From 7e2499c770db6ab6579e96374e5241afcf461560 Mon Sep 17 00:00:00 2001
From: francescalb <francesca.l.bleken@sintef.no>
Date: Wed, 29 Sep 2021 11:35:05 +0200
Subject: [PATCH 01/16] Added __hash__ and __eq__ to ontology.Ontology

---
 ontopy/ontology.py | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/ontopy/ontology.py b/ontopy/ontology.py
index 59403090e..96703a739 100644
--- a/ontopy/ontology.py
+++ b/ontopy/ontology.py
@@ -190,6 +190,26 @@ def __objclass__(self):
         # Play nice with inspect...
         pass
 
+    def __eq__(self, other):
+        return self.__hash__() == other.__hash__()
+
+    def __str__(self):
+        """TODO"""
+
+    def __iter__(self):
+        """TODO"""
+
+    def __delitem__(self):
+        """TODO"""
+
+    def __setitem__(self, key, value):
+        """ MAYBE TODO """
+        # self[key] = value
+        # emmo['HAtom'] = emmo.Atom
+
+    def __hash__(self):
+        return hash((self.base_iri, self.get_entities()))
+
     def get_by_label(self, label, label_annotations=None, namespace=None):
         """Returns entity with label annotation `label`.
 

From 7e6ab17633dc2182d58656a4251065883d67b90a Mon Sep 17 00:00:00 2001
From: francescalb <francesca.l.bleken@sintef.no>
Date: Wed, 29 Sep 2021 22:56:09 +0200
Subject: [PATCH 02/16] Sorting emmo classes with iris does not work. checkout

---
 ontopy/ontology.py | 15 +++++++++++++--
 ontopy/patch.py    | 17 +++++++++++++++--
 2 files changed, 28 insertions(+), 4 deletions(-)

diff --git a/ontopy/ontology.py b/ontopy/ontology.py
index 96703a739..4b4fd1b36 100644
--- a/ontopy/ontology.py
+++ b/ontopy/ontology.py
@@ -112,6 +112,9 @@ def get_ontology(self, base_iri='emmo-inferred'):
 
         return onto
 
+    def __hash__(self):
+        return hash(self.filename)
+
 
 class Ontology(owlready2.Ontology, OntoGraph):
     """A generic class extending owlready2.Ontology.
@@ -191,7 +194,7 @@ def __objclass__(self):
         pass
 
     def __eq__(self, other):
-        return self.__hash__() == other.__hash__()
+        return hash(self) == hash(other)
 
     def __str__(self):
         """TODO"""
@@ -208,7 +211,15 @@ def __setitem__(self, key, value):
         # emmo['HAtom'] = emmo.Atom
 
     def __hash__(self):
-        return hash((self.base_iri, self.get_entities()))
+        sorted_entities = sorted(
+            self.get_entities(imported=True,
+                              classes=True,
+                              individuals=False,
+                              object_properties=False,
+                              data_properties=False,
+                              annotation_properties=False,
+                             ), key=lambda e: e.name)
+        return hash((self.base_iri, tuple(sorted_entities)))
 
     def get_by_label(self, label, label_annotations=None, namespace=None):
         """Returns entity with label annotation `label`.
diff --git a/ontopy/patch.py b/ontopy/patch.py
index eeb1cae93..1e300cd30 100644
--- a/ontopy/patch.py
+++ b/ontopy/patch.py
@@ -3,7 +3,7 @@
 import types
 
 import owlready2
-from owlready2 import ThingClass, PropertyClass, Thing, Restriction, Namespace
+from owlready2 import ThingClass, PropertyClass, Thing, Restriction, Namespace, EntityClass
 from owlready2 import Metadata
 
 
@@ -67,6 +67,16 @@ def _dir(self):
     s.update(props)
     return sorted(s)
 
+def _hash(self):
+    """Define hash of ThingClass and PropertyClass."""
+    try:
+        return hash(self.iri)
+    except AttributeError:
+        return hash(self.name)
+
+def _eq(self, other):
+    """Define equality based on hash for ThingClass and PropertyClass."""
+    return hash(self) == hash(other)
 
 def get_class_annotations(self, all=False, imported=True):
     """Returns a dict with non-empty annotations.
@@ -121,6 +131,8 @@ def get_indirect_is_a(self, skip_classes=True):
 
 # Inject methods into ThingClass
 setattr(ThingClass, '__dir__', _dir)
+setattr(ThingClass, '__hash__', _hash)
+setattr(ThingClass, '__eq__', _eq)
 setattr(ThingClass, 'get_preferred_label', get_preferred_label)
 setattr(ThingClass, 'get_parents', get_parents)
 setattr(ThingClass, 'get_annotations', get_class_annotations)
@@ -147,7 +159,8 @@ def get_property_annotations(self, all=False, imported=True):
     else:
         return {k: v for k, v in d.items() if v}
 
-
+setattr(PropertyClass, '__hash__', _hash)
+#setattr(PropertyClass, '__eq__', _eq)
 setattr(PropertyClass, 'get_preferred_label', get_preferred_label)
 setattr(PropertyClass, 'get_parents', get_parents)
 setattr(PropertyClass, 'get_annotations', get_property_annotations)

From 180a05aca73b167f110e0ed193e472e92a2a1eef Mon Sep 17 00:00:00 2001
From: francescalb <francesca.l.bleken@sintef.no>
Date: Thu, 30 Sep 2021 08:21:46 +0200
Subject: [PATCH 03/16] Added test for ontology equality

---
 tests/test_load_emmo.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/tests/test_load_emmo.py b/tests/test_load_emmo.py
index 226c1bd56..4e9b74f00 100644
--- a/tests/test_load_emmo.py
+++ b/tests/test_load_emmo.py
@@ -12,5 +12,10 @@ def test_load_emmo() -> None:
     assert EMMO_inferred
     assert EMMO
 
-    assert EMMO_inferred.base_iri == get_emmo(None).base_iri
+    assert EMMO_inferred == get_emmo(None)
+    assert EMMO != EMMO_inferred
+
+    EMMO_inferred.new_entity('HydrogenAtom', EMMO_inferred.Atom)
+    EMMO_inferred.sync_attributes()
+    #assert EMMO_inferred != get_emmo(None)
 

From 475683d32488713975ee27e8a08aea11d0b73cb7 Mon Sep 17 00:00:00 2001
From: francescalb <francesca.l.bleken@sintef.no>
Date: Thu, 30 Sep 2021 18:03:19 +0200
Subject: [PATCH 04/16] Creating hash and testing ontology equality

It now works, but only when the test includes checking for classes
and base_iri of the ontology. The test does not include properties.
---
 ontopy/ontology.py      | 7 ++++++-
 tests/test_load_emmo.py | 2 +-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/ontopy/ontology.py b/ontopy/ontology.py
index 4b4fd1b36..28b33335e 100644
--- a/ontopy/ontology.py
+++ b/ontopy/ontology.py
@@ -211,6 +211,11 @@ def __setitem__(self, key, value):
         # emmo['HAtom'] = emmo.Atom
 
     def __hash__(self):
+        """Returns hash.
+
+        Note that entities must have iris for this to work, since entities are
+        sorted by their iris before creating the hash.
+        """
         sorted_entities = sorted(
             self.get_entities(imported=True,
                               classes=True,
@@ -218,7 +223,7 @@ def __hash__(self):
                               object_properties=False,
                               data_properties=False,
                               annotation_properties=False,
-                             ), key=lambda e: e.name)
+                             ), key=lambda e: e.iri)
         return hash((self.base_iri, tuple(sorted_entities)))
 
     def get_by_label(self, label, label_annotations=None, namespace=None):
diff --git a/tests/test_load_emmo.py b/tests/test_load_emmo.py
index 4e9b74f00..3a1384577 100644
--- a/tests/test_load_emmo.py
+++ b/tests/test_load_emmo.py
@@ -17,5 +17,5 @@ def test_load_emmo() -> None:
 
     EMMO_inferred.new_entity('HydrogenAtom', EMMO_inferred.Atom)
     EMMO_inferred.sync_attributes()
-    #assert EMMO_inferred != get_emmo(None)
+    assert EMMO_inferred != get_emmo(None)
 

From 3b6585e3dc8dec13d7b8bb6e48d973fbceadbafa Mon Sep 17 00:00:00 2001
From: francescalb <francesca.l.bleken@sintef.no>
Date: Thu, 30 Sep 2021 18:29:35 +0200
Subject: [PATCH 05/16] Extended possibilities for ThingClass hash

Preffered is hash on iri, second, try prefLabel, third try name
fourth try label
---
 ontopy/ontology.py      |  2 +-
 ontopy/patch.py         | 16 +++++++++++++---
 tests/test_load_emmo.py |  1 -
 3 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/ontopy/ontology.py b/ontopy/ontology.py
index 28b33335e..fea7f5660 100644
--- a/ontopy/ontology.py
+++ b/ontopy/ontology.py
@@ -223,7 +223,7 @@ def __hash__(self):
                               object_properties=False,
                               data_properties=False,
                               annotation_properties=False,
-                             ), key=lambda e: e.iri)
+                              ), key=lambda e: e.iri)
         return hash((self.base_iri, tuple(sorted_entities)))
 
     def get_by_label(self, label, label_annotations=None, namespace=None):
diff --git a/ontopy/patch.py b/ontopy/patch.py
index 1e300cd30..1d448c4a7 100644
--- a/ontopy/patch.py
+++ b/ontopy/patch.py
@@ -3,7 +3,7 @@
 import types
 
 import owlready2
-from owlready2 import ThingClass, PropertyClass, Thing, Restriction, Namespace, EntityClass
+from owlready2 import ThingClass, PropertyClass, Thing, Restriction, Namespace
 from owlready2 import Metadata
 
 
@@ -67,17 +67,26 @@ def _dir(self):
     s.update(props)
     return sorted(s)
 
+
 def _hash(self):
     """Define hash of ThingClass and PropertyClass."""
     try:
         return hash(self.iri)
     except AttributeError:
-        return hash(self.name)
+        try:
+            return hash(self.prefLabel)
+        except AttributeError:
+            try:
+                return hash(self.name)
+            except AttributeError:
+                return hash(self.label)
+
 
 def _eq(self, other):
     """Define equality based on hash for ThingClass and PropertyClass."""
     return hash(self) == hash(other)
 
+
 def get_class_annotations(self, all=False, imported=True):
     """Returns a dict with non-empty annotations.
 
@@ -159,8 +168,9 @@ def get_property_annotations(self, all=False, imported=True):
     else:
         return {k: v for k, v in d.items() if v}
 
+
 setattr(PropertyClass, '__hash__', _hash)
-#setattr(PropertyClass, '__eq__', _eq)
+# setattr(PropertyClass, '__eq__', _eq)
 setattr(PropertyClass, 'get_preferred_label', get_preferred_label)
 setattr(PropertyClass, 'get_parents', get_parents)
 setattr(PropertyClass, 'get_annotations', get_property_annotations)
diff --git a/tests/test_load_emmo.py b/tests/test_load_emmo.py
index 3a1384577..77c7e5324 100644
--- a/tests/test_load_emmo.py
+++ b/tests/test_load_emmo.py
@@ -18,4 +18,3 @@ def test_load_emmo() -> None:
     EMMO_inferred.new_entity('HydrogenAtom', EMMO_inferred.Atom)
     EMMO_inferred.sync_attributes()
     assert EMMO_inferred != get_emmo(None)
-

From d2ad9160d8751880cd3c3e54c4b5a457e71c333d Mon Sep 17 00:00:00 2001
From: francescalb <francesca.l.bleken@sintef.no>
Date: Mon, 25 Oct 2021 13:03:46 +0200
Subject: [PATCH 06/16] Only hash on iri for ThingClass in hash, and ontology
 hash including everything except annotation_properties and Individuals

---
 ontopy/ontology.py |  4 ++--
 ontopy/patch.py    | 12 +-----------
 2 files changed, 3 insertions(+), 13 deletions(-)

diff --git a/ontopy/ontology.py b/ontopy/ontology.py
index fea7f5660..944a3fd28 100644
--- a/ontopy/ontology.py
+++ b/ontopy/ontology.py
@@ -220,8 +220,8 @@ def __hash__(self):
             self.get_entities(imported=True,
                               classes=True,
                               individuals=False,
-                              object_properties=False,
-                              data_properties=False,
+                              object_properties=True,
+                              data_properties=True,
                               annotation_properties=False,
                               ), key=lambda e: e.iri)
         return hash((self.base_iri, tuple(sorted_entities)))
diff --git a/ontopy/patch.py b/ontopy/patch.py
index 1d448c4a7..72890d432 100644
--- a/ontopy/patch.py
+++ b/ontopy/patch.py
@@ -70,17 +70,7 @@ def _dir(self):
 
 def _hash(self):
     """Define hash of ThingClass and PropertyClass."""
-    try:
-        return hash(self.iri)
-    except AttributeError:
-        try:
-            return hash(self.prefLabel)
-        except AttributeError:
-            try:
-                return hash(self.name)
-            except AttributeError:
-                return hash(self.label)
-
+    return hash(self.iri)
 
 def _eq(self, other):
     """Define equality based on hash for ThingClass and PropertyClass."""

From 63513fe917abf421048576c7120621e5fe29ae5d Mon Sep 17 00:00:00 2001
From: francescalb <francesca.l.bleken@sintef.no>
Date: Wed, 29 Sep 2021 22:56:09 +0200
Subject: [PATCH 07/16] Sorting emmo classes with iris does not work.

---
 ontopy/patch.py | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/ontopy/patch.py b/ontopy/patch.py
index 72890d432..007d4e551 100644
--- a/ontopy/patch.py
+++ b/ontopy/patch.py
@@ -3,7 +3,7 @@
 import types
 
 import owlready2
-from owlready2 import ThingClass, PropertyClass, Thing, Restriction, Namespace
+from owlready2 import ThingClass, PropertyClass, Thing, Restriction, Namespace, EntityClass
 from owlready2 import Metadata
 
 
@@ -67,6 +67,16 @@ def _dir(self):
     s.update(props)
     return sorted(s)
 
+def _hash(self):
+    """Define hash of ThingClass and PropertyClass."""
+    try:
+        return hash(self.iri)
+    except AttributeError:
+        return hash(self.name)
+
+def _eq(self, other):
+    """Define equality based on hash for ThingClass and PropertyClass."""
+    return hash(self) == hash(other)
 
 def _hash(self):
     """Define hash of ThingClass and PropertyClass."""
@@ -158,7 +168,6 @@ def get_property_annotations(self, all=False, imported=True):
     else:
         return {k: v for k, v in d.items() if v}
 
-
 setattr(PropertyClass, '__hash__', _hash)
 # setattr(PropertyClass, '__eq__', _eq)
 setattr(PropertyClass, 'get_preferred_label', get_preferred_label)

From 3fa0e529fcccc1f707c8473a68f12f6cac56f0a7 Mon Sep 17 00:00:00 2001
From: francescalb <francesca.l.bleken@sintef.no>
Date: Thu, 30 Sep 2021 18:29:35 +0200
Subject: [PATCH 08/16] Only use iri for calculating the hash

---
 ontopy/patch.py | 14 +++-----------
 1 file changed, 3 insertions(+), 11 deletions(-)

diff --git a/ontopy/patch.py b/ontopy/patch.py
index 007d4e551..836c89fa4 100644
--- a/ontopy/patch.py
+++ b/ontopy/patch.py
@@ -3,7 +3,7 @@
 import types
 
 import owlready2
-from owlready2 import ThingClass, PropertyClass, Thing, Restriction, Namespace, EntityClass
+from owlready2 import ThingClass, PropertyClass, Thing, Restriction, Namespace
 from owlready2 import Metadata
 
 
@@ -67,21 +67,12 @@ def _dir(self):
     s.update(props)
     return sorted(s)
 
-def _hash(self):
-    """Define hash of ThingClass and PropertyClass."""
-    try:
-        return hash(self.iri)
-    except AttributeError:
-        return hash(self.name)
-
-def _eq(self, other):
-    """Define equality based on hash for ThingClass and PropertyClass."""
-    return hash(self) == hash(other)
 
 def _hash(self):
     """Define hash of ThingClass and PropertyClass."""
     return hash(self.iri)
 
+
 def _eq(self, other):
     """Define equality based on hash for ThingClass and PropertyClass."""
     return hash(self) == hash(other)
@@ -168,6 +159,7 @@ def get_property_annotations(self, all=False, imported=True):
     else:
         return {k: v for k, v in d.items() if v}
 
+
 setattr(PropertyClass, '__hash__', _hash)
 # setattr(PropertyClass, '__eq__', _eq)
 setattr(PropertyClass, 'get_preferred_label', get_preferred_label)

From 4b08fa6ea8fd0315ebfe7f4828c1e446b2651e9f Mon Sep 17 00:00:00 2001
From: francescalb <francesca.l.bleken@sintef.no>
Date: Mon, 25 Oct 2021 22:56:34 +0200
Subject: [PATCH 09/16] Added __eq__ in Ontology based on triples

Note that consistency of blank nodes is not checked.
---
 ontopy/ontology.py | 64 ++++++++++++++++++++++++----------------------
 ontopy/patch.py    | 14 ----------
 2 files changed, 34 insertions(+), 44 deletions(-)

diff --git a/ontopy/ontology.py b/ontopy/ontology.py
index 944a3fd28..6dabebabe 100644
--- a/ontopy/ontology.py
+++ b/ontopy/ontology.py
@@ -112,9 +112,6 @@ def get_ontology(self, base_iri='emmo-inferred'):
 
         return onto
 
-    def __hash__(self):
-        return hash(self.filename)
-
 
 class Ontology(owlready2.Ontology, OntoGraph):
     """A generic class extending owlready2.Ontology.
@@ -193,38 +190,45 @@ def __objclass__(self):
         # Play nice with inspect...
         pass
 
-    def __eq__(self, other):
-        return hash(self) == hash(other)
-
-    def __str__(self):
-        """TODO"""
-
-    def __iter__(self):
-        """TODO"""
+    def __hash__(self):
+        """ Returns hash based on base_iri
+        This is done to keep Ontology hashable when defining __eq__.
+        """
+        return hash(self.base_iri)
 
-    def __delitem__(self):
-        """TODO"""
+    def __eq__(self, other):
+        """Checks if this ontology is equal to other.
 
-    def __setitem__(self, key, value):
-        """ MAYBE TODO """
-        # self[key] = value
-        # emmo['HAtom'] = emmo.Atom
+        Equality of all triples obtained from self.get_triples(),
+        i.e. all triples except blank nodes.
+        """
+        return set(self.get_triples()) == set(other.get_triples())
 
-    def __hash__(self):
-        """Returns hash.
+    def _sorted_entities(self):
+        """Return sorted entities
+        """
+        return sorted(e.iri for e in self.get_entities(
+                imported=True, classes=True,
+                individuals=True, object_properties=True,
+                data_properties=True, annotation_properties=True))
 
-        Note that entities must have iris for this to work, since entities are
-        sorted by their iris before creating the hash.
+    def get_triples(self):
+        """ Returns all triples unabbreviated
         """
-        sorted_entities = sorted(
-            self.get_entities(imported=True,
-                              classes=True,
-                              individuals=False,
-                              object_properties=True,
-                              data_properties=True,
-                              annotation_properties=False,
-                              ), key=lambda e: e.iri)
-        return hash((self.base_iri, tuple(sorted_entities)))
+        def _unabbreviate(i):
+            if isinstance(i, int):
+                if i >= 0:
+                    return self._unabbreviate(i)
+                else:
+                    return "_:"  # blank nodes are given random neg. storid
+            else:
+                return i
+
+        for s, p, o in self.world.get_triples():
+            s = _unabbreviate(s)
+            p = _unabbreviate(p)
+            o = _unabbreviate(o)
+            yield s, p, o
 
     def get_by_label(self, label, label_annotations=None, namespace=None):
         """Returns entity with label annotation `label`.
diff --git a/ontopy/patch.py b/ontopy/patch.py
index 836c89fa4..eeb1cae93 100644
--- a/ontopy/patch.py
+++ b/ontopy/patch.py
@@ -68,16 +68,6 @@ def _dir(self):
     return sorted(s)
 
 
-def _hash(self):
-    """Define hash of ThingClass and PropertyClass."""
-    return hash(self.iri)
-
-
-def _eq(self, other):
-    """Define equality based on hash for ThingClass and PropertyClass."""
-    return hash(self) == hash(other)
-
-
 def get_class_annotations(self, all=False, imported=True):
     """Returns a dict with non-empty annotations.
 
@@ -131,8 +121,6 @@ def get_indirect_is_a(self, skip_classes=True):
 
 # Inject methods into ThingClass
 setattr(ThingClass, '__dir__', _dir)
-setattr(ThingClass, '__hash__', _hash)
-setattr(ThingClass, '__eq__', _eq)
 setattr(ThingClass, 'get_preferred_label', get_preferred_label)
 setattr(ThingClass, 'get_parents', get_parents)
 setattr(ThingClass, 'get_annotations', get_class_annotations)
@@ -160,8 +148,6 @@ def get_property_annotations(self, all=False, imported=True):
         return {k: v for k, v in d.items() if v}
 
 
-setattr(PropertyClass, '__hash__', _hash)
-# setattr(PropertyClass, '__eq__', _eq)
 setattr(PropertyClass, 'get_preferred_label', get_preferred_label)
 setattr(PropertyClass, 'get_parents', get_parents)
 setattr(PropertyClass, 'get_annotations', get_property_annotations)

From 61011d5fa2e05f1429d8ad2cf613e07359550ecc Mon Sep 17 00:00:00 2001
From: francescalb <francesca.l.bleken@sintef.no>
Date: Mon, 25 Oct 2021 23:02:53 +0200
Subject: [PATCH 10/16] Added testing of new relation

---
 tests/test_load_emmo.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/tests/test_load_emmo.py b/tests/test_load_emmo.py
index 77c7e5324..6398f3aa3 100644
--- a/tests/test_load_emmo.py
+++ b/tests/test_load_emmo.py
@@ -7,14 +7,19 @@ def test_load_emmo() -> None:
     from emmopy import get_emmo
 
     EMMO_inferred = get_emmo()
+    EMMO_inf = get_emmo(None)
     EMMO = get_emmo(inferred=False)
 
     assert EMMO_inferred
     assert EMMO
 
-    assert EMMO_inferred == get_emmo(None)
+    assert EMMO_inferred == EMMO_inf
     assert EMMO != EMMO_inferred
 
     EMMO_inferred.new_entity('HydrogenAtom', EMMO_inferred.Atom)
     EMMO_inferred.sync_attributes()
-    assert EMMO_inferred != get_emmo(None)
+    assert EMMO_inferred != EMMO_inf
+
+    EMMO_inferred2 = get_emmo()
+    EMMO_inferred2.Atom.comment.append('New triple')
+    assert EMMO_inferred2 != EMMO_inf

From b7371d089d5003ef54c1ef4f5395b710a71e6e38 Mon Sep 17 00:00:00 2001
From: "Francesca L. Bleken" <48128015+francescalb@users.noreply.github.com>
Date: Mon, 1 Nov 2021 13:32:51 +0100
Subject: [PATCH 11/16] Name of inferred ontology not shortened any longer

Co-authored-by: Casper Welzel Andersen <43357585+CasperWA@users.noreply.github.com>
---
 tests/test_load_emmo.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/tests/test_load_emmo.py b/tests/test_load_emmo.py
index 6398f3aa3..85d2b2f68 100644
--- a/tests/test_load_emmo.py
+++ b/tests/test_load_emmo.py
@@ -7,19 +7,20 @@ def test_load_emmo() -> None:
     from emmopy import get_emmo
 
     EMMO_inferred = get_emmo()
-    EMMO_inf = get_emmo(None)
+    EMMO_inferred_again = get_emmo(None)
     EMMO = get_emmo(inferred=False)
 
     assert EMMO_inferred
+    assert EMMO_inferred_again
     assert EMMO
 
-    assert EMMO_inferred == EMMO_inf
+    assert EMMO_inferred == EMMO_inferred_again
     assert EMMO != EMMO_inferred
 
     EMMO_inferred.new_entity('HydrogenAtom', EMMO_inferred.Atom)
     EMMO_inferred.sync_attributes()
-    assert EMMO_inferred != EMMO_inf
+    assert EMMO_inferred != EMMO_inferred_again
 
     EMMO_inferred2 = get_emmo()
     EMMO_inferred2.Atom.comment.append('New triple')
-    assert EMMO_inferred2 != EMMO_inf
+    assert EMMO_inferred2 != EMMO_inferred_again

From 14ff1c22c8d551477ba813fd5a2254c3e6fb3609 Mon Sep 17 00:00:00 2001
From: francescalb <francesca.l.bleken@sintef.no>
Date: Mon, 1 Nov 2021 13:54:16 +0100
Subject: [PATCH 12/16] Removed helper function to sort entities as it is no
 longer needed

---
 ontopy/ontology.py | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/ontopy/ontology.py b/ontopy/ontology.py
index 6dabebabe..2cc2385f3 100644
--- a/ontopy/ontology.py
+++ b/ontopy/ontology.py
@@ -204,14 +204,6 @@ def __eq__(self, other):
         """
         return set(self.get_triples()) == set(other.get_triples())
 
-    def _sorted_entities(self):
-        """Return sorted entities
-        """
-        return sorted(e.iri for e in self.get_entities(
-                imported=True, classes=True,
-                individuals=True, object_properties=True,
-                data_properties=True, annotation_properties=True))
-
     def get_triples(self):
         """ Returns all triples unabbreviated
         """

From b8e700d4d7e14fb83c350fb485b79b8f04311bb0 Mon Sep 17 00:00:00 2001
From: "Francesca L. Bleken" <48128015+francescalb@users.noreply.github.com>
Date: Mon, 1 Nov 2021 13:55:57 +0100
Subject: [PATCH 13/16] Improved on return of dummy variables

Co-authored-by: Casper Welzel Andersen <43357585+CasperWA@users.noreply.github.com>
---
 ontopy/ontology.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/ontopy/ontology.py b/ontopy/ontology.py
index 2cc2385f3..f57012482 100644
--- a/ontopy/ontology.py
+++ b/ontopy/ontology.py
@@ -211,10 +211,8 @@ def _unabbreviate(i):
             if isinstance(i, int):
                 if i >= 0:
                     return self._unabbreviate(i)
-                else:
-                    return "_:"  # blank nodes are given random neg. storid
-            else:
-                return i
+                return "_:"  # blank nodes are given random neg. storid
+            return i
 
         for s, p, o in self.world.get_triples():
             s = _unabbreviate(s)

From 1da61a5dfd58dba7a8684bdf318b533ce4f32cdf Mon Sep 17 00:00:00 2001
From: francescalb <francesca.l.bleken@sintef.no>
Date: Mon, 1 Nov 2021 13:58:28 +0100
Subject: [PATCH 14/16] Clarify documentation of __eq__ for Ontology

---
 ontopy/ontology.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/ontopy/ontology.py b/ontopy/ontology.py
index f57012482..e3f30bfdf 100644
--- a/ontopy/ontology.py
+++ b/ontopy/ontology.py
@@ -200,7 +200,8 @@ def __eq__(self, other):
         """Checks if this ontology is equal to other.
 
         Equality of all triples obtained from self.get_triples(),
-        i.e. all triples except blank nodes.
+        i.e. blank nodes are not distinguished, but relations
+        to blank nodes are included.
         """
         return set(self.get_triples()) == set(other.get_triples())
 

From 76edb29d965db08ab32405b4f711bb1d440c8b4a Mon Sep 17 00:00:00 2001
From: "Francesca L. Bleken" <48128015+francescalb@users.noreply.github.com>
Date: Mon, 1 Nov 2021 19:35:13 +0100
Subject: [PATCH 15/16] write out short names and skip unnecessary intermediate
 variables

Co-authored-by: Casper Welzel Andersen <43357585+CasperWA@users.noreply.github.com>
---
 ontopy/ontology.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/ontopy/ontology.py b/ontopy/ontology.py
index e3f30bfdf..87807a471 100644
--- a/ontopy/ontology.py
+++ b/ontopy/ontology.py
@@ -215,11 +215,8 @@ def _unabbreviate(i):
                 return "_:"  # blank nodes are given random neg. storid
             return i
 
-        for s, p, o in self.world.get_triples():
-            s = _unabbreviate(s)
-            p = _unabbreviate(p)
-            o = _unabbreviate(o)
-            yield s, p, o
+        for subject, predicate, obj in self.world.get_triples():
+            yield _unabbreviate(subject), _unabbreviate(predicate), _unabbreviate(obj)
 
     def get_by_label(self, label, label_annotations=None, namespace=None):
         """Returns entity with label annotation `label`.

From 1ea3bc9b0525affc052563511738228fd3fa0525 Mon Sep 17 00:00:00 2001
From: francescalb <francesca.l.bleken@sintef.no>
Date: Tue, 2 Nov 2021 12:43:08 +0100
Subject: [PATCH 16/16] Too long line with long variable names fixed

---
 ontopy/ontology.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/ontopy/ontology.py b/ontopy/ontology.py
index 87807a471..3947cdc9d 100644
--- a/ontopy/ontology.py
+++ b/ontopy/ontology.py
@@ -216,7 +216,9 @@ def _unabbreviate(i):
             return i
 
         for subject, predicate, obj in self.world.get_triples():
-            yield _unabbreviate(subject), _unabbreviate(predicate), _unabbreviate(obj)
+            yield (_unabbreviate(subject),
+                   _unabbreviate(predicate),
+                   _unabbreviate(obj))
 
     def get_by_label(self, label, label_annotations=None, namespace=None):
         """Returns entity with label annotation `label`.