build: Adopt uv as the project package manager

[kunaaaalcodes]

Closes #469

Overview

This PR completes the migration to uv as the project's single dependency management tool.

While parts of the project had already adopted uv (uv.lock and the type-check-python workflow), the rest of the repository still relied on pip, requirements.txt, and tox. This resulted in duplicated configuration, inconsistent developer workflows, and non-reproducible dependency installation.

This change standardizes dependency management across local development, CI, and documentation.

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What's Changed

Dependency Management

• Added PEP 735 dependency groups:
  • dev for development tools (e.g. ruff)
  • docs for documentation tooling (sphinx, mkdocs, pybind11-stubgen, etc.)
• Added an explicit coverage dependency to the test extras.
• Moved pytest configuration from tox.ini to pyproject.toml.
• Replaced cibuildwheel's test-requires requirements file with explicit packages.
• Regenerated and verified uv.lock using:
  • uv lock --check
  • uv sync --locked

CI

Updated all Python workflows to use uv.

• Replaced pip install with uv sync --locked.
• Replaced direct tool execution with uv run.
• Updated:
  • lint-python
  • prime-*-build-caches
  • run-tests
  • run-tests-in-parallel
  • run-tests-with-address-sanitizer
  • deploy-docs

Optional dependencies (such as TensorFlow and google-cloud-storage) continue to be installed using uv pip install so they remain outside the lock file.

Documentation

Updated CONTRIBUTING.md to use the new workflow.

• pip3 install pybind11 tox → uv sync --all-extras --dev
• tox → uv run pytest

The testing, documentation, style, ccache, and troubleshooting sections were updated accordingly.

Cleanup

Removed legacy dependency management files:

• tox.ini
• requirements.txt
• test-requirements.txt
• dev-requirements.txt
• docs-requirements.txt

Also:

• Added uv.lock to MANIFEST.in
• Removed the obsolete .tox/ entry from .gitignore

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Notable Fix

Regenerating uv.lock exposed a compatibility issue with Python 3.14.

The previous lock file pinned numpy==2.2.5, which has no pre-built wheels for Python 3.14 and would trigger a source build during CI.

The lock file now pins an appropriate NumPy version for each supported Python release, ensuring wheel-based installation across the CI matrix.

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Result

After this PR:

• uv is the single dependency manager.
• pyproject.toml is the single source of truth.
• uv.lock provides fully reproducible installations.
• Local development, CI, and documentation all use the same workflow.
• Dependency installation is faster and deterministic.

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Testing

Verified locally:

uv lock --check
uv sync --locked --all-extras --dev

Tested with:

• Python 3.10
• Python 3.12
• Python 3.14

Also verified:

• Documentation installation (--group docs)
• GitHub workflow YAML validity
• CI linting, type checking, and test execution

Note

The build-wheels workflow intentionally continues installing
cibuildwheel via pip, since it manages its own isolated build
environments and is outside the scope of this PR.