feat: Rust fixes, benchmarks, tests + Python tooling (pre-commit, CI, uv)

[vandan-revanur]

Summary

This PR brings together two workstreams:

1. Rust fixes, benchmarks & tests

• SMILES parser fixes (aromatic bonds, ring closures, 60+ bracket elements)
• Fingerprint replaced with ECFP2-style Morgan hashing (FNV-1a)
• Canonical SMILES rewritten with pre-pass DFS
• 481 tests, 0 failures (up from 64)
• Large-scale and extreme-scale benchmarks vs RDKit

2. Python tooling (from python-cookiecutter)

• .pre-commit-config.yaml — trailing-whitespace, ruff, detect-secrets, pytest-testmon (pre-commit), pytest-xdist (pre-push)
• .github/workflows/ci.yml — lint via pre-commit hooks → build+test (maturin+xdist) → RDKit cross-validation (main only)
• pyproject.toml — dev deps (maturin, pre-commit, pytest, ruff, mypy, testmon, xdist), ruff/mypy/pytest/coverage config
• .editorconfig, .secrets.baseline
• uv.lock for reproducible installs
• All lint errors resolved (71 → 0)
• README updated: uv-based setup, dev environment section, uv run commands throughout

CI pipeline

push / PR
│
├── lint  (pre-commit run --all-files, skipping pytest hooks)  ← fast gate
│
├── test  (maturin develop --release + pytest -n auto)          ← needs: lint
│
└── rdkit-validation  (main/master only)                        ← needs: test

Local setup

uv sync
uv run maturin develop --release
uv run pre-commit install --install-hooks
uv run pre-commit install --hook-type pre-push