[WIP] Move to new calculator API

CI/integration_tests/calculators/test_angular_distribution_function.py

@@ -62,8 +62,8 @@ def test_project(traj_file, true_values, tmp_path):
     project.add_experiment(
         "NaCl", simulation_data=traj_file, timestep=0.002, temperature=1400
     )
-
-    computation = project.run.AngularDistributionFunction(plot=False)
+    calculator = mds.calculators.AngularDistributionFunction(plot=False)
+    computation = project.execute_operation(calculator)
 
     for item in computation["NaCl"].data_dict:
         computation["NaCl"].data_dict[item].pop("max_peak")

CI/integration_tests/calculators/test_coordination_numbers.py

@@ -63,8 +63,10 @@ def test_project(traj_file, true_values, tmp_path):
         "NaCl", simulation_data=traj_file, timestep=0.002, temperature=1400
     )
 
-    computation = project.run.CoordinationNumbers(
-        savgol_order=3, savgol_window_length=111, plot=False
+    computation = project.execute_operation(
+        mds.calculators.CoordinationNumbers(
+            savgol_order=3, savgol_window_length=111, plot=False
+        )
     )
 
     data_dict = computation["NaCl"]["Na_Cl"]

CI/integration_tests/calculators/test_einstein_diffusion_coefficients.py

@@ -77,11 +77,12 @@ def test_calculator(tmp_path):
     data = TrajectoryChunkData(species_list=[species], chunk_size=n_step)
     data.add_data(pos, 0, species.name, pos_prop.name)
     proc = ScriptInput(data=data, metadata=metadata, name="test_name")
-    exp.add_data(proc)
+    exp.add_data(proc, update_with_pubchempy=False)
 
-    res = exp.run.EinsteinDiffusionCoefficients(
+    calculator = mds.calculators.EinsteinDiffusionCoefficients(
         plot=False, correlation_time=1, data_range=msd_range
-    )[species.name]
+    )
+    res = exp.execute_operation(calculator)[species.name]
 
     time_should_be = time_step * np.arange(0, msd_range) * units.time
     diff_coeff_should_be = diff_coeff * units.length**2 / units.time

CI/integration_tests/calculators/test_einstein_distinct_diffusion_coefficients.py

@@ -36,6 +36,9 @@
 from zinchub import DataHub
 
 import mdsuite as mds
+from mdsuite.calculators.einstein_distinct_diffusion_coefficients import (
+    EinsteinDistinctDiffusionCoefficients,
+)
 
 
 @pytest.fixture(scope="session")
@@ -68,8 +71,10 @@ def test_eddc_project(traj_file, true_values, tmp_path):
         "NaCl", simulation_data=traj_file, timestep=0.002, temperature=1400
     )
 
-    project.run.EinsteinDistinctDiffusionCoefficients(
-        plot=False, data_range=300, correlation_time=100
+    project.execute_operation(
+        EinsteinDistinctDiffusionCoefficients(
+            plot=False, data_range=300, correlation_time=300
+        )
     )
 
     # data_dict = project.load.EinsteinDistinctDiffusionCoefficients()[0].data_dict
@@ -97,8 +102,10 @@ def test_eddc_experiment(traj_file, true_values, tmp_path):
         "NaCl", simulation_data=traj_file, timestep=0.002, temperature=1400
     )
 
-    project.experiments["NaCl"].run.EinsteinDiffusionCoefficients(
-        plot=False, data_range=300, correlation_time=100
+    project.experiments["NaCl"].execute_operation(
+        EinsteinDistinctDiffusionCoefficients(
+            plot=False, data_range=300, correlation_time=300
+        )
     )
 
     # data_dict = (

CI/integration_tests/calculators/test_einstein_helfand_ionic_conductivity.py

@@ -30,6 +30,9 @@
 from zinchub import DataHub
 
 import mdsuite as mds
+from mdsuite.calculators.einstein_helfand_ionic_conductivity import (
+    EinsteinHelfandIonicConductivity,
+)
 
 
 @pytest.fixture(scope="session")
@@ -67,6 +70,6 @@ def test_project(traj_file, true_values, tmp_path):
         "NaCl", simulation_data=traj_file, timestep=0.002, temperature=1400
     )
 
-    # computation = project.run.EinsteinHelfandIonicConductivity(plot=False)
+    _ = project.execute_operation(EinsteinHelfandIonicConductivity(plot=False))
 
     # assertDeepAlmostEqual(computation["NaCl"].data_dict, true_values, decimal=-6)

CI/integration_tests/calculators/test_green_kubo_distinct_diffusion_coefficients.py

@@ -30,6 +30,9 @@
 from zinchub import DataHub
 
 import mdsuite as mds
+from mdsuite.calculators.green_kubo_distinct_diffusion_coefficients import (
+    GreenKuboDistinctDiffusionCoefficients,
+)
 
 
 @pytest.fixture(scope="session")
@@ -64,7 +67,9 @@ def test_project(traj_file, true_values, tmp_path):
         "NaCl", simulation_data=traj_file, timestep=0.002, temperature=1400
     )
 
-    project.run.GreenKuboDistinctDiffusionCoefficients(plot=False, correlation_time=100)
+    project.execute_operation(
+        GreenKuboDistinctDiffusionCoefficients(plot=False, correlation_time=300)
+    )
 
     # data_dict = project.load.GreenKuboDistinctDiffusionCoefficients()[0].data_dict
     #
@@ -91,8 +96,8 @@ def test_experiment(traj_file, true_values, tmp_path):
         "NaCl", simulation_data=traj_file, timestep=0.002, temperature=1400
     )
 
-    project.experiments["NaCl"].run.GreenKuboDistinctDiffusionCoefficients(
-        plot=False, correlation_time=100
+    project.experiments["NaCl"].execute_operation(
+        GreenKuboDistinctDiffusionCoefficients(plot=False, correlation_time=300)
     )
 
     # data_dict = (

CI/integration_tests/calculators/test_kirkwood_buff_integrals.py

@@ -30,6 +30,7 @@
 from zinchub import DataHub
 
 import mdsuite as mds
+from mdsuite.calculators.kirkwood_buff_integrals import KirkwoodBuffIntegral
 from mdsuite.utils.testing import assertDeepAlmostEqual
 
 
@@ -63,8 +64,8 @@ def test_project(traj_file, true_values, tmp_path):
         "NaCl", simulation_data=traj_file, timestep=0.002, temperature=1400
     )
 
-    computation = project.run.KirkwoodBuffIntegral(
-        plot=False, savgol_window_length=111, savgol_order=3
+    computation = project.execute_operation(
+        KirkwoodBuffIntegral(plot=False, savgol_window_length=111, savgol_order=3)
     )
 
     assertDeepAlmostEqual(computation["NaCl"].data_dict, true_values, decimal=1)

CI/integration_tests/calculators/test_potential_of_mean_force.py

@@ -30,6 +30,7 @@
 from zinchub import DataHub
 
 import mdsuite as mds
+from mdsuite.calculators import PotentialOfMeanForce
 from mdsuite.utils.testing import assertDeepAlmostEqual
 
 
@@ -63,8 +64,8 @@ def test_project(traj_file, true_values, tmp_path):
         "NaCl", simulation_data=traj_file, timestep=0.002, temperature=1400
     )
 
-    computation = project.run.PotentialOfMeanForce(
-        plot=False, savgol_window_length=111, savgol_order=3
+    computation = project.execute_operation(
+        PotentialOfMeanForce(plot=False, savgol_window_length=111, savgol_order=3)
     )
 
     assertDeepAlmostEqual(computation["NaCl"].data_dict, true_values, decimal=0)
@@ -78,8 +79,8 @@ def test_experiment(traj_file, true_values, tmp_path):
         "NaCl", simulation_data=traj_file, timestep=0.002, temperature=1400
     )
 
-    computation = project.experiments["NaCl"].run.PotentialOfMeanForce(
-        plot=False, savgol_window_length=111, savgol_order=3
+    computation = project.experiments["NaCl"].execute_operation(
+        PotentialOfMeanForce(plot=False, savgol_window_length=111, savgol_order=3)
     )
 
     assertDeepAlmostEqual(computation.data_dict, true_values, decimal=0)

CI/integration_tests/calculators/test_radial_distribution_function.py

@@ -63,7 +63,9 @@ def test_project(traj_file, true_values, tmp_path):
         "NaCl", simulation_data=traj_file, timestep=0.002, temperature=1400
     )
 
-    computation = project.run.RadialDistributionFunction(plot=False)
+    computation = project.execute_operation(
+        mds.calculators.RadialDistributionFunction(plot=False)
+    )
 
     assertDeepAlmostEqual(computation["NaCl"].data_dict, true_values, decimal=1)
 
@@ -76,7 +78,9 @@ def test_experiment(traj_file, true_values, tmp_path):
         "NaCl", simulation_data=traj_file, timestep=0.002, temperature=1400
     )
 
-    computation = project.experiments.NaCl.run.RadialDistributionFunction(plot=False)
+    computation = project.experiments.NaCl.execute_operation(
+        mds.calculators.RadialDistributionFunction(plot=False)
+    )
 
     assertDeepAlmostEqual(computation.data_dict, true_values, decimal=1)
 
@@ -88,12 +92,14 @@ def test_computation_parameter(traj_file, true_values, tmp_path):
         "NaCl", simulation_data=traj_file, timestep=0.002, temperature=1400
     )
 
-    computation = project.experiments.NaCl.run.RadialDistributionFunction(
-        plot=False,
-        number_of_bins=50,
-        cutoff=5,
-        number_of_configurations=150,
-        species=["Na"],
+    computation = project.experiments.NaCl.execute_operation(
+        mds.calculators.RadialDistributionFunction(
+            plot=False,
+            number_of_bins=50,
+            cutoff=5,
+            number_of_configurations=150,
+            species=["Na"],
+        )
     )
 
     assert computation.computation_parameter["number_of_bins"] == 50

CI/unit_tests/database/test_experiment_database.py

@@ -225,5 +225,8 @@ def test_experiment_units(tmp_path):
 
     project_2 = mds.Project()
 
-    assert project_2.experiments["Exp01"].units == si
-    assert project_2.experiments["Exp02"].units == custom_units
+    for key, val in project_2.experiments["Exp01"].units.items():
+        assert val == getattr(si, key)
+
+    for key, val in project_2.experiments["Exp02"].units.items():
+        assert val == getattr(custom_units, key)

CI/unit_tests/utils/test_helpers.py

@@ -0,0 +1,43 @@
+"""
+MDSuite: A Zincwarecode package.
+
+License
+-------
+This program and the accompanying materials are made available under the terms
+of the Eclipse Public License v2.0 which accompanies this distribution, and is
+available at https://www.eclipse.org/legal/epl-v20.html
+
+SPDX-License-Identifier: EPL-2.0
+
+Copyright Contributors to the Zincwarecode Project.
+
+Contact Information
+-------------------
+email: [email protected]
+github: https://github.com/zincware
+web: https://zincwarecode.com/
+
+Citation
+--------
+If you use this module please cite us with:
+
+Summary
+-------
+Test the helper functions module.
+"""
+from mdsuite.utils.helpers import generate_dataclass
+
+
+class TestHelpers:
+    """
+    Test all functions in the helpers file.
+    """
+
+    def test_generate_dataclass(self):
+        """
+        Test the generate dataclass function.
+        """
+        class_1 = generate_dataclass(par_a=5, par_b="hello", par_c=None)
+        assert class_1.par_a == 5
+        assert class_1.par_b == "hello"
+        assert class_1.par_c is None

CI/unit_tests/utils/test_scaling_functions.py

@@ -67,11 +67,11 @@ def test_linearithmic_scaling_function(self):
         """
         # Assert simple multiplication
         data = linearithmic_scale_function(10, 1)
-        self.assertAlmostEqual(data, 23.02585092994046, 5)
+        self.assertEqual(data, 23.02585092994046)
 
         # Assert scaled multiplication
         data = linearithmic_scale_function(10, 3)
-        self.assertAlmostEqual(data, 69.07755278982138, 5)
+        self.assertEqual(data, 69.07755278982138)
 
         # Assert array values
         data = linearithmic_scale_function(np.array([5, 10, 20]), 2)