updated to LLEPE

tests/multi_ree_settings.txt

@@ -1 +0,0 @@
-{"exp_csv_filename": "../data/csvs/Nd_exp_data.csv", "phases_xml_filename": "../data/xmls/twophase.xml", "opt_dict": {"Nd(H(A)2)3(org)": {"h0": -4662344.6400}}, "phase_names": ["HCl_electrolyte", "PC88A_liquid"], "aq_solvent_name": "H2O(L)", "extractant_name": "(HA)2(org)", "diluant_name": "dodecane", "complex_names": ["Nd(H(A)2)3(org)"], "rare_earth_ion_names": ["Nd+++"], "aq_solvent_rho": 1000.0, "extractant_rho": 960.0, "diluant_rho": 750.0}

tests/one_ree_settings.txt

@@ -1 +0,0 @@
-{"exp_csv_filename": "../data/csvs/exp_data.csv", "phases_xml_filename": "../data/xmls/twophase.xml", "opt_dict": {"Nd(H(A)2)3(org)": {"h0": -4662344.6400}}, "phase_names": ["HCl_electrolyte", "PC88A_liquid"], "aq_solvent_name": "H2O(L)", "extractant_name": "(HA)2(org)", "diluant_name": "dodecane", "complex_name": "Nd(H(A)2)3(org)", "rare_earth_ion_name": "Nd+++", "aq_solvent_rho": 1000.0, "extractant_rho": 960.0, "diluant_rho": 750.0}

tests/test_multi_reeps.py

@@ -1,37 +0,0 @@
-import json
-import numpy as np
-import sys
-sys.path.append('../')
-from reeps import REEPS
-
-with open('multi_ree_settings.txt') as file:
-    testing_params = json.load(file)
-
-beaker = REEPS(**testing_params)
-
-
-def optimizer(func, x_guess):
-    lb = np.array([1e-1])
-    ub = np.array([1e1])
-    bounds = (lb, ub)
-    options = {'c1': 1e-3, 'c2': 1e-3, 'w': 0.9}
-    mini_optimizer = ps.single.global_best.GlobalBestPSO(n_particles=100,
-                                                         dimensions=1,
-                                                         options=options,
-                                                         bounds=bounds)
-    f_opt, x_opt = mini_optimizer.optimize(func, iters=100)
-
-    return x_opt
-
-
-minimizer_kwargs = {"method": 'SLSQP',
-                    "bounds": [(1e-1, 1e1)],
-                    "constraints": (),
-                    "options": {'disp': True, 'maxiter': 1000, 'ftol': 1e-6}}
-# est_enthalpy = beaker.fit(optimizer=optimizer)
-est_enthalpy = beaker.fit()
-print(est_enthalpy)
-
-beaker.update_xml(est_enthalpy)
-# beaker.parity_plot('Nd_d_eq', print_r_squared=True)
-print(beaker.r_squared())

tests/test_reeps.py

@@ -1,165 +1,51 @@
 import json
-from unittest import TestCase
+from llepe import LLEPE
+import pkg_resources
 
-import numpy as np
-import pyswarms as ps
-from reeps import REEPS1
+validation_parameters_filename = pkg_resources.resource_filename(
+    'llepe',
+    r'..\tests\validation_parameters.txt')
+validation_values_filename = pkg_resources.resource_filename(
+    'llepe',
+    r'..\tests\validation_values.txt')
 
-with open('one_ree_settings.txt') as file:
-    testing_params = json.load(file)
-
-beaker = REEPS1(**testing_params)
+with open(validation_parameters_filename) as file:
+    validation_params = json.load(file)
+with open(validation_values_filename) as file:
+    validation_values = json.load(file)
+searcher = LLEPE(**validation_params)
 
 
-# def new_obj(predicted_dict, meas_df, epsilon):
-#     meas_cols = list(meas_df)
-#     pred_keys = list(predicted_dict.keys())
-#     meas = meas_df[meas_cols[2]]
-#     pred = (predicted_dict['re_org'] + epsilon) / (predicted_dict['re_aq'] + epsilon)
-#     log_pred = np.log10(pred)
-#     log_meas = np.log10(meas)
-#     obj = np.sum((log_pred - log_meas) ** 2)
-#     return obj
-# #
-# #
-# # def new_obj(ping):
-# #     print(ping)
-# beaker.set_objective_function(new_obj)
-# objective_kwargs = {"epsilon": 1e-14}
-# beaker.set
-# noinspection PyUnusedLocal
-def optimizer(func, x_guess):
-    lb = np.array([1e-1])
-    ub = np.array([1e1])
-    bounds = (lb, ub)
-    options = {'c1': 1e-3, 'c2': 1e-3, 'w': 0.9}
-    mini_optimizer = ps.single.global_best.GlobalBestPSO(n_particles=100, dimensions=1,
-                                                         options=options, bounds=bounds)
-    f_opt, x_opt = mini_optimizer.optimize(func, iters=100)
-
-    return x_opt
+def array_to_list_in_dict(dictionary):
+    new_dictionary = {}
+    for key, value in dictionary.items():
+        new_dictionary[key] = list(value)
+    return new_dictionary
 
 
-minimizer_kwargs = {"method": 'SLSQP',
-                    "bounds": [(1e-1, 1e1)],
-                    "constraints": (),
-                    "options": {'disp': True, 'maxiter': 1000, 'ftol': 1e-6}}
-# est_enthalpy = beaker.fit(optimizer=optimizer)
-est_enthalpy = beaker.fit()
-print(est_enthalpy)
+def test_init():
+    searcher.update_xml(validation_params['opt_dict'])
+    predicted_dict1 = searcher.get_predicted_dict()
+    predicted_dict1 = array_to_list_in_dict(predicted_dict1)
+    in_moles = searcher.get_in_moles().to_dict('list')
+    assert predicted_dict1 == validation_values['predicted_dict1'], \
+        "Prediction dicts are not equal. Error with set_in_moles, "
+    "update_predicted_dict, or changed xmls, or changed data"
+    assert in_moles == validation_values['in_moles'], \
+        "In_moles are different. Error with set_in_moles or data"
+    return None
 
 
-beaker.update_xml(est_enthalpy)
-# beaker.parity_plot()
-print(beaker.r_squared())
-# class TestREEPS1(TestCase):
-#     def test_slsqp_optimizer(self):
-#         self.fail()
-#
-#     def test_log_mean_squared_error(self):
-#         self.fail()
-#
-#     def test_get_exp_df(self):
-#         self.fail()
-#
-#     def test_set_exp_df(self):
-#         self.fail()
-#
-#     def test_get_phases(self):
-#         self.fail()
-#
-#     def test_set_phases(self):
-#         self.fail()
-#
-#     def test_get_opt_dict(self):
-#         self.fail()
-#
-#     def test_set_opt_dict(self):
-#         self.fail()
-#
-#     def test_get_aq_solvent_name(self):
-#         self.fail()
-#
-#     def test_set_aq_solvent_name(self):
-#         self.fail()
-#
-#     def test_get_extractant_name(self):
-#         self.fail()
-#
-#     def test_set_extractant_name(self):
-#         self.fail()
-#
-#     def test_get_diluant_name(self):
-#         self.fail()
-#
-#     def test_set_diluant_name(self):
-#         self.fail()
-#
-#     def test_get_complex_names(self):
-#         self.fail()
-#
-#     def test_set_complex_names(self):
-#         self.fail()
-#
-#     def test_get_rare_earth_ion_names(self):
-#         self.fail()
-#
-#     def test_set_rare_earth_ion_names(self):
-#         self.fail()
-#
-#     def test_get_aq_solvent_rho(self):
-#         self.fail()
-#
-#     def test_set_aq_solvent_rho(self):
-#         self.fail()
-#
-#     def test_get_extractant_rho(self):
-#         self.fail()
-#
-#     def test_set_extractant_rho(self):
-#         self.fail()
-#
-#     def test_get_diluant_rho(self):
-#         self.fail()
-#
-#     def test_set_diluant_rho(self):
-#         self.fail()
-#
-#     def test_set_in_moles(self):
-#         self.fail()
-#
-#     def test_get_in_moles(self):
-#         self.fail()
-#
-#     def test_set_objective_function(self):
-#         self.fail()
-#
-#     def test_get_objective_function(self):
-#         self.fail()
-#
-#     def test_set_optimizer(self):
-#         self.fail()
-#
-#     def test_get_optimizer(self):
-#         self.fail()
-#
-#     def test_update_predicted_dict(self):
-#         self.fail()
-#
-#     def test_get_predicted_dict(self):
-#         self.fail()
-#
-#     def test__internal_objective(self):
-#         self.fail()
-#
-#     def test_fit(self):
-#         self.fail()
-#
-#     def test_update_xml(self):
-#         self.fail()
-#
-#     def test_parity_plot(self):
-#         self.fail()
-#
-#     def test_r_squared(self):
-#         self.fail()
+def test_fit():
+    est_enthalpy, obj_value = searcher.fit()
+    searcher.update_xml(est_enthalpy)
+    predicted_dict2 = searcher.get_predicted_dict()
+    predicted_dict2 = array_to_list_in_dict(predicted_dict2)
+    r2 = searcher.r_squared()
+    assert est_enthalpy == validation_values['est_enthalpy'], \
+        "estimated enthalpy is not equal. Check fit method"
+    assert predicted_dict2 == validation_values['predicted_dict2'], \
+        "Prediction dicts are not equal. Error with set_in_moles, "
+    "update_predicted_dict, or changed xmls, or changed data"
+    assert r2 == validation_values['r2'], "r-squared value is off, check " \
+                                          "r_squared method"