Add pre-commit config, lint with Black 22.1.0 (#423)

openforcefield · Feb 21, 2022 · 89e9043 · 89e9043
1 parent 5c6f65d
commit 89e9043
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,18 @@
+ci:
+  autoupdate_schedule: "monthly"
+repos:
+- repo: https://github.com/psf/black
+  rev: 22.1.0
+  hooks:
+  - id: black
+    files: (^openff|^integration-tests)
+- repo: https://github.com/PyCQA/isort
+  rev: 5.10.1
+  hooks:
+  - id: isort
+    files: (^openff|^integration-tests)
+- repo: https://github.com/PyCQA/flake8
+  rev: 4.0.1
+  hooks:
+  - id: flake8
+    files: (^openff|^integration-tests)
diff --git a/openff/evaluator/properties/density.py b/openff/evaluator/properties/density.py
@@ -146,7 +146,7 @@ class ExcessMolarVolume(EstimableExcessProperty):
 
     @classmethod
     def default_unit(cls):
-        return unit.centimeter ** 3 / unit.mole
+        return unit.centimeter**3 / unit.mole
 
     @classmethod
     def _observable_type(cls) -> ObservableType:

diff --git a/openff/evaluator/protocols/reweighting.py b/openff/evaluator/protocols/reweighting.py
@@ -320,7 +320,7 @@ def _compute_effective_samples(
             .magnitude
         )
 
-        effective_samples = 1.0 / np.sum(weights ** 2)
+        effective_samples = 1.0 / np.sum(weights**2)
         return float(effective_samples)
 
     def _execute(self, directory, available_resources):

diff --git a/openff/evaluator/tests/test_datasets/test_datasets.py b/openff/evaluator/tests/test_datasets/test_datasets.py
@@ -122,8 +122,8 @@ def test_to_pandas():
             thermodynamic_state=thermodynamic_state,
             phase=PropertyPhase.Liquid,
             substance=binary_substance,
-            value=1 * unit.meter ** 3 / unit.mole,
-            uncertainty=0.11 * unit.meter ** 3 / unit.mole,
+            value=1 * unit.meter**3 / unit.mole,
+            uncertainty=0.11 * unit.meter**3 / unit.mole,
             source=source,
         )
 
@@ -171,8 +171,8 @@ def test_from_pandas():
             thermodynamic_state=thermodynamic_state,
             phase=PropertyPhase.Liquid,
             substance=Substance.from_components("CO", "O"),
-            value=1.0 * unit.kilogram / unit.meter ** 3,
-            uncertainty=1.0 * unit.kilogram / unit.meter ** 3,
+            value=1.0 * unit.kilogram / unit.meter**3,
+            uncertainty=1.0 * unit.kilogram / unit.meter**3,
             source=MeasurementSource(doi="10.5281/zenodo.596537"),
         ),
         EnthalpyOfVaporization(

diff --git a/openff/evaluator/tests/test_layers/test_reweighting.py b/openff/evaluator/tests/test_layers/test_reweighting.py
@@ -65,7 +65,7 @@ def test_storage_retrieval():
             thermodynamic_state=state,
         ),
         ExcessMolarVolume(
-            value=1.0 * unit.meter ** 3, substance=mixture, thermodynamic_state=state
+            value=1.0 * unit.meter**3, substance=mixture, thermodynamic_state=state
         ),
     ]
     expected_data_per_property = {

diff --git a/openff/evaluator/tests/test_protocols/test_analysis.py b/openff/evaluator/tests/test_protocols/test_analysis.py
@@ -44,7 +44,7 @@ def test_average_dielectric_constant():
             np.zeros((1, 3)) * unit.elementary_charge * unit.nanometer
         )
         average_observable.volumes = ObservableArray(
-            np.ones((1, 1)) * unit.nanometer ** 3
+            np.ones((1, 1)) * unit.nanometer**3
         )
         average_observable.thermodynamic_state = ThermodynamicState(
             298.15 * unit.kelvin, 1.0 * unit.atmosphere
@@ -175,7 +175,7 @@ def test_decorrelate_observables():
 
         protocol = DecorrelateObservables("")
         protocol.input_observables = ObservableArray(
-            np.ones((10, 1)) * unit.nanometer ** 3
+            np.ones((10, 1)) * unit.nanometer**3
         )
         protocol.time_series_statistics = TimeSeriesStatistics(10, 4, 2.0, 2)
         protocol.execute(temporary_directory)

diff --git a/openff/evaluator/tests/test_protocols/test_reweighting_protocols.py b/openff/evaluator/tests/test_protocols/test_reweighting_protocols.py
@@ -92,7 +92,7 @@ def test_reweight_dielectric_constant():
             value=np.zeros((10, 3)) * unit.elementary_charge * unit.nanometers
         )
         reweight_protocol.volumes = ObservableArray(
-            value=np.ones((10, 1)) * unit.nanometer ** 3
+            value=np.ones((10, 1)) * unit.nanometer**3
         )
         reweight_protocol.reference_reduced_potentials = [
             ObservableArray(value=np.zeros(10) * unit.dimensionless)

diff --git a/openff/evaluator/tests/test_server.py b/openff/evaluator/tests/test_server.py
@@ -125,7 +125,7 @@ def test_same_component_batching():
         Density(
             thermodynamic_state=thermodynamic_state,
             substance=Substance.from_components("O", "C"),
-            value=0.0 * unit.kilogram / unit.meter ** 3,
+            value=0.0 * unit.kilogram / unit.meter**3,
         ),
         EnthalpyOfVaporization(
             thermodynamic_state=thermodynamic_state,
@@ -135,7 +135,7 @@ def test_same_component_batching():
         Density(
             thermodynamic_state=thermodynamic_state,
             substance=Substance.from_components("O", "CO"),
-            value=0.0 * unit.kilogram / unit.meter ** 3,
+            value=0.0 * unit.kilogram / unit.meter**3,
         ),
         EnthalpyOfVaporization(
             thermodynamic_state=thermodynamic_state,
@@ -172,7 +172,7 @@ def test_shared_component_batching():
         Density(
             thermodynamic_state=thermodynamic_state,
             substance=Substance.from_components("O", "C"),
-            value=0.0 * unit.kilogram / unit.meter ** 3,
+            value=0.0 * unit.kilogram / unit.meter**3,
         ),
         EnthalpyOfVaporization(
             thermodynamic_state=thermodynamic_state,
@@ -182,7 +182,7 @@ def test_shared_component_batching():
         Density(
             thermodynamic_state=thermodynamic_state,
             substance=Substance.from_components("O", "CO"),
-            value=0.0 * unit.kilogram / unit.meter ** 3,
+            value=0.0 * unit.kilogram / unit.meter**3,
         ),
         EnthalpyOfVaporization(
             thermodynamic_state=thermodynamic_state,

diff --git a/openff/evaluator/tests/test_utils/test_observables.py b/openff/evaluator/tests/test_utils/test_observables.py
@@ -703,10 +703,10 @@ def test_subtract_observables(value_a, value_b, expected_value):
                     object_type,
                 ),
                 _mock_observable(
-                    8.0 * unit.kelvin ** 2,
+                    8.0 * unit.kelvin**2,
                     [
-                        ("vdW", "[#1:1]", "epsilon", 20.0 * unit.kelvin ** 2),
-                        ("vdW", "[#6:1]", "epsilon", 16.0 * unit.kelvin ** 2),
+                        ("vdW", "[#1:1]", "epsilon", 20.0 * unit.kelvin**2),
+                        ("vdW", "[#6:1]", "epsilon", 16.0 * unit.kelvin**2),
                     ],
                     object_type,
                 ),
@@ -722,10 +722,10 @@ def test_subtract_observables(value_a, value_b, expected_value):
                     object_type,
                 ),
                 _mock_observable(
-                    8.0 * unit.kelvin ** 2,
+                    8.0 * unit.kelvin**2,
                     [
-                        ("vdW", "[#1:1]", "epsilon", 4.0 * unit.kelvin ** 2),
-                        ("vdW", "[#6:1]", "epsilon", 8.0 * unit.kelvin ** 2),
+                        ("vdW", "[#1:1]", "epsilon", 4.0 * unit.kelvin**2),
+                        ("vdW", "[#6:1]", "epsilon", 8.0 * unit.kelvin**2),
                     ],
                     object_type,
                 ),
@@ -954,7 +954,7 @@ def test_frame_magic_functions(key):
                 {"Temperature": ObservableArray(value=numpy.ones(2) * unit.kelvin)}
             ),
             "Volume",
-            numpy.ones(1) * unit.nanometer ** 3,
+            numpy.ones(1) * unit.nanometer**3,
             pytest.raises(ValueError),
             "The length of the data (1) must match the length of the data already in "
             "the frame (2).",
@@ -1002,7 +1002,7 @@ def test_frame_from_openmm(pressure):
         ObservableType.KineticEnergy: 5939.683117957521 * unit.kilojoule / unit.mole,
         ObservableType.TotalEnergy: 13874.51498645249 * unit.kilojoule / unit.mole,
         ObservableType.Temperature: 286.38157154881503 * unit.kelvin,
-        ObservableType.Volume: 26.342326662784938 * unit.nanometer ** 3,
+        ObservableType.Volume: 26.342326662784938 * unit.nanometer**3,
         ObservableType.Density: 0.6139877476363793 * unit.gram / unit.milliliter,
     }
 
@@ -1014,7 +1014,7 @@ def test_frame_from_openmm(pressure):
             13874.51498645249 * unit.kilojoule / unit.mole
             + pressure
             * 26.342326662784938
-            * unit.nanometer ** 3
+            * unit.nanometer**3
             * unit.avogadro_constant
         )
         assert numpy.isclose(observable_frame["Enthalpy"].value[0], expected_enthalpy)
@@ -1105,7 +1105,7 @@ def test_frame_join():
                 ObservableFrame(
                     {
                         "Volume": ObservableArray(
-                            value=numpy.ones(2) * unit.nanometer ** 3
+                            value=numpy.ones(2) * unit.nanometer**3
                         )
                     }
                 ),

diff --git a/openff/evaluator/utils/observables.py b/openff/evaluator/utils/observables.py
@@ -552,7 +552,7 @@ class ObservableFrame(MutableMapping[Union[str, ObservableType], ObservableArray
         ObservableType.KineticEnergy: unit.kilojoules / unit.mole,
         ObservableType.TotalEnergy: unit.kilojoules / unit.mole,
         ObservableType.Temperature: unit.kelvin,
-        ObservableType.Volume: unit.nanometer ** 3,
+        ObservableType.Volume: unit.nanometer**3,
         ObservableType.Density: unit.gram / unit.milliliter,
         ObservableType.Enthalpy: unit.kilojoules / unit.mole,
         ObservableType.ReducedPotential: unit.dimensionless,
@@ -687,7 +687,7 @@ def from_openmm(
             "Kinetic Energy (kJ/mole)": unit.kilojoules / unit.mole,
             "Total Energy (kJ/mole)": unit.kilojoules / unit.mole,
             "Temperature (K)": unit.kelvin,
-            "Box Volume (nm^3)": unit.nanometer ** 3,
+            "Box Volume (nm^3)": unit.nanometer**3,
             "Density (g/mL)": unit.gram / unit.milliliter,
         }
 

diff --git a/openff/evaluator/utils/packmol.py b/openff/evaluator/utils/packmol.py
@@ -141,7 +141,7 @@ def _approximate_box_size_by_density(
         A list of the three box lengths in units compatible with angstroms.
     """
 
-    volume = 0.0 * unit.angstrom ** 3
+    volume = 0.0 * unit.angstrom**3
 
     for (molecule, number) in zip(molecules, n_copies):
 

diff --git a/openff/evaluator/utils/timeseries.py b/openff/evaluator/utils/timeseries.py
@@ -107,17 +107,14 @@ def _statistical_inefficiency(
 
     while current_timestep < number_of_timesteps - 1:
 
-        autocorrelation_function = (
+        autocorrelation_function = np.sum(
             np.sum(
-                np.sum(
-                    time_series_shifted[0 : (number_of_timesteps - current_timestep)]
-                    * time_series_shifted[current_timestep:number_of_timesteps],
-                    axis=1,
-                ),
-                axis=0,
-            )
-            / (float(number_of_timesteps - current_timestep) * sigma_squared)
-        )
+                time_series_shifted[0 : (number_of_timesteps - current_timestep)]
+                * time_series_shifted[current_timestep:number_of_timesteps],
+                axis=1,
+            ),
+            axis=0,
+        ) / (float(number_of_timesteps - current_timestep) * sigma_squared)
 
         if autocorrelation_function <= 0.0 and current_timestep > minimum_samples:
             break