Merge pull request #253 from mwang87/revert-247-dependency-slimming

Revert "Dependency slimming"

Author: mwang87

massql/msql_fileloading.py

@@ -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')
@@ -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
 

requirements.txt

@@ -1,9 +1,10 @@
+pymzml
 lark>=1.0
 pandas
 pyarrow
 tqdm
 py_expression_eval
-pymzml
+matchms
 pyteomics
 psims
 plotly

setup.py

@@ -28,12 +28,13 @@
     ],
     packages=["massql"],
     install_requires=[
+        "pymzml",
         "lark-parser",
         "pandas",
         "pyarrow",
         "tqdm",
         "py_expression_eval",
-        "pymzml",
+        "matchms",
         "pyteomics",
         "psims",
         "plotly",

tests/test_file_loading.py

@@ -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__":