Use flake8 directly

pytest-flake8 seems to have some issues with ignores behaving
differently locally and on Travis-CI

Author: Kai Wohlfahrt

.travis.yml

@@ -14,7 +14,7 @@ matrix:
         - pip install pytest-flake8
         - pip install .
       script:
-        - pytest --flake8 -m flake8
+        - flake8 nuc_processing test setup.py
       after_success: []
 install:
   - pip install pytest-cov codecov

nuc_processing/NucProcess.py

@@ -1449,7 +1449,7 @@ def map_reads(fastq_file, genome_index, align_exe, num_cpu, ambig, qual_scheme,
   patt_4 = re.compile('(\d+) \(.+\) aligned >1 times')
 
   cmd_args = [align_exe,
-              '-D', '20', '-R', '3', '-N', '0',  '-L', '20',  '-i', 'S,1,0.50',
+              '-D', '20', '-R', '3', '-N', '0', '-L', '20', '-i', 'S,1,0.50',
               '-x', genome_index,
               '-k', '2',
               '--reorder',
@@ -2654,7 +2654,7 @@ def pie_values(data, names):
   hist, edges = frag_sizes
   data_set = [(int(edges[i]), int(val)) for i, val in enumerate(hist)]
   svg_doc.graph(x1, y+chart_height, table_width/2, th-chart_height-40, [data_set], 'Size', 'Count',
-                names=None, colors=None,  graph_type='line',
+                names=None, colors=None, graph_type='line',
                 symbols=None, line_widths=None, symbol_sizes=None,
                 legend=False, title=None, plot_offset=(80, 20))
   y += th

nuc_processing/NucSvg.py

@@ -465,7 +465,7 @@ def color_func(x, p=pos_color, n=neg_color, b=bg_color):
       self.text(y_axis_label, (x3, y), anchor='middle', size=font_size, bold=False, font=font, color=line_color, angle=270, vert_align=None)
 
   def graph(self, x, y, width, height, data_lists, x_label, y_label,
-            names=None, colors=None,  graph_type=LINE_TYPE,
+            names=None, colors=None, graph_type=LINE_TYPE,
             symbols=None, line_widths=None, symbol_sizes=None,
             legend=False, title=None, x_labels=None, plot_offset=(100, 50),
             axis_color='black', bg_color='#F0F0F0', font=None, font_size=16, line_width=1,

nuc_processing/split_fastq_barcodes.py

@@ -820,7 +820,7 @@ def get_bc_file_name(path_root, bc_key, sample_names, nsn, file_ext):
       msg = '{} barcode: {} count {:,} ({:.2f}%)'.format(sample_names[bc_key], bc_key, nb, nb/float(100.0*n_reads))
       info(msg)
 
-  _write_analysis_file(bc_counts, sample_names,  analysis_file_path)
+  _write_analysis_file(bc_counts, sample_names, analysis_file_path)
 
 
 if __name__ == '__main__':

setup.cfg

@@ -1,10 +1,15 @@
-[tool:pytest]
-flake8-ignore =
+[flake8]
+ignore =
   E401
   E261
   E111
   E114
   E129
-  nuc_processing/test/*.py F403 F405
-  nuc_processing/nuc_processing/*.py E501 E231 E228 E741
-flake8-max-line-length = 101
+  E121
+  E226
+  W503
+  W504
+
+  test/*.py F403 F405
+  nuc_processing/*.py E501 E231 E228 E741
+max-line-length = 100