added pytest to most

Author: simongravelle

docs/source/chapters/chapter1.rst

@@ -280,8 +280,10 @@ and copy the following lines into it:
         assert not issubclass(Utilities, MonteCarlo), "Utilities should not inherit from MonteCarlo"
         print("Utilities does not inherit from MonteCarlo, as expected")
 
-    test_utilities_does_not_inherit_from_montecarlo()
-    test_montecarlo_inherits_from_utilities()
+    # In the script is launched with Python, call Pytest
+    if __name__ == "__main__":
+        import pytest
+        pytest.main(["-s", __file__])
 
 .. label:: end_test_1a_class
 
@@ -318,8 +320,10 @@ called *test_1b.py*, copy the following lines:
         except Exception as e:
             print(f"Method call raised an error: {e}")
 
-    # Make sure that the method call succeeded
-    test_init_method()
+    # In the script is launched with Python, call Pytest
+    if __name__ == "__main__":
+        import pytest
+        pytest.main(["-s", __file__])
 
 .. label:: end_test_1b_class
 

docs/source/chapters/chapter2.rst

@@ -382,20 +382,25 @@ type 1, and 3 atoms of type 2:
     import numpy as np
     from Prepare import Prepare
 
-    prep = Prepare(number_atoms=[2, 3],
+    # Initialize the Prepare object
+    prep = Prepare(
+        number_atoms=[2, 3],
         epsilon=[0.2, 0.4], # kcal/mol
         sigma=[3, 4], # A
         atom_mass=[10, 20], # g/mol
-        )
+    )
 
-    def test_array(result, expected):
-        """Test function comparing *result* and *expected*"""
+    # Test function using pytest
+    def test_atoms_epsilon():
+        expected = np.array([1., 1., 2., 2., 2.])
+        result = prep.atoms_epsilon
         assert np.array_equal(result, expected), f"Test failed: {result} != {expected}"
         print("Test passed")
 
-    # Make sure the *atoms_epsilon* gives the expected values
-    # of 1 1 2 2 2 (in LJ units)
-    test_array(prep.atoms_epsilon, np.array([1., 1., 2., 2., 2.]))
+    # In the script is launched with Python, call Pytest
+    if __name__ == "__main__":
+        import pytest
+        pytest.main(["-s", __file__])
 
 .. label:: end_test_2a_class
 

docs/source/chapters/chapter3.rst

@@ -229,19 +229,28 @@ boundaries along all 3 dimensions of space:
     import numpy as np
     from InitializeSimulation import InitializeSimulation
 
-    init = InitializeSimulation(number_atoms=[2, 3],
+    # Initialize the InitializeSimulation object
+    init = InitializeSimulation(
+        number_atoms=[2, 3],
         epsilon=[0.2, 0.4], # kcal/mol
         sigma=[3, 4], # A
         atom_mass=[10, 20], # g/mol
         box_dimensions=[20, 20, 20], # A
-        )
+    )
 
-    def test_placement(box_boundaries, atoms_positions):
-        """Ensure that atoms are placed within the box"""
+    # Test function using pytest
+    def test_placement():
+        box_boundaries = init.box_boundaries
+        atoms_positions = init.atoms_positions
         for atom_position in atoms_positions:
             for x, boundary in zip(atom_position, box_boundaries):
-                assert (x >= boundary[0]) & (x <= boundary[1]), f"Test failed: Atoms outside of the box"
+                assert (x >= boundary[0]) and (x <= boundary[1]), f"Test failed: Atoms outside of the box at position {atom_position}"
         print("Test passed")
-    test_placement(init.box_boundaries, init.atoms_positions)
+
+    # If the script is run directly, execute the tests
+    if __name__ == "__main__":
+        import pytest
+        # Run pytest programmatically
+        pytest.main(["-s", __file__])
 
 .. label:: end_test_3a_class

docs/source/chapters/chapter4.rst

@@ -353,20 +353,31 @@ typically negative.
 
     from MinimizeEnergy import MinimizeEnergy
 
-    min = MinimizeEnergy(maximum_steps=100,
+    # Initialize the MinimizeEnergy object and run the minimization
+    minimizer = MinimizeEnergy(
+        maximum_steps=100,
         number_atoms=[2, 3],
         epsilon=[0.2, 0.4], # kcal/mol
         sigma=[3, 4], # A
         atom_mass=[10, 20], # g/mol
         box_dimensions=[20, 20, 20], # A
-        )
-    min.run()
-
-    Final_Epot = min.Epot
-    Final_MaxF = min.MaxF
-    assert Final_Epot < 0, f"Test failed: Final energy too large"
-    assert Final_MaxF < 10, f"Test failed: Final max force too large"
-    print("Test passed")
+    )
+    minimizer.run()
+
+    # Test function using pytest
+    def test_energy_and_force():
+        Final_Epot = minimizer.Epot
+        Final_MaxF = minimizer.MaxF
+        assert Final_Epot < 0, f"Test failed: Final energy too large: {Final_Epot}"
+        assert Final_MaxF < 10, f"Test failed: Final max force too large: {Final_MaxF}"
+        print("Test passed")
+
+    # If the script is run directly, execute the tests
+    if __name__ == "__main__":
+        import pytest
+        # Run pytest programmatically
+        pytest.main(["-s", __file__])
+
 
 .. label:: end_test_4a_class
 

docs/source/chapters/chapter5.rst

@@ -211,21 +211,32 @@ files were indeed created without the *Outputs/* folder:
     import os
     from MinimizeEnergy import MinimizeEnergy
 
-    min = MinimizeEnergy(maximum_steps=100,
+    # Initialize the MinimizeEnergy object and run the minimization
+    minimizer = MinimizeEnergy(
+        maximum_steps=100,
         thermo_period=25,
         dumping_period=25,
-        thermo_outputs = "Epot-MaxF",
+        thermo_outputs="Epot-MaxF",
         number_atoms=[2, 3],
         epsilon=[0.1, 1.0], # kcal/mol
         sigma=[3, 4], # A
         atom_mass=[10, 20], # g/mol
         box_dimensions=[20, 20, 20], # A
         data_folder="Outputs/",
-        )
-    min.run()
-
-    assert os.path.exists("Outputs/dump.min.lammpstrj"), f"Test failed: dump file was not created"
-    assert os.path.exists("Outputs/simulation.log"), f"Test failed: log file was not created"
+    )
+    minimizer.run()
+
+    # Test function using pytest
+    def test_output_files():
+        assert os.path.exists("Outputs/dump.min.lammpstrj"), "Test failed: dump file was not created"
+        assert os.path.exists("Outputs/simulation.log"), "Test failed: log file was not created"
+        print("Test passed")
+
+    # If the script is run directly, execute the tests
+    if __name__ == "__main__":
+        import pytest
+        # Run pytest programmatically
+        pytest.main(["-s", __file__])
 
 .. label:: end_test_5a_class
 

docs/source/chapters/chapter7.rst

@@ -96,53 +96,69 @@ chosen to make the calculation faster.
 
     import numpy as np
     from MonteCarlo import MonteCarlo
-
     from scipy import constants as cst
     from pint import UnitRegistry
+    from reader import import_data
+
+    # Initialize the unit registry
     ureg = UnitRegistry()
 
     # Constants
-    kB = cst.Boltzmann*ureg.J/ureg.kelvin # boltzman constant
-    Na = cst.Avogadro/ureg.mole # avogadro
-    R = kB*Na # gas constant
+    kB = cst.Boltzmann * ureg.J / ureg.kelvin  # Boltzmann constant
+    Na = cst.Avogadro / ureg.mole  # Avogadro's number
+    R = kB * Na  # Gas constant
 
     # Parameters taken from Wood1957
-    tau = 2 # ratio between volume / reduced volume
-    epsilon = (119.76*ureg.kelvin*kB*Na).to(ureg.kcal/ureg.mol) # kcal/mol
-    r_star = 3.822*ureg.angstrom # angstrom
-    sigma = r_star / 2**(1/6) # angstrom
-    N_atom = 50 # no units
-    m_argon = 39.948*ureg.gram/ureg.mol # g/mol
-    T =  328.15 * ureg.degK # 328 K or 55°C
+    tau = 2  # Ratio between volume / reduced volume
+    epsilon = (119.76 * ureg.kelvin * kB * Na).to(ureg.kcal / ureg.mol)  # kcal/mol
+    r_star = 3.822 * ureg.angstrom  # Angstrom
+    sigma = r_star / 2**(1/6)  # Angstrom
+    N_atom = 50  # Number of atoms
+    m_argon = 39.948 * ureg.gram / ureg.mol  # g/mol
+    T = 328.15 * ureg.degK  # 328 K or 55°C
     volume_star = r_star**3 * Na * 2**(-0.5)
-    cut_off = sigma*2.5 # angstrom
-    displace_mc = sigma/5 # angstrom
-    volume = N_atom*volume_star*tau/Na # angstrom**3
-    box_size = volume**(1/3) # angstrom
-
-    mc = MonteCarlo(maximum_steps=15000,
+    cut_off = sigma * 2.5  # Angstrom
+    displace_mc = sigma / 5  # Angstrom
+    volume = N_atom * volume_star * tau / Na  # Angstrom^3
+    box_size = volume**(1/3)  # Angstrom
+
+    # Initialize and run the Monte Carlo simulation
+    mc = MonteCarlo(
+        maximum_steps=15000,
         dumping_period=1000,
         thermo_period=1000,
-        thermo_outputs = "Epot-press",
+        thermo_outputs="Epot-press",
         neighbor=50,
         number_atoms=[N_atom],
         epsilon=[epsilon.magnitude],
         sigma=[sigma.magnitude],
         atom_mass=[m_argon.magnitude],
         box_dimensions=[box_size.magnitude, box_size.magnitude, box_size.magnitude],
-        displace_mc = displace_mc.magnitude,
-        desired_temperature = T.magnitude,
-        cut_off = cut_off.magnitude,
-        data_folder = "Outputs/",
-        )
+        displace_mc=displace_mc.magnitude,
+        desired_temperature=T.magnitude,
+        cut_off=cut_off.magnitude,
+        data_folder="Outputs/",
+    )
     mc.run()
 
-    # Import the data and calculate p V / R T
-    # output = np.mean(np.loadtxt("Outputs/pressure.dat")[:,1][10:])
-    # pressure = (output*ureg.atm).to(ureg.pascal)
-    # volume = (volume_star * tau / Na).to(ureg.meter**3)
-    # pV_over_RT = np.round((pressure * volume / (R * T) * Na).magnitude,2)
-    # print("p v / R T =", pV_over_RT, " --- (The expected value from Wood1957 is 1.5)")
+    # Test function using pytest
+    def test_pV_over_RT():
+        # Import the data and calculate pV / RT
+        pressure_data = np.array(import_data("Outputs/simulation.log")[1:])[0][:,2][10:]  # Skip initial values
+        pressure_atm = np.mean(pressure_data) # atm
+        pressure_Pa = (pressure_atm * ureg.atm).to(ureg.pascal) # Pa
+        volume = (volume_star * tau / Na).to(ureg.meter**3) # m3
+        pV_over_RT = (pressure_Pa * volume / (R * T) * Na).magnitude
+        
+        # Assert that pV_over_RT is close to 1.5
+        assert np.isclose(pV_over_RT, 1.5, atol=1.0), f"Test failed: pV/Rt = {pV_over_RT}, expected close to 1.5"
+        print(f"pV/RT = {pV_over_RT:.2f} --- (The expected value from Wood1957 is 1.5)")
+
+    # If the script is run directly, execute the tests
+    if __name__ == "__main__":
+        import pytest
+        # Run pytest programmatically
+        pytest.main(["-s", __file__])
 
 .. label:: end_test_7a_class
 
@@ -154,4 +170,4 @@ of 1.5 by Wood and Parker for :math:`\tau = V/V^* = 2` (see Fig. 4 in Ref. :cite
     (...)
     p v / R T = 1.56  --- (The expected value from Wood1957 is 1.5)
 
-The exact value will varie from one simulation to the other due to noise.
+The exact value will vary from one simulation to the other due to noise.

tests/build-documentation.py

@@ -18,7 +18,7 @@
     os.mkdir("generated-codes/")
 
 # loop on the different chapter
-for chapter_id in [1]:
+for chapter_id in [1, 2, 3, 4, 5, 6, 7]:
     # for each chapter, create the corresponding code
     RST_EXISTS, created_tests, folder = sphinx_to_python(path_to_docs, chapter_id)
     if RST_EXISTS: