Merge branch 'dev' of https://github.com/cmap/cmapPy.git into dev

cmap · Oct 30, 2019 · a9bf5dc · a9bf5dc
2 parents 7dc505d + 4520702
commit a9bf5dc
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Showing 4 changed files with 17 additions and 11 deletions.
diff --git a/cmapPy/visualization/__init__.py b/cmapPy/visualization/__init__.py
@@ -1,3 +1,3 @@
-import scattergram
-import stratogram
-import cohort_view
+from . import scattergram
+from . import stratogram
+from . import cohort_view
diff --git a/cmapPy/visualization/cohort_view.py b/cmapPy/visualization/cohort_view.py
@@ -1,8 +1,13 @@
 
 
+import logging
+
 from IPython.display import display
-import pandas as pd 
+
 import numpy as np
+import pandas as pd 
+
+logger = logging.getLogger()
 
 
 
@@ -69,7 +74,7 @@ def cohort_view_table(df,
 
  df = df.T
  num_categories = len(df.columns)
- print "num_categories: {}".format(num_categories)
+ logger.info("num_categories: {}".format(num_categories))
 
  # Test comopound fields
  cpd_columns = [c for c in df.columns if 'Test subset' in c]
@@ -158,7 +163,6 @@ def display_cohort_stats_table(table, barplot_column):
  # indexes of the rows corresponding to categories, exludes 
  # the last "total" sums
  group_ids = [x for x in table.index if 'Total' not in x]
- print group_ids
 
  # Sum of numbers in Total column (excluding Grand Total, obviously)
  total = table.loc['Grand Total', 'Total']
@@ -220,4 +224,4 @@ def display_cohort_stats_table(table, barplot_column):
  )
  )
 
-
+
diff --git a/cmapPy/visualization/scattergram.py b/cmapPy/visualization/scattergram.py
@@ -4,14 +4,18 @@
 @contact: [email protected]
 '''
 
-import matplotlib
+import logging
 import os
 
+import matplotlib
+
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
 import seaborn as sns
 
+logger = logging.getLogger()
+
 
 def scattergram(
  df, columns, column_names, title="",

diff --git a/cmapPy/visualization/stratogram.py b/cmapPy/visualization/stratogram.py
@@ -14,7 +14,6 @@
 import seaborn as sns
 
 logger = logging.getLogger()
-logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(name)s - %(levelname)s - %(message)s')
 
 figure_dpi = 150
 
@@ -102,7 +101,6 @@ def stratogram(
  for name, group in grouped:
  row_is_test_compounds = is_test_category(name)
  name = group[category_label].unique()
- print name
  assert len(name) == 1
  name = name[0]
 
@@ -272,7 +270,7 @@ def plot_row_of_histograms(
 
  except Exception as e:
  plt.text(0.01, 0.5, 'ERROR')
- print str(e)
+ logger.errot(str(e))
 
  if row_id == 0:
  plt.xlabel(colname + " ",