fix: clean denaturant blacklist and fix exp-method regex#4
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fix: clean denaturant blacklist and fix exp-method regex#4
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- Remove duplicate entries (*.txt was listed twice) - Organize into logical sections with comments - Add exception for trizod/potenci/data/ directory - Use proper gitignore patterns (directories with trailing /) - POTENCI data files are now included as required dependencies
- Add 6 CSV tables extracted from inline strings - Add comprehensive README documenting data format - Data sourced from Nielsen & Mulder (2018) POTENCI algorithm Files added: - tablecent.csv: Central residue chemical shifts - tablenei.csv: Neighbor residue corrections - tabletermcorrs.csv: Terminal corrections - tabletempk.csv: Temperature coefficients - tablecombdevs.csv: Combinatorial deviations - tablephshifts.csv: pH-dependent shifts - README.md: Comprehensive documentation
- Add comprehensive type hints (ShiftDict, CorrectionDict, etc.) - Replace unsafe eval() calls with safe float conversion - Implement CSV-based data loading with caching - Add PhysicalConstants dataclass - Remove all backward compatibility wrappers - Update module docstring with academic references Security: Eliminates eval() vulnerability Performance: Cached data loading with lru_cache Maintainability: Type-safe, well-documented API
- Add comprehensive module docstring - Fix typo: logging.waring() to logging.warning() - Update outdated comments (python2.x to python3.10+) - Replace ##-style comments with proper documentation - Update to use new constants API (PHYSICAL_CONSTANTS, load_* functions) - Improve CLI documentation in main()
- Export modern API: load_central_shifts, PHYSICAL_CONSTANTS, etc. - Remove legacy exports: R, a, b, cutoff, e, ncycles - Add module docstring - Update __all__ for clean public API
- Remove setup.py (replaced by pyproject.toml) - Add uv.lock for reproducible dependencies - Configure hatchling to include potenci/data files - Update build system to use modern Python packaging standards Migration: setup.py → pyproject.toml + uv Build backend: hatchling Lock file: uv.lock for reproducibility
- Run ruff check --fix --unsafe-fixes on all modules - Apply ruff format for consistent code style - Fix import ordering, comparison operators, nested if statements - Remove unused variables and imports - Add explicit exception handling (no bare excepts) - Rename functions to follow snake_case convention: - get_pH → get_ph - convChi2CDF → conv_chi2_cdf - get_offset_corrected_wSCS → get_offset_corrected_wscs - Rename exceptions to follow Error suffix convention: - Found → FoundError - OffsetTooLargeException → OffsetTooLargeError - OffsetCausedFilterException → OffsetCausedFilterError - FilterException → FilterError - Fix lambda loop variable binding issue - Add exception chaining with "from e"
…equires-python - Replace deprecated np.float with np.float64 (removed in NumPy 1.24+) - Replace eval() with float() in read_csv_pkaoutput (security fix) - Fix argument count mismatch in getpredshifts_arr -> getphcorrs_arr call - Remove dead code: unused log_fun(), no-op str(i+1) statements - Bump requires-python from >=3.8 to >=3.9 (BooleanOptionalAction, dict |) - Exclude test/ from ruff config (pre-existing issues, not part of package) - Add implementation plan document for BMRB expert suggestions Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Replace blanket *.csv/*.txt/*.zip patterns with specific directory rules for clarity and transparency. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Remove 9 non-denaturant items (reducing agents, NMR reference standard, buffers) from strict chemical-denaturants list. Fix exp-method-blacklist by removing 'state' substring which incorrectly matched 'solution-state' and 'liquid-state' entries. Addresses expert suggestions #3 and #5. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Summary
chemical-denaturantslist: reducing agents (BME, 2-ME, mercaptoethanol, DTT, dithiothreitol), NMR reference standard (dss), and NMR buffers (acetic acid, CD3COOH, deuterated sodium acetate)exp-method-blacklistby removing"state"substring from regex list, which incorrectly matched"solution-state"and"liquid-state"entries, excluding valid NMR dataTest plan
exp-method-blacklistfilterssolidbut notsolution-stateorliquid-stateAddresses expert suggestions #3 and #5.
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