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gh-248: a few fixes for ignored and recommended ruff rules (#360)

Fixed:
- missing-trailing-comma
- commented-out-code
- single-line-implicit-string-concatenation
- numpy-legacy-random
- pytest-raises-too-broad

Refs: #248

146 of 276 branches covered (52.9%)

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1054 of 1734 relevant lines covered (60.78%)

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Source Files on job run-3.11 - 11345132033.4