From 7d99a9dab28637e3515dc67cdad8c1f5829a5b6c Mon Sep 17 00:00:00 2001
From: Emmanuelle Vargas-Gonzalez <emmanuelle@mitre.org>
Date: Fri, 16 Oct 2020 16:40:25 -0400
Subject: [PATCH 1/6] remove docs in wrong locations or directories

---
 docs/api/equivalence/graph/stix2.equivalence.graph.rst       | 5 -----
 docs/api/equivalence/object/stix2.equivalence.object.rst     | 5 -----
 .../compare/stix2.equivalence.pattern.compare.comparison.rst | 5 -----
 .../stix2.equivalence.pattern.compare.observation.rst        | 5 -----
 .../stix2.equivalence.pattern.transform.comparison.rst       | 5 -----
 .../stix2.equivalence.pattern.transform.observation.rst      | 5 -----
 .../stix2.equivalence.pattern.transform.specials.rst         | 5 -----
 7 files changed, 35 deletions(-)
 delete mode 100644 docs/api/equivalence/graph/stix2.equivalence.graph.rst
 delete mode 100644 docs/api/equivalence/object/stix2.equivalence.object.rst
 delete mode 100644 docs/api/equivalence/pattern/compare/stix2.equivalence.pattern.compare.comparison.rst
 delete mode 100644 docs/api/equivalence/pattern/compare/stix2.equivalence.pattern.compare.observation.rst
 delete mode 100644 docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.comparison.rst
 delete mode 100644 docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.observation.rst
 delete mode 100644 docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.specials.rst

diff --git a/docs/api/equivalence/graph/stix2.equivalence.graph.rst b/docs/api/equivalence/graph/stix2.equivalence.graph.rst
deleted file mode 100644
index deb3dde..0000000
--- a/docs/api/equivalence/graph/stix2.equivalence.graph.rst
+++ /dev/null
@@ -1,5 +0,0 @@
-graph
-=====
-
-.. automodule:: stix2.equivalence.graph
-   :members:
diff --git a/docs/api/equivalence/object/stix2.equivalence.object.rst b/docs/api/equivalence/object/stix2.equivalence.object.rst
deleted file mode 100644
index 41c8f52..0000000
--- a/docs/api/equivalence/object/stix2.equivalence.object.rst
+++ /dev/null
@@ -1,5 +0,0 @@
-object
-======
-
-.. automodule:: stix2.equivalence.object
-   :members:
diff --git a/docs/api/equivalence/pattern/compare/stix2.equivalence.pattern.compare.comparison.rst b/docs/api/equivalence/pattern/compare/stix2.equivalence.pattern.compare.comparison.rst
deleted file mode 100644
index 0b886be..0000000
--- a/docs/api/equivalence/pattern/compare/stix2.equivalence.pattern.compare.comparison.rst
+++ /dev/null
@@ -1,5 +0,0 @@
-comparison
-==============
-
-.. automodule:: stix2.equivalence.pattern.compare.comparison
-   :members:
diff --git a/docs/api/equivalence/pattern/compare/stix2.equivalence.pattern.compare.observation.rst b/docs/api/equivalence/pattern/compare/stix2.equivalence.pattern.compare.observation.rst
deleted file mode 100644
index 16bd619..0000000
--- a/docs/api/equivalence/pattern/compare/stix2.equivalence.pattern.compare.observation.rst
+++ /dev/null
@@ -1,5 +0,0 @@
-observation
-==============
-
-.. automodule:: stix2.equivalence.pattern.compare.observation
-   :members:
diff --git a/docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.comparison.rst b/docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.comparison.rst
deleted file mode 100644
index 6364561..0000000
--- a/docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.comparison.rst
+++ /dev/null
@@ -1,5 +0,0 @@
-comparison
-==============
-
-.. automodule:: stix2.equivalence.pattern.transform.comparison
-   :members:
diff --git a/docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.observation.rst b/docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.observation.rst
deleted file mode 100644
index f67fb1b..0000000
--- a/docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.observation.rst
+++ /dev/null
@@ -1,5 +0,0 @@
-observation
-==============
-
-.. automodule:: stix2.equivalence.pattern.transform.observation
-   :members:
diff --git a/docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.specials.rst b/docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.specials.rst
deleted file mode 100644
index 8b61b69..0000000
--- a/docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.specials.rst
+++ /dev/null
@@ -1,5 +0,0 @@
-specials
-==============
-
-.. automodule:: stix2.equivalence.pattern.transform.specials
-   :members:

From 5ec001d3244203936adbc13aec85f3ff7d5513d6 Mon Sep 17 00:00:00 2001
From: Emmanuelle Vargas-Gonzalez <emmanuelle@mitre.org>
Date: Fri, 16 Oct 2020 16:42:17 -0400
Subject: [PATCH 2/6] add new rst files and directories

---
 .../compare/stix2.equivalence.pattern.compare.comparison.rst | 5 +++++
 .../stix2.equivalence.pattern.compare.observation.rst        | 5 +++++
 .../pattern/stix2.equivalence.pattern.compare.rst            | 5 +++++
 .../pattern/stix2.equivalence.pattern.transform.rst          | 5 +++++
 .../stix2.equivalence.pattern.transform.comparison.rst       | 5 +++++
 .../stix2.equivalence.pattern.transform.observation.rst      | 5 +++++
 .../stix2.equivalence.pattern.transform.specials.rst         | 5 +++++
 docs/api/equivalence/stix2.equivalence.graph.rst             | 5 +++++
 docs/api/equivalence/stix2.equivalence.object.rst            | 5 +++++
 9 files changed, 45 insertions(+)
 create mode 100644 docs/api/equivalence/pattern/compare/stix2.equivalence.pattern.compare.comparison.rst
 create mode 100644 docs/api/equivalence/pattern/compare/stix2.equivalence.pattern.compare.observation.rst
 create mode 100644 docs/api/equivalence/pattern/stix2.equivalence.pattern.compare.rst
 create mode 100644 docs/api/equivalence/pattern/stix2.equivalence.pattern.transform.rst
 create mode 100644 docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.comparison.rst
 create mode 100644 docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.observation.rst
 create mode 100644 docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.specials.rst
 create mode 100644 docs/api/equivalence/stix2.equivalence.graph.rst
 create mode 100644 docs/api/equivalence/stix2.equivalence.object.rst

diff --git a/docs/api/equivalence/pattern/compare/stix2.equivalence.pattern.compare.comparison.rst b/docs/api/equivalence/pattern/compare/stix2.equivalence.pattern.compare.comparison.rst
new file mode 100644
index 0000000..37c6cc0
--- /dev/null
+++ b/docs/api/equivalence/pattern/compare/stix2.equivalence.pattern.compare.comparison.rst
@@ -0,0 +1,5 @@
+comparison
+============================================
+
+.. automodule:: stix2.equivalence.pattern.compare.comparison
+   :members:
\ No newline at end of file
diff --git a/docs/api/equivalence/pattern/compare/stix2.equivalence.pattern.compare.observation.rst b/docs/api/equivalence/pattern/compare/stix2.equivalence.pattern.compare.observation.rst
new file mode 100644
index 0000000..463e11f
--- /dev/null
+++ b/docs/api/equivalence/pattern/compare/stix2.equivalence.pattern.compare.observation.rst
@@ -0,0 +1,5 @@
+observation
+=============================================
+
+.. automodule:: stix2.equivalence.pattern.compare.observation
+   :members:
\ No newline at end of file
diff --git a/docs/api/equivalence/pattern/stix2.equivalence.pattern.compare.rst b/docs/api/equivalence/pattern/stix2.equivalence.pattern.compare.rst
new file mode 100644
index 0000000..3f64bea
--- /dev/null
+++ b/docs/api/equivalence/pattern/stix2.equivalence.pattern.compare.rst
@@ -0,0 +1,5 @@
+compare
+=================================
+
+.. automodule:: stix2.equivalence.pattern.compare
+   :members:
\ No newline at end of file
diff --git a/docs/api/equivalence/pattern/stix2.equivalence.pattern.transform.rst b/docs/api/equivalence/pattern/stix2.equivalence.pattern.transform.rst
new file mode 100644
index 0000000..a26102b
--- /dev/null
+++ b/docs/api/equivalence/pattern/stix2.equivalence.pattern.transform.rst
@@ -0,0 +1,5 @@
+transform
+===================================
+
+.. automodule:: stix2.equivalence.pattern.transform
+   :members:
\ No newline at end of file
diff --git a/docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.comparison.rst b/docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.comparison.rst
new file mode 100644
index 0000000..e2b5d42
--- /dev/null
+++ b/docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.comparison.rst
@@ -0,0 +1,5 @@
+comparison
+==============================================
+
+.. automodule:: stix2.equivalence.pattern.transform.comparison
+   :members:
\ No newline at end of file
diff --git a/docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.observation.rst b/docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.observation.rst
new file mode 100644
index 0000000..607bdcf
--- /dev/null
+++ b/docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.observation.rst
@@ -0,0 +1,5 @@
+observation
+===============================================
+
+.. automodule:: stix2.equivalence.pattern.transform.observation
+   :members:
\ No newline at end of file
diff --git a/docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.specials.rst b/docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.specials.rst
new file mode 100644
index 0000000..f8191c3
--- /dev/null
+++ b/docs/api/equivalence/pattern/transform/stix2.equivalence.pattern.transform.specials.rst
@@ -0,0 +1,5 @@
+specials
+============================================
+
+.. automodule:: stix2.equivalence.pattern.transform.specials
+   :members:
\ No newline at end of file
diff --git a/docs/api/equivalence/stix2.equivalence.graph.rst b/docs/api/equivalence/stix2.equivalence.graph.rst
new file mode 100644
index 0000000..0cc2922
--- /dev/null
+++ b/docs/api/equivalence/stix2.equivalence.graph.rst
@@ -0,0 +1,5 @@
+graph
+=======================
+
+.. automodule:: stix2.equivalence.graph
+   :members:
\ No newline at end of file
diff --git a/docs/api/equivalence/stix2.equivalence.object.rst b/docs/api/equivalence/stix2.equivalence.object.rst
new file mode 100644
index 0000000..76f5274
--- /dev/null
+++ b/docs/api/equivalence/stix2.equivalence.object.rst
@@ -0,0 +1,5 @@
+object
+========================
+
+.. automodule:: stix2.equivalence.object
+   :members:
\ No newline at end of file

From fc600df5f16c25ec768a1412c3a3d73cdf081f31 Mon Sep 17 00:00:00 2001
From: Emmanuelle Vargas-Gonzalez <emmanuelle@mitre.org>
Date: Fri, 16 Oct 2020 16:43:12 -0400
Subject: [PATCH 3/6] update .gitignore and conf.py

---
 .gitignore   |  3 ++-
 docs/conf.py | 22 +++++++++++++++-------
 2 files changed, 17 insertions(+), 8 deletions(-)

diff --git a/.gitignore b/.gitignore
index 9758937..72b31cd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -55,7 +55,8 @@ coverage.xml
 # Sphinx documentation
 docs/_build/
 .ipynb_checkpoints
-default_sem_eq_weights.rst
+graph_default_sem_eq_weights.rst
+object_default_sem_eq_weights.rst
 
 # PyBuilder
 target/
diff --git a/docs/conf.py b/docs/conf.py
index 8b372d5..9723e39 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -8,7 +8,8 @@ from six import class_types
 from sphinx.ext.autodoc import ClassDocumenter
 
 from stix2.base import _STIXBase
-from stix2.environment import WEIGHTS
+from stix2.equivalence.graph import GRAPH_WEIGHTS
+from stix2.equivalence.object import WEIGHTS
 from stix2.version import __version__
 
 sys.path.insert(0, os.path.abspath('..'))
@@ -62,12 +63,19 @@ latex_documents = [
 ]
 
 # Add a formatted version of environment.WEIGHTS
-default_sem_eq_weights = json.dumps(WEIGHTS, indent=4, default=lambda o: o.__name__)
-default_sem_eq_weights = default_sem_eq_weights.replace('\n', '\n    ')
-default_sem_eq_weights = default_sem_eq_weights.replace('               "', '               ')
-default_sem_eq_weights = default_sem_eq_weights.replace('"\n', '\n')
-with open('default_sem_eq_weights.rst', 'w') as f:
-    f.write(".. code-block:: py\n\n   {}\n\n".format(default_sem_eq_weights))
+object_default_sem_eq_weights = json.dumps(WEIGHTS, indent=4, default=lambda o: o.__name__)
+object_default_sem_eq_weights = object_default_sem_eq_weights.replace('\n', '\n    ')
+object_default_sem_eq_weights = object_default_sem_eq_weights.replace('               "', '               ')
+object_default_sem_eq_weights = object_default_sem_eq_weights.replace('"\n', '\n')
+with open('object_default_sem_eq_weights.rst', 'w') as f:
+    f.write(".. code-block:: python\n\n   {}\n\n".format(object_default_sem_eq_weights))
+
+graph_default_sem_eq_weights = json.dumps(GRAPH_WEIGHTS, indent=4, default=lambda o: o.__name__)
+graph_default_sem_eq_weights = graph_default_sem_eq_weights.replace('\n', '\n    ')
+graph_default_sem_eq_weights = graph_default_sem_eq_weights.replace('               "', '               ')
+graph_default_sem_eq_weights = graph_default_sem_eq_weights.replace('"\n', '\n')
+with open('graph_default_sem_eq_weights.rst', 'w') as f:
+    f.write(".. code-block:: python\n\n   {}\n\n".format(graph_default_sem_eq_weights))
 
 
 def get_property_type(prop):

From 92ab1227edd28cf3da366e792a626c6f5c9a1d85 Mon Sep 17 00:00:00 2001
From: Emmanuelle Vargas-Gonzalez <emmanuelle@mitre.org>
Date: Fri, 16 Oct 2020 17:12:52 -0400
Subject: [PATCH 4/6] docstrings, changes to equivalence.ipynb

---
 docs/guide/equivalence.ipynb          | 18 ++++++++++--------
 stix2/environment.py                  |  6 +++---
 stix2/equivalence/graph/__init__.py   |  5 +++--
 stix2/equivalence/object/__init__.py  |  5 +++--
 stix2/equivalence/pattern/__init__.py |  2 +-
 5 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/docs/guide/equivalence.ipynb b/docs/guide/equivalence.ipynb
index c0b9331..8393495 100644
--- a/docs/guide/equivalence.ipynb
+++ b/docs/guide/equivalence.ipynb
@@ -2165,15 +2165,17 @@
     "The weights dictionary should contain both the weight and the comparison function for each property. You may use the default weights and functions, or provide your own.\n",
     "\n",
     "##### Existing comparison functions\n",
-    "For reference, here is a list of the comparison functions already built in the codebase (found in [stix2/environment.py](../api/stix2.environment.rst#stix2.environment.Environment)):\n",
+    "For reference, here is a list of the comparison functions already built in the codebase (found in [stix2/equivalence/object](../api/equivalence/stix2.equivalence.object.rst#module-stix2.equivalence.object)):\n",
     "\n",
-    " - [custom_pattern_based](../api/stix2.environment.rst#stix2.environment.custom_pattern_based)\n",
-    " - [exact_match](../api/stix2.environment.rst#stix2.environment.exact_match)\n",
-    " - [partial_external_reference_based](../api/stix2.environment.rst#stix2.environment.partial_external_reference_based)\n",
-    " - [partial_list_based](../api/stix2.environment.rst#stix2.environment.partial_list_based)\n",
-    " - [partial_location_distance](../api/stix2.environment.rst#stix2.environment.partial_location_distance)\n",
-    " - [partial_string_based](../api/stix2.environment.rst#stix2.environment.partial_string_based)\n",
-    " - [partial_timestamp_based](../api/stix2.environment.rst#stix2.environment.partial_timestamp_based)\n",
+    " - [custom_pattern_based](../api/equivalence/stix2.equivalence.object.rst#stix2.equivalence.object.custom_pattern_based)\n",
+    " - [exact_match](../api/equivalence/stix2.equivalence.object.rst#stix2.equivalence.object.exact_match)\n",
+    " - [list_reference_check](../api/equivalence/stix2.equivalence.object.rst#stix2.equivalence.object.list_reference_check)\n",
+    " - [partial_external_reference_based](../api/equivalence/stix2.equivalence.object.rst#stix2.equivalence.object.partial_external_reference_based)\n",
+    " - [partial_list_based](../api/equivalence/stix2.equivalence.object.rst#stix2.equivalence.object.partial_list_based)\n",
+    " - [partial_location_distance](../api/equivalence/stix2.equivalence.object.rst#stix2.equivalence.object.partial_location_distance)\n",
+    " - [partial_string_based](../api/equivalence/stix2.equivalence.object.rst#stix2.equivalence.object.partial_string_based)\n",
+    " - [partial_timestamp_based](../api/equivalence/stix2.equivalence.object.rst#stix2.equivalence.object.partial_timestamp_based)\n",
+    " - [reference_check](../api/equivalence/stix2.equivalence.object.rst#stix2.equivalence.object.reference_check)\n",
     "\n",
     "For instance, if we wanted to compare two of the `ThreatActor`s from before, but use our own weights, then we could do the following:"
    ]
diff --git a/stix2/environment.py b/stix2/environment.py
index ea93a83..f31762c 100644
--- a/stix2/environment.py
+++ b/stix2/environment.py
@@ -4,7 +4,7 @@ import copy
 from .datastore import CompositeDataSource, DataStoreMixin
 from .equivalence.graph import graphically_equivalent
 from .equivalence.object import (  # noqa: F401
-    check_property_present, custom_pattern_based, exact_match,
+    WEIGHTS, check_property_present, custom_pattern_based, exact_match,
     list_reference_check, partial_external_reference_based, partial_list_based,
     partial_location_distance, partial_string_based, partial_timestamp_based,
     reference_check, semantically_equivalent,
@@ -222,7 +222,7 @@ class Environment(DataStoreMixin):
         Note:
             Default weights_dict:
 
-            .. include:: ../default_sem_eq_weights.rst
+            .. include:: ../object_default_sem_eq_weights.rst
 
         Note:
             This implementation follows the Semantic Equivalence Committee Note.
@@ -260,7 +260,7 @@ class Environment(DataStoreMixin):
         Note:
             Default weights_dict:
 
-            .. include:: ../default_sem_eq_weights.rst
+            .. include:: ../graph_default_sem_eq_weights.rst
 
         Note:
             This implementation follows the Semantic Equivalence Committee Note.
diff --git a/stix2/equivalence/graph/__init__.py b/stix2/equivalence/graph/__init__.py
index 3c8730a..680f42f 100644
--- a/stix2/equivalence/graph/__init__.py
+++ b/stix2/equivalence/graph/__init__.py
@@ -1,3 +1,4 @@
+"""Python APIs for STIX 2 Graph-based Semantic Equivalence."""
 import logging
 
 from ..object import (
@@ -36,7 +37,7 @@ def graphically_equivalent(ds1, ds2, prop_scores={}, **weight_dict):
     Note:
         Default weights_dict:
 
-        .. include:: ../default_sem_eq_weights.rst
+        .. include:: ../../graph_default_sem_eq_weights.rst
 
     Note:
         This implementation follows the Semantic Equivalence Committee Note.
@@ -133,4 +134,4 @@ GRAPH_WEIGHTS.update({
         "ds2": None,
         "max_depth": 1,
     },
-})  #: :autodoc-skip:
+})  # :autodoc-skip:
diff --git a/stix2/equivalence/object/__init__.py b/stix2/equivalence/object/__init__.py
index c24fa3c..8333ceb 100644
--- a/stix2/equivalence/object/__init__.py
+++ b/stix2/equivalence/object/__init__.py
@@ -1,3 +1,4 @@
+"""Python APIs for STIX 2 Object-based Semantic Equivalence."""
 import logging
 import time
 
@@ -32,7 +33,7 @@ def semantically_equivalent(obj1, obj2, prop_scores={}, **weight_dict):
     Note:
         Default weights_dict:
 
-        .. include:: ../default_sem_eq_weights.rst
+        .. include:: ../../object_default_sem_eq_weights.rst
 
     Note:
         This implementation follows the Semantic Equivalence Committee Note.
@@ -448,4 +449,4 @@ WEIGHTS = {
     "_internal": {
         "ignore_spec_version": False,
     },
-}  #: :autodoc-skip:
+}  # :autodoc-skip:
diff --git a/stix2/equivalence/pattern/__init__.py b/stix2/equivalence/pattern/__init__.py
index 10494f7..b2e5421 100644
--- a/stix2/equivalence/pattern/__init__.py
+++ b/stix2/equivalence/pattern/__init__.py
@@ -1,7 +1,7 @@
 """Python APIs for STIX 2 Pattern Semantic Equivalence.
 
 .. autosummary::
-   :toctree: patterns
+   :toctree: pattern
 
    compare
    transform

From bb3b1e141af13a3fce1654fc03b0e6e823878336 Mon Sep 17 00:00:00 2001
From: Emmanuelle Vargas-Gonzalez <emmanuelle@mitre.org>
Date: Fri, 16 Oct 2020 17:36:20 -0400
Subject: [PATCH 5/6] add requirement to prevent breaking change to fail build

---
 requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements.txt b/requirements.txt
index 8a5e4a2..fa1773a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,6 @@
 bumpversion
 ipython
+nbconvert<6
 nbsphinx==0.4.3
 pre-commit
 pygments<3,>=2.4.1

From e08a26a39cab2839705875ed782bbbe327f752da Mon Sep 17 00:00:00 2001
From: Chris Lenk <clenk@mitre.org>
Date: Sun, 18 Oct 2020 21:09:07 -0400
Subject: [PATCH 6/6] Correct variable name

---
 stix2/environment.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/stix2/environment.py b/stix2/environment.py
index f31762c..4dc6ff0 100644
--- a/stix2/environment.py
+++ b/stix2/environment.py
@@ -220,7 +220,7 @@ class Environment(DataStoreMixin):
             or methods can be fine tuned for a particular use case.
 
         Note:
-            Default weights_dict:
+            Default weight_dict:
 
             .. include:: ../object_default_sem_eq_weights.rst
 
@@ -258,7 +258,7 @@ class Environment(DataStoreMixin):
             or methods can be fine tuned for a particular use case.
 
         Note:
-            Default weights_dict:
+            Default weight_dict:
 
             .. include:: ../graph_default_sem_eq_weights.rst