codequality

mdrasmus · May 18, 2014 · 996a03b · 996a03b
1 parent d05cf29
commit 996a03b
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Showing 3 changed files with 18 additions and 6 deletions.
diff --git a/argweaver/argweaverc.py b/argweaver/argweaverc.py
@@ -329,11 +329,11 @@
         [POINTER(C.c_int * 2), "path"])
     argweaver_get_nstates = export(
         argweaverclib, "arghmm_get_nstates", int,
-        [C.c_void_p, "trees",  C.c_int, "ntimes", C.c_bool, "internal",
+        [C.c_void_p, "trees", C.c_int, "ntimes", C.c_bool, "internal",
          C.c_out(C.c_int_list), "nstates"])
     get_state_spaces = export(
         argweaverclib, "get_state_spaces", POINTER(POINTER(C.c_int * 2)),
-        [C.c_void_p, "trees",  C.c_int, "ntimes", C.c_bool, "internal"])
+        [C.c_void_p, "trees", C.c_int, "ntimes", C.c_bool, "internal"])
     delete_state_spaces = export(
         argweaverclib, "delete_state_spaces", C.c_int,
         [POINTER(POINTER(C.c_int * 2)), "all_states", C.c_int, "ntrees"])
@@ -1411,7 +1411,7 @@ def iter_local_ptrees(arg, times, start=None, end=None):
 
         # setup last tree
         last_tree2 = tree2
-        last_ptree, last_nodes, last_nodelookup = ptree, nodes, nodelookup
+        last_nodes, last_nodelookup = nodes, nodelookup
 
 
 def get_treeset(arg, times, start=None, end=None):

diff --git a/bin/arg-extract-recomb b/bin/arg-extract-recomb
@@ -77,8 +77,8 @@ for filename in filenames:
 avg_treelens = [[s, e, stats.mean(util.cget(group, 2))]
                 for s, e, group in intervals.iter_intersections(
                     sorted(util.concat(*treelens)))]
-recombs = util.hist_dict(util.concat(*[[t[0] for t in treelen]
-                                       for treelen in treelens]))
+recombs = util.hist_dict(util.concat(*[[t[0] for t in _treelen]
+                                       for _treelen in treelens]))
 
 # Calcuate recombination rate.
 recomb_rate = []

diff --git a/test/test_codequality.py b/test/test_codequality.py
@@ -32,7 +32,19 @@ def run_pep8(filenames, key=lambda line: True):
     """
     Run pep8 and return all errors.
     """
-    cmd = " ".join(["pep8"] + filenames)
+
+    options = []
+    ignore = []
+
+    # E265 block comment should start with '# '
+    ignore.append('E265')
+
+    # E226 missing whitespace around arithmetic operator
+    ignore.append('E226')
+
+    options.extend(['--ignore', ','.join(ignore)])
+
+    cmd = " ".join(["pep8"] + options + filenames)
     print cmd
     pipe = subprocess.Popen(cmd, stdout=subprocess.PIPE, shell=True)
     lines = [line for line in pipe.stdout if key(line)]