moved OperationConstraint to utils, wrote __init__ in surrogate folder and...

moved OperationConstraint to utils, wrote __init__ in surrogate folder and changed some class names to have capital letters, changed candidate_operations folder to candidates

surrogate/__init__.py

+from surrogate.gpr import GPR
+from surrogate.descriptor.fingerprint import Fingerprint
+from surrogate.prior.prior import RepulsivePrior
+
+__all__ = ['GPR', 'Fingerprint', 'RepulsivePrior']
\ No newline at end of file

surrogate/gpr.py

@@ -2,9 +2,9 @@ import numpy as np
 from scipy.linalg import cholesky, cho_solve, solve_triangular
 from scipy.optimize import fmin_l_bfgs_b
 
-from surrogate.kernel import gauss_kernel, double_gauss_kernel
-from surrogate.descriptor.fingerprint import Fingerprint
-from surrogate.prior.prior import repulsive_prior
+from surrogate.kernel import GaussKernel, DoubleGaussKernel
+from surrogate import Fingerprint
+from surrogate import RepulsivePrior
 from surrogate.gpr_calculator import gpr_calculator
 
 class gpr_memory():
@@ -89,14 +89,14 @@ class GPR():
                     Nsplit_eta = self.descriptor.Nelements_2body
 
         if kernel is 'single':
-            self.kernel = gauss_kernel(Nsplit_eta=Nsplit_eta)
+            self.kernel = GaussKernel(Nsplit_eta=Nsplit_eta)
         elif kernel is 'double':
-            self.kernel = double_gauss_kernel(Nsplit_eta=Nsplit_eta)
+            self.kernel = DoubleGaussKernel(Nsplit_eta=Nsplit_eta)
         else:
             self.kernel = kernel
 
         if prior is None:
-            self.prior = repulsive_prior()
+            self.prior = RepulsivePrior()
         else:
             self.prior = prior
 

surrogate/kernel.py

@@ -5,7 +5,7 @@ from scipy.spatial.distance import pdist, cdist, squareform
 
 from time import time
 
-class kernel(ABC):
+class Kernel(ABC):
     def __init__(self):
         self._theta = None
 
@@ -79,7 +79,7 @@ class kernel(ABC):
         return dK_dTheta
 
 
-class gauss_kernel(kernel):
+class GaussKernel(Kernel):
     def __init__(self, amplitude=100.0, amplitude_bounds=(1e0, 1e5),
                  length_scale=10.0, length_scale_bounds=(1e0, 1e3),
                  noise=1e-5, noise_bounds=None,
@@ -284,7 +284,7 @@ class gauss_kernel(kernel):
 
     
 
-class double_gauss_kernel(kernel):
+class DoubleGaussKernel(Kernel):
     def __init__(self, amplitude=100., amplitude_bounds=(1e1,1e5),
                  length_scale1=10.0, length_scale1_bounds=(1e0, 1e3),
                  length_scale2=10.0, length_scale2_bounds=(1e0, 1e3),

surrogate/prior/prior.pyx

@@ -44,8 +44,7 @@ def convert_atom_types(num):
                 num_converted[i] = j
     return num_converted
 
-class repulsive_prior():
-
+class RepulsivePrior():
     def __init__(self, rcut=6, ratio_of_covalent_radii=0.7):
         self.rcut = rcut
         self.ratio_of_covalent_radii = ratio_of_covalent_radii

surrogate/test_gpr.py

@@ -17,7 +17,6 @@ class test_gpr(unittest.TestCase):
 
     def setUp(self):
         print('setUp')
-        #self.kernel = gauss_kernel()
         a = read('structures.traj', index='0')
         #self.gpr = gpr()
         #self.gpr = gpr(kernel='double', template_structure=a)

surrogate/test_kernel.py

 import numpy as np
 import unittest
-from kernel import gauss_kernel, double_gauss_kernel
+from kernel import GaussKernel, DoubleGaussKernel
 
 class test_kernel(unittest.TestCase):
 
@@ -14,11 +14,11 @@ class test_kernel(unittest.TestCase):
 
     def setUp(self):
         print('setUp')
-        #self.kernel = gauss_kernel()
+        #self.kernel = GaussKernel()
         #self.kernel_old = C(10, (1e1, 1e6)) * RBF(10, (1,1000))
         
-        #self.kernel = double_gauss_kernel(Nsplit_eta=2, eta=10)
-        self.kernel = gauss_kernel(Nsplit_eta=2, eta=10)
+        #self.kernel = DoubleGaussKernel(Nsplit_eta=2, eta=10)
+        self.kernel = GaussKernel(Nsplit_eta=2, eta=10)
 
     def tearDown(self):
         print('tearDown\n')