fix(deps): update all non-major dependencies (#378)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: James Braza <[email protected]>

Author: renovate[bot]

.github/renovate.json5

@@ -31,5 +31,10 @@
       matchPackageNames: ["torch"],
       allowedVersions: "<2.6",
     },
+    {
+      // Match pyproject.toml
+      matchPackageNames: ["dask-cuda"],
+      allowedVersions: "<25.10.0",
+    },
   ],
 }

.pre-commit-config.yaml

@@ -20,17 +20,17 @@ repos:
       - id: mixed-line-ending
       - id: trailing-whitespace
   - repo: https://github.com/jsh9/markdown-toc-creator
-    rev: 0.0.10
+    rev: 0.1.3
     hooks:
       - id: markdown-toc-creator
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.0
+    rev: v0.14.7
     hooks:
       - id: ruff-check
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
   - repo: https://github.com/rbubley/mirrors-prettier
-    rev: v3.6.2
+    rev: v3.7.3
     hooks:
       - id: prettier
   - repo: https://github.com/Yelp/detect-secrets
@@ -47,7 +47,7 @@ repos:
     hooks:
       - id: blacken-docs
   - repo: https://github.com/jsh9/markdown-toc-creator
-    rev: 0.0.10
+    rev: 0.1.3
     hooks:
       - id: markdown-toc-creator
   - repo: https://github.com/jumanjihouse/pre-commit-hooks
@@ -70,15 +70,15 @@ repos:
       - id: nb-clean
         args: [--preserve-cell-outputs, --remove-empty-cells]
   - repo: https://github.com/jackdewinter/pymarkdown
-    rev: v0.9.32
+    rev: v0.9.33
     hooks:
       - id: pymarkdown
   - repo: https://github.com/henryiii/validate-pyproject-schema-store
-    rev: 2025.10.03
+    rev: 2025.11.21
     hooks:
       - id: validate-pyproject
   - repo: https://github.com/astral-sh/uv-pre-commit
-    rev: 0.9.0
+    rev: 0.9.13
     hooks:
       - id: uv-lock
   - repo: local

packages/lmi/README.md

@@ -20,6 +20,10 @@ pip install fhlmi
 
 <!--TOC-->
 
+---
+
+**Table of Contents**
+
 - [Installation](#installation)
 - [Quick start](#quick-start)
 - [Documentation](#documentation)
@@ -41,6 +45,8 @@ pip install fhlmi
     - [HybridEmbeddingModel](#hybridembeddingmodel)
     - [SentenceTransformerEmbeddingModel](#sentencetransformerembeddingmodel)
 
+---
+
 <!--TOC-->
 
 ## Quick start

pyproject.toml

@@ -114,6 +114,10 @@ check-hidden = true
 ignore-words-list = "astroid,ser"
 skip = "**tests/cassettes/*,**/tests/cassettes/*"
 
+[tool.markdown_toc_creator]
+horizontal-rule-style = "prettier"
+proactive = false
+
 [tool.mypy]
 # Type-checks the interior of functions without type annotations.
 check_untyped_defs = true
@@ -202,6 +206,12 @@ max-attributes = 12
 max-line-length = 88  # Match ruff line-length
 
 [tool.pylint.main]
+# Files or directories matching the regular expression patterns are skipped.
+# The regex matches against base names, not paths. The default value ignores
+# Emacs file locks
+ignore-patterns = [
+    "^version\\.py$",  # Version files made by setuptools_scm
+]
 # Use multiple processes to speed up Pylint. Specifying 0 will auto-detect the
 # number of processors available to use, and will cap the count on Windows to
 # avoid hangs.
@@ -359,6 +369,7 @@ extend-select = [
     "B909",
     "B912",
     "CPY001",
+    "DOC102",
     "DOC201",
     "DOC202",
     "DOC402",
@@ -560,6 +571,7 @@ mypy-init-return = true
     "E501",  # Tests can have long strings
     "F841",  # Tests can have unused locals
     "N802",  # Tests function names can match class names
+    "PLC2701",  # Test can import private names if needed
     "PLR2004",  # Tests can have magic values
     "PLR6301",  # Test classes can ignore self
     "S101",  # Tests can have assertions

tests/test_context_managers.py

@@ -15,7 +15,7 @@
     set_training_mode,
     train_mode,
 )
-from ldp.graph.op_utils import _RUN_ID  # noqa: PLC2701
+from ldp.graph.op_utils import _RUN_ID
 
 
 @pytest.mark.asyncio

tests/test_torch_ops.py

@@ -12,7 +12,7 @@
 from ldp.graph import ConfigOp, FxnOp, PromptOp, compute_graph, set_training_mode
 from ldp.graph.async_torch import (
     AsyncTorchModule,
-    _get_autocast_context,  # noqa: PLC2701
+    _get_autocast_context,
     async_protect_torch_call,
 )
 from ldp.graph.gradient_estimators import straight_through_estimator as ste