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🎨 Palette: Add progress bar for library cleaning #12

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🎨 Palette: Add progress bar for library cleaning #12

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1 change: 1 addition & 0 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ dependencies = [
"matchms>=0.23",
"numpy>=1.24",
"PyYAML>=6.0",
"tqdm>=4.66",
]

[project.optional-dependencies]
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22 changes: 7 additions & 15 deletions yogimass/processing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
from __future__ import annotations

import logging
from tqdm import tqdm
from matchms.importing import load_from_mgf, load_from_msp
from matchms.filtering import (
default_filters,
Expand All @@ -25,9 +26,6 @@

logger = logging.getLogger(__name__)

# Interval for progress logging
LOG_INTERVAL = 1000


def metadata_processing(spectrum):
"""
Expand Down Expand Up @@ -78,19 +76,16 @@ def clean_mgf_library(mgf_path: str) -> list:
"""
logger.info(f"Cleaning {mgf_path} library spectra...")
library_list = list(load_from_mgf(mgf_path))

# Apply filters sequentially
processed_spectra = []
for i, s in enumerate(library_list):
if (i + 1) % LOG_INTERVAL == 0:
logger.info(f"Processed {i + 1} / {len(library_list)} spectra...")

for s in tqdm(library_list, desc="Cleaning spectra", unit="spectrum"):
meta_processed = metadata_processing(s)
if meta_processed:
peak_processed = peak_processing(meta_processed)
if peak_processed:
processed_spectra.append(peak_processed)

logger.info(f"Retained {len(processed_spectra)} spectra after cleaning.")
return processed_spectra

Expand All @@ -101,17 +96,14 @@ def clean_msp_library(msp_path: str) -> list:
"""
logger.info(f"Cleaning {msp_path} library spectra...")
library_list = list(load_from_msp(msp_path))

processed_spectra = []
for i, s in enumerate(library_list):
if (i + 1) % LOG_INTERVAL == 0:
logger.info(f"Processed {i + 1} / {len(library_list)} spectra...")

processed_spectra = []
for s in tqdm(library_list, desc="Cleaning spectra", unit="spectrum"):
meta_processed = metadata_processing(s)
if meta_processed:
peak_processed = peak_processing(meta_processed)
if peak_processed:
processed_spectra.append(peak_processed)

logger.info(f"Retained {len(processed_spectra)} spectra after cleaning.")
return processed_spectra