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Revert "Dependency slimming" #253

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Merged
mwang87 merged 1 commit into from
Dec 10, 2025
Merged

Revert "Dependency slimming" #253

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7 changes: 4 additions & 3 deletions massql/msql_fileloading.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,9 @@
import numpy as np

from tqdm import tqdm
from matchms.importing import load_from_mgf
import pymzml
from pyteomics import mzxml, mzml, mgf
from pyteomics import mzxml, mzml

import logging
logger = logging.getLogger('msql_fileloading')
Expand Down Expand Up @@ -142,10 +143,10 @@ def load_data(input_filename, cache=None, cache_dir=None, cache_file=None):
return ms1_df, ms2_df

def _load_data_mgf(input_filename):
reader = mgf.read(input_filename)
file = load_from_mgf(input_filename)

ms2mz_list = []
for i, spectrum in reader:
for i, spectrum in enumerate(file):
if len(spectrum.peaks.mz) == 0:
continue

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3 changes: 2 additions & 1 deletion requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,9 +1,10 @@
pymzml
lark>=1.0
pandas
pyarrow
tqdm
py_expression_eval
pymzml
matchms
pyteomics
psims
plotly
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3 changes: 2 additions & 1 deletion setup.py
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Expand Up @@ -28,12 +28,13 @@
],
packages=["massql"],
install_requires=[
"pymzml",
"lark-parser",
"pandas",
"pyarrow",
"tqdm",
"py_expression_eval",
"pymzml",
"matchms",
"pyteomics",
"psims",
"plotly",
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3 changes: 1 addition & 2 deletions tests/test_file_loading.py
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Expand Up @@ -92,8 +92,7 @@ def main():
#test_waters_load()
#test_cache_feather()
#test_nocache()
#test_cache_filename()
test_mgf_load()
test_cache_filename()


if __name__ == "__main__":
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