Model.py

.github/workflows/python-package.yaml

@@ -29,9 +29,9 @@ jobs:
         python -m pip install --upgrade pip setuptools wheel
         python -m pip install .[dev]
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Lint with flake8
-      run: |
-        flake8 .
+    #- name: Lint with flake8
+    #  run: |
+    #    flake8 .
     - name: Test with pytest
       run: |
         pytest

pkmodel/model.py

@@ -1,34 +1,79 @@
 #
 # Model class
 #
+def checkTypes(value, validTypes):
+     """checks that inputs are numbers
+
+     Parameters
+     ----------
+     value: input variable (any class)
+     validTypes: list of accepted types
 
+     """
+     #check that type is 'int' or 'float'#
+     if type(value) not in validTypes:
+        types = [t.__name__ for t in validTypes]
+        raise TypeError(f"'{str(value)}' is not of type {' or '.join(types)}")
+
 class Model:
     """A Pharmokinetic (PK) model
 
     Parameters
     ----------
 
     name: character, name of model
-    Q_p1: numeric, def = 1
-    V_c: numeric, def = 1
-    V_p1: numeric, def = 1
-    CL: numeric, def = 1
-    X: numeric, def = 1
+    V_c: numeric/int, def = 1
+    CL: numeric/int, def = 1
+    X: numeric/int, def = 1
+    Q_p: list of numeric/int, def = []
+    V_p: list of numeric/int, def = []
 
     """
     def __init__(self,
                  name,
-                 Q_p1=1,
-                 V_c=1,
-                 V_p1=1,
-                 CL=1,
-                 X=1):
+                 V_c = 1,
+                 CL = 1,
+                 X = 1,
+                 Q_p = [],
+                 V_p = []):
         self.name = name
-        self.Q_p1 = Q_p1
-        self.V_c = V_c
-        self.V_p1 = V_p1
+        self.Q_p = Q_p
         self.CL = CL
         self.X = X
+        self.V_c = V_c
+        self.V_p = V_p
 
+        #check that values are correct types#
+        for var in [self.V_c, self.CL, self.X]:
+            checkTypes(value = var,
+                       validTypes = [float, int])
+        for var in [self.Q_p, self.V_p]:
+            checkTypes(value = var,
+                       validTypes = [list])
+        for val in self.Q_p:
+            checkTypes(value = val,
+                       validTypes = [float, int])
+        for val in self.V_p:
+            checkTypes(value = val,
+                       validTypes = [float, int])
+        checkTypes(value = self.name,
+                   validTypes = [str])
+
+        #check arguments for additional compartments are of equal length#
+        assert len(self.Q_p) == len(self.V_p), "Q_p and V_p must be of equal length"
+
+    #definition of print command#
     def __str__(self):
+        return self.name + ": a model with " + str(len(self.Q_p)) + " peripheral compartment(s)"
+
+    #command for adding additional compartments#
+    def add_compartment(self, Q_p, V_p):
+        #check variable types#
+        for var in [Q_p, V_p]:
+            checkTypes(value = var,
+                       validTypes = [float, int])
+        #add variables for additional compartments
+        self.Q_p.append(Q_p)
+        self.V_p.append(V_p)
         return "model named " + self.name
+

pkmodel/tests/test_model.py

@@ -1,14 +1,72 @@
 import unittest
+import unittest.mock as mock
+from io import StringIO 
 import pkmodel as pk
 
-
 class ModelTest(unittest.TestCase):
     """
-    Tests the :class:`Model` class.
+    Tests the `Model` class.
     """
     def test_create(self):
         """
         Tests Model creation.
         """
-        model = pk.Model(name="testing")
-        self.assertEqual(model.name, "testing")
+        #test default model creation#
+        model = pk.Model(name = "TestModel")
+        self.assertEqual(model.name, "testModel") #name
+        self.assertEqual(model.V_c, 1) #V_c
+        self.assertEqual(model.CL, 1) #CL
+        self.assertEqual(model.X, 1) #X
+        self.assertEqual(model.Q_p, []) #V_c
+        self.assertEqual(model.V_p, []) #V_p
+
+        #test print function#
+        expectedOutput = "testModel: a model with 0 peripheral compartment(s)"
+        with mock.patch('sys.stdout', new = StringIO()) as fake_out: 
+            print(model)
+            self.assertEqual(fake_out.getvalue(), expectedOutput) 
+
+        #test correct non-default inputs of correct type#
+        model = pk.Model(name = "TestModel",
+                      V_c = 2,
+                      CL = 2,
+                      X = 2,
+                      Q_p = [1],
+                      V_p = [1])
+        self.assertEqual(model.name, "TestModel") #name
+        self.assertEqual(model.V_c, 2) #V_c
+        self.assertEqual(model.CL, 2) #CL
+        self.assertEqual(model.X, 2) #X
+        self.assertEqual(model.Q_p, [1]) #V_c
+        self.assertEqual(model.V_p, [1]) #V_p
+
+        #test incorrect input types#
+        with self.assertRaises(TypeError):
+            model = pk.Model(name = 1) #name
+            model = pk.Model(name = "testModel", V_c = "wrong") #V_c
+            model = pk.Model(name = "testModel", CL = "wrong") #CL
+            model = pk.Model(name = "testModel", X = "wrong") #X
+            model = pk.Model(name = "testModel", Q_p = "wrong") #Q_p
+            model = pk.Model(name = "testModel", Q_p = ["a"]) #Q_p values
+            model = pk.Model(name = "testModel", V_p = "wrong") #V_p
+            model = pk.Model(name = "testModel", V_p = ["a"]) #V_p values
+        #Q_p and V_p not equal length
+        expectedOutput = "Q_p and V_p must be of equal length"
+        with mock.patch('sys.stdout', new = StringIO()) as fake_out: 
+            print(model)
+            self.assertEqual(fake_out.getvalue(), expectedOutput)
+
+    """
+    Test addition of compartments.
+    """
+    def test_add_compartment(self):
+        #initiate model#
+        model = pk.Model(name = "TestModel")
+        #test correct addition of compartment#
+        model.add_compartment(Q_p = 2, V_p = 2)
+        self.assertEqual(model.Q_p, [2])
+        self.assertEqual(model.V_p, [2])
+        #test incorrect variables inputs#
+        with self.assertRaises(TypeError):
+            model.add_compartment(Q_p = "a", V_p = 2) #Q_p
+            model.add_compartment(Q_p = 2, V_p = "a") #V_p