Dependency update sweep: bump all deps to latest and re-lock

.agents/skills/update-deps/references/migration-gotchas.md

@@ -24,10 +24,7 @@ Fix — split positional indices instead of the frame, then select rows with `il
 return [pd.DataFrame(fold) for fold in np.array_split(reports, n)]
 
 # Fixed — preserves columns, dtypes, and even fold sizes
-return [
-    reports.iloc[indices]
-    for indices in np.array_split(np.arange(len(reports)), n)
-]
+return [reports.iloc[indices] for indices in np.array_split(np.arange(len(reports)), n)]
 ```
 
 ### `copy=` keyword removed from `merge`/`concat`/`join`/`set_axis` etc.

.semversioner/next-release/patch-20260818203711168483.json

@@ -0,0 +1,4 @@
+{
+  "type": "patch",
+  "description": "Update dependencies to their latest versions."
+}

docs/config/models.md

@@ -89,10 +89,12 @@ Once you have a model implementation, you need to register it with our completio
 ```python
 from graphrag_llm.completion import LLMCompletion, register_completion
 
+
 class MyCustomCompletionModel(LLMCompletion):
     ...
     # implementation
 
+
 # elsewhere...
 register_completion("my-custom-completion-model", MyCustomCompletionModel)
 ```

packages/graphrag-cache/README.md

@@ -35,8 +35,9 @@ from graphrag_cache.json_cache import JsonCache
 # May also register a custom implementation, see above for example.
 cache_factory.register("my_cache_impl", JsonCache)
 
-cache = cache_factory.create(strategy="my_cache_impl", init_args={"some_setting": "..."})
+cache = cache_factory.create(
+    strategy="my_cache_impl", init_args={"some_setting": "..."}
+)
 
 ...
-
 ```

packages/graphrag-chunking/pyproject.toml

@@ -31,7 +31,7 @@ classifiers = [
 ]
 dependencies = [
     "graphrag-common==3.1.1",
-    "pydantic~=2.10",
+    "pydantic~=2.13",
 ]
 
 [project.urls]

packages/graphrag-common/pyproject.toml

@@ -30,7 +30,7 @@ classifiers = [
     "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
-    "python-dotenv~=1.0",
+    "python-dotenv~=1.2",
     "pyyaml~=6.0",
     "toml~=0.10",
 ]

packages/graphrag-input/pyproject.toml

@@ -32,7 +32,7 @@ classifiers = [
 dependencies = [
     "graphrag-common==3.1.1",
     "graphrag-storage==3.1.1",
-    "pydantic~=2.10",
+    "pydantic~=2.13",
     "markitdown[pdf]~=0.1.0",
     "pyarrow>=14.0.0"
 ]

packages/graphrag-llm/pyproject.toml

@@ -38,12 +38,12 @@ dependencies = [
     "graphrag-cache==3.1.1",
     "graphrag-common==3.1.1",
     "jinja2~=3.1",
-    "litellm==1.92.0",
+    "litellm==1.97.0",
     "nest-asyncio2~=1.7",
     # orjson is required for litellm tool calling. https://github.com/BerriAI/litellm/issues/32993
     "orjson>=3.11.6,<4.0",
-    "pydantic~=2.10",
-    "typing-extensions~=4.12",
+    "pydantic~=2.13",
+    "typing-extensions~=4.16",
 ]
 
 [project.urls]

packages/graphrag-storage/README.md

@@ -37,8 +37,9 @@ from graphrag_storage.file_storage import FileStorage
 # May also register a custom implementation, see above for example.
 storage_factory.register("my_storage_key", FileStorage)
 
-storage = storage_factory.create(strategy="my_storage_key", init_args={"base_dir": "...", "other_settings": "..."})
+storage = storage_factory.create(
+    strategy="my_storage_key", init_args={"base_dir": "...", "other_settings": "..."}
+)
 
 ...
-
 ```

packages/graphrag-storage/pyproject.toml

@@ -31,12 +31,12 @@ classifiers = [
 ]
 dependencies = [
     "aiofiles~=25.1",
-    "azure-cosmos~=4.9",
+    "azure-cosmos~=4.16",
     "azure-identity~=1.25",
-    "azure-storage-blob~=12.24",
+    "azure-storage-blob~=12.30",
     "graphrag-common==3.1.1",
     "pandas~=3.0",
-    "pydantic~=2.10",
+    "pydantic~=2.13",
 ]
 
 [project.urls]

packages/graphrag-vectors/pyproject.toml

@@ -30,15 +30,15 @@ classifiers = [
     "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
-    "azure-core~=1.32",
-    "azure-cosmos~=4.9",
+    "azure-core~=1.41",
+    "azure-cosmos~=4.16",
     "azure-identity~=1.25",
     "azure-search-documents~=12.0",
     "graphrag-common==3.1.1",
-    "lancedb~=0.34.0",
+    "lancedb~=0.37.0",
     "numpy~=2.1",
     "pyarrow~=25.0",
-    "pydantic~=2.10",
+    "pydantic~=2.13",
 ]
 
 [project.urls]

packages/graphrag/pyproject.toml

@@ -34,7 +34,7 @@ classifiers = [
 dependencies = [
     "azure-identity~=1.25",
     "azure-search-documents~=12.0",
-    "azure-storage-blob~=12.24",
+    "azure-storage-blob~=12.30",
     "devtools~=0.12",
     "graphrag-cache==3.1.1",
     "graphrag-chunking==3.1.1",
@@ -47,19 +47,19 @@ dependencies = [
     # output (community counts/levels), which breaks pinned regression tests and the
     # golden community data. Revisit deliberately with a golden-data refresh.
     "graspologic-native>=1.2,<1.3",
-    "json-repair~=0.30",
-    "networkx~=3.4",
-    "nltk~=3.9",
+    "json-repair~=0.63",
+    "networkx~=3.6",
+    "nltk~=3.10",
     "numpy~=2.1",
     "pandas~=3.0",
     "pyarrow~=25.0",
-    "pydantic~=2.10",
+    "pydantic~=2.13",
     "spacy~=3.8",
-    "blis~=1.0",
-    "textblob~=0.18",
-    "tqdm~=4.67",
-    "typing-extensions~=4.12",
-    "typer~=0.16",
+    "blis~=1.3",
+    "textblob~=0.20",
+    "tqdm~=4.70",
+    "typing-extensions~=4.16",
+    "typer~=0.27",
 ]
 
 [project.scripts]

pyproject.toml

@@ -25,23 +25,23 @@ requires-python = ">=3.11,<3.14"
 
 [dependency-groups]
 dev = [
-    "coverage~=7.6",
-    "deptry~=0.21",
+    "coverage~=7.15",
+    "deptry~=0.25",
     "ipykernel~=7.3",
     "jupyter~=1.1",
-    "mkdocs-material~=9.5",
-    "mkdocs-jupyter~=0.25",
+    "mkdocs-material~=9.7",
+    "mkdocs-jupyter~=0.26",
     "mkdocs-exclude-search~=0.6",
     "mkdocs-typer~=0.0.3",
-    "nbconvert~=7.16",
+    "nbconvert~=7.17",
     "pandas-stubs~=3.0",
-    "poethepoet~=0.31",
+    "poethepoet~=0.48",
     "pyright~=1.1",
     "pytest~=9.1",
     "pytest-asyncio~=1.4",
     "pytest-dotenv~=0.5",
-    "pytest-timeout~=2.3",
-    "ruff~=0.8",
+    "pytest-timeout~=2.4",
+    "ruff~=0.16",
     "semversioner~=3.0",
     "update-toml~=0.2",
     "pytest-xdist[psutil]~=3.8.0",
@@ -224,7 +224,13 @@ ignore = [
     "PERF203", # Needs restructuring of errors, we should bail-out on first error
     "C901",    # needs refactoring to remove cyclomatic complexity
     "B008", # Needs to restructure our cli params with Typer into constants
-    "ASYNC240"
+    "ASYNC240",
+    # Opinionated preview rule (ruff >=0.16) that flags `# noqa` in favor of
+    # `# ruff: ignore`; we intentionally keep `# noqa` comments.
+    "RUF105",
+    # Opinionated preview rule (ruff >=0.16) that flags rule codes (instead of
+    # names) in the lint selectors below; we intentionally use rule codes.
+    "RUF201",
 ]
 
 [tool.ruff.lint.per-file-ignores]