Improve autodoc output

- Add markings and sources
- Tidy up some docstrings

docs/api/api/stix2.markings.granular_markings.rst

@@ -0,0 +1,5 @@
+granular_markings
+================================
+
+.. automodule:: stix2.markings.granular_markings
+   :members:

docs/api/api/stix2.markings.object_markings.rst

@@ -0,0 +1,5 @@
+object_markings
+==============================
+
+.. automodule:: stix2.markings.object_markings
+   :members:

docs/api/api/stix2.markings.utils.rst

@@ -0,0 +1,5 @@
+utils
+====================
+
+.. automodule:: stix2.markings.utils
+   :members:

docs/api/api/stix2.sources.filesystem.rst

@@ -0,0 +1,5 @@
+filesystem
+========================
+
+.. automodule:: stix2.sources.filesystem
+   :members:

docs/api/api/stix2.sources.filters.rst

@@ -0,0 +1,5 @@
+filters
+=====================
+
+.. automodule:: stix2.sources.filters
+   :members:

docs/api/api/stix2.sources.memory.rst

@@ -0,0 +1,5 @@
+memory
+====================
+
+.. automodule:: stix2.sources.memory
+   :members:

docs/api/api/stix2.sources.taxii.rst

@@ -0,0 +1,5 @@
+taxii
+===================
+
+.. automodule:: stix2.sources.taxii
+   :members:

docs/api/stix2.markings.rst

@@ -0,0 +1,5 @@
+markings
+==============
+
+.. automodule:: stix2.markings
+   :members:

docs/api/stix2.sources.rst

@@ -0,0 +1,5 @@
+sources
+=============
+
+.. automodule:: stix2.sources
+   :members:

docs/conf.py

@@ -9,6 +9,7 @@ extensions = [
     'sphinx.ext.autodoc',
     'sphinx.ext.autosummary',
     'sphinx.ext.napoleon',
+    'sphinx.ext.todo',
 ]
 autodoc_default_flags = [
     'show-inheritance',

stix2/__init__.py

@@ -8,10 +8,12 @@
    core
    environment
    exceptions
+   markings
    observables
    patterns
    properties
    sdo
+   sources
    sro
    utils
 """

stix2/markings/__init__.py

@@ -3,6 +3,18 @@ Python STIX 2.0 Data Markings API.
 
 These high level functions will operate on both object level markings and
 granular markings unless otherwise noted in each of the functions.
+
+
+.. autosummary::
+   :toctree: api
+
+   granular_markings
+   object_markings
+   utils
+
+.. raw:: html
+
+   <br/><hr/><br/>
 """
 
 from stix2.markings import granular_markings, object_markings

stix2/markings/utils.py

@@ -7,14 +7,14 @@ from stix2 import exceptions
 
 
 def _evaluate_expression(obj, selector):
-    """
-    Walks an SDO or SRO generating selectors to match against ``selector``. If
-    a match is found and the the value of this property is present in the
+    """Walks an SDO or SRO generating selectors to match against ``selector``.
+
+    If a match is found and the the value of this property is present in the
     objects. Matching value of the property will be returned.
 
     Args:
         obj: An SDO or SRO object.
-        selector: A string following the selector syntax.
+        selector (str): A string following the selector syntax.
 
     Returns:
         list: Values contained in matching property. Otherwise empty list.
@@ -58,28 +58,26 @@ def convert_to_list(data):
 
 
 def compress_markings(granular_markings):
-    """
-    Compress granular markings list. If there is more than one marking
-    identifier matches. It will collapse into a single granular marking.
+    """Compress granular markings list.
 
-    Examples:
-        Input:
-        [
-            {
-                "selectors": [
-                    "description"
-                ],
-                "marking_ref": "marking-definition--613f2e26-407d-48c7-9eca-b8e91df99dc9"
-            },
-            {
-                "selectors": [
-                    "name"
-                ],
-                "marking_ref": "marking-definition--613f2e26-407d-48c7-9eca-b8e91df99dc9"
-            }
-        ]
+    If there is more than one marking identifier matches. It will collapse into
+    a single granular marking.
 
-        Output:
+    Example:
+        >>> compress_markings([
+        ...     {
+        ...         "selectors": [
+        ...             "description"
+        ...         ],
+        ...         "marking_ref": "marking-definition--613f2e26-407d-48c7-9eca-b8e91df99dc9"
+        ...     },
+        ...     {
+        ...         "selectors": [
+        ...             "name"
+        ...         ],
+        ...         "marking_ref": "marking-definition--613f2e26-407d-48c7-9eca-b8e91df99dc9"
+        ...     }
+        ... ])
         [
             {
                 "selectors": [
@@ -117,23 +115,21 @@ def compress_markings(granular_markings):
 
 
 def expand_markings(granular_markings):
-    """
-    Expands granular markings list. If there is more than one selector per
-    granular marking. It will be expanded using the same marking_ref.
+    """Expands granular markings list.
 
-    Examples:
-        Input:
-        [
-            {
-                "selectors": [
-                    "description",
-                    "name"
-                ],
-                "marking_ref": "marking-definition--613f2e26-407d-48c7-9eca-b8e91df99dc9"
-            }
-        ]
+    If there is more than one selector per granular marking. It will be
+    expanded using the same marking_ref.
 
-        Output:
+    Example:
+        >>> expand_markings([
+        ...     {
+        ...         "selectors": [
+        ...             "description",
+        ...             "name"
+        ...         ],
+        ...         "marking_ref": "marking-definition--613f2e26-407d-48c7-9eca-b8e91df99dc9"
+        ...     }
+        ... ])
         [
             {
                 "selectors": [
@@ -174,15 +170,16 @@ def expand_markings(granular_markings):
 
 
 def build_granular_marking(granular_marking):
-    """Returns a dictionary with the required structure for a granular
-    marking"""
+    """Returns a dictionary with the required structure for a granular marking.
+    """
     return {"granular_markings": expand_markings(granular_marking)}
 
 
 def iterpath(obj, path=None):
-    """
-    Generator which walks the input ``obj`` model. Each iteration yields a
-    tuple containing a list of ancestors and the property value.
+    """Generator which walks the input ``obj`` model.
+
+    Each iteration yields a tuple containing a list of ancestors and the
+    property value.
 
     Args:
         obj: An SDO or SRO object.

stix2/properties.py

@@ -1,3 +1,5 @@
+"""Classes for representing properties of STIX Objects and Cyber Observables.
+"""
 import base64
 import binascii
 import collections

stix2/sdo.py

@@ -288,30 +288,28 @@ class Vulnerability(_STIXBase):
 
 
 def CustomObject(type='x-custom-type', properties=None):
-    """Custom STIX Object type decorator
+    """Custom STIX Object type decorator.
 
-    Example 1:
-
-    @CustomObject('x-type-name', [
-        ('property1', StringProperty(required=True)),
-        ('property2', IntegerProperty()),
-    ])
-    class MyNewObjectType():
-        pass
+    Example:
+        >>> @CustomObject('x-type-name', [
+        ...     ('property1', StringProperty(required=True)),
+        ...     ('property2', IntegerProperty()),
+        ... ])
+        ... class MyNewObjectType():
+        ...     pass
 
     Supply an __init__() function to add any special validations to the custom
     type. Don't call super().__init__() though - doing so will cause an error.
 
-    Example 2:
-
-    @CustomObject('x-type-name', [
-        ('property1', StringProperty(required=True)),
-        ('property2', IntegerProperty()),
-    ])
-    class MyNewObjectType():
-        def __init__(self, property2=None, **kwargs):
-            if property2 and property2 < 10:
-                raise ValueError("'property2' is too small.")
+    Example:
+        >>> @CustomObject('x-type-name', [
+        ...     ('property1', StringProperty(required=True)),
+        ...     ('property2', IntegerProperty()),
+        ... ])
+        ... class MyNewObjectType():
+        ...     def __init__(self, property2=None, **kwargs):
+        ...         if property2 and property2 < 10:
+        ...             raise ValueError("'property2' is too small.")
     """
 
     def custom_builder(cls):

stix2/sources/__init__.py

@@ -1,5 +1,4 @@
-"""
-Python STIX 2.0 Sources
+"""Python STIX 2.0 Sources
 
 Classes:
     DataStore
@@ -7,13 +6,26 @@ Classes:
     DataSource
     CompositeDataSource
 
-TODO:Test everything
+TODO:
+    Test everything
 
-Notes:
+Note:
     add_filter(), remove_filter(), deduplicate() - if these functions remain
     the exact same for DataSource, DataSink, CompositeDataSource etc... -> just
     make those functions an interface to inherit?
 
+
+.. autosummary::
+   :toctree: api
+
+   filters
+   filesystem
+   memory
+   taxii
+
+.. raw:: html
+
+   <br/><hr/><br/>
 """
 
 import uuid
@@ -29,8 +41,7 @@ def make_id():
 
 
 class DataStore(object):
-    """
-    An implementer will create a concrete subclass from
+    """An implementer will create a concrete subclass from
     this abstract class for the specific data store.
 
     Attributes:
@@ -47,7 +58,7 @@ class DataStore(object):
     def get(self, stix_id):
         """Retrieve the most recent version of a single STIX object by ID.
 
-        Notes:
+        Note:
             Translate API get() call to the appropriate DataSource call.
 
         Args:
@@ -79,7 +90,7 @@ class DataStore(object):
     def query(self, query):
         """Retrieve STIX objects matching a set of filters.
 
-        Notes:
+        Note:
             Implement the specific data source API calls, processing,
             functionality required for retrieving query from the data source.
 
@@ -97,7 +108,7 @@ class DataStore(object):
     def add(self, stix_objs):
         """Store STIX objects.
 
-        Notes:
+        Note:
             Translate add() to the appropriate DataSink call().
 
         Args:
@@ -109,9 +120,9 @@ class DataStore(object):
 
 
 class DataSink(object):
-    """
-    Abstract class for defining a data sink. Intended for subclassing into
-    different sink components.
+    """Abstract class for defining a data sink.
+
+    Intended for subclassing into different sink components.
 
     Attributes:
         id (str): A unique UUIDv4 to identify this DataSink.
@@ -123,7 +134,7 @@ class DataSink(object):
     def add(self, stix_objs):
         """Store STIX objects.
 
-        Notes:
+        Note:
             Implement the specific data sink API calls, processing,
             functionality required for adding data to the sink
 
@@ -136,9 +147,9 @@ class DataSink(object):
 
 
 class DataSource(object):
-    """
-    Abstract class for defining a data source. Intended for subclassing into
-    different source components.
+    """Abstract class for defining a data source.
+
+    Intended for subclassing into different source components.
 
     Attributes:
         id (str): A unique UUIDv4 to identify this DataSource.
@@ -171,7 +182,7 @@ class DataSource(object):
 
     def all_versions(self, stix_id, _composite_filters=None):
         """
-        Notes:
+        Note:
             Similar to get() except returns list of all object versions of
             the specified "id". In addition, implement the specific data
             source API calls, processing, functionality required for retrieving
@@ -294,7 +305,7 @@ class DataSource(object):
         return filtered_stix_objs
 
     def deduplicate(self, stix_obj_list):
-        """Deduplicate a list of STIX objects to a unique set
+        """Deduplicate a list of STIX objects to a unique set.
 
         Reduces a set of STIX objects to unique set by looking
         at 'id' and 'modified' fields - as a unique object version
@@ -348,7 +359,7 @@ class CompositeDataSource(DataSource):
         function does a federated retrieval and consolidation of the data
         returned from all the STIX data sources.
 
-        Notes:
+        Note:
              A composite data source will pass its attached filters to
              each configured data source, pushing filtering to them to handle.
 
@@ -387,7 +398,7 @@ class CompositeDataSource(DataSource):
         Federated all_versions retrieve method - iterates through all STIX data
         sources defined in "data_sources"
 
-        Notes:
+        Note:
             A composite data source will pass its attached filters to
             each configured data source, pushing filtering to them to handle
 

stix2/sources/filesystem.py

@@ -6,7 +6,8 @@ Classes:
     FileSystemSink
     FileSystemSource
 
-TODO: Test everything
+TODO:
+    Test everything
 """
 
 import json
@@ -88,7 +89,7 @@ class FileSystemSource(DataSource):
 
     def all_versions(self, stix_id, _composite_filters=None):
         """
-        Notes:
+        Note:
             Since FileSystem sources/sinks don't handle multiple versions
             of a STIX object, this operation is unnecessary. Pass call to get().
 

stix2/sources/filters.py

@@ -4,10 +4,11 @@ Filters for Python STIX 2.0 DataSources, DataSinks, DataStores
 Classes:
     Filter
 
-TODO: The script at the bottom of the module works (to capture
-all the callable filter methods), however it causes this module
-to be imported by itself twice. Not sure how big of deal that is,
-or if cleaner solution possible.
+TODO:
+    The script at the bottom of the module works (to capture
+    all the callable filter methods), however it causes this module
+    to be imported by itself twice. Not sure how big of deal that is,
+    or if cleaner solution possible.
 """
 
 import collections

stix2/sources/memory.py

@@ -6,12 +6,14 @@ Classes:
     MemorySink
     MemorySource
 
-TODO: Test everything.
+TODO:
+    Test everything.
 
-TODO: Use deduplicate() calls only when memory corpus is dirty (been added to)
-      can save a lot of time for successive queries
+TODO:
+    Use deduplicate() calls only when memory corpus is dirty (been added to)
+    can save a lot of time for successive queries
 
-Notes:
+Note:
     Not worrying about STIX versioning. The in memory STIX data at anytime
     will only hold one version of a STIX object. As such, when save() is called,
     the single versions of all the STIX objects are what is written to file.
@@ -47,7 +49,7 @@ class MemoryStore(DataStore):
     """
     def __init__(self, stix_data=None):
         """
-        Notes:
+        Note:
             It doesn't make sense to create a MemoryStore by passing
             in existing MemorySource and MemorySink because there could
             be data concurrency issues. Just as easy to create new MemoryStore.
@@ -144,7 +146,7 @@ class MemorySource(DataSource):
 
     def all_versions(self, stix_id, _composite_filters=None):
         """
-        Notes:
+        Note:
             Since Memory sources/sinks don't handle multiple versions of a
             STIX object, this operation is unnecessary. Translate call to get().
 

stix2/sources/taxii.py

@@ -6,7 +6,8 @@ Classes:
     TAXIICollectionSink
     TAXIICollectionSource
 
-TODO: Test everything
+TODO:
+    Test everything
 
 """
 
@@ -127,7 +128,7 @@ class TAXIICollectionSource(DataSource):
     def _parse_taxii_filters(self, query):
         """Parse out TAXII filters that the TAXII server can filter on.
 
-        Notes:
+        Note:
             For instance - "?match[type]=indicator,sighting" should be in a
             query dict as follows: