fix linter errors

.travis.yml

@@ -30,6 +30,7 @@ install:
 
 script:
   - python setup.py test
-  - check-manifest --ignore "tox.ini,test*,devtools*,docs*"
+  - check-manifest --ignore
+    "tox.ini,test*,devtools*,docs*,taxtastic/data,taxtastic/data/*"
   - python setup.py check --metadata --restructuredtext --strict
   - flake8 taxtastic

MANIFEST.in

@@ -2,6 +2,7 @@ exclude docker docker/*
 exclude singularity singularity/*
 exclude dev dev/*
 exclude README.txt readme.txt
+include *.py
 include *.in
 include *.rst
 include *.txt

taxtastic/refpkg.py

@@ -136,7 +136,7 @@ def transaction(f, self, *args, **kwargs):
             r = f(self, *args, **kwargs)
             self.commit_transaction()
             return r
-        except:
+        except Exception:
             self.contents = self.current_transaction['rollback']
             self._sync_to_disk()
             raise
@@ -675,9 +675,9 @@ def is_ill_formed(self):
             for req_header in 'seqname', 'tax_id':
                 if req_header not in headers:
                     return "seq_info is missing {0}".format(req_header)
-            lens = [len(l) for l in lines]
-            if not(all([l == lens[0] and l > 1 for l in lens])):
-                return "seq_info is not valid CSV."
+            lengths = {len(line) for line in lines}
+            if len(lengths) > 1:
+                return "some lines in seq_info differ in field cout"
             csv_names = {line[0] for line in lines[1:]}
 
         with self.open_resource('aln_sto') as f:
@@ -693,7 +693,7 @@ def is_ill_formed(self):
                 case_sensitive_taxon_labels=True,
                 preserve_underscores=True)
             tree_names = set(tree.taxon_namespace.labels())
-        except:
+        except Exception:
             return 'tree file is not valid Newick.'
 
         d = fasta_names.symmetric_difference(sto_names)
@@ -712,9 +712,10 @@ def is_ill_formed(self):
         # Next make sure that taxonomy is valid CSV, phylo_model is valid JSON
         with self.open_resource('taxonomy') as f:
             lines = list(csv.reader(f))
-            lens = [len(l) for l in lines]
-            if not(all([l == lens[0] and l > 1 for l in lens])):
-                return "Taxonomy is invalid: not all lines had the same number of fields."
+            lengths = {len(line) for line in lines}
+            if len(lengths) > 1:
+                return ("Taxonomy is invalid: not all lines had "
+                        "the same number of fields.")
             # I don't try to check if the taxids match up to those
             # mentioned in aln_fasta, since that would make taxtastic
             # depend on RefsetInternalFasta in romperroom.

taxtastic/subcommands/create.py

@@ -22,7 +22,6 @@
 import logging
 import shutil
 import os
-import sys
 
 from taxtastic import refpkg, utils
 

taxtastic/taxonomy.py

@@ -688,8 +688,8 @@ def sibling_of(self, tax_id):
     def is_ancestor_of(self, node, ancestor):
         if node is None or ancestor is None:
             return False
-        l = self.lineage(node)
-        return ancestor in list(l.values())
+        lineage = self.lineage(node)
+        return ancestor in list(lineage.values())
 
     def rank(self, tax_id):
         if tax_id is None:

taxtastic/taxtable.py

@@ -180,9 +180,9 @@ def lineage(self):
         if not self.parent:
             return [self]
         else:
-            l = self.parent.lineage()
-            l.append(self)
-            return l
+            L = self.parent.lineage()
+            L.append(self)
+            return L
 
     def __repr__(self):
         return ("<TaxNode {0.tax_id}:{0.name} [rank={0.rank};"
@@ -208,8 +208,8 @@ def node_record(node):
                  'tax_name': node.name,
                  'parent_id': parent_id,
                  'rank': node.rank}
-            l = {i.rank: i.tax_id for i in node.lineage()}
-            d.update(l)
+            L = {i.rank: i.tax_id for i in node.lineage()}
+            d.update(L)
             return d
 
         header = ['tax_id', 'parent_id', 'rank', 'tax_name'] + ranks

taxtastic/utils.py

@@ -137,7 +137,7 @@ def parse_fasttree(fobj):
         elif splut[0] == 'GTRRates':
             data['subs_rates'] = dict(
                 list(zip(['ac', 'ag', 'at', 'cg', 'ct', 'gt'],
-                    list(map(float, splut[1:])))))
+                         list(map(float, splut[1:])))))
         elif line.strip() == JTT_MODEL:
             data['subs_model'] = 'JTT'
             data['datatype'] = 'AA'