Add pre-commit

.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: ^physical_validation
+- repo: https://github.com/PyCQA/isort
+  rev: 5.10.1
+  hooks:
+  - id: isort
+    files: ^physical_validation
+- repo: https://github.com/PyCQA/flake8
+  rev: 4.0.1
+  hooks:
+  - id: flake8
+    files: ^physical_validation

physical_validation/tests/test_data_lammps_parser.py

@@ -32,7 +32,7 @@ def test_read_lammps() -> None:
         lammps_files = database.lammps_files(system_name)
         parser = pv.data.LammpsParser()
         ensemble = pv.data.EnsembleData(
-            ensemble="NVT", natoms=100 * 3, volume=20 ** 3, temperature=300
+            ensemble="NVT", natoms=100 * 3, volume=20**3, temperature=300
         )
         lammps_simulation_data = parser.get_simulation_data(
             ensemble=ensemble,

physical_validation/tests/test_system_database/Argon1000/system.py

@@ -34,7 +34,7 @@
         "liquid": pv.data.EnsembleData(
             ensemble="NVE",
             natoms=1000,
-            volume=3.60140 ** 3,
+            volume=3.60140**3,
             energy=1,
         ),
     },

physical_validation/tests/test_system_database/Water300/system.py

@@ -40,7 +40,7 @@
     # Hack ensemble to also distinguish trajectories
     ensemble={
         "NVT": pv.data.EnsembleData(
-            ensemble="NVT", natoms=100 * 3, volume=20 ** 3, temperature=300
+            ensemble="NVT", natoms=100 * 3, volume=20**3, temperature=300
         ),
     },
     description="100 water molecules, energy and trajectory data",

physical_validation/tests/test_system_database/Water5/system.py

@@ -39,10 +39,10 @@
     # Hack ensemble to also distinguish trajectories
     ensemble={
         "NVT full trajectory": pv.data.EnsembleData(
-            ensemble="NVT", natoms=5 * 3, volume=1.86210 ** 3, temperature=300
+            ensemble="NVT", natoms=5 * 3, volume=1.86210**3, temperature=300
         ),
         "NVT last frame only": pv.data.EnsembleData(
-            ensemble="NVT", natoms=5 * 3, volume=1.86210 ** 3, temperature=300
+            ensemble="NVT", natoms=5 * 3, volume=1.86210**3, temperature=300
         ),
         "NPT full trajectory": pv.data.EnsembleData(
             ensemble="NPT", natoms=5 * 3, pressure=1, temperature=300

physical_validation/tests/test_system_database/Water900/system.py

@@ -34,13 +34,13 @@
         "NVT-low": pv.data.EnsembleData(
             ensemble="NVT",
             natoms=900 * 3,
-            volume=3.01125 ** 3,
+            volume=3.01125**3,
             temperature=298.15,
         ),
         "NVT-high": pv.data.EnsembleData(
             ensemble="NVT",
             natoms=900 * 3,
-            volume=3.01125 ** 3,
+            volume=3.01125**3,
             temperature=308.15,
         ),
         "NPT-lowT-lowP": pv.data.EnsembleData(

physical_validation/util/gromacs_interface.py

@@ -495,7 +495,7 @@ def _check_exe(self, quiet: bool = False, exe: Optional[str] = None) -> bool:
             else:
                 raise e
         # check that output is as expected
-        return bool(re.search(br":-\) GROMACS - gmx.* \(-:", exe_out))
+        return bool(re.search(rb":-\) GROMACS - gmx.* \(-:", exe_out))
 
     def _run(
         self,

physical_validation/util/integrator.py

@@ -99,7 +99,7 @@ def check_convergence(
                         results[dt][0],
                         results[dt][1],
                         results[dt][2],
-                        prev[0] ** 2 / dt ** 2,
+                        prev[0] ** 2 / dt**2,
                         prev[1] / results[dt][1],
                     )
                 )