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pyiron_dataclasses/v1/atomistic.py

@@ -1,6 +1,8 @@
 from dataclasses import dataclass
+from typing import List, Optional
+
 import numpy as np
-from typing import Optional, List
+
 from pyiron_dataclasses.v1.dft import OutputGenericDFT
 
 

pyiron_dataclasses/v1/converter.py

@@ -1,63 +1,63 @@
 from pint import UnitRegistry
 
-from pyiron_dataclasses.v1.job import (
-    Executable,
-    Interactive,
-    GenericDict,
-    Server,
-)
 from pyiron_dataclasses.v1.atomistic import (
+    Cell,
     GenericInput,
     GenericOutput,
     Structure,
     Units,
-    Cell,
 )
 from pyiron_dataclasses.v1.dft import (
-    OutputGenericDFT,
-    ElectronicStructure,
-    DensityOfStates,
     ChargeDensity,
+    DensityOfStates,
+    ElectronicStructure,
+    OutputGenericDFT,
+)
+from pyiron_dataclasses.v1.job import (
+    Executable,
+    GenericDict,
+    Interactive,
+    Server,
 )
 from pyiron_dataclasses.v1.lammps import (
-    LammpsJob,
     LammpsInput,
+    LammpsInputFiles,
+    LammpsJob,
     LammpsOutput,
     LammpsPotential,
-    LammpsInputFiles,
 )
 from pyiron_dataclasses.v1.sphinx import (
-    SphinxJob,
-    SphinxInput,
-    SphinxInputParameters,
-    SphinxRho,
+    BornOppenheimer,
+    PawPot,
+    ScfDiag,
+    Species,
     SphinxAtom,
-    SphinxMain,
     SphinxBasis,
-    SphinxWaves,
-    SphinxOutput,
-    SphinxKpoint,
+    SphinxElectrostaticPotential,
     SphinxElement,
     SphinxEvalForces,
-    SphinxStructure,
-    SphinxRicQN,
-    SphinxInternalInput,
-    Species,
     SphinxInitialGuess,
+    SphinxInput,
+    SphinxInputParameters,
+    SphinxInternalInput,
+    SphinxJob,
+    SphinxKpoint,
+    SphinxMain,
+    SphinxOutput,
     SphinxPawHamiltonian,
     SphinxPreConditioner,
-    SphinxElectrostaticPotential,
-    ScfDiag,
-    PawPot,
-    BornOppenheimer,
+    SphinxRho,
+    SphinxRicQN,
+    SphinxStructure,
+    SphinxWaves,
 )
 from pyiron_dataclasses.v1.vasp import (
-    VaspJob,
+    OutCar,
+    PotCar,
     VaspInput,
+    VaspJob,
     VaspOutput,
     VaspResources,
-    PotCar,
-    OutCar,
 )
 
 

pyiron_dataclasses/v1/dft.py

@@ -1,6 +1,7 @@
 from dataclasses import dataclass
+from typing import List, Optional
+
 import numpy as np
-from typing import Optional, List
 
 
 @dataclass

pyiron_dataclasses/v1/lammps.py

@@ -1,6 +1,5 @@
 from dataclasses import dataclass
-from typing import Optional, List
-
+from typing import List, Optional
 
 from pyiron_dataclasses.v1.atomistic import (
     GenericInput,

pyiron_dataclasses/v1/sphinx.py

@@ -1,16 +1,16 @@
 from dataclasses import dataclass
-import numpy as np
 from typing import List, Optional
 
+import numpy as np
 
 from pyiron_dataclasses.v1.atomistic import (
     GenericInput,
     GenericOutput,
     Structure,
 )
 from pyiron_dataclasses.v1.dft import (
-    ElectronicStructure,
     ChargeDensity,
+    ElectronicStructure,
 )
 from pyiron_dataclasses.v1.job import (
     Executable,

pyiron_dataclasses/v1/vasp.py

@@ -1,15 +1,15 @@
 from dataclasses import dataclass
-import numpy as np
 
+import numpy as np
 
 from pyiron_dataclasses.v1.atomistic import (
     GenericInput,
     GenericOutput,
     Structure,
 )
 from pyiron_dataclasses.v1.dft import (
-    ElectronicStructure,
     ChargeDensity,
+    ElectronicStructure,
 )
 from pyiron_dataclasses.v1.job import (
     Executable,

tests/test_pyiron_atomistics_live.py

@@ -7,6 +7,7 @@
 
 try:
     from pyiron_atomistics import Project
+
     skip_pyiron_atomistics_test = False
 except ImportError:
     skip_pyiron_atomistics_test = True
@@ -21,7 +22,8 @@ def get_node_from_job_dict(job_dict, node):
 
 
 @unittest.skipIf(
-    skip_pyiron_atomistics_test, "pyiron_atomistics is not installed, so the pyiron_atomistics tests are skipped."
+    skip_pyiron_atomistics_test,
+    "pyiron_atomistics is not installed, so the pyiron_atomistics tests are skipped.",
 )
 class TestPyironAtomisticsLive(unittest.TestCase):
     def setUp(self):
@@ -40,10 +42,13 @@ def test_sphinx_calc_minimize(self):
             file_name=job.project_hdf5.file_name,
             h5_path="/",
             recursive=True,
-            slash='ignore',
+            slash="ignore",
         )
         job_sphinx = get_dataclass(job_dict[job.job_name])
-        self.assertEqual(job_sphinx.calculation_output.generic.energy_tot[-1], -228.78315943905295 * ureg.eV)
+        self.assertEqual(
+            job_sphinx.calculation_output.generic.energy_tot[-1],
+            -228.78315943905295 * ureg.eV,
+        )
 
     def test_sphinx_calc_static(self):
         ureg = UnitRegistry()
@@ -54,37 +59,43 @@ def test_sphinx_calc_static(self):
             file_name=job.project_hdf5.file_name,
             h5_path="/",
             recursive=True,
-            slash='ignore',
+            slash="ignore",
         )
         job_sphinx = get_dataclass(job_dict[job.job_name])
-        self.assertEqual(job_sphinx.calculation_output.generic.energy_tot[-1], -228.78315953829286 * ureg.eV)
+        self.assertEqual(
+            job_sphinx.calculation_output.generic.energy_tot[-1],
+            -228.78315953829286 * ureg.eV,
+        )
 
     def test_lammps_calc_static(self):
         ureg = UnitRegistry()
         job = self.project.create.job.Lammps("lmp_static")
         job.structure = self.project.create.structure.ase.bulk("Al", cubic=True)
-        job.potential = '2002--Mishin-Y--Ni-Al--LAMMPS--ipr1'
+        job.potential = "2002--Mishin-Y--Ni-Al--LAMMPS--ipr1"
         job.run()
         job_dict = read_dict_from_hdf(
             file_name=job.project_hdf5.file_name,
             h5_path="/",
             recursive=True,
-            slash='ignore',
+            slash="ignore",
         )
         job_lammps = get_dataclass(job_dict[job.job_name])
-        self.assertEqual(job_lammps.calculation_output.generic.energy_tot[-1], -13.4486826111902 * ureg.eV)
+        self.assertEqual(
+            job_lammps.calculation_output.generic.energy_tot[-1],
+            -13.4486826111902 * ureg.eV,
+        )
 
     def test_lammps_calc_md(self):
         job = self.project.create.job.Lammps("lmp_md")
         job.structure = self.project.create.structure.ase.bulk("Al", cubic=True)
-        job.potential = '2002--Mishin-Y--Ni-Al--LAMMPS--ipr1'
+        job.potential = "2002--Mishin-Y--Ni-Al--LAMMPS--ipr1"
         job.calc_md(temperature=200.0, n_ionic_steps=1000, n_print=100)
         job.run()
         job_dict = read_dict_from_hdf(
             file_name=job.project_hdf5.file_name,
             h5_path="/",
             recursive=True,
-            slash='ignore',
+            slash="ignore",
         )
         job_lammps = get_dataclass(job_dict[job.job_name])
         self.assertEqual(len(job_lammps.calculation_output.generic.energy_tot), 11)
@@ -93,13 +104,16 @@ def test_lammps_calc_minimize(self):
         ureg = UnitRegistry()
         job = self.project.create.job.Lammps("lmp_mini")
         job.structure = self.project.create.structure.ase.bulk("Al", cubic=True)
-        job.potential = '2002--Mishin-Y--Ni-Al--LAMMPS--ipr1'
+        job.potential = "2002--Mishin-Y--Ni-Al--LAMMPS--ipr1"
         job.run()
         job_dict = read_dict_from_hdf(
             file_name=job.project_hdf5.file_name,
             h5_path="/",
             recursive=True,
-            slash='ignore',
+            slash="ignore",
         )
         job_lammps = get_dataclass(job_dict[job.job_name])
-        self.assertEqual(job_lammps.calculation_output.generic.energy_tot[-1], -13.4486826111902 * ureg.eV)
+        self.assertEqual(
+            job_lammps.calculation_output.generic.energy_tot[-1],
+            -13.4486826111902 * ureg.eV,
+        )

tests/test_pyiron_atomistics_static.py

@@ -12,7 +12,9 @@
 class TestPyironAtomisticsStatic(TestCase):
     def test_all(self):
         ureg = UnitRegistry()
-        static_folder = os.path.join(os.path.dirname(__file__), "pyiron_atomistics_0_6_13")
+        static_folder = os.path.join(
+            os.path.dirname(__file__), "pyiron_atomistics_0_6_13"
+        )
         energy_dict = {
             "sx.h5": -228.7831594379917 * ureg.eV,
             "lmp.h5": -9428.45286561574 * ureg.eV,
@@ -23,9 +25,11 @@ def test_all(self):
                 file_name=os.path.join(static_folder, hdf5_file),
                 h5_path="/",
                 recursive=True,
-                slash='ignore',
+                slash="ignore",
             )[hdf5_file.split(".")[0]]
             self.assertEqual(
-                get_dataclass(job_dict=job_dict).calculation_output.generic.energy_tot[-1],
-                energy_dict[hdf5_file]
+                get_dataclass(job_dict=job_dict).calculation_output.generic.energy_tot[
+                    -1
+                ],
+                energy_dict[hdf5_file],
             )