Add comprehensive repository audit report#3
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Full audit covering security, code quality, CI/CD, testing, and documentation. Key findings: no security vulnerabilities, 2 bugs (README API examples use wrong params, gaps rendered in wrong color), and several low-severity improvement items. https://claude.ai/code/session_0131auyCkmPyg7DpokpeA1Vw
tests/output/ contains reference rendered images so users can browse example output without running tests. Added an explanatory comment to .gitignore to prevent future confusion about why it's not ignored. https://claude.ai/code/session_0131auyCkmPyg7DpokpeA1Vw
Bugs fixed: - README API examples now use correct `columns` parameter (#1) - Gaps render in grey (GAP_COLOR) instead of black (TEXT_COLOR) (#2) Testing: - Added test_bam.py with 17 tests: 12 unit tests for CIGAR ops (match, insertion, deletion, soft-clip, ref-skip, windowing, complex mixed CIGARs) + 5 integration tests using example BAMs (#3) CI/CD: - Added lint job (black --check, isort --check) to CI workflow (#4) - Added Python 3.12 to test matrix (#10) Config & docs: - Fixed homepage URLs to tmsincomb/tview (#5) - Added [compose] optional-dependency extra for patchworklib, moved patchworklib from core deps since it's not imported (#6) - Replaced print() with logging.info() in renderer (#7) - mono_sm tick-label font now uses 0.8x fontsize (#8) - Panel.ins_columns uses field(default_factory=set) (#11) Test output images updated to reflect gap color and font changes. https://claude.ai/code/session_0131auyCkmPyg7DpokpeA1Vw
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Full audit covering security, code quality, CI/CD, testing,
and documentation. Key findings: no security vulnerabilities,
2 bugs (README API examples use wrong params, gaps rendered
in wrong color), and several low-severity improvement items.
https://claude.ai/code/session_0131auyCkmPyg7DpokpeA1Vw