Add version number in TMD installation

Change-Id: I3604c15e7ee8bbe6f61f43be84c0aea26d999ded

setup.py

@@ -1,9 +1,9 @@
 """ Distribution configuration for TMD
 """
-import os
 from setuptools import setup
 from setuptools import find_packages
-import pip
+
+execfile('tmd/version.py')
 
 config = {
     'description': 'TMD: a python package for the topological analysis of neurons',
@@ -22,6 +22,7 @@
     'scripts': [],
     'name': 'tmd',
     'include_package_data': True,
+    'version': VERSION,  # pylint: disable=undefined-variable
 }
 
 setup(**config)

tmd/Population/Population.py

@@ -66,7 +66,7 @@ def try_except(tree, ntree, feature, output_folder, ttype='basal'):
                     output_file=os.path.join(output_folder, ttype +
                                              '_' + str(ntree) + '.txt'))
             except ValueError:
-                print tree
+                print(tree)
 
         if neurite_type == 'all':
             _ = [try_except(ap, enap, feature, output_folder, ttype='apical')
@@ -99,7 +99,7 @@ def try_except(tree, ntree, feature, output_folder, ttype='basal'):
                     output_file=os.path.join(output_folder, ttype +
                                              '_' + str(ntree) + '.txt'))
             except ValueError:
-                print tree
+                print(tree)
 
         if neurite_type == 'all':
             _ = [[try_except(ap, enap, feature, output_folder,
@@ -137,7 +137,7 @@ def try_except(neuron, feature, output_folder, ttype=neurite_type):
                     output_file=os.path.join(output_folder, neuron.name + '.txt'))
 
             except ValueError:
-                print neuron.name
+                print(neuron.name)
 
         _ = [try_except(n, feature, output_folder, ttype=neurite_type)
              for n in self.neurons]

tmd/Topology/methods.py

@@ -86,7 +86,7 @@ def get_persistence_diagram(tree, feature='radial_distances', **kwargs):
 
                 rd[p] = rd[mx_id]
 
-    ph.append([rd[np.where(active)[0][0]], 0]) # Add the last alive component
+    ph.append([rd[np.where(active)[0][0]], 0])  # Add the last alive component
 
     return ph
 
@@ -119,10 +119,10 @@ def phi_theta(u, v):
     phi2 = np.arctan2(v[1], v[0])
     theta2 = np.arccos(v[2] / np.linalg.norm(v))
 
-    delta_phi = phi2 - phi1 # np.abs(phi1 - phi2)
-    delta_theta = theta2 - theta1 # np.abs(theta1 - theta2)
+    delta_phi = phi2 - phi1  # np.abs(phi1 - phi2)
+    delta_theta = theta2 - theta1  # np.abs(theta1 - theta2)
 
-    return delta_phi, delta_theta # dphi, dtheta
+    return delta_phi, delta_theta  # dphi, dtheta
 
 
 def get_angles(tree, beg, parents, children):
@@ -252,7 +252,7 @@ def get_ph_radii(tree, feature='radial_distances', **kwargs):
 
                 rd[p] = rd[mx_id]
 
-    ph.append([rd[np.where(active)[0][0]], 0, radii[beg[0]]]) # Add the last alive component
+    ph.append([rd[np.where(active)[0][0]], 0, radii[beg[0]]])  # Add the last alive component
 
     return ph
 
@@ -302,7 +302,7 @@ def extract_ph(tree, feature='radial_distances', output_file='test.txt',
 
     write_ph(ph, output_file)
 
-    print 'File ' + output_file + ' completed!'
+    print('File ' + output_file + ' completed!')
 
 
 def extract_ph_neuron(neuron, feature='radial_distances', output_file=None,
@@ -319,7 +319,7 @@ def extract_ph_neuron(neuron, feature='radial_distances', output_file=None,
 
     write_ph(ph, output_file)
 
-    print 'File ' + output_file + ' completed!'
+    print('File ' + output_file + ' completed!')
 
 
 def get_lifetime(tree, feature='point_radial_distances'):

tmd/io/io.py

@@ -78,7 +78,7 @@ def load_neuron(input_file, line_delimiter='\n', soma_type=None, tree_types=None
     # Save soma in Neuron
     neuron.set_soma(soma)
     p = _np.array(_np.transpose(data)[6], dtype=int) - _np.transpose(data)[0][0]
-    #return p, soma_ids
+    # return p, soma_ids
     dA = sp.csr_matrix((_np.ones(len(p) - len(soma_ids)),
                         (range(len(soma_ids), len(p)),
                          p[len(soma_ids):])), shape=(len(p), len(p)))
@@ -108,11 +108,10 @@ def load_population(input_directory, tree_types=None):
     pop = Population.Population(name=os.path.relpath(input_directory))
 
     for i in files_h5 + files_swc:
-        #print 'Loading ' + i + ' ...'
         try:
             pop.append_neuron(load_neuron(os.path.join(input_directory, i),
                                           tree_types=tree_types))
         except:
-            print 'File failed to load: ', i
+            print('File failed to load: {}'.format(i))
 
     return pop