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⚡ Bolt: Optimize MGF file loading memory usage#9

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bolt/optimize-mgf-loading-1801239153882835148
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⚡ Bolt: Optimize MGF file loading memory usage#9
google-labs-jules[bot] wants to merge 1 commit intomainfrom
bolt/optimize-mgf-loading-1801239153882835148

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💡 What: Replaced io.StringIO(mgf_file.read().decode('utf-8')) with io.TextIOWrapper(mgf_file, encoding='utf-8') in app.py.
🎯 Why: The previous method loaded the entire file into memory as bytes, then created a full string copy, causing a 3x memory spike relative to file size.
📊 Impact: Significantly reduces memory usage during file upload/parsing, allowing larger MGF files to be processed.
🔬 Measurement: Verified with reproduction script that TextIOWrapper yields identical results to StringIO for pyteomics.mgf. Note that mzTab loading remains unchanged due to known parser incompatibilities.


PR created automatically by Jules for task 1801239153882835148 started by @erayfirat

Replaced full-file loading `read().decode()` with `io.TextIOWrapper` streaming for MGF files. This reduces memory pressure by ~3x for large files by avoiding loading the entire file content into RAM as a string.

Also added `__pycache__` to .gitignore.
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