⚡ Bolt: Streaming File Loading Optimization

[erayfirat]

💡 What: Replaced the file loading mechanism in app.py. Instead of reading the entire streamlit.UploadedFile content into memory (read().decode()) and wrapping it in StringIO, we now use io.TextIOWrapper to stream and decode the file content on-the-fly.

🎯 Why: The previous approach required allocating memory for:

1. The raw bytes of the file.
2. The decoded string of the file (which can be larger).
3. The StringIO buffer.
   For large proteomics files (hundreds of MBs to GBs), this caused significant memory pressure and potentially Out-Of-Memory errors.

📊 Impact:

• Memory: Reduces peak memory usage during file loading by avoiding full-file in-memory duplication. The file is now processed in chunks.
• Speed: Reduces initial load time by avoiding the synchronous read() and decode() of the entire file before parsing begins.

🔬 Measurement:

• Verified with tests/test_streaming_io.py which confirms pyteomics can read from io.TextIOWrapper correctly.
• Integration tests pass, ensuring no regression in app functionality.

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PR created automatically by Jules for task 7318918625458296556 started by @erayfirat

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