Adding to tox.ini D100

src/cluto.py

@@ -6,20 +6,19 @@ from __future__ import print_function
 import json
 import re
 import io
-
-import numpy as _np
 import os
 import shutil
 import tempfile
-
 from subprocess import call
+
+import numpy as _np
 from sklearn.externals import joblib
 import xlsxwriter
 
 verbose = False
 
 
-def loadData(inputFile):
+def load_data(inputFile):
     """Loading data."""
     with open(inputFile) as json_ifs:
         jsonVal = json.load(json_ifs)
@@ -29,7 +28,7 @@ def loadData(inputFile):
         return data, rowlabels
 
 
-def saveXLSX(names, clustering_path, outfile):
+def save_XLSX(names, clustering_path, outfile):
     """Saving to XLSX."""
     srow = 3
     scol = 4
@@ -49,7 +48,7 @@ def saveXLSX(names, clustering_path, outfile):
     workbook.close()
 
 
-def toHeatMapJSON(cluto_path, clustering_path, names, outfile):
+def to_heat_map_json(cluto_path, clustering_path, names, outfile):
     """Saving to JSON."""
     with open(clustering_path) as f:
         groups = f.readlines()
@@ -105,8 +104,8 @@ def number_of_clusters(options, rowlabels):
     return no_clusters
 
 
-def save_clutofiles(mat, rlabels, clabels, cluto_path, rlabel_path,
-                    clabel_path):
+def save_cluto_files(mat, rlabels, clabels, cluto_path, rlabel_path,
+                     clabel_path):
     """Saving cluto file."""
     with open(cluto_path, 'w') as cluto_ofs:
         # Print header:
@@ -156,12 +155,12 @@ def write_node(node_id, tree_dict, name2group):
                                                  name2group))
     if len(child_node_strings) == 0:
         node_str = '{"id":"node_' + node_id + '", "group":' + \
-                   str(name2group[node_id]) +\
+                   str(name2group[node_id]) + \
                    ', "name":"' + \
                    node_id + \
                    '", "data":{}, "children":['
     else:
-        node_str = '{"id":"node_' + node_id + '", "name":"' + node_id +\
+        node_str = '{"id":"node_' + node_id + '", "name":"' + node_id + \
                    '", "data":{}, "children":['
     node_str += ', '.join(child_node_strings)
     node_str += ']}'
@@ -209,10 +208,10 @@ def run_convert(cl_out_file, out_file, options, rowlabels):
     if len(rowlabels) < 25:
         density = '50'
 
-#    if options['analysis_type'] == 'plottree':
-#       resize = '50%'
-#   else:
-#       resize = '100%'
+    #    if options['analysis_type'] == 'plottree':
+    #       resize = '50%'
+    #   else:
+    #       resize = '100%'
 
     # print density
     call(['convert', '-density', density, cl_out_file, 'png:' + out_file])
@@ -220,7 +219,7 @@ def run_convert(cl_out_file, out_file, options, rowlabels):
 
 def run(inputFile, outputFile, options):
     """Running cluto worker."""
-    data, rowlabels = loadData(inputFile + "/similarity.json")
+    data, rowlabels = load_data(inputFile + "/similarity.json")
     if "analysis_type" not in options:
         options["analysis_type"] = "plottree"
     no_clusters = number_of_clusters(options, rowlabels)
@@ -254,10 +253,10 @@ def run(inputFile, outputFile, options):
                 options, rowlabels)
 
     # for heatmap
-    toHeatMapJSON(cluto_path, os.path.join(temp_folder,
-                                           'matrix.txt.clustering.' +
-                                           str(no_clusters)), rowlabels,
-                  outputFile + "/data.json")
+    to_heat_map_json(cluto_path, os.path.join(temp_folder,
+                                              'matrix.txt.clustering.' +
+                                              str(no_clusters)), rowlabels,
+                     outputFile + "/data.json")
 
     # Check if they are required by any tool
     shutil.copyfile(os.path.join(temp_folder, 'matrix.txt.clustering.' +
@@ -276,16 +275,16 @@ def run(inputFile, outputFile, options):
     with open(os.path.join(outputFile, 'clusters.json'), 'w') as outfile:
         json.dump(res, outfile)
 
-    labels = getLablesFromNames(rowlabels)
+    labels = get_lables_from_names(rowlabels)
     labels["groupnames"]["clusters"] = list(set(clusters))
     labels["groups"]["clusters"] = clusters
     with open(os.path.join(outputFile, 'labels.json'), 'w') as outfile:
         json.dump(labels, outfile)
 
     # results in XLSX
-    saveXLSX(rowlabels, os.path.join(temp_folder, 'matrix.txt.clustering.' +
-                                     str(no_clusters)),
-             os.path.join(outputFile, 'result.xlsx'))
+    save_XLSX(rowlabels, os.path.join(temp_folder, 'matrix.txt.clustering.' +
+                                      str(no_clusters)),
+              os.path.join(outputFile, 'result.xlsx'))
 
     # Coping results for next tools
     # for visulisation (mds)
@@ -304,7 +303,7 @@ def run(inputFile, outputFile, options):
     shutil.rmtree(temp_folder)
 
 
-def getLablesFromNames(row_labels):
+def get_lables_from_names(row_labels):
     """Getting labels from names."""
     # data, data_cleaned,shortest_row_len, row_labels = get_data(row)
     shortest_row_len = 10000000

tox.ini

@@ -39,7 +39,7 @@ max-line-length = 80
 # D409 Section underline should match the length of its name
 # D410 Missing blank line after section
 # D411 Missing blank line before section
-ignore = D104,D203,D213,D214,D215,D401,D405,D406,D407,D408,D409,D410,D411
+ignore = D104,D203,D213,D214,D215,D401,D405,D406,D407,D408,D409,D410,D411,D100
 match-dir = ^(?!\.tox|venv).*
 match = ^(?!setup).*\.py