Reduce warnings (#3085)

* build(deps-dev): bump ruff from 0.9.2 to 0.9.6

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.9.2 to 0.9.6.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.9.2...0.9.6)

---
updated-dependencies:
- dependency-name: ruff
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* add readthedocs sphynx.configuration

* replace ConjunctiveGraph() with Dataset() in tests

* tidy some notation

* align black version

* fix black & ruff

* poetry --check -> poetry-check --lock

* more CG -> Datasets

* ruff

* GC -> Dataset

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Author: nicholascar

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
         args: ["--fix"]
   - repo: https://github.com/psf/black-pre-commit-mirror
     # WARNING: Black version should be the same as in `pyproject.toml`
-    rev: "25.1.0"
+    rev: "24.4.2"
     hooks:
     - id: black
       pass_filenames: false
@@ -24,6 +24,5 @@ repos:
     rev: 2.1.1
     hooks:
     - id: poetry-check
-    - id: poetry-lock
       # sadly `--no-update` does not work on pre-commit.ci
-      args: ["--check"]
+      args: ["--lock"]

rdflib/plugins/parsers/notation3.py

@@ -57,7 +57,7 @@
 
 from rdflib.compat import long_type
 from rdflib.exceptions import ParserError
-from rdflib.graph import ConjunctiveGraph, Graph, QuotedGraph
+from rdflib.graph import Dataset, Graph, QuotedGraph
 from rdflib.term import (
     _XSD_PFX,
     BNode,
@@ -2047,7 +2047,7 @@ def parse(  # type: ignore[override]
         elif not fa:
             raise ParserError("Cannot parse N3 into non-formula-aware store.")
 
-        conj_graph = ConjunctiveGraph(store=graph.store)
+        conj_graph = Dataset(store=graph.store)
         conj_graph.default_context = graph  # TODO: CG __init__ should have a
         # default_context arg
         # TODO: update N3Processor so that it can use conj_graph as the sink

test/test_graph/test_diff.py

@@ -9,7 +9,7 @@
 import rdflib
 from rdflib import Graph
 from rdflib.compare import graph_diff
-from rdflib.graph import ConjunctiveGraph, Dataset
+from rdflib.graph import Dataset
 from rdflib.namespace import FOAF, RDF
 from rdflib.term import BNode, Literal
 from test.utils import (
@@ -111,7 +111,7 @@ def as_element_set(self, value: _ElementSetTypeOrStr) -> _ElementSetType:
         if isinstance(value, str):
             graph = self.graph_type()
             graph.parse(data=value, format=self.format)
-            if isinstance(graph, ConjunctiveGraph):
+            if isinstance(graph, Dataset):
                 return GraphHelper.quad_set(graph, BNodeHandling.COLLAPSE)
             else:
                 return GraphHelper.triple_set(graph, BNodeHandling.COLLAPSE)

test/test_graph/test_graph_context.py

@@ -291,71 +291,63 @@ def test_triples(self):
 
         for c in [graph, self.graph.get_context(c1)]:
             # unbound subjects
-            asserte(set(c.subjects(likes, pizza)), set((michel, tarek)))
-            asserte(set(c.subjects(hates, pizza)), set((bob,)))
-            asserte(set(c.subjects(likes, cheese)), set([tarek, bob, michel]))
+            asserte(set(c.subjects(likes, pizza)), {michel, tarek})
+            asserte(set(c.subjects(hates, pizza)), {bob})
+            asserte(set(c.subjects(likes, cheese)), {tarek, bob, michel})
             asserte(set(c.subjects(hates, cheese)), set())
 
             # unbound objects
-            asserte(set(c.objects(michel, likes)), set([cheese, pizza]))
-            asserte(set(c.objects(tarek, likes)), set([cheese, pizza]))
-            asserte(set(c.objects(bob, hates)), set([michel, pizza]))
-            asserte(set(c.objects(bob, likes)), set([cheese]))
+            asserte(set(c.objects(michel, likes)), {cheese, pizza})
+            asserte(set(c.objects(tarek, likes)), {cheese, pizza})
+            asserte(set(c.objects(bob, hates)), {michel, pizza})
+            asserte(set(c.objects(bob, likes)), {cheese})
 
             # unbound predicates
-            asserte(set(c.predicates(michel, cheese)), set([likes]))
-            asserte(set(c.predicates(tarek, cheese)), set([likes]))
-            asserte(set(c.predicates(bob, pizza)), set([hates]))
-            asserte(set(c.predicates(bob, michel)), set([hates]))
+            asserte(set(c.predicates(michel, cheese)), {likes})
+            asserte(set(c.predicates(tarek, cheese)), {likes})
+            asserte(set(c.predicates(bob, pizza)), {hates})
+            asserte(set(c.predicates(bob, michel)), {hates})
 
-            asserte(set(c.subject_objects(hates)), set([(bob, pizza), (bob, michel)]))
+            asserte(set(c.subject_objects(hates)), {(bob, pizza), (bob, michel)})
             asserte(
                 set(c.subject_objects(likes)),
-                set(
-                    [
-                        (tarek, cheese),
-                        (michel, cheese),
-                        (michel, pizza),
-                        (bob, cheese),
-                        (tarek, pizza),
-                    ]
-                ),
+                {
+                    (tarek, cheese),
+                    (michel, cheese),
+                    (michel, pizza),
+                    (bob, cheese),
+                    (tarek, pizza),
+                },
             )
 
-            asserte(
-                set(c.predicate_objects(michel)), set([(likes, cheese), (likes, pizza)])
-            )
+            asserte(set(c.predicate_objects(michel)), {(likes, cheese), (likes, pizza)})
             asserte(
                 set(c.predicate_objects(bob)),
-                set([(likes, cheese), (hates, pizza), (hates, michel)]),
-            )
-            asserte(
-                set(c.predicate_objects(tarek)), set([(likes, cheese), (likes, pizza)])
+                {(likes, cheese), (hates, pizza), (hates, michel)},
             )
+            asserte(set(c.predicate_objects(tarek)), {(likes, cheese), (likes, pizza)})
 
             asserte(
                 set(c.subject_predicates(pizza)),
-                set([(bob, hates), (tarek, likes), (michel, likes)]),
+                {(bob, hates), (tarek, likes), (michel, likes)},
             )
             asserte(
                 set(c.subject_predicates(cheese)),
-                set([(bob, likes), (tarek, likes), (michel, likes)]),
+                {(bob, likes), (tarek, likes), (michel, likes)},
             )
-            asserte(set(c.subject_predicates(michel)), set([(bob, hates)]))
+            asserte(set(c.subject_predicates(michel)), {(bob, hates)})
 
             asserte(
                 set(c),
-                set(
-                    [
-                        (bob, hates, michel),
-                        (bob, likes, cheese),
-                        (tarek, likes, pizza),
-                        (michel, likes, pizza),
-                        (michel, likes, cheese),
-                        (bob, hates, pizza),
-                        (tarek, likes, cheese),
-                    ]
-                ),
+                {
+                    (bob, hates, michel),
+                    (bob, likes, cheese),
+                    (tarek, likes, pizza),
+                    (michel, likes, pizza),
+                    (michel, likes, cheese),
+                    (bob, hates, pizza),
+                    (tarek, likes, cheese),
+                },
             )
 
         # remove stuff and make sure the graph is empty again

test/test_graph/test_graph_formula.py

@@ -4,7 +4,7 @@
 import pytest
 
 from rdflib import RDF, RDFS, BNode, URIRef, Variable, plugin
-from rdflib.graph import ConjunctiveGraph, QuotedGraph
+from rdflib.graph import Dataset, QuotedGraph
 
 implies = URIRef("http://www.w3.org/2000/10/swap/log#implies")
 testN3 = """
@@ -21,7 +21,7 @@
 
 def checkFormulaStore(store="default", configString=None):  # noqa: N802, N803
     try:
-        g = ConjunctiveGraph(store=store)
+        g = Dataset(store=store)
     except ImportError:
         pytest.skip("Dependencies for store '%s' not available!" % store)
 
@@ -48,7 +48,7 @@ def checkFormulaStore(store="default", configString=None):  # noqa: N802, N803
         d = URIRef("http://test/d")
         v = Variable("y")
 
-        universe = ConjunctiveGraph(g.store)
+        universe = Dataset(g.store)
 
         # test formula as terms
         assert len(list(universe.triples((formulaA, implies, formulaB)))) == 1

test/test_graph/test_namespace_rebinding.py

@@ -1,6 +1,6 @@
 import pytest
 
-from rdflib import ConjunctiveGraph, Graph, Literal
+from rdflib import Dataset, Graph, Literal
 from rdflib.namespace import OWL, Namespace, NamespaceManager
 from rdflib.plugins.stores.memory import Memory
 from rdflib.term import URIRef
@@ -292,12 +292,11 @@ def test_multigraph_bindings():
     assert list(g1.namespaces()) == [("friend-of-a-friend", foaf1_uri)]
 
     # Including newly-created objects that use the store
-    cg = ConjunctiveGraph(store=store)
+    cg = Dataset(store=store, default_union=True)
     cg.namespace_manager = NamespaceManager(cg, bind_namespaces="core")
 
     assert ("foaf", foaf1_uri) not in list(cg.namespaces())
     assert ("friend-of-a-friend", foaf1_uri) in list(cg.namespaces())
-
     assert len(list(g1.namespaces())) == 6
     assert len(list(g2.namespaces())) == 6
     assert len(list(cg.namespaces())) == 6

test/test_n3.py

@@ -4,7 +4,7 @@
 
 import pytest
 
-from rdflib.graph import ConjunctiveGraph, Graph
+from rdflib.graph import Dataset, Graph
 from rdflib.plugins.parsers.notation3 import BadSyntax, exponent_syntax
 from rdflib.term import Literal, URIRef
 from test import TEST_DIR
@@ -44,7 +44,7 @@
                 n3:predicate :p;
                 n3:object :y ] a log:Truth}.
 
-# Needs more thought ... ideally, we have the implcit AND rules of
+# Needs more thought ... ideally, we have the implicit AND rules of
 # juxtaposition (introduction and elimination)
 
 {
@@ -125,9 +125,9 @@ def test_base_serialize(self):
         )
         s = g.serialize(base="http://example.com/", format="n3", encoding="latin-1")
         assert b"<people/Bob>" in s
-        g2 = ConjunctiveGraph()
-        g2.parse(data=s, publicID="http://example.com/", format="n3")
-        assert list(g) == list(g2)
+        g2 = Dataset()
+        g2.parse(data=s, format="n3")
+        assert list(g) == list(g2.triples((None, None, None)))
 
     def test_issue23(self):
         input = """<http://example.com/article1> <http://example.com/title> "this word is in \\u201Cquotes\\u201D"."""
@@ -195,24 +195,24 @@ def test_dot_in_prefix(self):
         )
 
     def test_model(self):
-        g = ConjunctiveGraph()
+        g = Dataset()
         g.parse(data=test_data, format="n3")
         i = 0
-        for s, p, o in g:
+        for s, p, o, c in g:
             if isinstance(s, Graph):
                 i += 1
         assert i == 3
-        assert len(list(g.contexts())) == 13
+        assert len(list(g.graphs())) == 13
 
         g.close()
 
     def test_quoted_serialization(self):
-        g = ConjunctiveGraph()
+        g = Dataset()
         g.parse(data=test_data, format="n3")
         g.serialize(format="n3")
 
     def test_parse(self):
-        g = ConjunctiveGraph()
+        g = Dataset()
         try:
             g.parse(
                 "http://groups.csail.mit.edu/dig/2005/09/rein/examples/troop42-policy.n3",
@@ -229,14 +229,14 @@ def test_single_quoted_literals(self):
 
         for data in test_data:
             # N3 doesn't accept single quotes around string literals
-            g = ConjunctiveGraph()
+            g = Dataset()
             with pytest.raises(BadSyntax):
                 g.parse(data=data, format="n3")
 
-            g = ConjunctiveGraph()
+            g = Dataset()
             g.parse(data=data, format="turtle")
             assert len(g) == 1
-            for _, _, o in g:
+            for _, _, o, c in g:
                 assert o == Literal("o")
 
     def test_empty_prefix(self):

test/test_parsers/test_empty_xml_base.py

@@ -5,7 +5,7 @@
 and RDF/XML dependence on it
 """
 
-from rdflib.graph import ConjunctiveGraph
+from rdflib.graph import Dataset
 from rdflib.namespace import FOAF, RDF
 from rdflib.term import URIRef
 
@@ -36,7 +36,7 @@
 
 class TestEmptyBase:
     def test_empty_base_ref(self):
-        self.graph = ConjunctiveGraph()
+        self.graph = Dataset()
         self.graph.parse(data=test_data, publicID=baseUri, format="xml")
         assert (
             len(list(self.graph)) > 0
@@ -50,7 +50,7 @@ def test_empty_base_ref(self):
 
 class TestRelativeBase:
     def test_relative_base_ref(self):
-        self.graph = ConjunctiveGraph()
+        self.graph = Dataset()
         self.graph.parse(data=test_data2, publicID=baseUri2, format="xml")
         assert (
             len(self.graph) > 0