Only lint source code, run pre-commit run --all-files

shirtsgroup · Feb 4, 2022 · 0953684 · 0953684
1 parent f30856a
commit 0953684
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Showing 8 changed files with 12 additions and 9 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -5,11 +5,14 @@ repos:
   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
diff --git a/physical_validation/tests/test_data_lammps_parser.py b/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,

diff --git a/physical_validation/tests/test_system_database/Argon1000/system.py b/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,
         ),
     },

diff --git a/physical_validation/tests/test_system_database/Water300/system.py b/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",

diff --git a/physical_validation/tests/test_system_database/Water5/system.py b/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

diff --git a/physical_validation/tests/test_system_database/Water900/system.py b/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(

diff --git a/physical_validation/util/gromacs_interface.py b/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,

diff --git a/physical_validation/util/integrator.py b/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],
                     )
                 )