Combined dependency updates (10 dependabot PRs)

[xhan97]

Combines the 10 open dependabot PRs into a single branch, plus one fix needed to unblock the notebook upgrade.

Included PRs

Python deps

• Bump ruff from 0.15.7 to 0.15.16 #43 ruff 0.15.7 → 0.15.16 (lock only)
• Bump tqdm from 4.67.3 to 4.68.0 #42 tqdm 4.67.3 → 4.68.0 (lock only)
• Bump notebook from 6.4.12 to 7.5.7 #41 notebook 6.4.12 → 7.5.7
• Bump mkdocs-jupyter from 0.26.1 to 0.26.3 #35 mkdocs-jupyter 0.26.1 → 0.26.3
• Bump mike from 2.1.4 to 2.2.0 #33 mike 2.1.4 → 2.2.0

GitHub Actions

• Bump codecov/codecov-action from 4.5.0 to 6.0.0 #29 codecov/codecov-action 4.5.0 → 6.0.0
• Bump actions/setup-python from 5 to 6 #28 actions/setup-python 5 → 6
• Bump actions/download-artifact from 4 to 8 #14 actions/download-artifact 4 → 8
• Bump actions/checkout from 4 to 6 #13 actions/checkout 4 → 6
• Bump actions/upload-artifact from 4 to 7 #12 actions/upload-artifact 4 → 7

All nine branches merged without conflicts.

Fix: drop jupyter-contrib-nbextensions

#41 was the only PR with failing CI — both docs jobs failed at mkdocs build --strict.

Root cause: jupyter-contrib-nbextensions==0.7.0 registers nbconvert exporters via entry points. When nbconvert's get_export_names() loads them, it hits from notebook.services.config import ConfigManager — a classic-notebook module removed in notebook 7:

File ".../jupyter_contrib_nbextensions/nbconvert_support/collapsible_headings.py", line 6
from notebook.services.config import ConfigManager
ModuleNotFoundError: No module named 'notebook.services'

Nothing in the project or mkdocs.yml references nbextensions — the pin is a leftover from the old poetry config (it still appears in pyproject_old.toml). The package is also unmaintained and hard-pinned to classic notebook <7, so it would block every future notebook upgrade. Removed it.

Verification

Ran the equivalent of all three CI workflows locally on this branch:

• uv run mkdocs build --strict — passes
• uv run pytest — 125 passed
• uv run black --check . — clean
• uv run ruff check . — clean
• uv lock --check — lockfile consistent

Note

notebook is now likely unnecessary in the docs group too — mkdocs-jupyter pulls in nbconvert/nbclient itself, and nbextensions was the only thing that needed the notebook package. Left it in place here to keep this PR scoped to the dependency bumps; worth a follow-up.

Closes#43, closes#42, closes#41, closes#35, closes#33, closes#29, closes#28, closes#14, closes#13, closes#12