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🎨 Palette: Add progress bar and improve CLI feedback #9

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🎨 Palette: Add progress bar and improve CLI feedback #9

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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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8 changes: 7 additions & 1 deletion yogimass/cli.py
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Expand Up @@ -72,8 +72,13 @@ def run_clean(args):
output_dir = args.output_dir
export_format = args.format

if not os.path.exists(input_path):
logger.error(f"Input file not found: {input_path}")
return 1

if not os.path.exists(output_dir):
os.makedirs(output_dir)
logger.info(f"Created output directory: {output_dir}")

logger.info(f"Starting clean operation on {input_path}")

Expand Down Expand Up @@ -101,7 +106,8 @@ def run_clean(args):
io.save_spectra_to_mgf(spectra, output_dir, lib_name)
elif export_format == "json":
io.save_spectra_to_json(spectra, output_dir, lib_name)


logger.info(f"Successfully processed {len(spectra)} spectra and saved to {output_dir}")
return 0


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14 changes: 3 additions & 11 deletions yogimass/processing.py
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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 @@ -81,10 +79,7 @@ def clean_mgf_library(mgf_path: str) -> list:

# 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="Processing MGF library", unit="spectra"):
meta_processed = metadata_processing(s)
if meta_processed:
peak_processed = peak_processing(meta_processed)
Expand All @@ -103,10 +98,7 @@ def clean_msp_library(msp_path: str) -> list:
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...")

for s in tqdm(library_list, desc="Processing MSP library", unit="spectra"):
meta_processed = metadata_processing(s)
if meta_processed:
peak_processed = peak_processing(meta_processed)
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