pep8 style adjustments , implemented deterministic case into simulati…

…on function and read process and changed all assert statements in the test directory such that they work now as they should do

development/working/run.py

@@ -1,13 +1,13 @@
 """ This module allows to manually explore the capabilities of the grmpy package.
 """
 import sys
-import os
-sys.path.insert(0, "../../")
-
 from grmpy.simulation.simulation import simulate
 from grmpy.read.read import read
 from grmpy.test.random_init import generate_random_dict
-from grmpy.read.print_init import print_dict
+from grmpy.test.random_init import print_dict
+
+sys.path.insert(0, "../../")
+
 dict_ = generate_random_dict()
 print_dict(dict_)
 dict_ = read('test.grmpy.ini')

docs/conf.py

@@ -152,9 +152,6 @@
      author, 'grmpy', 'One line description of project.',
      'Miscellaneous'),
 ]
-
-
-
 # -- Options for Epub output ----------------------------------------------
 
 # Bibliographic Dublin Core info.

grmpy/read/read.py

@@ -2,12 +2,12 @@
 
 import shlex
 
-from grmpy.read.read_auxiliary import _auxiliary
-from grmpy.read.read_auxiliary import _process
+from grmpy.read.read_auxiliary import auxiliary
+from grmpy.read.read_auxiliary import process
 
 
 def read(file_):
-    '''reads the initialization file and provides an dictionary with parameters for the simulation'''
+    """reads the initialization file and provides an dictionary with parameters for the simulation"""
     dict_ = {}
     for line in open(file_).readlines():
 
@@ -28,9 +28,9 @@ def read(file_):
             dict_[keyword] = {}
             continue
 
-        _process(list_, dict_, keyword)
+        process(list_, dict_, keyword)
 
-    dict_ = _auxiliary(dict_)
+    dict_ = auxiliary(dict_)
 
     return dict_
 

grmpy/read/read_auxiliary.py

@@ -1,14 +1,12 @@
 import numpy as np
 
-def _process(list_, dict_, keyword):
-    '''processes keyword parameters'''
-    name, val = list_[0], list_[1]
-
-    if name not in dict_[keyword].keys():
-        if name in ['coeff']:
-            dict_[keyword][name] = []
 
+def process(list_, dict_, keyword):
+    """processes keyword parameters"""
+    name, val = list_[0], list_[1]
 
+    if name not in dict_[keyword].keys() and name in ['coeff']:
+        dict_[keyword][name] = []
     # Type conversion
     if name in ['agents', 'seed']:
         val = int(val)
@@ -26,31 +24,23 @@ def _process(list_, dict_, keyword):
     return dict_
 
 
-def _auxiliary(dict_):
+def auxiliary(dict_):
     """
     """
     dict_['AUX'] = {}
-    if 'coeff' not in dict_['TREATED'].keys():
+    if dict_['DIST']['coeff'] == [0.0] * len(dict_['DIST']['coeff']):
         is_deterministic = True
     else:
         is_deterministic = False
 
-
     for key_ in ['UNTREATED', 'TREATED', 'COST', 'DIST']:
         if key_ in ['UNTREATED', 'TREATED', 'COST']:
-            if not is_deterministic:
                 dict_[key_]['all'] = dict_[key_]['coeff']
                 dict_[key_]['all'] = np.array(dict_[key_]['all'])
-            else:
-                dict_[key_]['all'] = np.array([])
         else:
             dict_[key_]['all'] = dict_[key_]['coeff']
             dict_[key_]['all'] = np.array(dict_[key_]['all'])
 
-
-
-
-
     # Create keys that contain all standard deviation and covariance parameters
 
     # Number of covariates
@@ -63,8 +53,7 @@ def _auxiliary(dict_):
     # Number of parameters
     dict_['AUX']['num_paras'] = 2 * num_covars_out + num_covars_cost + 2 + 2
 
-
-    #Starting values
+    # Starting values
     dict_['AUX']['init_values'] = []
 
     for key_ in ['TREATED', 'UNTREATED', 'COST', 'DIST']:
@@ -75,14 +64,6 @@ def _auxiliary(dict_):
                 pass
             else:
                 del dict_[key_][j]
-    dict_['DETERMINISTIC']= is_deterministic
+    dict_['DETERMINISTIC'] = is_deterministic
 
     return dict_
-
-
-
-
-
-
-
-

grmpy/simulation/simulation.py

@@ -4,11 +4,16 @@
 from grmpy.simulation.simulation_auxiliary import simulate_outcomes
 from grmpy.simulation.simulation_auxiliary import write_output
 from grmpy.simulation.simulation_auxiliary import print_info
+from grmpy.read.read import read
 
 
-def simulate(init_dict):
+def simulate(init_file):
     """ This function simulated a user-specified version of the generalized Roy model
     """
+
+    # Transform init file to dictionary
+
+    init_dict = read(init_file)
     # Distribute information
     is_deterministic = init_dict['DETERMINISTIC']
     num_agents = init_dict['SIMULATION']['agents']
@@ -29,18 +34,14 @@ def simulate(init_dict):
     num_covars_cost = C_coeffs.shape[0]
 
     # Simulate observables
-    if not is_deterministic:
-        means = np.tile(0.0, num_covars_out)
-        covs = np.identity(num_covars_out)
-        X = np.random.multivariate_normal(means, covs, num_agents)
-
-        means = np.tile(0.0, num_covars_cost)
-        covs = np.identity(num_covars_cost)
-        Z = np.random.multivariate_normal(means, covs, num_agents)
-        Z[:, 0], X[:, 0] = 1.0, 1.0
-    else:
-        X = np.array([])
-        Z = np.array([])
+    means = np.tile(.0, num_covars_out)
+    covs = np.identity(num_covars_out)
+    X = np.random.multivariate_normal(means, covs, num_agents)
+
+    means = np.tile(.0, num_covars_cost)
+    covs = np.identity(num_covars_cost)
+    Z = np.random.multivariate_normal(means, covs, num_agents)
+    Z[:, 0], X[:, 0] = 1.0, 1.0
 
     # Simulate unobservables
     # Read information about the distribution and the specific means from the init dic