chore(deps): consolidate dependabot updates and bump all dependencies (#266)

Bump all pending dependabot PRs in one commit and reconfigure
dependabot to run weekly with max 1 open PR per ecosystem.

- psutil 6.1.1 → 7.2.2
- transformers 4.57.1 → 5.4.0
- protobuf 6.33.5 → 7.34.1
- sphinx 8.2.3 → 9.1.0
- sphinx-rtd-theme 3.0.2 → 3.1.0
- sphinx-autodoc-typehints 3.1.0 → 3.9.11
- myst-parser 4.0.1 → 5.0.0
- pytest-cov 7.0.0 → 7.1.0
- scipy 1.16.3 → 1.17.1
- aiohttp 3.13.4 → 3.13.5

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: viraatc

.github/dependabot.yml

@@ -3,18 +3,23 @@ updates:
   - package-ecosystem: "pip"
     directory: "/"
     schedule:
-      interval: "daily"
-    open-pull-requests-limit: 10
+      interval: "weekly"
+      day: "monday"
+    open-pull-requests-limit: 1
     labels: ["dependencies", "security"]
 
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-      interval: "daily"
+      interval: "weekly"
+      day: "monday"
+    open-pull-requests-limit: 1
     labels: ["dependencies", "ci"]
 
   - package-ecosystem: "docker"
     directory: "/scripts"
     schedule:
-      interval: "daily"
+      interval: "weekly"
+      day: "monday"
+    open-pull-requests-limit: 1
     labels: ["dependencies", "docker"]

pyproject.toml

@@ -29,7 +29,7 @@ dependencies = [
     # Core Python dependencies
     "typing-extensions==4.15.0",
     # System utilities
-    "psutil==6.1.1",
+    "psutil==7.2.2",
     # Async and networking
     "pyzmq==27.1.0",
     "uvloop==0.22.1",
@@ -44,12 +44,12 @@ dependencies = [
     "cyclopts==4.10.0",
     "rich==14.3.3",
     # Needed for tokenization and OSL reporting
-    "transformers==4.57.1",
+    "transformers==5.4.0",
     "numpy==2.4.4",
     "datasets==4.8.4",
     "Pillow==12.1.1",
     "sentencepiece==0.2.1",
-    "protobuf==6.33.5",
+    "protobuf==7.34.1",
     "openai_harmony==0.0.8",
     # Color support for cross-platform terminals
     "colorama==0.4.6",
@@ -71,10 +71,10 @@ dev = [
     "line-profiler==5.0.2",
     "Pympler==1.1",
     # Documentation
-    "sphinx==8.2.3",
-    "sphinx-rtd-theme==3.0.2",
-    "sphinx-autodoc-typehints==3.1.0",
-    "myst-parser==4.0.1",
+    "sphinx==9.1.0",
+    "sphinx-rtd-theme==3.1.0",
+    "sphinx-autodoc-typehints==3.9.11",
+    "myst-parser==5.0.0",
     # Security auditing
     "pip-audit==2.10.0",
 ]
@@ -84,17 +84,17 @@ test = [
     # Testing framework
     "pytest==9.0.2",
     "pytest-asyncio==1.3.0",
-    "pytest-cov==7.0.0",
+    "pytest-cov==7.1.0",
     "pytest-benchmark==5.2.3",
     "pytest-timeout==2.4.0",
     "pytest-xdist==3.8.0",
     # Test utilities
     "coverage==7.13.4",
     "line-profiler==5.0.2",
     "Pympler==1.1",
-    "scipy==1.16.3",
+    "scipy==1.17.1",
     # HTTP server and client for mock server fixture
-    "aiohttp==3.13.4",
+    "aiohttp==3.13.5",
     # Plotting for benchmark sweep mode
     "matplotlib==3.10.8",
 ]