style: correct new flake8 errors (#229)

Author: Midnighter

cameo/core/strain_design.py

@@ -188,9 +188,9 @@ def plot(self, grid=None, width=None, height=None, title=None, *args, **kwargs):
         counts = DataFrame(columns=['count'])
         for design in self._designs:
             for target in design:
-                    if target.id not in counts.index:
-                        counts.loc[target.id, 'count'] = 0
-                    counts.loc[target.id, 'count'] += 1
+                if target.id not in counts.index:
+                    counts.loc[target.id, 'count'] = 0
+                counts.loc[target.id, 'count'] += 1
             counts['frequency'] = counts['count'].apply(lambda c: c / len(self._designs))
 
         plotter.frequency(counts, title=title, width=width, height=height, **kwargs)

cameo/strain_design/heuristic/evolutionary/variators.py

@@ -112,9 +112,9 @@ def set_mutation(random, individual, args):
     mutation_rate = float(args.get('mutation_rate', .1))
     for value in individual:
         if random.random() < mutation_rate and len(indices) > 0:
-                index = random.sample(indices, 1)[0]
-                indices.remove(index)
-                new_individual.append(index)
+            index = random.sample(indices, 1)[0]
+            indices.remove(index)
+            new_individual.append(index)
         else:
             new_individual.append(value)
 
@@ -234,9 +234,9 @@ def multiple_chromosome_set_indel(random, individual, args):
         indel_rate = args.get('%s_indel_rate' % key, .1)
         if random.random() < indel_rate:
             if random.random() > 0.5 and len(new_individual[key]) < max_size and len(indices) > 0:
-                    index = random.sample(indices, 1)[0]
-                    indices.remove(index)
-                    new_individual[key].append(index)
+                index = random.sample(indices, 1)[0]
+                indices.remove(index)
+                new_individual[key].append(index)
             else:
                 if len(individual[key]) > 1:
                     new_individual[key] = random.sample(new_individual[key], len(new_individual[key]) - 1)

cameo/strain_design/heuristic/evolutionary_based.py

@@ -134,15 +134,15 @@ def run(self, target=None, biomass=None, substrate=None, max_knockouts=5, variab
             objective_function = biomass_product_coupled_min_yield(biomass, target, substrate)
         else:
             objective_function = biomass_product_coupled_yield(biomass, target, substrate)
-        if self.manipulation_type is "genes":
+        if self.manipulation_type == "genes":
             optimization_algorithm = GeneKnockoutOptimization(
                 model=self._model,
                 heuristic_method=self._algorithm,
                 essential_genes=self._essential_genes,
                 plot=self.plot,
                 objective_function=objective_function,
                 use_nullspace_simplification=use_nullspace_simplification)
-        elif self.manipulation_type is "reactions":
+        elif self.manipulation_type == "reactions":
             optimization_algorithm = ReactionKnockoutOptimization(
                 model=self._model,
                 heuristic_method=self._algorithm,

cameo/visualization/plotting/with_plotly.py

@@ -342,7 +342,7 @@ def frequency(self, dataframe, width=None, height=None, palette=None, title="Fre
 
     @property
     def _display(self):
-        if self.get_option('mode') is "offline":
+        if self.get_option('mode') == "offline":
             from plotly.offline import iplot
             self._oflline()
         else: