Updated dependencies using deptry, modernized tooling

[jamesbraza]

This PR updates our tooling:

• Pulled in pytest v9
• Linting dependencies using https://github.com/osprey-oss/deptry
• Modernized pre-commit stack

[Copilot]

Pull request overview

This PR modernizes the project’s Python tooling stack by upgrading core dev dependencies (notably pytest v9), introducing deptry for dependency-linting, and updating pre-commit hooks and related configuration across the monorepo packages.

Changes:

• Upgrade testing/tooling dependencies (incl. pytest>=9) and refresh pre-commit hook revisions.
• Add deptry configuration (root + packages) and run deptry in CI for the root project and each packages/* project.
• Adjust tests and lockfile/package extras to align with updated dev dependency layout.

Reviewed changes

Copilot reviewed 15 out of 16 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
uv.lock	Updates locked dependency set; adds deptry and related deps; adjusts extras/dev requirements across packages.
pyproject.toml	Adds deptry config, updates dev deps (incl. pytest>=9), adds pydantic-core, and modifies pytest configuration location/format.
.github/workflows/tests.yml	Runs deptry in the lint job for root and each package directory.
.pre-commit-config.yaml	Bumps revisions for ruff, prettier, toml-sort, uv-pre-commit, and pyproject schema validation hooks.
tests/test_utils.py	Removes pytest_subtests import and updates subtests annotation.
tests/test_tools.py	Removes pytest_subtests import and updates subtests annotation.
tests/test_envs.py	Removes pytest_subtests import and updates subtests annotation.
src/aviary/utils.py	Docstring section ordering tweak (Returns/Raises).
src/aviary/core.py	Removes duplicate eval_answer entry in exported names list.
packages/notebook/src/aviary/envs/notebook/utils.py	Docstring section ordering tweak (Returns/Raises).
packages/notebook/pyproject.toml	Adds dev deps for tests + deptry config; adds typing-extensions for <3.13.
packages/lfrqa/pyproject.toml	Expands dev deps to include pytest tooling + adds deptry config.
packages/labbench/tests/test_tasks.py	Removes pytest_subtests import and updates subtests annotation.
packages/labbench/pyproject.toml	Adjusts dependencies/dev deps (incl. pytest>=9) and adds deptry config.
packages/hotpotqa/pyproject.toml	Adds a dev extra (pytest tooling) and deptry config.
packages/gsm8k/pyproject.toml	Adds a dev extra (pytest tooling) and deptry config.

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[jabra]

LGTM