setup and __init__ are pep8 compliant

cobra/__init__.py

@@ -9,14 +9,17 @@
     _warning_base = "%s:%s \x1b[1;31m%s\x1b[0m: %s\n"  # colors
 else:
     _warning_base = "%s:%s %s: %s\n"
+
+
 def _warn_format(message, category, filename, lineno, file=None, line=None):
     shortname = filename.replace(_cobra_path, "cobra", 1)
     return _warning_base % (shortname, lineno, category.__name__, message)
 _warnings.formatwarning = _warn_format
 
 from .version import get_version
 __version__ = get_version()
-from .core import Object, Formula, Metabolite, Gene, Reaction, Model, DictList, Species
+from .core import Object, Formula, Metabolite, Gene, Reaction, Model, \
+    DictList, Species
 from . import io, flux_analysis
 
 try:

cobra/test/__init__.py

@@ -13,7 +13,6 @@
 salmonella_sbml = join(data_directory, "salmonella.xml")
 salmonella_fbc_sbml = join(data_directory, "salmonella_fbc.xml")
 salmonella_pickle = join(data_directory, "salmonella.pickle")
-salmonella_reaction_p_values_pickle = join(data_directory, "salmonella_reaction_p_values.pickle")
 ecoli_sbml = join(data_directory, "iJO1366.xml")
 ecoli_pickle = join(data_directory, "iJO1366.pickle")
 ecoli_mat = join(data_directory, "iJO1366.mat")
@@ -35,10 +34,10 @@ def create_test_model(test_pickle=salmonella_pickle):
     version of the Salmonella enterica Typhimurium LT2 model published in
     Thiele et al. 2011 BMC Sys Bio 5:8
 
-    test_pickle: The complete file name of a pickled cobra.Model or SBML XML
-    file to be read.  We currently provide Salmonella enterica Typhimurium
-    and Escherichia coli models whose paths are stored in cobra.test.salmonella_pickle
-    and cobra.test.ecoli_pickle, respectively.  The ecoli model is a variant of the
+    test_pickle: The filename of a pickled cobra.Model
+    We currently provide Salmonella enterica Typhimurium and Escherichia coli
+    models whose paths are stored in cobra.test.salmonella_pickle and
+    cobra.test.ecoli_pickle, respectively.  The ecoli model is a variant of the
     model published in Orth et al. 2011 Mol Syst Biol 7:535
 
     """
@@ -54,6 +53,7 @@ def create_test_model(test_pickle=salmonella_pickle):
     with open(test_pickle, "rb") as infile:
         return load(infile)
 
+
 def create_test_suite():
     """create a unittest.TestSuite with available tests"""
     from unittest import TestLoader, TestSuite
@@ -66,6 +66,7 @@ def create_test_suite():
 
 suite = create_test_suite()
 
+
 def test_all():
     """###running unit tests on cobra py###"""
     from unittest import TextTestRunner

setup.py

@@ -110,7 +110,7 @@ def get_tag(self):
     # https://gist.github.com/aebrahim/94a2b231d86821f7f225
     include_dirs = []
     library_dirs = []
-    if isfile("libglpk.a") or isfile ("libgmp.a"):
+    if isfile("libglpk.a") or isfile("libgmp.a"):
         library_dirs.append(abspath("."))
     if isfile("glpk.h"):
         include_dirs.append(dirname(abspath("glpk.h")))