Merge pull request #481 from Climate-REF/dependabot/uv/python-dependencies-cbfbb3c6eb

Author: lewisjared

changelog/480.trivial.md

@@ -1 +1 @@
-oIgnore changelog requirement for dependabot PRs
+Ignore changelog requirement for dependabot PRs

packages/climate-ref-example/src/climate_ref_example/example.py

@@ -168,9 +168,11 @@ def execute(self, definition: ExecutionDefinition) -> None:
 
         input_datasets = definition.datasets[SourceDatasetType.CMIP6]
 
-        calculate_annual_mean_timeseries(input_files=input_datasets.path.to_list()).to_netcdf(
-            definition.output_directory / "annual_mean_global_mean_timeseries.nc"
-        )
+        result = calculate_annual_mean_timeseries(input_files=input_datasets.path.to_list())
+        # Drop time_bnds to avoid xarray cftime bounds encoding regression (xarray >= 2025.11.0)
+        if "time_bnds" in result:
+            result = result.drop_vars("time_bnds")
+        result.to_netcdf(definition.output_directory / "annual_mean_global_mean_timeseries.nc")
 
     def build_execution_result(self, definition: ExecutionDefinition) -> ExecutionResult:
         """

packages/climate-ref-ilamb/pyproject.toml

@@ -25,7 +25,8 @@ classifiers = [
 dependencies = [
   "climate-ref-core",
   "ilamb3>=2025.9.9",
-  "scipy<1.16",       # https://github.com/statsmodels/statsmodels/issues/9584
+  "scipy<1.16",        # https://github.com/statsmodels/statsmodels/issues/9584
+  "xarray<2025.11",    # ilamb3 incompatibility with integrate_space units handling
 ]
 [project.entry-points."climate-ref.providers"]
 ilamb = "climate_ref_ilamb:provider"

packages/climate-ref/src/climate_ref/datasets/base.py

@@ -219,7 +219,9 @@ def register_dataset(  # noqa: PLR0915
         slug = unique_slugs[0]
 
         # Upsert the dataset (create a new dataset or update the metadata)
-        dataset_metadata = data_catalog_dataset[list(self.dataset_specific_metadata)].iloc[0].to_dict()
+        dataset_metadata = cast(
+            dict[str, Any], data_catalog_dataset[list(self.dataset_specific_metadata)].iloc[0].to_dict()
+        )
         dataset, dataset_state = db.update_or_create(DatasetModel, defaults=dataset_metadata, slug=slug)
         if dataset_state == ModelState.CREATED:
             logger.info(f"Created new dataset: {dataset}")

packages/climate-ref/src/climate_ref/datasets/cmip6.py

@@ -53,7 +53,7 @@ def _fix_parent_variant_label(group: pd.DataFrame) -> pd.DataFrame:
     if "parent_variant_label" in data_catalog:
         data_catalog = (
             data_catalog.groupby("instance_id")
-            .apply(_fix_parent_variant_label, include_groups=False)
+            .apply(_fix_parent_variant_label, include_groups=False)  # type: ignore[call-overload]
             .reset_index(level="instance_id")
         )
 

packages/climate-ref/src/climate_ref/solver.py

@@ -130,7 +130,7 @@ def extract_covered_datasets(
         # Use a single group
         groups = [((), subset)]
     else:
-        groups = list(subset.groupby(list(requirement.group_by)))
+        groups = list(subset.groupby(list(requirement.group_by)))  # type: ignore[arg-type]
 
     results = {}
 

pyproject.toml

@@ -47,7 +47,7 @@ dev = [
     "mkdocs-autorefs>=1.0.1",
     "mkdocs-jupyter>=0.24.0",
     "mkdocs-panzoom-plugin>=0.1.3",
-    "beautifulsoup4>=4.12,<4.13",
+    "beautifulsoup4>=4.12,<4.15",
     "cartopy>=0.24.1",
     "intake-esgf>=2025.7.16",
     "ipython>=9.2.0",