chore(deps): bump the python-deps group with 16 updates (#497)

Bumps the python-deps group with 16 updates:

| Package | From | To |
| --- | --- | --- |
| [click](https://github.com/pallets/click) | `8.3.2` | `8.4.1` |
| [pandas](https://github.com/pandas-dev/pandas) | `3.0.2` | `3.0.3` |
| [pymongo](https://github.com/mongodb/mongo-python-driver) | `4.16.0` | `4.17.0` |
| [requests](https://github.com/psf/requests) | `2.33.1` | `2.34.2` |
| [tqdm](https://github.com/tqdm/tqdm) | `4.67.3` | `4.68.1` |
| [openai](https://github.com/openai/openai-python) | `2.31.0` | `2.41.0` |
| [black](https://github.com/psf/black) | `26.3.1` | `26.5.1` |
| [ruff](https://github.com/astral-sh/ruff) | `0.15.10` | `0.15.16` |
| [mypy](https://github.com/python/mypy) | `1.20.1` | `2.1.0` |
| [pre-commit](https://github.com/pre-commit/pre-commit) | `4.5.1` | `4.6.0` |
| [types-requests](https://github.com/python/typeshed) | `2.33.0.20260408` | `2.33.0.20260518` |
| [linkml](https://github.com/linkml/linkml) | `1.9.3` | `1.11.1` |
| [notebook](https://github.com/jupyter/notebook) | `7.5.6` | `7.5.7` |
| [matplotlib](https://github.com/matplotlib/matplotlib) | `3.10.8` | `3.10.9` |
| [numpy](https://github.com/numpy/numpy) | `2.4.4` | `2.4.6` |
| [chromadb](https://github.com/chroma-core/chroma) | `1.5.7` | `1.5.9` |


Updates `click` from 8.3.2 to 8.4.1
- [Release notes](https://github.com/pallets/click/releases)
- [Changelog](https://github.com/pallets/click/blob/main/CHANGES.rst)
- [Commits](pallets/click@8.3.2...8.4.1)

Updates `pandas` from 3.0.2 to 3.0.3
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Commits](pandas-dev/pandas@v3.0.2...v3.0.3)

Updates `pymongo` from 4.16.0 to 4.17.0
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](mongodb/mongo-python-driver@4.16.0...4.17.0)

Updates `requests` from 2.33.1 to 2.34.2
- [Release notes](https://github.com/psf/requests/releases)
- [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md)
- [Commits](psf/requests@v2.33.1...v2.34.2)

Updates `tqdm` from 4.67.3 to 4.68.1
- [Release notes](https://github.com/tqdm/tqdm/releases)
- [Commits](tqdm/tqdm@v4.67.3...v4.68.1)

Updates `openai` from 2.31.0 to 2.41.0
- [Release notes](https://github.com/openai/openai-python/releases)
- [Changelog](https://github.com/openai/openai-python/blob/main/CHANGELOG.md)
- [Commits](openai/openai-python@v2.31.0...v2.41.0)

Updates `black` from 26.3.1 to 26.5.1
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](psf/black@26.3.1...26.5.1)

Updates `ruff` from 0.15.10 to 0.15.16
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.15.10...0.15.16)

Updates `mypy` from 1.20.1 to 2.1.0
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.20.1...v2.1.0)

Updates `pre-commit` from 4.5.1 to 4.6.0
- [Release notes](https://github.com/pre-commit/pre-commit/releases)
- [Changelog](https://github.com/pre-commit/pre-commit/blob/main/CHANGELOG.md)
- [Commits](pre-commit/pre-commit@v4.5.1...v4.6.0)

Updates `types-requests` from 2.33.0.20260408 to 2.33.0.20260518
- [Commits](https://github.com/python/typeshed/commits)

Updates `linkml` from 1.9.3 to 1.11.1
- [Release notes](https://github.com/linkml/linkml/releases)
- [Commits](linkml/linkml@v1.9.3...v1.11.1)

Updates `notebook` from 7.5.6 to 7.5.7
- [Release notes](https://github.com/jupyter/notebook/releases)
- [Changelog](https://github.com/jupyter/notebook/blob/@jupyter-notebook/tree@7.5.7/CHANGELOG.md)
- [Commits](https://github.com/jupyter/notebook/compare/@jupyter-notebook/tree@7.5.6...@jupyter-notebook/tree@7.5.7)

Updates `matplotlib` from 3.10.8 to 3.10.9
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](matplotlib/matplotlib@v3.10.8...v3.10.9)

Updates `numpy` from 2.4.4 to 2.4.6
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v2.4.4...v2.4.6)

Updates `chromadb` from 1.5.7 to 1.5.9
- [Release notes](https://github.com/chroma-core/chroma/releases)
- [Changelog](https://github.com/chroma-core/chroma/blob/main/RELEASE_PROCESS.md)
- [Commits](chroma-core/chroma@1.5.7...1.5.9)

---
updated-dependencies:
- dependency-name: click
  dependency-version: 8.4.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-deps
- dependency-name: pandas
  dependency-version: 3.0.3
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-deps
- dependency-name: pymongo
  dependency-version: 4.17.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-deps
- dependency-name: requests
  dependency-version: 2.34.2
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-deps
- dependency-name: tqdm
  dependency-version: 4.68.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-deps
- dependency-name: openai
  dependency-version: 2.41.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-deps
- dependency-name: black
  dependency-version: 26.5.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-deps
- dependency-name: ruff
  dependency-version: 0.15.16
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-deps
- dependency-name: mypy
  dependency-version: 2.1.0
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: python-deps
- dependency-name: pre-commit
  dependency-version: 4.6.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-deps
- dependency-name: types-requests
  dependency-version: 2.33.0.20260518
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-deps
- dependency-name: linkml
  dependency-version: 1.11.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-deps
- dependency-name: notebook
  dependency-version: 7.5.7
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-deps
- dependency-name: matplotlib
  dependency-version: 3.10.9
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-deps
- dependency-name: numpy
  dependency-version: 2.4.6
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-deps
- dependency-name: chromadb
  dependency-version: 1.5.9
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-deps
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Author: dependabot[bot]

pyproject.toml

@@ -24,16 +24,16 @@ classifiers = [
 ]
 
 dependencies = [
-    "click>=8.3.0",
+    "click>=8.4.1",
     "kgx>=2.1.0",
-    "pandas>=2.3.3",
-    "pymongo>=4.15.3",
+    "pandas>=3.0.3",
+    "pymongo>=4.17.0",
     "python-dotenv>=1.2.1",
     "pyyaml>=6.0.3",
     "rdflib>=7.1.4",
-    "requests>=2.32.5",
+    "requests>=2.34.2",
     "rich>=13.0.0",
-    "tqdm>=4.67.1",
+    "tqdm>=4.68.1",
 ]
 
 [project.urls]
@@ -48,43 +48,43 @@ test = [
 ]
 dev = [
     "oaklib>=0.6.23",
-    "pandas>=2.3.3",
-    "pymongo>=4.15.3",
+    "pandas>=3.0.3",
+    "pymongo>=4.17.0",
     "rdflib>=7.1.4",
     "semsql>=0.4.0",
-    "tqdm>=4.67.1",
-    "openai>=2.6.1",
+    "tqdm>=4.68.1",
+    "openai>=2.41.0",
     # Testing
     "pytest>=9.0.3",
     # Code quality tools
-    "black>=24.0.0",
-    "ruff>=0.8.4",
-    "mypy>=1.13.0",
-    "pre-commit>=4.0.1",
+    "black>=26.5.1",
+    "ruff>=0.15.16",
+    "mypy>=2.1.0",
+    "pre-commit>=4.6.0",
     "types-PyYAML>=6.0.12",
-    "types-requests>=2.32.0",
+    "types-requests>=2.33.0.20260518",
 ]
 literature = [
     "artl-mcp>=0.34.0",
-    "linkml>=1.8.5",
+    "linkml>=1.11.1",
     "oaklib>=0.6.23",
-    "pandas>=2.3.3",
-    "openai>=2.6.1",
+    "pandas>=3.0.3",
+    "openai>=2.41.0",
     "semsql>=0.4.0",
 ]
 databases = [
-    "pandas>=2.3.3",
-    "pymongo>=4.15.3",
+    "pandas>=3.0.3",
+    "pymongo>=4.17.0",
 ]
 notebooks = [
     "jupyter>=1.1.1",
-    "notebook>=7.5.6",
-    "matplotlib>=3.10.7",
-    "numpy>=2.0.2",
+    "notebook>=7.5.7",
+    "matplotlib>=3.10.9",
+    "numpy>=2.4.6",
     "python-levenshtein>=0.27.1",
-    "chromadb>=1.2.2",
-    "tqdm>=4.67.1",
-    "openai>=2.6.1",
+    "chromadb>=1.5.9",
+    "tqdm>=4.68.1",
+    "openai>=2.41.0",
 ]
 
 [project.scripts]