Update dependencies 2025-10

.gitignore

@@ -204,3 +204,6 @@ build-iPhoneSimulator/
 
 # Avoid accidental commiting of dev notebooks
 examples/dev/*
+
+# Datasets from loaders such as OGBLoader
+dataset/

changelog.md

@@ -11,3 +11,8 @@
 ## Improvements
 
 ## Other changes
+
+- Add support for PyArrow 21.0.0
+- Drop support for PyArrow 17.0
+- Support numpy 1.24.0
+- Add support for neo4j 6.0

graphdatascience/error/cypher_warning_handler.py

@@ -27,6 +27,17 @@ def wrapper(self: CallerBase, *args: Any, **kwargs: Any) -> Any:
                 message=r"The query used a deprecated function. \('id'.*",
             )
 
+            # with neo4j driver 6.0.0
+            warnings.filterwarnings(
+                "ignore",
+                message=r"warn: feature deprecated with replacement\. id is deprecated. It is replaced by elementId or consider using an application-generated id\.",
+            )
+            # with neo4j driver 6.0.0 + Neo4j 5.X
+            warnings.filterwarnings(
+                "ignore",
+                message=r"warn: feature deprecated without replacement\. id is deprecated and will be removed without a replacement\.",
+            )
+
             return func(self, *args, **kwargs)
 
         return cast(F, wrapper)

graphdatascience/graph/ogb_loader.py

@@ -111,7 +111,7 @@ def _parse_homogeneous(self, dataset: HomogeneousOGBNDataset) -> tuple[list[pd.D
             node_dict["features"] = graph["node_feat"].tolist()  # type: ignore
 
         if len(dataset.labels[0]) == 1:
-            node_dict["classLabel"] = [cl[0] for cl in dataset.labels]
+            node_dict["classLabel"] = [cl[0] for cl in dataset.labels]  # type: ignore
         else:
             node_dict["classLabel"] = dataset.labels.tolist()  # type: ignore
 
@@ -174,7 +174,7 @@ def _parse_heterogeneous(self, dataset: HeterogeneousOGBNDataset) -> tuple[list[
 
             if node_label in class_labels:
                 if len(class_labels[node_label]) == 1:
-                    node_dict["classLabel"] = [cl[0] for cl in class_labels[node_label]]
+                    node_dict["classLabel"] = [cl[0] for cl in class_labels[node_label]]  # type: ignore
                 else:
                     node_dict["classLabel"] = class_labels[node_label].tolist()  # type: ignore
 

graphdatascience/query_runner/neo4j_query_runner.py

@@ -196,14 +196,12 @@ def run_cypher(
             df = result.to_df()
 
             if self._NEO4J_DRIVER_VERSION < SemanticVersion(5, 0, 0):
-                self._last_bookmarks = [session.last_bookmark()]
+                self._last_bookmarks = [session.last_bookmark()]  # type: ignore
             else:
                 self._last_bookmarks = session.last_bookmarks()
 
-            notifications = result.consume().notifications
-            if notifications:
-                for notification in notifications:
-                    self._forward_cypher_warnings(notification)
+            result_summary = result.consume()
+            self._handle_notifications(result_summary)
 
             return df
 
@@ -321,7 +319,21 @@ def encrypted(self) -> bool:
     def driver_config(self) -> dict[str, Any]:
         return self._config
 
-    def _forward_cypher_warnings(self, notification: dict[str, Any]) -> None:
+    def _handle_notifications(self, result_summary: neo4j.ResultSummary) -> None:
+        if self._NEO4J_DRIVER_VERSION < SemanticVersion(6, 0, 0):
+            notifications = result_summary.notifications
+            if notifications:
+                for notification in notifications:
+                    self._forward_cypher_notification(notification)
+        if self._NEO4J_DRIVER_VERSION >= SemanticVersion(6, 0, 0):
+            status_objects = result_summary.gql_status_objects
+            for status in status_objects:
+                if status.raw_classification == "DEPRECATION" and not re.match(
+                    r"(.*returned by the procedure.*)|(.*procedure field deprecated.*)", status.status_description
+                ):
+                    warnings.warn(DeprecationWarning(status.status_description))
+
+    def _forward_cypher_notification(self, notification: dict[str, Any]) -> None:
         # (see https://neo4j.com/docs/status-codes/current/notifications/ for more details)
         severity = notification["severity"]
         if severity == "WARNING":
@@ -434,7 +446,7 @@ def _verify_connectivity(
                         category=neo4j.ExperimentalWarning,
                         message=r"^The configuration may change in the future.$",
                     )
-                else:
+                elif self._NEO4J_DRIVER_VERSION < SemanticVersion(6, 0, 0):
                     warnings.filterwarnings(
                         "ignore",
                         category=neo4j.ExperimentalWarning,
@@ -443,6 +455,13 @@ def _verify_connectivity(
                             "They might be changed or removed in any future version without prior notice.$"
                         ),
                     )
+                else:
+                    warnings.filterwarnings(
+                        "ignore",
+                        category=neo4j.warnings.PreviewWarning,  # type: ignore[attr-defined]
+                        message=(r"^Passing key-word arguments to verify_connectivity\(\) is a preview feature.*"),
+                    )
+
                 self._driver.verify_connectivity(database=database)
                 break
             except neo4j.exceptions.DriverError as e:
@@ -478,6 +497,9 @@ def __configure_warnings_filter(self) -> None:
         warnings.filterwarnings("ignore", message=r".*The procedure has a deprecated field.*by 'gds.*")
         # neo4j driver 4.4
         warnings.filterwarnings("ignore", message=r".*The query used a deprecated field from a procedure.*by 'gds.*")
+        # neo4j driver 6.0
+        warnings.filterwarnings("ignore", message=r".*returned by the procedure.* is deprecated.*")
+        warnings.filterwarnings("ignore", message=r".*procedure field deprecated..*")
 
     class ConnectivityRetriesConfig(NamedTuple):
         max_retries: int = 600

graphdatascience/tests/integration/conftest.py

@@ -131,6 +131,13 @@ def is_neo4j_44(gds: GraphDataScience) -> bool:
         return False
 
 
+def id_warning_pattern() -> str:
+    if neo4j.__version__.startswith("6."):
+        return r"(.*feature deprecated without replacement\. id is deprecated and will be removed without a replacement.*)|(.*feature deprecated with replacement\. id is deprecated.*)"
+    else:
+        return r".*The query used a deprecated function.*[`']id[`'].*"
+
+
 @pytest.fixture(autouse=True)
 def clean_up(gds: GraphDataScience) -> Generator[None, None, None]:
     yield

graphdatascience/tests/integration/test_error_handling.py

@@ -5,7 +5,7 @@
 
 from graphdatascience import GraphDataScience
 from graphdatascience.server_version.server_version import ServerVersion
-from graphdatascience.tests.integration.conftest import AUTH, URI, is_neo4j_44
+from graphdatascience.tests.integration.conftest import AUTH, URI, id_warning_pattern, is_neo4j_44
 
 GRAPH_NAME = "g"
 
@@ -207,7 +207,7 @@ def test_forward_server_side_warning(gds: GraphDataScience) -> None:
     if is_neo4j_44(gds):
         return
 
-    with pytest.raises(Warning, match="The query used a deprecated function.*[`']id[`'].*"):
+    with pytest.raises(Warning, match=id_warning_pattern()):
         gds.run_cypher("MATCH (n) RETURN id(n)")
 
 
@@ -219,7 +219,7 @@ def test_forward_driver_configured_warning(warning_driver: Driver) -> None:
     if is_neo4j_44(gds):
         return
 
-    with pytest.raises(Warning, match="The query used a deprecated function.*[`']id[`'].*"):
+    with pytest.raises(Warning, match=id_warning_pattern()):
         gds.run_cypher("MATCH (n) RETURN id(n)")
 
 

graphdatascience/tests/integration/test_graph_ops.py

@@ -9,7 +9,7 @@
 from graphdatascience.query_runner.arrow_query_runner import ArrowQueryRunner
 from graphdatascience.query_runner.query_runner import QueryRunner
 from graphdatascience.server_version.server_version import ServerVersion
-from graphdatascience.tests.integration.conftest import AUTH, DB, URI, is_neo4j_44
+from graphdatascience.tests.integration.conftest import AUTH, DB, URI, id_warning_pattern, is_neo4j_44
 
 GRAPH_NAME = "g"
 
@@ -844,7 +844,7 @@ def test_graph_relationships_stream_without_arrow(gds_without_arrow: GraphDataSc
     else:
         result = gds_without_arrow.beta.graph.relationships.stream(G, ["REL", "REL2"])
 
-    warnings.filterwarnings("ignore", category=DeprecationWarning, message="The query used a deprecated function")
+    warnings.filterwarnings("ignore", category=DeprecationWarning, message=id_warning_pattern())
     expected = gds_without_arrow.run_cypher(
         "MATCH (n)-[r]->(m) RETURN id(n) AS src_id, id(m) AS trg_id, type(r) AS rel_type"
     )

graphdatascience/tests/integration/test_model_ops.py

@@ -321,6 +321,7 @@ def test_missing_model_drop(gds: GraphDataScience) -> None:
 
 @pytest.mark.model_store_location
 @pytest.mark.filterwarnings("ignore: The query used a deprecated procedure.")
+@pytest.mark.filterwarnings("ignore: .*feature deprecated with replacement")
 def test_deprecated_model_Functions_still_work(gds: GraphDataScience, gs_model: GraphSageModel) -> None:
     gds.beta.model.list()
     gds.alpha.model.store(gs_model)

graphdatascience/tests/integration/test_system_ops.py

@@ -70,6 +70,7 @@ def test_list_defaults(gds: GraphDataScience) -> None:
 
 
 @pytest.mark.filterwarnings("ignore: The query used a deprecated procedure")
+@pytest.mark.filterwarnings("ignore: .*feature deprecated with replacement")
 @pytest.mark.enterprise
 @pytest.mark.skip_on_aura
 def test_alpha_backup(gds: GraphDataScience) -> None:
@@ -88,6 +89,7 @@ def test_backup(gds: GraphDataScience) -> None:
 
 
 @pytest.mark.filterwarnings("ignore: The query used a deprecated procedure")
+@pytest.mark.filterwarnings("ignore: .*feature deprecated with replacement")
 @pytest.mark.enterprise
 @pytest.mark.skip_on_aura
 def test_alpha_restore(gds: GraphDataScience) -> None:
@@ -106,6 +108,7 @@ def test_restore(gds: GraphDataScience) -> None:
 
 
 @pytest.mark.filterwarnings("ignore: The query used a deprecated procedure")
+@pytest.mark.filterwarnings("ignore: .*feature deprecated with replacement.")
 @pytest.mark.compatible_with(min_inclusive=ServerVersion(2, 5, 0))
 def test_deprecated_endpoints(gds: GraphDataScience) -> None:
     gds.beta.listProgress()

requirements/base/base.txt

@@ -1,8 +1,8 @@
 multimethod >= 1.0, < 3.0
-neo4j >= 4.4.12, < 6.0
-numpy < 2.3
+neo4j >= 4.4.12, < 7.0
+numpy < 2.4
 pandas >= 1.0, < 3.0
-pyarrow >= 17.0, < 21.0
+pyarrow >= 17.0, < 22.0
 textdistance >= 4.0, < 5.0
 tqdm >= 4.0, < 5.0
 typing-extensions >= 4.0, < 5.0

requirements/dev/dev.txt

@@ -2,7 +2,7 @@ ruff == 0.11.7
 mypy == 1.13.0
 nbconvert == 7.16.4
 pandas-stubs == 2.2.3.241009
-tox == 4.11.3
+tox == 4.30.2
 types-setuptools == 75.8.0.20250110
 sphinx == 7.3.7
 enum-tools[sphinx] == 0.12.0

requirements/dev/test.txt

@@ -1,5 +1,5 @@
 pytest == 8.3.3
 requests_mock == 1.11.0
-pytest_mock == 3.12.0
+pytest_mock == 3.15.1
 testcontainers >= 4.0, < 4.13.0
 python-dateutil >= 2.9

tox.ini

@@ -1,29 +1,33 @@
 [tox]
 envlist =
-	# Vary Neo4j & Pandas versions
-	py{39, 310}-neo4j{4,5}-pandas{1,2}-main-{standard,encrypted},
-	# Vary Pandas 1.x + PyArrow
-	py{39,310}-pandas1-pyarrow{17, 18, 19, 20}-main-{standard,encrypted},
-	py311-pandas1-pyarrow{17, 18, 19, 20}-main-{standard,encrypted},
-	# Vary Pandas 2.x + PyArrow
-	py{39,310,311}-pandas2-pyarrow{19, 20}-main-{standard,encrypted},
+	# Vary Pandas versions
+	py310-neo4j6-pandas{1,2}-main-standard,
+	# Vary Neo4j versions
+	py310-neo4j{4,5,6}-pandas2-main-standard,
+	# Vary Pandas
+	py310-pandas{1,2}-pyarrow21-main-standard,
+	# Vary PyArrow
+	py311-pandas2-pyarrow{18, 19, 20, 21}-main-standard,
 	# Vary Python version
-	py3{12,13}-pandas2-pyarrow{20}-main-{standard,encrypted},
+	py3{9, 10, 11, 12, 13}-pandas2-pyarrow21-main-standard,
 
-	# PR envs
-	py{39,310}-neo4j{4,5}-pullrequest-{standard,encrypted},
-	py{311,312,313}-pullrequest-{standard,encrypted},
+	# encrypted tests
+	py310-neo4j6-pandas2-pyarrow21-main-encrypted,
 
-	# Aura
+	# against an AuraDS instance
 	py311-main-aura,
 
+	# Vary networkx & neo4j versions only for relevant tests
+	py311-neo4j{4,5,6}-pandas2-pyarrow20-networkx{2,3}-main-nx,
+
 	# Session tests
 	py39-neo4j{5}-pyarrow17-main-{cloud-architecture}
-	py39-pullrequest-{cloud-architecture}
 
-	# Vary networkx versions only for relevant tests
-	py311-neo4j{4,5}-pandas1-pyarrow20-networkx{2,3}-main-nx
-	py311-neo4j{4,5}-pandas2-pyarrow20-networkx{2,3}-main-nx
+
+	# PR envs
+	py10-neo4j{4,5,6}-pullrequest-{standard,encrypted},
+	py{39,311,312,313}-pullrequest-standard,
+	py39-pullrequest-{cloud-architecture}
 	py311-networkx3-pullrequest-nx
 
 	# Notebooks
@@ -45,14 +49,15 @@ deps =
 	-r {toxinidir}/requirements/dev/test.txt
 	neo4j4: neo4j >= 4.4.2, < 5.0
 	neo4j5: neo4j >= 5.0, < 6.0
+	neo4j6: neo4j >= 6.0, < 7.0
 	pandas1: pandas >= 1.0, < 2.0
 	pandas1: numpy == 1.24.3
 	pandas2: pandas >= 2.2.2, < 3.0
 	pandas2: numpy >= 2.0
-	pyarrow17: pyarrow >= 17.0, < 18.0
 	pyarrow18: pyarrow >= 18.0, < 19.0
 	pyarrow19: pyarrow >= 19.0, < 20.0
 	pyarrow20: pyarrow >= 20.0, < 21.0
+	pyarrow21: pyarrow >= 21.0, < 22.0
 	networkx2: networkx >= 2.0, < 3.0
 	networkx3: networkx >= 3.0, < 4.0
 commands =