Add unit tests

Makefile

@@ -20,6 +20,7 @@ docs:
 	PDOC_ALLOW_EXEC=0 ${PYTHON} -m pdoc ./pyMBE.py -o ./documentation --docformat google
 
 unit_tests:
+	${PYTHON} testsuite/serialization_test.py
 	${PYTHON} testsuite/lj_tests.py
 	${PYTHON} testsuite/set_particle_acidity_test.py
 	${PYTHON} testsuite/bond_tests.py

lib/analysis.py

@@ -136,7 +136,7 @@ def get_params_from_dir_name(name):
     entries = name.split('_')
     params = {}
     for entry in entries:
-        sp_entry = entry.split('-')
+        sp_entry = entry.split('-', 1)
         params[sp_entry[0]] = sp_entry[-1]     #float(sp_entry[-1])     # creates a dictionary of parameters and their values.
     return params
 
@@ -343,7 +343,6 @@ def get_distribution_from_df(df, key):
         distribution_list (`lst`): list stored under `key`
 
     """
-    import pandas as pd
     distribution_list=[]
     for row in df[key]:
         if pd.isnull(row):

pyMBE.py

@@ -2157,10 +2157,10 @@ def print_reduced_units(self):
         unit_length=self.units.Quantity(1,'reduced_length')
         unit_energy=self.units.Quantity(1,'reduced_energy')
         unit_charge=self.units.Quantity(1,'reduced_charge')
-        print(unit_length.to('nm'), "=", unit_length)
-        print(unit_energy.to('J'), "=", unit_energy)
-        print('Temperature:', (self.kT/self.Kb).to("K"))
-        print(unit_charge.to('C'), "=", unit_charge)
+        print(f"{unit_length.to('nm'):.5g} = {unit_length}")
+        print(f"{unit_energy.to('J'):.5g} = {unit_energy}")
+        print(f"{unit_charge.to('C'):.5g} = {unit_charge}")
+        print(f"Temperature: {(self.kT/self.Kb).to('K'):.5g}")
         print()
 
     def propose_unused_type(self):

testsuite/serialization_test.py

@@ -0,0 +1,52 @@
+import io
+import json
+import contextlib
+import unittest as ut
+import numpy as np
+import pandas as pd
+import pyMBE
+import lib.analysis
+
+
+class Serialization(ut.TestCase):
+
+    def test_json_encoder(self):
+        encoder = pyMBE.pymbe_library.NumpyEncoder
+        # Python types
+        self.assertEqual(json.dumps(1, cls=encoder), "1")
+        self.assertEqual(json.dumps([1, 2], cls=encoder), "[1, 2]")
+        self.assertEqual(json.dumps((1, 2), cls=encoder), "[1, 2]")
+        self.assertEqual(json.dumps({1: 2}, cls=encoder), """{"1": 2}""")
+        # NumPy types
+        self.assertEqual(json.dumps(np.array([1, 2]), cls=encoder), "[1, 2]")
+        self.assertEqual(json.dumps(np.array(1), cls=encoder), "1")
+        self.assertEqual(json.dumps(np.int32(1), cls=encoder), "1")
+        # Pandas types
+        with self.assertRaisesRegex(TypeError, "Object of type Series is not JSON serializable"):
+            json.dumps(pd.Series([1, 2]), cls=encoder)
+
+    def test_parameters_to_path(self):
+        params = {"kT": 2., "phi": -np.pi, "n": 3, "fene": True, "name": "pep"}
+        name = lib.analysis.built_output_name(params)
+        self.assertEqual(name, "kT-2_phi--3.14_n-3_fene-True_name-pep")
+        params_out = lib.analysis.get_params_from_dir_name(name)
+        params_ref = {"kT": "2", "phi": "-3.14", "n": "3",
+                      "fene": "True", "name": "pep"}
+        self.assertEqual(params_out, params_ref)
+
+    def test_pint_units(self):
+        ref_output = [
+            "Current set of reduced units:",
+            "0.355 nanometer = 1 reduced_length",
+            "4.1164e-21 joule = 1 reduced_energy",
+            "1.6022e-19 coulomb = 1 reduced_charge",
+            "Temperature: 298.15 kelvin",
+        ]
+        pmb = pyMBE.pymbe_library(SEED=42)
+        with contextlib.redirect_stdout(io.StringIO()) as f:
+            pmb.print_reduced_units()
+        self.assertEqual(f.getvalue().strip("\n").split("\n"), ref_output)
+
+
+if __name__ == "__main__":
+    ut.main()