Merge pull request #25 from Krxsy/master

Ported Python 2 Code to Python 3

pyfanova/fanova.py

@@ -13,13 +13,13 @@
 def check_java_version():
     import re
     from subprocess import STDOUT, check_output
-    out = check_output(["java", "-version"], stderr=STDOUT).split("\n")
+    out = check_output(["java".encode("utf-8"), "-version".encode("utf-8")], stderr=STDOUT).split("\n".encode("utf-8"))
     if len(out) < 1:
-        print "Failed checking Java version. Make sure Java version 7 or greater is installed."
+        print("Failed checking Java version. Make sure Java version 7 or greater is installed.")
         return False
-    m = re.match('java version "\d+.(\d+)..*', out[0])
+    m = re.match('java version "\d+.(\d+)..*'.encode("utf-8"), out[0])
     if m is None or len(m.groups()) < 1:
-        print "Failed checking Java version. Make sure Java version 7 or greater is installed."
+        print("Failed checking Java version. Make sure Java version 7 or greater is installed.")
         return False
     java_version = int(m.group(1))
     if java_version < 7:
@@ -75,7 +75,7 @@ def __init__(self, smac_output, num_trees=30,
             self._config_space = ConfigSpace(self._remote)
 
             param_names = self._config_space.get_parameter_names()
-            self.param_name2dmin = dict(zip(param_names, range(len(param_names))))
+            self.param_name2dmin = dict(list(zip(param_names, list(range(len(param_names))))))
         else:
             stdout, stderr = self._process.communicate()
             error_msg = "Failed starting fanova. Did you start it from a SMAC state-run directory?"
@@ -179,7 +179,7 @@ def get_categorical_marginal_for_value(self, param, value):
         """
         size = self._config_space.get_categorical_size(param)
         if(value >= size):
-            print "Categorical value %d is out of bounds [%d, %d] for parameter %s" %(value, 0, size, param)
+            print("Categorical value %d is out of bounds [%d, %d] for parameter %s" %(value, 0, size, param))
             return
         else:
             return self._get_marginal_for_value(param, value)
@@ -272,7 +272,7 @@ def print_all_marginals(self, max_num=30, pairwise=True):
         for marginal, param_name in zip(main_marginal_performances, param_names):
             labelled_performances.append((marginal, "%.2f%% due to main effect: %s" % (marginal, param_name), param_name))
 
-        print "Sum of fractions for main effects %.2f%%" % (sum(main_marginal_performances))
+        print("Sum of fractions for main effects %.2f%%" % (sum(main_marginal_performances)))
 
         if pairwise:
             pairwise_marginal_performance = self.get_all_pairwise_marginals()
@@ -282,14 +282,14 @@ def print_all_marginals(self, max_num=30, pairwise=True):
                     label = "%.2f%% due to interaction: %s x %s" % (pairwise_marginal_performance, param_name1, param_name2)
                     labelled_performances.append((pairwise_marginal_performance, label, param_name1 + " x " + param_name2))
 
-            print "Sum of fractions for pairwise interaction effects %.2f%%" % (sum_of_pairwise_marginals)
+            print("Sum of fractions for pairwise interaction effects %.2f%%" % (sum_of_pairwise_marginals))
 
         sorted_performances = sorted(labelled_performances, reverse=True)
         return_values = []
         if max_num is not None:
             sorted_performances = sorted_performances[:max_num]
         for marginal, label, name in sorted_performances:
-            print label
+            print(label)
             return_values.append((marginal, name))
         return return_values
 

pyfanova/fanova_from_csv.py

@@ -60,7 +60,7 @@ def _write_runs_and_results_file(self, values):
         writer.writerow(("Run Number", "Run History Configuration ID", "Instance ID", "Response Value (y)", "Censored?", "Cutoff Time Used",
                                       "Seed", "Runtime", "Run Length", "Run Result Code", "Run Quality", "SMAC Iteration", "SMAC Cumulative Runtime", "Run Result"))
 
-        for i in xrange(0, len(values)):
+        for i in range(0, len(values)):
             line = (i, i, 1, 0, 0, 0, 1, 0, 0, 0, values[i], 0, 0, "SAT")
             writer.writerow(line)
 
@@ -69,7 +69,7 @@ def _write_runs_and_results_file(self, values):
     def _write_param_file(self):
 
         fh = open(os.path.join(self._scenario_dir, "param-file.txt"), "w")
-        for i in xrange(0, self._num_of_params):
+        for i in range(0, self._num_of_params):
             param_string = "X" + str(i) + " " + str(self._bounds[i]) + " " + "[" + str(self._defaults[i]) + "]\n"
             logging.debug(param_string)
             fh.write(param_string)
@@ -79,9 +79,9 @@ def _write_param_file(self):
     def _write_paramstrings_file(self, params):
 
         fh = open(os.path.join(self._scenario_dir, "paramstrings.txt"), "w")
-        for i in xrange(0, params.shape[0]):
+        for i in range(0, params.shape[0]):
             line = str(i) + ": "
-            for j in xrange(0, params.shape[1]):
+            for j in range(0, params.shape[1]):
                 line = line + "X" + str(j) + "='" + str(params[i][j]) + "', "
             #remove the last comma and whitespace from the string again
             line = line[:-2]
@@ -114,7 +114,7 @@ def _read_csv_file(self, filename):
         fh.seek(0)
         rownum = 0
         for line in reader:
-            for param in xrange(0, self._num_of_params):
+            for param in range(0, self._num_of_params):
                 X[rownum][param] = line[param]
             y[rownum] = line[-1]
             rownum += 1
@@ -123,7 +123,7 @@ def _read_csv_file(self, filename):
 
         self._bounds = []
         self._defaults = []
-        for i in xrange(0, self._num_of_params):
+        for i in range(0, self._num_of_params):
             #Take min and max value as bounds for smac parameter file
             self._bounds.append([np.min(X[:, i]), np.max(X[:, i])])
             #Set min value as default value for smac parameter file

pyfanova/fanova_from_hpolib.py

@@ -53,7 +53,7 @@ def _load_pkl(self, pkl):
 
     def _clean_trials(self):
         trials = []
-        for i in xrange(0, len(self.trials)):
+        for i in range(0, len(self.trials)):
             result = self.trials[i]["result"]
             if not np.isfinite(result):
                 logging.warning("skipping result, that's not finite...")
@@ -93,7 +93,7 @@ def _write_runs_and_results_file(self):
         writer.writerow(("Run Number", "Run History Configuration ID", "Instance ID", "Response Value (y)", "Censored?", "Cutoff Time Used",
                                       "Seed", "Runtime", "Run Length", "Run Result Code", "Run Quality", "SMAC Iteration", "SMAC Cumulative Runtime", "Run Result"))
 
-        for i in xrange(0, len(self.trials)):
+        for i in range(0, len(self.trials)):
             result = self.trials[i]["result"]
             line = (i, i, 1, 0, 0, 0, 1, 0, 0, 0, result, 0, 0, "SAT")
             writer.writerow(line)
@@ -108,15 +108,15 @@ def _write_param_file(self):
 
     def _write_paramstrings_file(self):
         fh = open(os.path.join(self._scenario_dir, "paramstrings.txt"), "w")
-        for i in xrange(0, len(self.trials)):
+        for i in range(0, len(self.trials)):
             params = self.trials[i]["params"]
             clean_params = {}
-            for param_name, param_value in params.iteritems():
+            for param_name, param_value in params.items():
                 #FIX of a hpolib bug, where the parameter names in the pkl contain a - infront of their name
                 if param_name[0] == '-':
                     param_name = param_name[1:]
                 clean_params[param_name] = param_value
-            param_list = ["%s='%s'" % (key, value) for key, value in clean_params.iteritems()]
+            param_list = ["%s='%s'" % (key, value) for key, value in clean_params.items()]
             line = "%d: %s\n" % (i, ", ".join(param_list))
             fh.write(line)
         fh.close()

pyfanova/visualizer.py

@@ -11,11 +11,11 @@ class Visualizer(object):
     def __init__(self, fanova):
         self._fanova = fanova
         self._latex_template = '''\documentclass[letterpaper]{article}
-\usepackage{times}
-\usepackage{graphicx}
-\usepackage{epsfig}
-\usepackage{subfigure}
-\usepackage{lscape}
+\\usepackage{times}
+\\usepackage{graphicx}
+\\usepackage{epsfig}
+\\usepackage{subfigure}
+\\usepackage{lscape}
 \begin{document}
 \title{Functional ANOVA Analysis}
 \maketitle
@@ -39,7 +39,7 @@ def create_all_plots(self, directory, **kwargs):
         for param_name in self._fanova.get_config_space().get_categorical_parameters():
             plt.clf()
             outfile_name = os.path.join(directory, param_name.replace(os.sep, "_") + ".png")
-            print "creating %s" % outfile_name
+            print("creating %s" % outfile_name)
             self.plot_categorical_marginal(param_name)
             plt.savefig(outfile_name)
 
@@ -50,7 +50,7 @@ def create_all_plots(self, directory, **kwargs):
         for param_name in params_to_plot:
             plt.clf()
             outfile_name = os.path.join(directory, param_name.replace(os.sep, "_") + ".png")
-            print "creating %s" % outfile_name
+            print("creating %s" % outfile_name)
             self.plot_marginal(param_name, **kwargs)
             plt.savefig(outfile_name)
 
@@ -60,11 +60,11 @@ def create_most_important_pairwise_marginal_plots(self, directory, n=20):
         most_important_pairwise_marginals = self._fanova.get_most_important_pairwise_marginals(n)
         for param1, param2 in most_important_pairwise_marginals:
             if param1 in categorical_parameters or param2 in categorical_parameters:
-                print "skipping pairwise marginal plot %s x %s, because one of them is categorical" % (param1, param2)
+                print("skipping pairwise marginal plot %s x %s, because one of them is categorical" % (param1, param2))
                 continue
             outfile_name = os.path.join(directory, param1.replace(os.sep, "_") + "x" + param2.replace(os.sep, "_") + ".png")
             plt.clf()
-            print "creating %s" % outfile_name
+            print("creating %s" % outfile_name)
             self.plot_pairwise_marginal(param1, param2)
             plt.savefig(outfile_name)
 
@@ -74,7 +74,7 @@ def plot_categorical_marginal(self, param):
             param_name = self._fanova.get_config_space().get_parameter_names()[dim]
         else:
             if param not in self._fanova.param_name2dmin:
-                print "Parameter %s not known" % param
+                print("Parameter %s not known" % param)
                 return
             dim = self._fanova.param_name2dmin[param]
             param_name = param
@@ -84,15 +84,15 @@ def plot_categorical_marginal(self, param):
         labels = self._fanova.get_config_space().get_categorical_values(param)
 
         if param_name not in self._fanova.get_config_space().get_categorical_parameters():
-            print "Parameter %s is not a categorical parameter!" % (param_name)
+            print("Parameter %s is not a categorical parameter!" % (param_name))
 
-        indices = np.asarray(range(categorical_size))
+        indices = np.asarray(list(range(categorical_size)))
         width = 0.5
         marginals = [self._fanova.get_categorical_marginal_for_value(param_name, i) for i in range(categorical_size)]
-        mean, std = zip(*marginals)
+        mean, std = list(zip(*marginals))
         #plt.bar(indices, mean, width, color='red', yerr=std)
         #plot mean
-        b = plt.boxplot(map(lambda x: [x], mean), 0, '', labels=labels)
+        b = plt.boxplot([[x] for x in mean], 0, '', labels=labels)
         min_y = mean[0]
         max_y = mean[0]
         # blow up boxes 
@@ -161,20 +161,20 @@ def plot_marginal(self, param, lower_bound=0, upper_bound=1, is_int=False, resol
             param_name = self._fanova.get_config_space().get_parameter_names()[dim]
         else:
             if param not in self._fanova.param_name2dmin:
-                print "Parameter %s not known" % param
+                print("Parameter %s not known" % param)
                 return
             dim = self._fanova.param_name2dmin[param]
             param_name = param
 
         if param_name not in self._fanova.get_config_space().get_integer_parameters() and param_name not in self._fanova.get_config_space().get_continuous_parameters():
-            print "Parameter %s is not a continuous or integer parameter!" % (param_name) 
+            print("Parameter %s is not a continuous or integer parameter!" % (param_name)) 
             return 
         grid = np.linspace(lower_bound, upper_bound, resolution)
         display_grid = [self._fanova.get_config_space().unormalize_value(param_name, value) for value in grid]
 
         mean = np.zeros(resolution)
         std = np.zeros(resolution)
-        for i in xrange(0, resolution):
+        for i in range(0, resolution):
             (m, s) = self._fanova.get_marginal_for_value(dim, grid[i])
             mean[i] = m
             std[i] = s

setup.py

@@ -10,13 +10,13 @@
 def check_java_version():
     import re
     from subprocess import STDOUT, check_output
-    out = check_output(["java", "-version"], stderr=STDOUT).split("\n")
+    out = check_output(["java".encode("utf-8"), "-version".encode("utf-8")], stderr=STDOUT).split("\n".encode("utf-8"))
     if len(out) < 1:
-        print "failed checking Java version. Make sure Java version 7 or greater is installed."
+        print("failed checking Java version. Make sure Java version 7 or greater is installed.")
         return False
-    m = re.match('java version "\d+.(\d+)..*', out[0])
+    m = re.match('java version "\d+.(\d+)..*'.encode("utf-8"), out[0])
     if m is None or len(m.groups()) < 1:
-        print "failed checking Java version. Make sure Java version 7 or greater is installed."
+        print("failed checking Java version. Make sure Java version 7 or greater is installed.")
         return False
     java_version = int(m.group(1))
     if java_version < 7: