chore: slim DiffBio runtime dependencies

[mahdi-shafiei]

chore: slim DiffBio runtime dependencies

What

Removes pre-commit and ruff from the runtime dependency list, along with the
# Development essentials comment that grouped them.

Why

pip install diffbio installed a git hook manager and a linter. Neither appears anywhere in
src/ or in tests/; they are development tooling that was placed in [project] dependencies
rather than in an extra.

Why this is safe

Verified absent from the shipped and tested code:

DiffBio / pre-commit : src=0  tests=0
DiffBio / ruff       : src=0  tests=0

Positive control on the same search: pytest returns tests=273 in the sibling repo, so a zero
here is a true negative rather than a broken search.

Deliberately not changed

rdkit stays in the base dependencies. It is module-level in
src/diffbio/operators/drug_discovery/primitives.py and it is a legitimate cheminformatics
dependency for a bioinformatics library, not incidental weight.

pandas continues to appear in the resolution. It arrives through anndata, which requires
pandas>=2.3, and anndata is core to the single-cell operators. Correct, and left alone.

Measured effect

Resolution with Avitai sibling packages excluded: 100 packages before, 90 after. The larger
share of DiffBio's install weight comes from its siblings and is addressed by their own patches
in this series.

Verification before merge

• pip install diffbio then python -c "import diffbio" in a clean virtual environment
• Confirm CI installs the test or dev extra, since pre-commit and ruff are no longer implied