fix: correct imports and __all__ (#2340)

Disable
[`implicit_reexport`](https://mypy.readthedocs.io/en/stable/config_file.html#confval-implicit_reexport)
and eliminate all errors reported by mypy after this.

This helps ensure that import statements import from the right module and that
the `__all__` variable is correct.

docs/conf.py

@@ -16,8 +16,10 @@
 import os
 import re
 import sys
+from typing import Any, Dict
 
 import sphinx
+import sphinx.application
 
 import rdflib
 
@@ -47,6 +49,7 @@
     "sphinx.ext.autosectionlabel",
 ]
 
+# https://github.com/sphinx-contrib/apidoc/blob/master/README.rst#configuration
 apidoc_module_dir = "../rdflib"
 apidoc_output_dir = "apidocs"
 
@@ -328,3 +331,50 @@ def find_version(filename):
 
 if sys.version_info < (3, 8):
     nitpick_ignore.extend([("py:class", "importlib_metadata.EntryPoint")])
+
+
+def autodoc_skip_member_handler(
+    app: sphinx.application.Sphinx,
+    what: str,
+    name: str,
+    obj: Any,
+    skip: bool,
+    options: Dict[str, Any],
+):
+    """
+    This function will be called by Sphinx when it is deciding whether to skip a
+    member of a class or module.
+    """
+    # https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#event-autodoc-skip-member
+    if (
+        app.env.docname == "apidocs/rdflib"
+        and what == "module"
+        and type(obj).__name__.endswith("DefinedNamespaceMeta")
+    ):
+        # Don't document namespaces in the `rdflib` module, they will be
+        # documented in the `rdflib.namespace` module instead and Sphinx does
+        # not like when these are documented in two places.
+        #
+        # An example of the WARNINGS that occur without this is:
+        #
+        # "WARNING: duplicate object description of rdflib.namespace._SDO.SDO,
+        # other instance in apidocs/rdflib, use :noindex: for one of them"
+        logging.info(
+            "Skipping %s %s in %s, it will be documented in ",
+            what,
+            name,
+            app.env.docname,
+        )
+        return True
+    return None
+
+
+# https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#skipping-members
+def setup(app: sphinx.application.Sphinx) -> None:
+    """
+    Setup the Sphinx application.
+    """
+
+    # Register a autodoc-skip-member handler so that certain members can be
+    # skipped.
+    app.connect("autodoc-skip-member", autodoc_skip_member_handler)

docs/rdf_terms.rst

@@ -150,7 +150,7 @@ Common XSD datatypes
 ^^^^^^^^^^^^^^^^^^^^
 
 Most simple literals such as *string* or *integer* have XML Schema (XSD) datatypes defined for them, see the figure 
-below. Additionally, these XSD datatypes are listed in the :class:`XSD Namespace class <rdflib.XSD>` that 
+below. Additionally, these XSD datatypes are listed in the :class:`XSD Namespace class <rdflib.namespace.XSD>` that 
 ships with RDFLib, so many Python code editors will prompt you with autocomplete for them when using it.
 
 Remember, you don't *have* to use XSD datatypes and can always make up your own, as GeoSPARQL does, as described above.

pyproject.toml

@@ -211,6 +211,7 @@ disallow_subclassing_any = false
 warn_unreachable = true
 warn_unused_ignores = true
 no_implicit_optional = false
+implicit_reexport = false
 
 [[tool.mypy.overrides]]
 module = "pyparsing.*"

rdflib/namespace/_GEO.py

@@ -9,18 +9,20 @@ class GEO(DefinedNamespace):
     Generated from: http://schemas.opengis.net/geosparql/1.0/geosparql_vocab_all.rdf
     Date: 2021-12-27 17:38:15.101187
 
-    <http://www.opengis.net/ont/geosparql> dc:creator "Open Geospatial Consortium"^^xsd:string
-    dc:date "2012-04-30"^^xsd:date
-    dc:source <http://www.opengis.net/doc/IS/geosparql/1.0>
-        "OGC GeoSPARQL – A Geographic Query Language for RDF Data OGC 11-052r5"^^xsd:string
-    rdfs:seeAlso <http://www.opengis.net/def/function/ogc-geosparql/1.0>
-        <http://www.opengis.net/def/rule/ogc-geosparql/1.0>
-        <http://www.opengis.net/doc/IS/geosparql/1.0>
-    owl:imports dc:
-        <http://www.opengis.net/ont/gml>
-        <http://www.opengis.net/ont/sf>
-        <http://www.w3.org/2004/02/skos/core>
-    owl:versionInfo "OGC GeoSPARQL 1.0"^^xsd:string
+    .. code-block:: Turtle
+
+        <http://www.opengis.net/ont/geosparql> dc:creator "Open Geospatial Consortium"^^xsd:string
+        dc:date "2012-04-30"^^xsd:date
+        dc:source <http://www.opengis.net/doc/IS/geosparql/1.0>
+            "OGC GeoSPARQL – A Geographic Query Language for RDF Data OGC 11-052r5"^^xsd:string
+        rdfs:seeAlso <http://www.opengis.net/def/function/ogc-geosparql/1.0>
+            <http://www.opengis.net/def/rule/ogc-geosparql/1.0>
+            <http://www.opengis.net/doc/IS/geosparql/1.0>
+        owl:imports dc:
+            <http://www.opengis.net/ont/gml>
+            <http://www.opengis.net/ont/sf>
+            <http://www.w3.org/2004/02/skos/core>
+        owl:versionInfo "OGC GeoSPARQL 1.0"^^xsd:string
     """
 
     # http://www.w3.org/2000/01/rdf-schema#Datatype

rdflib/namespace/__init__.py

@@ -91,6 +91,34 @@
     "ClosedNamespace",
     "DefinedNamespace",
     "NamespaceManager",
+    "BRICK",
+    "CSVW",
+    "DC",
+    "DCAM",
+    "DCAT",
+    "DCMITYPE",
+    "DCTERMS",
+    "DOAP",
+    "FOAF",
+    "GEO",
+    "ODRL2",
+    "ORG",
+    "OWL",
+    "PROF",
+    "PROV",
+    "QB",
+    "RDF",
+    "RDFS",
+    "SDO",
+    "SH",
+    "SKOS",
+    "SOSA",
+    "SSN",
+    "TIME",
+    "VANN",
+    "VOID",
+    "WGS",
+    "XSD",
 ]
 
 logger = logging.getLogger(__name__)

rdflib/plugins/stores/sparqlconnector.py

@@ -185,3 +185,6 @@ def update(
                 self.update_endpoint + qsa, data=query.encode(), headers=args["headers"]
             )
         )
+
+
+__all__ = ["SPARQLConnector", "SPARQLConnectorException"]

rdflib/plugins/stores/sparqlstore.py

@@ -1011,3 +1011,6 @@ def predicate_objects(
         """A generator of (predicate, object) tuples for the given subject"""
         for t, c in self.triples((subject, None, None)):
             yield t[1], t[2]
+
+
+__all__ = ["SPARQLUpdateStore", "SPARQLStore"]

test/jsonld/runner.py

@@ -1,21 +1,21 @@
 # -*- coding: UTF-8 -*-
 import json
 
-from rdflib import ConjunctiveGraph
+from rdflib import BNode, ConjunctiveGraph
 from rdflib.compare import isomorphic
 from rdflib.parser import InputSource
 from rdflib.plugins.parsers.jsonld import JsonLDParser, to_rdf
 
 # monkey-patch N-Quads parser via it's underlying W3CNTriplesParser to keep source bnode id:s ..
-from rdflib.plugins.parsers.ntriples import W3CNTriplesParser, bNode, r_nodeid
+from rdflib.plugins.parsers.ntriples import W3CNTriplesParser, r_nodeid
 from rdflib.plugins.serializers.jsonld import from_rdf
 from rdflib.plugins.shared.jsonld.keys import CONTEXT, GRAPH
 
 
 def _preserving_nodeid(self, bnode_context=None):
     if not self.peek("_"):
         return False
-    return bNode(self.eat(r_nodeid).group(1))
+    return BNode(self.eat(r_nodeid).group(1))
 
 
 DEFAULT_PARSER_VERSION = 1.0

test/jsonld/test_api.py

@@ -1,5 +1,7 @@
 # -*- coding: UTF-8 -*-
-from rdflib.plugin import Parser, Serializer, register
+from rdflib.parser import Parser
+from rdflib.plugin import register
+from rdflib.serializer import Serializer
 
 register("json-ld", Parser, "rdflib.plugins.parsers.jsonld", "JsonLDParser")
 register("json-ld", Serializer, "rdflib.plugins.serializers.jsonld", "JsonLDSerializer")

test/jsonld/test_compaction.py

@@ -7,7 +7,8 @@
 import pytest
 
 from rdflib import Graph
-from rdflib.plugin import Serializer, register
+from rdflib.plugin import register
+from rdflib.serializer import Serializer
 
 register("json-ld", Serializer, "rdflib.plugins.serializers.jsonld", "JsonLDSerializer")
 

test/jsonld/test_context.py

@@ -134,7 +134,8 @@ def test_prefix_like_vocab():
 
 # Mock external sources loading
 SOURCES: Dict[str, Dict[str, Any]] = {}
-_source_to_json = context.source_to_json
+# type error: Module "rdflib.plugins.shared.jsonld.context" does not explicitly export attribute "source_to_json"
+_source_to_json = context.source_to_json  # type: ignore[attr-defined]
 
 
 def _mock_source_loader(f):

test/jsonld/test_named_graphs.py

@@ -1,6 +1,7 @@
 # -*- coding: UTF-8 -*-
 from rdflib import *
-from rdflib.plugin import Parser, register
+from rdflib.parser import Parser
+from rdflib.plugin import register
 
 register("json-ld", Parser, "rdflib.plugins.parsers.jsonld", "JsonLDParser")
 register("application/ld+json", Parser, "rdflib.plugins.parsers.jsonld", "JsonLDParser")

test/test_dataset/test_dataset.py

@@ -7,7 +7,9 @@
 import pytest
 
 from rdflib import URIRef, plugin
-from rdflib.graph import DATASET_DEFAULT_GRAPH_ID, Dataset, Graph, Namespace
+from rdflib.graph import DATASET_DEFAULT_GRAPH_ID, Dataset, Graph
+from rdflib.namespace import Namespace
+from rdflib.store import Store
 
 # Will also run SPARQLUpdateStore tests against local SPARQL1.1 endpoint if
 # available. This assumes SPARQL1.1 query/update endpoints running locally at
@@ -26,7 +28,7 @@
 
 pluginstores = []
 
-for s in plugin.plugins(None, plugin.Store):
+for s in plugin.plugins(None, Store):
     if s.name in ("Memory", "Auditable", "Concurrent", "SPARQLStore"):
         continue  # these are tested by default
 

test/test_graph/test_graph.py

@@ -10,7 +10,7 @@
 
 import pytest
 
-from rdflib import Graph, URIRef, plugin
+from rdflib import Graph, URIRef
 from rdflib.exceptions import ParserError
 from rdflib.namespace import Namespace, NamespaceManager
 from rdflib.plugin import PluginException
@@ -62,7 +62,7 @@ def test_property_namespace_manager() -> None:
 
 
 def get_store_names() -> Set[Optional[str]]:
-    names: Set[Optional[str]] = {*get_unique_plugin_names(plugin.Store)}
+    names: Set[Optional[str]] = {*get_unique_plugin_names(Store)}
     names.difference_update(
         {
             "default",

test/test_graph/test_graph_context.py

@@ -7,6 +7,7 @@
 import pytest
 
 from rdflib import BNode, ConjunctiveGraph, Graph, URIRef, plugin
+from rdflib.store import Store
 
 
 class ContextTestCase(unittest.TestCase):
@@ -367,7 +368,7 @@ def testTriples(self):
         pluginname = sys.argv[1]
 
 tests = 0
-for s in plugin.plugins(pluginname, plugin.Store):
+for s in plugin.plugins(pluginname, Store):
     if s.name in (
         "default",
         "Memory",

test/test_graph/test_graph_http.py

@@ -6,14 +6,12 @@
 from test.utils.graph import cached_graph
 from test.utils.http import (
     MOCK_HTTP_REQUEST_WILDCARD,
-    MockHTTPRequest,
-    ctx_http_handler,
-)
-from test.utils.httpservermock import (
     MethodName,
+    MockHTTPRequest,
     MockHTTPResponse,
-    ServedBaseHTTPServerMock,
+    ctx_http_handler,
 )
+from test.utils.httpservermock import ServedBaseHTTPServerMock
 from test.utils.wildcard import URL_PARSE_RESULT_WILDCARD
 from urllib.error import HTTPError
 

test/test_namespace/test_namespace.py

@@ -5,7 +5,7 @@
 import pytest
 
 from rdflib import DCTERMS
-from rdflib.graph import BNode, Graph, Literal
+from rdflib.graph import Graph
 from rdflib.namespace import (
     FOAF,
     OWL,
@@ -17,7 +17,7 @@
     Namespace,
     URIPattern,
 )
-from rdflib.term import URIRef
+from rdflib.term import BNode, Literal, URIRef
 
 
 class TestNamespace:

test/test_roundtrip.py

@@ -14,8 +14,9 @@
 import rdflib.compare
 from rdflib.graph import ConjunctiveGraph, Graph
 from rdflib.namespace import XSD
-from rdflib.parser import create_input_source
+from rdflib.parser import Parser, create_input_source
 from rdflib.plugins.parsers.notation3 import BadSyntax
+from rdflib.serializer import Serializer
 from rdflib.util import guess_format
 
 logger = logging.getLogger(__name__)
@@ -302,10 +303,8 @@ def roundtrip(
 def get_formats() -> Set[str]:
     global _formats
     if not _formats:
-        serializers = set(
-            x.name for x in rdflib.plugin.plugins(None, rdflib.plugin.Serializer)
-        )
-        parsers = set(x.name for x in rdflib.plugin.plugins(None, rdflib.plugin.Parser))
+        serializers = set(x.name for x in rdflib.plugin.plugins(None, Serializer))
+        parsers = set(x.name for x in rdflib.plugin.plugins(None, Parser))
         _formats = {
             format for format in parsers.intersection(serializers) if "/" not in format
         }

test/test_sparql/test_service.py

@@ -1,11 +1,8 @@
 import json
 from contextlib import ExitStack
 from test.utils import helper
-from test.utils.httpservermock import (
-    MethodName,
-    MockHTTPResponse,
-    ServedBaseHTTPServerMock,
-)
+from test.utils.http import MethodName, MockHTTPResponse
+from test.utils.httpservermock import ServedBaseHTTPServerMock
 from typing import (
     Dict,
     FrozenSet,

test/test_store/test_store_sparqlstore.py

@@ -3,11 +3,8 @@
 import socket
 from http.server import BaseHTTPRequestHandler, HTTPServer
 from test.utils import helper
-from test.utils.httpservermock import (
-    MethodName,
-    MockHTTPResponse,
-    ServedBaseHTTPServerMock,
-)
+from test.utils.http import MethodName, MockHTTPResponse
+from test.utils.httpservermock import ServedBaseHTTPServerMock
 from threading import Thread
 from typing import Callable, ClassVar, Type
 from unittest.mock import patch
@@ -16,7 +13,7 @@
 
 from rdflib import Graph, Literal, URIRef
 from rdflib.namespace import FOAF, RDF, RDFS, XMLNS, XSD
-from rdflib.plugins.stores.sparqlstore import SPARQLConnector
+from rdflib.plugins.stores.sparqlconnector import SPARQLConnector
 
 
 class TestSPARQLStoreGraph:

test/test_store/test_store_sparqlstore_query.py

@@ -3,11 +3,8 @@
 import itertools
 import logging
 from test.utils import GraphHelper
-from test.utils.httpservermock import (
-    MethodName,
-    MockHTTPResponse,
-    ServedBaseHTTPServerMock,
-)
+from test.utils.http import MethodName, MockHTTPResponse
+from test.utils.httpservermock import ServedBaseHTTPServerMock
 from typing import Dict, Iterable, List, Optional, Set, Tuple
 
 import pytest