100% coverage

LotkaVolterraModel.py

@@ -136,5 +136,6 @@ def check_equilibrium(a=1.0, b=0.1, c=1.5, d=0.75):
 
 if __name__ == "__main__":
     import doctest
+
     print("Starting doctests")  # not required!
     doctest.testmod()

README.md

@@ -11,7 +11,7 @@ This is an openly developed project and we welcome community contributions, espe
 We are happy to receive code extensions, bug fixes, documentation updates, etc.
 If you are a new user, we recommend checking out the detailed Github Guides.
 
-# Testing the code
+# Unit-tests 
 
 We use [doctests](https://docs.python.org/3/library/doctest.html) and [pytest](https://docs.pytest.org/en/6.2.x/contents.html). 
 
@@ -42,3 +42,4 @@ coverage run -m pytest
 coverage report
 ```
 
+This is also available via a bash script `./tests.sh`.

test_LVM.py

@@ -27,6 +27,57 @@ def test_jacobian():
     target_jac = np.array([[2.0, -0.0], [0.0, -1.2]])
     assert (jac == target_jac).all()
 
+
 def test_equilibria():
-    eq = LotkaVolterraModel.population_equilibrium(a=1.0, b=0.1, c=1.5, d=0.75)
-    assert sum(eq[0])==0 # equal to 0
+    a=1.0
+    b=0.1
+    c=1.5
+    d=0.75
+    eq = LotkaVolterraModel.population_equilibrium(a=a, b=b, c=c, d=d)
+
+    # Checking the first and second fixpoint:
+    assert sum(np.abs(eq[0])) == 0  # equal to 0
+    assert (eq[1] == (c / (d * b), a / b)).all()
+
+def test_check_equilibrium():
+    return_value = LotkaVolterraModel.check_equilibrium()
+    assert return_value == None 
+
+import sys 
+
+def test_printoutput_checkeq(capsys): 
+    ''' 
+    Unit-test that check the print statements in LotkaVolterraModel.check_equilibrium()
+    
+    Notes: 
+    ------
+    Based on capture: https://docs.pytest.org/en/6.2.x/capture.html 
+    '''
+    LotkaVolterraModel.check_equilibrium()      # run check equlibrium and 
+    captured = capsys.readouterr()              # capture the output
+
+    first, second,_ = (captured.out).split('\n')      # separating different lines
+    assert first == "[0. 0.]  is a fix point!"
+    assert second == "[20. 10.]  is a fix point!"
+
+def test_printoutput_checkeq_notfixpoint(capsys):
+
+    # Overwrite dX_dt (with a different version so that equilibria are no longer fixpoints)
+    def dX_dt(X, a=1.0, b=0.1, c=1.5, d=0.75):
+        return np.array([a + X[0] - b * X[0] * X[1], -c * X[1] + d * b * X[0] * X[1]])
+
+    LotkaVolterraModel.dX_dt = dX_dt
+    LotkaVolterraModel.check_equilibrium()      # run check equlibrium and 
+    captured = capsys.readouterr()              # capture the output
+
+    first, second,_ = (captured.out).split('\n')      # separating different lines
+    assert first == "[0. 0.]  is not a fix point!"
+    assert second == "[20. 10.]  is not a fix point!"
+
+def test_main(capsys):
+    ''' Silly test that runs LVM.py as script.py '''
+    import imp
+    runpy = imp.load_source('__main__', 'LotkaVolterraModel.py')
+    captured = capsys.readouterr()              # capture the output
+    first, _ = (captured.out).split('\n')       # separating different lines
+    assert first == "Starting doctests"

tests.sh

@@ -0,0 +1,3 @@
+# Run tests 
+coverage run -m pytest
+coverage report