setup.cfg update; flake8 fixes

Update setup.cfg file:
    - remove line length cheat from
    - add .py to * (unsure why this was needed)

fix flake8 errors accordingly

ghosttree/filter.py

@@ -25,9 +25,11 @@ def filter_positions(alignment_fh, maximum_gap_frequency,
 
 def _filter_gap_positions(aln, maximum_gap_frequency):
 
-    aln_gap_frequencies = (aln.gap_frequencies(axis='sequence',
-                                               relative=False) / aln._seqs.count())
-    aln_gap_frequencies_boolean = (aln_gap_frequencies <= maximum_gap_frequency)
+    aln_gap_frequencies = (aln.gap_frequencies(
+                           axis='sequence',
+                           relative=False) / aln._seqs.count())
+    aln_gap_frequencies_boolean = (aln_gap_frequencies <=
+                                   maximum_gap_frequency)
     aln = aln.iloc[:, aln_gap_frequencies_boolean]
 
     return aln

ghosttree/scaffold/tests/test_hybridtree.py

@@ -36,8 +36,10 @@ def test_make_nr_foundation_alignment_few(self):
                                                self.extension_genus_dic_few)
 
         self.assertEqual(list(result), [
-            Sequence("AAA---", metadata={"id": "PBB1", "description": "Phoma"}),
-            Sequence("AAG---", metadata={"id": "CBB1", "description": "Candida"}),
+            Sequence("AAA---", metadata={"id": "PBB1",
+                                         "description": "Phoma"}),
+            Sequence("AAG---", metadata={"id": "CBB1",
+                                         "description": "Candida"}),
         ])
 
     def test_make_nr_foundation_alignment_none(self):

ghosttree/silva/tests/test_filter.py

@@ -35,7 +35,8 @@ def test_fasta_with_fungi(self):
                                   self.accession,
                                   self.taxonomy_with_fungi)
         self.assertEqual(list(result),
-                         [Sequence("ATCG", metadata={'id': "AB21", 'description': "Fungi"})])
+                         [Sequence("ATCG", metadata={'id': "AB21",
+                                                     'description': "Fungi"})])
 
     def test_fasta_with_many_fungi(self):
         result = fungi_from_fasta(self.fasta_many_fungi,

setup.cfg

@@ -1,5 +1,4 @@
 [flake8]
-filename = *
+filename = *.py
 exclude = *.pyc, __pycache__
-max-line-length = 120
 ignore = E722