Add ruff format linter and fix current codebase

[scal444]

No description provided.

[greptile-apps]

Greptile Summary

This PR introduces ruff format as a new automated formatter for the Python codebase, adding a CI workflow job and a helper shell script, and then applies the formatter's output across all 15 changed Python files. The pyproject.toml include list is simultaneously widened to cover all of nvmolkit, benchmarks, and setup.py, so the new CI gate enforces consistent formatting going forward.

• All Python changes are purely cosmetic — single quotes → double quotes, blank lines between top-level definitions, long lines wrapped with parentheses, and alignment-style spaces removed. No logic, control flow, or API surface was altered.
• admin/run_ruff_format.sh checks that ruff is installed, warns (but does not fail) on version mismatch, and accepts -d for dry-run mode via --check; this mirrors the pattern of the existing run_cmake_format_lint.sh.
• CI job pins ruff to 0.15.8 and runs the dry-run script; the job structure is consistent with the other lint jobs already in lint.yml.
• pyproject.toml scope expansion is coherent with the files touched in this PR — nothing is left out that was reformatted, and nothing extra is included beyond what is reasonable for a library of this size.

Confidence Score: 5/5

Safe to merge — all changes are pure formatting with no semantic or logic modifications.

Every Python file change is a mechanical ruff format output (quote style, whitespace, line wrapping). The new CI job and script are well-structured and consistent with existing tooling. No P0 or P1 findings were identified.

No files require special attention.

Important Files Changed

Filename	Overview
.github/workflows/lint.yml	Adds new ruff-format CI job that installs ruff 0.15.8 and runs the format check in dry-run mode; straightforward and consistent with the existing lint job pattern.
admin/run_ruff_format.sh	New shell script that validates the installed ruff version, accepts a -d flag for dry-run (--check) mode, and runs ruff format over the repo root; well-structured and consistent with sibling scripts.
pyproject.toml	Expands ruff's include list from just nvmolkit/tests/conftest.py to all Python files in nvmolkit, benchmarks, and setup.py, aligning the linter scope with the files actually reformatted in this PR.
nvmolkit/similarity.py	Pure formatting changes: function signatures reformatted to one parameter per line, long ternary expressions wrapped in parentheses, blank lines added between top-level definitions; no logic changes.
nvmolkit/tests/test_substructure.py	Large formatting-only pass: blank lines added before class definitions, trailing whitespace removed from docstrings, multi-line assert messages reformatted, alignment-style spaces removed from list literals.

_{Reviews (2): Last reviewed commit: "Ruff version pin and chekc" | Re-trigger Greptile}

[evasnow1992]

Changes look good to me. Thank you!