:22:56 +0900
Subject: [PATCH 40/45] edit docs

---
 package/MDAnalysis/core/groups.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 18667058889..49fc8c954a5 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3341,12 +3341,12 @@ def sort(self, key='ix', keyfunc=None):
             is ignored when the attribute is one dimensional.
 
         Returns
-        -------
-        output:
+        ----------
+        Group
             Sorted ``AtomGroup``.
 
         Example
-        -------
+        ----------
 
         .. code-block:: python
 
@@ -3372,7 +3372,7 @@ def sort(self, key='ix', keyfunc=None):
                    [-12.44 ,  27.042,  10.926]], dtype=float32)
 
         Note
-        ----
+        ----------
         This uses a stable sort as implemented by
         `numpy.argsort(kind='stable')`.
 

From 325a3d9655889201c95dea4099a4c24b4e7472ec Mon Sep 17 00:00:00 2001
From: 1ut <69892398+1ut@users.noreply.github.com>
Date: Fri, 9 Apr 2021 18:44:18 +0900
Subject: [PATCH 41/45] Update package/MDAnalysis/core/groups.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
---
 package/MDAnalysis/core/groups.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 49fc8c954a5..b147853535e 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3342,7 +3342,7 @@ def sort(self, key='ix', keyfunc=None):
 
         Returns
         ----------
-        Group
+        :class:`AtomGroup`
             Sorted ``AtomGroup``.
 
         Example

From 1de2d9748893fd759903f52dadbd0659bc3a4ab1 Mon Sep 17 00:00:00 2001
From: 1ut <69892398+1ut@users.noreply.github.com>
Date: Fri, 9 Apr 2021 18:44:30 +0900
Subject: [PATCH 42/45] Update package/MDAnalysis/core/groups.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
---
 package/MDAnalysis/core/groups.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index b147853535e..5fbe511a762 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3376,6 +3376,7 @@ def sort(self, key='ix', keyfunc=None):
         This uses a stable sort as implemented by
         `numpy.argsort(kind='stable')`.
 
+
         .. versionadded:: 2.0.0
         """
         idx = getattr(self.atoms, key)

From 705cdd72f21fb8a340e029582d424bdd5d6f5846 Mon Sep 17 00:00:00 2001
From: 1ut <69892398+1ut@users.noreply.github.com>
Date: Fri, 9 Apr 2021 18:44:38 +0900
Subject: [PATCH 43/45] Update package/MDAnalysis/core/groups.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
---
 package/MDAnalysis/core/groups.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 5fbe511a762..7d057151cc8 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3396,7 +3396,7 @@ def sort(self, key='ix', keyfunc=None):
             sortkeys = keyfunc(idx)
             if sortkeys.ndim != 1:
                 raise ValueError("The function assigned to the argument "
-                                 "'keyfunc':{} doesn't return 1D array."
+                                 "'keyfunc':{} doesn't return a 1D array."
                                  .format(keyfunc))
             order = np.argsort(sortkeys, kind='stable')
         return self.atoms[order]

From 33776558e9dc6ce659dfc57537d98aeb80209ea7 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Fri, 9 Apr 2021 18:49:40 +0900
Subject: [PATCH 44/45] Unecessary \

---
 package/MDAnalysis/core/groups.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 7d057151cc8..53e9e8529b6 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -3325,8 +3325,8 @@ def write(self, filename=None, file_format=None,
         raise ValueError("No writer found for format: {}".format(filename))
 
     def sort(self, key='ix', keyfunc=None):
-        """Returns a sorted ``AtomGroup`` using a specified attribute as \
-           the key.
+        """
+        Returns a sorted ``AtomGroup`` using a specified attribute as the key.
 
         Parameters
         ----------

From c2f734260ee05bd387572144b5a0a15463cf53e0 Mon Sep 17 00:00:00 2001
From: 1ut <kosukex910@gmail.com>
Date: Fri, 9 Apr 2021 18:54:42 +0900
Subject: [PATCH 45/45] remove unnecessary .*

---
 testsuite/MDAnalysisTests/core/test_atomgroup.py | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/testsuite/MDAnalysisTests/core/test_atomgroup.py b/testsuite/MDAnalysisTests/core/test_atomgroup.py
index eabb89ad9b7..a719ccdfbb5 100644
--- a/testsuite/MDAnalysisTests/core/test_atomgroup.py
+++ b/testsuite/MDAnalysisTests/core/test_atomgroup.py
@@ -1735,18 +1735,16 @@ def test_sort(self, ag, inputs, expected):
 
     def test_sort_bonds(self, ag):
         with pytest.raises(ValueError, match=r"The array returned by the "
-                           "attribute.*"):
+                           "attribute"):
             ag.sort("bonds")
 
     def test_sort_positions_2D(self, ag):
-        with pytest.raises(ValueError, match=r"The function assigned to"
-                           ".*"):
+        with pytest.raises(ValueError, match=r"The function assigned to"):
             ag.sort("positions", keyfunc=lambda x: x)
 
     def test_sort_position_no_keyfunc(self, ag):
         with pytest.raises(NameError, match=r"The .* attribute returns a "
-                           "multidimensional array. In order to sort it, "
-                           ".*"):
+                           "multidimensional array. In order to sort it, "):
             ag.sort("positions")
 
     def test_sort_position(self, ag):