modified moduse structure, added test of imports and changed documentation...

modified moduse structure, added test of imports and changed documentation accordingly as some import statements have changed as a result

gofee.py → gofee/gofee.py

@@ -5,21 +5,20 @@ import numpy as np
 import pickle
 from os.path import isfile
 
-from surrogate.gpr import GPR
-from population import population
-
 from ase import Atoms
 from ase.io import read, write, Trajectory
 from ase.calculators.singlepoint import SinglePointCalculator
 from ase.calculators.dftb import Dftb
 
-from utils import array_to_string
-from parallel_utils import split, parallel_function_eval
+from gofee.surrogate import GPR
+from gofee.population import Population
+from gofee.utils import array_to_string
+from gofee.parallel_utils import split, parallel_function_eval
 
-from bfgslinesearch_constrained import relax
+from gofee.bfgslinesearch_constrained import relax
 
-from candidate_operations.candidate_generation import CandidateGenerator
-from candidate_operations.basic_mutations import RattleMutation
+from gofee.candidates import CandidateGenerator
+from gofee.candidates import RattleMutation
 
 from mpi4py import MPI
 world = MPI.COMM_WORLD
@@ -213,7 +212,7 @@ class GOFEE():
                 self.gpr = GPR(template_structure=self.structures[0])
             
             # Initialize population
-            self.population = population(population_size=population_size, gpr=self.gpr, similarity2equal=0.9999)
+            self.population = Population(population_size=population_size, gpr=self.gpr, similarity2equal=0.9999)
         else:
             self.read()
             self.comm.barrier()

population.py → gofee/population.py

@@ -2,7 +2,7 @@ import numpy as np
 from ase.calculators.singlepoint import SinglePointCalculator
 from ase import Atoms
 
-class population():
+class Population():
 
     def __init__(self, population_size, gpr, similarity2equal=0.9999):
         self.pop_size = population_size

gofee/surrogate/__init__.py

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