chore(deps): refresh pyproject lower bounds + dependabot config

[jphein]

Summary

• pyproject.toml: bump direct lower bounds to current latest where reasonable
• .github/dependabot.yml: target main explicitly, group security updates, ignore chromadb

Pin bumps (direct deps only)

package	before	after	latest on PyPI
huggingface_hub	>=0.20	>=1.0	1.16.1
tokenizers	>=0.15	>=0.23	0.23.1
numpy	>=1.24	>=2.0	2.4.6
python-dateutil	>=2.8	>=2.9	2.9.0.post0
httpx (kg-extract extra)	>=0.27	>=0.28	0.28.1

pyyaml already at >=6.0,<7 — left alone (matches the target floor).
chromadb (<2) untouched per JP's call: we don't use it directly but the
import path still resolves through it.

pydantic was on the bump request but it's transitive (via chromadb,
not in our direct deps list) — pinning it directly would expand our surface
without benefit, so it's deliberately omitted. Happy to add it as a direct
pin if the team wants explicit control over the version.

Dependabot config changes

 - package-ecosystem: "pip"
   directory: "/"
+  target-branch: "main"
   schedule:
     interval: "weekly"
   open-pull-requests-limit: 5
+  groups:
+    security-updates:
+      applies-to: security-updates
+      patterns: ["*"]
+  ignore:
+    - dependency-name: "chromadb"

 - package-ecosystem: "github-actions"
   directory: "/"
+  target-branch: "main"
   schedule:
     interval: "weekly"
   open-pull-requests-limit: 3
+  groups:
+    security-updates:
+      applies-to: security-updates
+      patterns: ["*"]

Test plan

• pip install --dry-run -e . resolves cleanly with new floors (numpy 2.4.6, huggingface_hub 1.16.1, tokenizers 0.23.1, python-dateutil 2.9.0.post0, httpx 0.28.1) on Python 3.12
• tomllib.load() parses pyproject.toml without error
• yaml.safe_load() parses dependabot.yml; both ecosystems show target=main, security-updates group, chromadb ignored on pip
• Dependabot picks up the new config on next weekly run (will land in main after merge)
• requires-python>=3.9 preserved — numpy 2.0 and huggingface_hub 1.0 both still ship 3.9 wheels at the requested floor

🤖 Generated with Claude Code

[gemini-code-assist]

Summary of Changes

Hello, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request updates the project's dependency floor requirements to align with current stable versions and refines the automated dependency management configuration. These changes improve security maintenance and ensure that the project remains compatible with modern package versions while maintaining explicit control over specific transitive dependencies.

Highlights

• Dependency Version Bumps: Updated the lower bounds for several direct dependencies in pyproject.toml, including huggingface_hub, tokenizers, numpy, python-dateutil, and httpx, to ensure compatibility with recent releases.
• Dependabot Configuration: Enhanced the Dependabot configuration to target the main branch, introduced grouping for security updates, and added an ignore rule for chromadb.

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[gemini-code-assist]

Code Review

This pull request updates the Dependabot configuration to target the main branch and group security updates, while also bumping several minimum dependency versions in pyproject.toml (including huggingface_hub, tokenizers, numpy, python-dateutil, and httpx). The review feedback points out two important issues: first, ignoring chromadb entirely in Dependabot prevents critical security alerts, so it is recommended to only ignore regular version updates; second, bumping numpy to >=2.0 may cause compatibility issues with older versions of onnxruntime (versions 1.16 to 1.18), so the minimum onnxruntime version in optional dependencies should be bumped to >=1.19.0.

[gemini-code-assist]

Ignoring chromadb entirely will also prevent Dependabot from opening pull requests for critical security vulnerabilities in this dependency. Since chromadb is still installed and resolved in your environment, it is safer to only ignore regular version updates while allowing security updates to go through.

You can achieve this by adding update-types: ["version-update"] to the ignore rule.

    ignore:
      # chromadb is pinned <2 deliberately — we don't use it but the import
      # path still resolves through it. Skip until we drop the dep entirely.
      - dependency-name: "chromadb"
        update-types:
          - "version-update"

[gemini-code-assist]

Bumping the minimum numpy version to >=2.0 may introduce compatibility issues with onnxruntime (specified in the gpu, dml, and coreml extras as >=1.16).

Official support for NumPy 2.0 was only introduced in onnxruntime version 1.19.0. Users installing these extras might encounter runtime errors if an older version of onnxruntime (e.g., 1.16 to 1.18) is resolved alongside NumPy 2.0.

Consider bumping the minimum onnxruntime versions in the optional dependencies to >=1.19.0 to ensure compatibility.

[Copilot]

Pull request overview

This PR refreshes the project’s direct dependency lower bounds in pyproject.toml and adjusts Dependabot configuration to target main, group security updates, and ignore chromadb updates.

Changes:

• Bumped lower bounds for huggingface_hub, tokenizers, numpy, python-dateutil, and httpx (kg-extract extra).
• Updated Dependabot config to explicitly target main and group security updates.
• Configured Dependabot to ignore chromadb updates.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
pyproject.toml	Raises minimum versions for several direct runtime dependencies and the kg-extract extra.
.github/dependabot.yml	Adds target-branch: main, groups security updates, and ignores chromadb for pip updates.

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