RDFLib · ashleysommer · Aug 15, 2024
diff --git a/docs/source/Closure.rst b/docs/source/Closure.rst
@@ -5,4 +5,4 @@ Closure
     :members:
     :undoc-members:
     :inherited-members:
-    :show-inheritance:
+    :show-inheritance:
diff --git a/docs/source/owlrl.rst → docs/source/OWLRL.rst b/docs/source/owlrl.rst → docs/source/OWLRL.rst
@@ -1,7 +1,7 @@
-owlrl
+OWLRL
 =====
 
-.. automodule:: owlrl
+.. automodule:: owlrl.OWLRL
     :members:
     :undoc-members:
     :inherited-members:

diff --git a/docs/source/OWLRLExtras.rst b/docs/source/OWLRLExtras.rst
@@ -5,4 +5,6 @@ OWLRLExtras
     :members:
     :undoc-members:
     :inherited-members:
-    :show-inheritance:
+    :show-inheritance:
+
+.. autofunction:: owlrl.OWLRLExtras._strToRational
diff --git a/docs/source/XsdDatatypes_source.rst b/docs/source/XsdDatatypes_source.rst
@@ -4,4 +4,4 @@ XsdDatatypes.py
 ---------------
 
 .. literalinclude:: ../../owlrl/XsdDatatypes.py
-    :linenos:
+    :linenos:
diff --git a/docs/source/_static/.gitkeep b/docs/source/_static/.gitkeep
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -66,8 +66,8 @@
 # for a list of supported languages.
 #
 # This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = None
+# Usually you set "language" from the command lihttps://rdflib.readthedocs.io/en/stable/ne for these cases.
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -194,4 +194,8 @@
 # -- Options for intersphinx extension ---------------------------------------
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {"https://docs.python.org/": None}
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/", None),
+    "rdflib": ("https://rdflib.readthedocs.io/en/stable/", None)
+}
+
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -22,7 +22,8 @@ OWL-RL Documentation
    :maxdepth: 2
    :caption: Modules
 
-   owlrl
+   stubs/owlrl.__index__
+   stubs/owlrl.DeductiveClosure
    AxiomaticTriples
    Closure
    CombinedClosure
@@ -33,3 +34,10 @@ OWL-RL Documentation
    RestrictedDatatype
    XsdDatatypes
 
+.. toctree::
+   :maxdepth: 1
+   :caption: Reference Source
+
+   AxiomaticTriples_source
+   DatatypeHandling_source
+   XsdDatatypes_source
diff --git a/docs/source/stubs/owlrl.Closure.rst b/docs/source/stubs/owlrl.Closure.rst
diff --git a/docs/source/stubs/owlrl.DeductiveClosure.rst b/docs/source/stubs/owlrl.DeductiveClosure.rst
@@ -7,7 +7,10 @@ owlrl.DeductiveClosure
 
 
    .. automethod:: __init__
-
+   .. automethod:: expand
+   .. automethod:: use_improved_datatypes_conversions
+   .. automethod:: use_rdflib_datatypes_conversions
+   .. autoattribute:: improved_datatype_generic
 
    .. rubric:: Methods
 
@@ -24,8 +27,6 @@ owlrl.DeductiveClosure
 
    .. rubric:: Attributes
 
-   .. autosummary::
-
-      ~DeductiveClosure.improved_datatype_generic
+   .. autosummary:: improved_datatype_generic
 
 
diff --git a/docs/source/stubs/owlrl.rst → docs/source/stubs/owlrl.__index__.rst b/docs/source/stubs/owlrl.rst → docs/source/stubs/owlrl.__index__.rst
@@ -7,23 +7,21 @@ owlrl
 
    .. rubric:: Functions
 
-   .. autosummary::
-
-      convert_graph
-      interpret_owl_imports
-      return_closure_class
+   .. autofunction:: convert_graph
+   .. autofunction:: interpret_owl_imports
+   .. autofunction:: return_closure_class
+
 
 
 
 
-
    .. rubric:: Classes
 
    .. autosummary::
 
       DeductiveClosure
-   
-   
+
+
 
 
 

diff --git a/owlrl/Closure.py b/owlrl/Closure.py
@@ -53,7 +53,7 @@ class Core:
     There are some methods that are implemented in the subclasses only, ie, this class cannot be used by itself!
 
     :param graph: The RDF graph to be extended.
-    :type graph: :class:`rdflib.Graph`
+    :type graph: :class:`rdflib.graph.Graph`
 
     :param axioms: Whether axioms should be added or not.
     :type axioms: bool
@@ -65,13 +65,13 @@ class Core:
     :type rdfs: bool
 
     :param destination: The destination graph to which the results are written. If None, use the source graph.
-    :type destination: :class:`rdflib.Graph`
+    :type destination: :class:`rdflib.graph.Graph`
 
     :var IMaxNum: Maximal index of :code:`rdf:_i` occurrence in the graph.
     :type IMaxNum: int
 
     :var graph: The real graph.
-    :type graph: :class:`rdflib.Graph`
+    :type graph: :class:`rdflib.graph.Graph`
 
     :var axioms: Whether axioms should be added or not.
     :type axioms: bool
@@ -96,15 +96,15 @@ def __init__(self, graph: Graph, axioms, daxioms, rdfs: bool = False, destinatio
         The parameter descriptions here are from the old documentation.
 
         @param graph: the RDF graph to be extended
-        @type graph: rdflib.Graph
+        @type graph: Graph
         @param axioms: whether axioms should be added or not
         @type axioms: boolean
         @param daxioms: whether datatype axioms should be added or not
         @type daxioms: boolean
         @param rdfs: whether RDFS inference is also done (used in subclassed only)
         @type rdfs: boolean
         @param destination: the destination graph to which the results are written. If None, use the source graph.
-        @type destination: rdflib.Graph
+        @type destination: Graph
         """
         self._debug = debugGlobal
 
@@ -248,7 +248,7 @@ def store_triple(self, t):
         added any new triple, and the full processing can stop.
 
         :param t: The triple to be added to the graph, unless it is already there
-        :type t: tuple (s,p,o)
+        :type t: tuple
         """
         (s, p, o) = t
         if not isinstance(p, Literal) and not (t in self.destination or t in self.graph):
@@ -261,7 +261,7 @@ def closure(self):
         """
         Generate the closure the graph. This is the real 'core'.
 
-        The processing rules store new triples via the separate method :func:`.Core.store_triple` which stores
+        The processing rules store new triples via the separate method :func:`owlrl.Closure.Core.store_triple` which stores
         them in the :code:`added_triples` array. If that array is empty at the end of a cycle,
         it means that the whole process can be stopped.
 

diff --git a/owlrl/DatatypeHandling.py b/owlrl/DatatypeHandling.py
@@ -684,7 +684,7 @@ def _strToPlainLiteral(v):
 def use_Alt_lexical_conversions():
     """
     Registering the datatypes item for RDFLib, ie, bind the dictionary values. The 'bind' method of RDFLib adds
-    extra datatypes to the registered ones in RDFLib, though the table used here (I.e., :py:data:`.AltXSDToPYTHON`) actually
+    extra datatypes to the registered ones in RDFLib, though the table used here (I.e., :code:`AltXSDToPYTHON`) actually
     overrides all of the default conversion routines. The method also add a Decimal entry to the :code:`PythonToXSD` list of
     RDFLib.
     """

diff --git a/owlrl/OWLRLExtras.py b/owlrl/OWLRLExtras.py
@@ -100,7 +100,7 @@ def _strToRational(v):
 class OWLRL_Extension(RDFS_OWLRL_Semantics):
     """
     Additional rules to OWL 2 RL. The initialization method also adds the :code:`owl:rational` datatype to the set of
-    allowed datatypes with the :py:func:`._strToRational` function as a conversion between the literal form and a Rational. The
+    allowed datatypes with the :func:`owlrl.OWLRLExtras._strToRational` function as a conversion between the literal form and a Rational. The
     :code:`xsd:decimal` datatype is also set to be a subclass of :code:`owl:rational`. Furthermore, the restricted datatypes are
     extracted from the graph using a separate method in a different module
     (:py:func:`.RestrictedDatatype.extract_faceted_datatypes`), and all those datatypes are also added to the set of allowed
@@ -227,7 +227,7 @@ def one_time_rules(self):
 
     def add_axioms(self):
         """
-        Add the :class:`.OWLRL_Extension.extra_axioms`, related to the self restrictions.
+        Add the :class:`owlrl.OWLRLExtras.OWLRL_Extension.extra_axioms`, related to the self restrictions. This method is invoked only once at the beginning, and prior of, the forward chaining process.
         """
         RDFS_OWLRL_Semantics.add_axioms(self)
         for t in self.extra_axioms:

diff --git a/owlrl/RestrictedDatatype.py b/owlrl/RestrictedDatatype.py
@@ -57,7 +57,7 @@
 import re
 
 from rdflib.namespace import OWL, RDF, RDFS, XSD
-from rdflib import Literal as rdflibLiteral
+from rdflib import Literal as rdflibLiteral, Graph
 
 from .DatatypeHandling import AltXSDToPYTHON
 from functools import reduce
@@ -197,15 +197,15 @@ def _match(r, l):
 #######################################################################################################
 
 
-def extract_faceted_datatypes(core, graph):
+def extract_faceted_datatypes(core, graph: Graph):
     """
     Extractions of restricted (i.e., faceted) datatypes from the graph.
 
     :param core: The core closure instance that is being handled.
     :type core: :class:`.Closure.Core`
 
     :param graph: RDFLib graph.
-    :type graph: :class:`RDFLib.Graph`
+    :type graph: :class:`rdflib.graph.Graph`
 
     :return: List of :class:`.RestrictedDatatype` instances.
     :rtype: list

diff --git a/owlrl/__init__.py b/owlrl/__init__.py
@@ -26,7 +26,7 @@
 
 The main entry point to the package is via the :class:`.DeductiveClosure` class. This class should be
 initialized to control the parameters of the deductive closure; the forward chaining is done via the
-L{expand<DeductiveClosure.expand>} method.
+L{expand<owlrl.DeductiveClosure.expand>} method.
 The simplest way to use the package from an RDFLib application is as follows::
 
     graph = Graph()                                 # creation of an RDFLib graph
@@ -48,7 +48,7 @@
 expand function does not change any state.
 
 For convenience, a second entry point to the package is provided in the form of a function called
-:func:`.convert_graph`, that expects a directory with various options, including a file name. The function
+:func:`owlrl.convert_graph`, that expects a directory with various options, including a file name. The function
 parses the file, creates the expanded graph, and serializes the result into RDF/XML or Turtle. This function is
 particularly useful as an entry point for a CGI call (where the HTML form parameters are in a directory) and is easy to
 use with a command line interface. The package distribution contains an example for both.
@@ -87,13 +87,6 @@
 methods that are executed only once either at the beginning or at the end of the full processing cycle. Adding axiomatic
 triples is handled separately, which allows a finer user control over these features.
 
-Literals must be handled separately. Indeed, the functionality relies on 'extended' RDF graphs, that allows literals
-to be in a subject position, too. Because RDFLib does not allow that, processing begins by exchanging all literals in
-the graph for bnodes (identical literals get the same associated bnode). Processing occurs on these bnodes; at the end
-of the process all these bnodes are replaced by their corresponding literals if possible (if the bnode occurs in a
-subject position, that triple is removed from the resulting graph). Details of this processing is handled in the
-separate :class:`.Literals.LiteralProxies` class.
-
 The OWL specification includes references to datatypes that are not in the core RDFS specification, consequently not
 directly implemented by RDFLib. These are added in a separate module of the package.
 
@@ -102,8 +95,10 @@
 -------------------------------------
 
 The current distribution of RDFLib is fairly poor in handling datatypes, particularly in checking whether a lexical form
-of a literal is "proper" as for its declared datatype. A typical example is::
+of a literal is "proper" as for its declared datatype. A typical example is ::
+
   "-1234"^^xsd:nonNegativeInteger
+
 which should not be accepted as valid literal. Because the requirements of OWL 2 RL are much stricter in this respect,
 an alternative set of datatype handling (essentially, conversions) had to be implemented (see the :py:mod:`.XsdDatatypes`
 module).
@@ -233,15 +228,13 @@ def interpret_owl_imports(iformat, graph):
     Interpret the owl import statements. Essentially, recursively merge with all the objects in the owl import
     statement, and remove the corresponding triples from the graph.
 
-    This method can be used by an application prior to expansion. It is *not* done by the the :class:`.DeductiveClosure`
+    This method can be used by an application prior to expansion. It is *not* done by the :class:`.DeductiveClosure`
     class.
 
-    :param iformat: Input format; can be one of :code:`AUTO`, :code:`TURTLE`, or :code:`RDFXML`. :code:`AUTO` means that
-    the suffix of the file name or URI will decide: '.ttl' means Turtle, RDF/XML otherwise.
+    :param iformat: Input format; can be one of :code:`AUTO`, :code:`TURTLE`, or :code:`RDFXML`. :code:`AUTO` means that the suffix of the file name or URI will decide: '.ttl' means Turtle, RDF/XML otherwise.
     :type iformat: str
-
     :param graph: The RDFLib Graph instance to parse into.
-    :type graph: :class:`RDFLib.Graph`
+    :type graph: :class:`rdflib.graph.Graph`
     """
     while True:
         # 1. collect the import statements:
@@ -330,7 +323,7 @@ class DeductiveClosure:
     :type datatype_axioms: bool
 
     :var improved_datatype_generic: Whether the improved set of lexical-to-Python conversions should be used for datatype handling *in general*, I.e., not only for a particular instance and not only for inference purposes. Default: False.
-    :type improved_Datatype_generic: bool
+    :type improved_datatype_generic: bool
     """
 
     # This is the original set of param definitions in the class definition
@@ -380,6 +373,8 @@ def __init__(
             if not isinstance(closure_class, type):
                 raise ValueError("The closure type argument must be a class reference")
             else:
+
+
                 self.closure_class = closure_class
         self.axiomatic_triples = axiomatic_triples
         self.datatype_axioms = datatype_axioms