Mechanical lint cleanup across the package

[galjos]

Behaviour-preserving lint cleanup, driven by ruff + pylint and guarded by the full test suite (159 passed with the DFTB+ binaries, 0 skipped). No logic changes.

Changes (all mechanical)

• Strip trailing whitespace; add missing final newlines.
• Remove useless return / return None at the end of functions.
• Drop superfluous else after return (dedent only; the prior else bodies call logger.error(..., exception=...), which raises, so control flow is unchanged).
• == None -> is None.
• Convert leftover %-formatted strings to f-strings.
• Add module docstrings (skipping the setuptools_scm-generated __version__.py).

Result

• pylint 7.40 -> 8.79.
• Remaining lint is structural and intentionally left out of this pass: attribute-defined-outside-init (Thermo sets totals in run()), invalid-name (overlaps Clean up rotational inertia naming #37), inconsistent-return-statements (the log-and-raise pattern), too-many-arguments, cyclic-import. Those want dedicated, careful PRs.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.25%. Comparing base (714a996) to head (ca7950f).

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #57      +/-   ##
==========================================
- Coverage   95.30%   95.25%   -0.05%     
==========================================
  Files          22       22              
  Lines        1321     1286      -35     
==========================================
- Hits         1259     1225      -34     
+ Misses         62       61       -1     

Flag	Coverage Δ
unittests	95.25% <100.00%> (-0.05%)	⬇️

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