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Dependency slimming #247

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Dependency slimming #247

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e3b4b2d
refining requirements
mwang87 Apr 26, 2024
452e0a4
refine
mwang87 Apr 26, 2024
815b9ae
adding testing
mwang87 Jul 11, 2024
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7 changes: 3 additions & 4 deletions massql/msql_fileloading.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,8 @@
import numpy as np

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

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

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

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

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


if __name__ == "__main__":
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