Add more unit tests

environment-dev.yml

@@ -3,7 +3,7 @@ channels:
 - conda-forge
 dependencies:
 - cuda-version=11.8
-- freud >=2.13
+- freud =2.13.2
 - gsd >=3.0
 - hoomd >=4.0
 - python >=3.9

environment.yml

@@ -3,7 +3,7 @@ channels:
 - conda-forge
 dependencies:
 - cuda-version=11.8
-- freud >=2.13
+- freud =2.13.2
 - gsd >=3.0
 - hoomd >=4.0
 - python >=3.9

msibi/forces.py

@@ -84,12 +84,6 @@ def __init__(
         self._tail_correction_history = []
         self._learned_potential_history = []
 
-        if optimize and nbins is None:
-            raise ValueError(
-                    "If this force is set to be optimized, the nbins "
-                    "must be set as a non-zero value"
-            )
-
     def __repr__(self):
         return (
                 f"Type: {self.__class__}; "
@@ -131,7 +125,7 @@ def smoothing_window(self) -> int:
 
     @smoothing_window.setter
     def smoothing_window(self, value: int):
-        if not isinstance(value, int):
+        if not isinstance(value, int) or value <= 0:
             raise ValueError("The smoothing window must be an integer.")
         self._smoothing_window = value
         for state in self._states:
@@ -144,7 +138,7 @@ def smoothing_order(self) -> int:
 
     @smoothing_order.setter
     def smoothing_order(self, value: int):
-        if not isinstance(value, int):
+        if not isinstance(value, int) or value <= 0:
             raise ValueError("The smoothing order must be an integer.")
         self._smoothing_order = value
         for state in self._states:
@@ -157,7 +151,7 @@ def nbins(self) -> int:
 
     @nbins.setter
     def nbins(self, value: int):
-        if not isinstance(value, int):
+        if not isinstance(value, int) or value <= 0:
             raise ValueError("nbins must be an integer.")
         self._nbins =  value
         for state in self._states:

msibi/tests/test_forces.py

@@ -31,6 +31,7 @@ def test_potential_setter(self, bond):
         initial_pot = np.copy(bond.potential)
         bond.potential = bond.potential * 2
         assert np.allclose(bond.potential, initial_pot * 2)
+        assert bond.format == "table"
 
     def test_smooth_potential(self, bond):
         bond.set_quadratic(
@@ -49,6 +50,37 @@ def test_smooth_potential(self, bond):
         for i, j in zip(bond.potential, noisy_pot):
             assert i != j
 
+    def test_set_from_file(self):
+        bond = Bond(type1="A", type2="B", optimize=True, nbins=60)
+        bond.set_quadratic(x_min=0.0, x_max=3.0, x0=1, k2=200, k3=0, k4=0)
+        bond.save_potential("test.csv")
+        bond2 = Bond(type1="A", type2="B", optimize=True, nbins=60)
+        bond2.set_from_file("test.csv")
+        assert np.allclose(bond.potential, bond2.potential)
+        os.remove("test.csv")
+
+    def test_fit_scores(self, msibi, stateX, stateY):
+        msibi.gsd_period = 10
+        bond = Bond(type1="A", type2="B", optimize=True, nbins=60)
+        bond.set_quadratic(x_min=0.0, x_max=3.0, x0=1, k2=200, k3=0, k4=0)
+        angle = Angle(type1="A", type2="B", type3="A", optimize=False)
+        angle.set_harmonic(k=500, t0=2)
+        angle2 = Angle(type1="B", type2="A", type3="B", optimize=False)
+        angle2.set_harmonic(k=500, t0=2)
+        msibi.add_state(stateX)
+        msibi.add_state(stateY)
+        msibi.add_force(bond)
+        msibi.add_force(angle)
+        msibi.add_force(angle2)
+        init_bond_pot = np.copy(bond.potential)
+        msibi.run_optimization(n_steps=500, n_iterations=1)
+        assert len(bond._states[stateY]["f_fit"]) == 1
+        assert len(bond._states[stateX]["f_fit"]) == 1
+        bond.plot_fit_scores(state=stateY)
+        bond.plot_fit_scores(state=stateX)
+        with pytest.raises(RuntimeError):
+            angle.plot_fit_scores(state=stateY)
+
     def test_smoothing_window(self, bond):
         bond.smoothing_window = 5
         assert bond.smoothing_window == 5
@@ -61,6 +93,48 @@ def test_nbins(self, bond):
         bond.nbins = 60
         assert bond.nbins == 60
 
+    def test_set_potential_error(self):
+        bond = Bond(type1="A", type2="B", optimize=False)
+        bond.set_harmonic(k=500, r0=2)
+        with pytest.raises(ValueError):
+            bond.potential = np.array([1, 2, 3])
+
+    def test_plot_target_dist(self, stateX):
+        angle = Angle(type1="A", type2="B", type3="A", optimize=True, nbins=60)
+        angle.set_quadratic(x0=2, k4=0, k3=0, k2=100, x_min=0, x_max=np.pi)
+        angle._add_state(stateX)
+        angle.plot_target_distribution(state=stateX)
+
+    def test_static_warnings(self):
+        bond = Bond(type1="A", type2="B", optimize=False)
+        bond.set_harmonic(k=500, r0=2)
+        with pytest.warns(UserWarning):
+            bond.potential
+            bond.force
+
+    def test_bad_smoothing_args(self, bond):
+        with pytest.raises(ValueError):
+            bond.smoothing_window = 0
+        with pytest.raises(ValueError):
+            bond.smoothing_window = 4.5
+        with pytest.raises(ValueError):
+            bond.smoothing_order = 0
+        with pytest.raises(ValueError):
+            bond.smoothing_order = 2.2
+        with pytest.raises(ValueError):
+            bond.nbins = 20.5
+        with pytest.raises(ValueError):
+            bond.nbins = 0
+        angle = Angle(type1="A", type2="B", type3="A", optimize=False)
+        angle.set_harmonic(k=500, t0=2)
+        with pytest.raises(RuntimeError):
+            angle.smooth_potential()
+
+    def test_save_static_force(self):
+        angle = Angle(type1="A", type2="B", type3="A", optimize=False)
+        angle.set_harmonic(k=500, t0=2)
+        with pytest.raises(RuntimeError):
+            angle.save_potential("test.csv")
 
 class TestBond(BaseTest):
     def test_bond_name(self, bond):

msibi/tests/test_optimize.py

@@ -49,6 +49,11 @@ def test_run(self, msibi, stateX, stateY):
         assert msibi.n_iterations == 1
         ff = msibi._build_force_objects()
         assert len(ff) == 1
+        assert len(bond.distribution_history(state=stateX)) == 1
+        assert len(bond.potential_history) == 2
+        assert len(bond._head_correction_history) == 1
+        assert len(bond._tail_correction_history) == 1
+        assert len(bond._learned_potential_history) == 1
 
     def test_run_with_static_force(self, msibi, stateX, stateY):
         msibi.gsd_period = 10
@@ -68,4 +73,55 @@ def test_run_with_static_force(self, msibi, stateX, stateY):
         assert not np.array_equal(bond.potential, init_bond_pot)
         assert msibi.n_iterations == 1
         ff = msibi._build_force_objects()
-        assert len(ff) == 2
+        assert len(ff) == 2
+
+    def test_run_with_all_forces(self, msibi, stateX, stateY):
+        msibi.add_state(stateX)
+        msibi.add_state(stateY)
+
+        bond = Bond(type1="A", type2="B", optimize=False, nbins=60)
+        bond.set_harmonic(r0=1.1, k=100)
+        msibi.add_force(bond)
+
+        angle = Angle(type1="A", type2="B", type3="A", optimize=False)
+        angle.set_harmonic(t0=1.9, k=100)
+        msibi.add_force(angle)
+        angle2 = Angle(type1="B", type2="A", type3="B", optimize=False)
+        angle2.set_harmonic(t0=2.3, k=100)
+        msibi.add_force(angle2)
+
+        pair = Pair(type1="A", type2="B", r_cut=3.0, nbins=60, optimize=True, exclude_bonded=True)
+        pair.set_lj(sigma=1.5, epsilon=1, r_cut=3.0, r_min=0.1)
+        msibi.add_force(pair)
+        pair2 = Pair(type1="A", type2="A", r_cut=3.0, nbins=60, optimize=True, exclude_bonded=True)
+        pair2.set_lj(sigma=2, epsilon=2, r_cut=3.0, r_min=0.1)
+        msibi.add_force(pair2)
+        pair3 = Pair(type1="B", type2="B", r_cut=3.0, nbins=60, optimize=True, exclude_bonded=True)
+        pair3.set_lj(sigma=1.5, epsilon=1, r_cut=3.0, r_min=0.1)
+        msibi.add_force(pair3)
+        dihedral = Dihedral(type1="A", type2="B", type3="A", type4="B", optimize=False)
+        dihedral.set_harmonic(k=100, phi0=0, d=-1, n=1)
+        msibi.add_force(dihedral)
+
+        msibi.run_optimization(n_steps=500, n_iterations=0)
+
+    def test_raise_errors(self, msibi, stateX, stateY):
+        with pytest.raises(RuntimeError):
+            msibi.pickle_forces(file_path="test.pkl")
+
+        bond = Bond(type1="A", type2="B", optimize=True, nbins=60)
+        angle = Angle(type1="A", type2="B", type3="A", optimize=True, nbins=60)
+        with pytest.raises(RuntimeError):
+            msibi.add_force(bond)
+            msibi.add_force(angle)
+
+        with pytest.raises(ValueError):
+            msibi = MSIBI(
+                nlist=hoomd.md.nlist.Cell,
+                integrator_method=hoomd.md.methods.DisplacementCapped,
+                method_kwargs=dict(),
+                thermostat=hoomd.md.methods.thermostats.MTTK,
+                thermostat_kwargs=dict(tau=0.01),
+                dt=0.003,
+                gsd_period=int(1e3),
+            )