Enable tqdm logger (#11)

* initialize logger with tqdm

* removing redundant tqdm.pandas()

* adding pyarrow.parquet to phosphoproteomics

* removing unused imports

* fixed kinase-substrates typo

src/kinase_library/__init__.py

@@ -17,6 +17,10 @@
 from .modules.data import *
 from .modules.enrichment import *
 
+from .logger import TqdmToLoggerWithStatus, logger
+tqdm_out = TqdmToLoggerWithStatus(logger)
+tqdm.pandas(file=tqdm_out, ascii=False)
+
 #%%
 
 __version__ = "1.0.1"

src/kinase_library/enrichment/binary_enrichment.py

@@ -9,14 +9,10 @@
 import pandas as pd
 import scipy.stats as st
 from statsmodels.stats import multitest
-from tqdm import tqdm
-tqdm.pandas()
 
 from ..utils import _global_vars, exceptions, utils
 from ..modules import data, enrichment
-from ..objects import core
 from ..objects import phosphoproteomics as pps
-from ..logger import logger
 
 #%%
 

src/kinase_library/enrichment/differential_phosphorylation.py

@@ -4,19 +4,15 @@
 #####################################################
 """
 
-import numpy as np
 import pandas as pd
-from tqdm import tqdm
 import matplotlib.pyplot as plt
 import warnings
 
 from ..utils import _global_vars, exceptions
-from ..modules import data, enrichment
-from ..objects import core
+from ..modules import enrichment
 from ..objects import phosphoproteomics as pps
 from ..enrichment import binary_enrichment as be
 from ..logger import logger
-tqdm.pandas()
 
 plt.rcParams['font.family'] = 'Arial'
 plt.rcParams['pdf.fonttype'] = 42

src/kinase_library/enrichment/mea.py

@@ -4,15 +4,11 @@
 ########################################################
 """
 
-import numpy as np
 import pandas as pd
-from tqdm import tqdm
 import gseapy as gp
-tqdm.pandas()
 
-from ..utils import _global_vars, exceptions, utils
+from ..utils import _global_vars, exceptions
 from ..modules import data, enrichment
-from ..objects import core
 from ..objects import phosphoproteomics as pps
 from ..logger import logger
 
@@ -105,8 +101,8 @@ def submit_percentiles(self, kin_type, percentiles, phosprot_name=None, suppress
 
     def _create_kin_sub_sets(self, thresh, comp_direction):
 
-        print('\nGenerating kinase-substartes sets')
-        logger.info('Generating kinase-substartes sets')
+        print('\nGenerating kinase-substrates sets')
+        logger.info('Generating kinase-substrates sets')
         kin_sub_sets = enrichment.create_kin_sub_sets(data_values=self.data_kl_values, threshold=thresh, comp_direction=comp_direction)
         self.kin_sub_sets = kin_sub_sets
 

src/kinase_library/objects/phosphoproteomics.py

@@ -3,18 +3,12 @@
 # The Kinase Library - Phosphoproteomics #
 ##########################################
 """
-
-import os
 import numpy as np
 import pandas as pd
-import scipy.stats as st
-from statsmodels.stats import multitest
-from tqdm import tqdm
-import gseapy as gp
-tqdm.pandas()
+import pyarrow.parquet as pq
 
 from ..utils import _global_vars, exceptions, utils
-from ..modules import data, enrichment
+from ..modules import data
 from . import core
 from ..logger import logger
 
@@ -461,7 +455,6 @@ def percentile(self, kin_type=None, kinases=None,
 
         print('Calculating percentile for '+str(len(getattr(self,kin_type+'_substrates')))+' '+kin_type+' substrates')
         logger.info('Calculating percentile for '+str(len(getattr(self,kin_type+'_substrates')))+' '+kin_type+' substrates')
-        tqdm.pandas()
         percent_output = scored_phosprot.progress_apply(lambda x: x.sort_values().searchsorted(score[x.name], side='right'))/len(scored_phosprot)*100
         percent_output.index = score.index