⚡ Bolt: Optimized DataFrame construction in map_psms_to_spectra#27
⚡ Bolt: Optimized DataFrame construction in map_psms_to_spectra#27
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- Use `.tolist()` when iterating over `matched_spec_series` to create `specs_list`. This avoids the overhead of iterating over a pandas Series directly, resulting in a ~2.7x speedup for this operation. - Update `.gitignore` to include `__pycache__/` to keep the repository clean. Co-authored-by: erayfirat <59361860+erayfirat@users.noreply.github.com>
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💡 What: Optimized the iteration over
matched_spec_seriesinprocessing.pyby converting it to a list using.tolist()before the list comprehension. Also updated.gitignoreto exclude__pycache__files.🎯 Why: Iterating directly over a pandas Series is slow due to index access and boxing overhead. Converting to a native Python list removes this overhead.
📊 Impact: The iteration step is approximately 2.7x faster (measured in synthetic benchmark). This improves the performance of the PSM-to-spectrum mapping process, especially for large datasets.
🔬 Measurement:
Ran a benchmark comparing
[x for x in series]vs[x for x in series.tolist()].Result: 0.0177s vs 0.0065s (~2.7x faster).
Existing tests passed.
PR created automatically by Jules for task 14220710222280695807 started by @erayfirat