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fix logging for spectral library prediction #257

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Merged
RalfG merged 2 commits into from
Feb 10, 2026
Merged

fix logging for spectral library prediction #257

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7ed80dd
don't disable logging
paretje Feb 10, 2026
18b204c
drop console instance and use rich.print
paretje Feb 10, 2026
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9 changes: 4 additions & 5 deletions ms2pip/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@
from typing import Optional

import click
import rich
from psm_utils.io import READERS
from rich.console import Console
from rich.logging import RichHandler
from werkzeug.utils import secure_filename

Expand All @@ -17,7 +17,6 @@
from ms2pip.result import write_correlations
from ms2pip.spectrum_output import SUPPORTED_FORMATS, write_spectra

console = Console()
logger = logging.getLogger(__name__)

LOGGING_LEVELS = {
Expand Down Expand Up @@ -52,10 +51,10 @@ def cli(*args, **kwargs):
datefmt="%Y-%m-%d %H:%M:%S",
level=LOGGING_LEVELS[kwargs["logging_level"]],
handlers=[
RichHandler(rich_tracebacks=True, console=console, show_level=True, show_path=False)
RichHandler(rich_tracebacks=True, show_level=True, show_path=False)
],
)
console.print(build_credits())
rich.print(build_credits())


@cli.command(help=ms2pip.core.predict_single.__doc__)
Expand All @@ -78,7 +77,7 @@ def predict_single(*args, **kwargs):
predicted_spectrum, _ = result.as_spectra()

# Write output
console.print(build_prediction_table(predicted_spectrum))
rich.print(build_prediction_table(predicted_spectrum))
write_spectra(output_name, [result], output_format)
if plot:
spectrum_to_png(predicted_spectrum, output_name)
Expand Down
2 changes: 0 additions & 2 deletions ms2pip/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -196,7 +196,6 @@ def predict_library(
description="Predicting spectra...",
total=ceil(len(search_space) / batch_size),
):
logging.disable(logging.CRITICAL)
yield predict_batch(
search_space.filter_psms_by_mz(PSMList(psm_list=list(batch))),
add_retention_time=add_retention_time,
Expand All @@ -205,7 +204,6 @@ def predict_library(
model_dir=model_dir,
processes=processes,
)
logging.disable(logging.NOTSET)


def correlate(
Expand Down