[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -18,7 +18,7 @@ repos:
     -   id: check-toml
 # Python
 -   repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 23.1.0
     hooks:
     -   id: black-jupyter
 -   repo: https://github.com/PyCQA/isort

dpdata/bond_order_system.py

@@ -1,4 +1,4 @@
-#%%
+# %%
 # Bond Order System
 from copy import deepcopy
 

dpdata/cli.py

@@ -65,7 +65,7 @@ def convert(
     no_labeled: bool = False,
     multi: bool = False,
     type_map: Optional[list] = None,
-    **kwargs
+    **kwargs,
 ):
     """Convert files from one format to another one.
 

dpdata/cp2k/cell.py

@@ -1,4 +1,4 @@
-#%%
+# %%
 import re
 from collections import OrderedDict
 

dpdata/cp2k/output.py

@@ -1,4 +1,4 @@
-#%%
+# %%
 import re
 from collections import OrderedDict
 
@@ -13,7 +13,7 @@
 )
 from .cell import cell_to_low_triangle
 
-#%%
+# %%
 AU_TO_ANG = LengthConversion("bohr", "angstrom").value()
 AU_TO_EV = EnergyConversion("hartree", "eV").value()
 AU_TO_EV_EVERY_ANG = ForceConversion("hartree/bohr", "eV/angstrom").value()
@@ -370,7 +370,7 @@ def handle_single_xyz_frame(self, lines):
         return info_dict
 
 
-#%%
+# %%
 
 
 def get_frames(fname):

dpdata/fhi_aims/output.py

@@ -14,7 +14,6 @@
 
 
 def get_info(lines, type_idx_zero=False):
-
     atom_types = []
     atom_names = []
     cell = []
@@ -159,7 +158,6 @@ def analyze_block(lines, first_blk=False, md=True):
         natom = 0
 
     if first_blk:
-
         if md:
             _tmp = re.findall(pos_patt_other, contents)[:]
             for ii in _tmp[slice(int(len(_tmp) / 2), len(_tmp))]:

dpdata/plugins/3dmol.py

@@ -19,7 +19,7 @@ def to_system(
         f_idx: int = 0,
         size: Tuple[int] = (300, 300),
         style: dict = {"stick": {}, "sphere": {"radius": 0.4}},
-        **kwargs
+        **kwargs,
     ):
         """Show 3D structure of a frame in jupyter.
 

dpdata/plugins/ase.py

@@ -106,7 +106,7 @@ def from_multi_systems(
         end: Optional[int] = None,
         step: Optional[int] = None,
         ase_fmt: Optional[str] = None,
-        **kwargs
+        **kwargs,
     ) -> "ase.Atoms":
         """Convert a ASE supported file to ASE Atoms.
 

dpdata/plugins/deepmd.py

@@ -205,7 +205,7 @@ def from_system(
         self,
         file_name: Union[str, h5py.Group, h5py.File],
         type_map: Optional[List[str]] = None,
-        **kwargs
+        **kwargs,
     ) -> dict:
         """Convert HDF5 file to System data.
 
@@ -233,7 +233,7 @@ def from_labeled_system(
         self,
         file_name: Union[str, h5py.Group, h5py.File],
         type_map: Optional[List[str]] = None,
-        **kwargs
+        **kwargs,
     ) -> dict:
         """Convert HDF5 file to LabeledSystem data.
 
@@ -263,7 +263,7 @@ def to_system(
         file_name: Union[str, h5py.Group, h5py.File],
         set_size: int = 5000,
         comp_prec: np.dtype = np.float64,
-        **kwargs
+        **kwargs,
     ):
         """Convert System data to HDF5 file.
 

dpdata/siesta/aiMD_output.py

@@ -5,6 +5,7 @@
 ev2ev = 1
 ang2ang = 1
 
+
 #############################read output#####################################
 def get_single_line_tail(fin, keyword, num=1):
     file = open(fin, "r")

dpdata/system.py

@@ -1,4 +1,4 @@
-#%%
+# %%
 import glob
 import inspect
 import os

dpdata/xyz/quip_gap_xyz.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
-#%%
+# %%
 import re
 from collections import OrderedDict
 

tests/test_cp2k_aimd_output.py

@@ -1,4 +1,4 @@
-#%%
+# %%
 import os
 import unittest
 
@@ -7,7 +7,7 @@
 from context import dpdata
 
 
-#%%
+# %%
 class TestCp2kAimdOutput(unittest.TestCase, CompLabeledSys):
     def setUp(self):
         self.system_1 = dpdata.LabeledSystem("cp2k/aimd", fmt="cp2k/aimd_output")
@@ -51,7 +51,7 @@ def setUp(self):
     unittest.main()
 
 
-#%%
+# %%
 # print(1)
 # system_1 = dpda.La
 # system_1 = dpdata.LabeledSystem('cp2k/restart_aimd',fmt='cp2k/aimd_output', restart=True)

tests/test_pwmat_mlmd.py

@@ -13,7 +13,6 @@ def setUp(self):
         )
 
     def test_mlmd(self):
-
         self.assertEqual(self.LabeledSystem1["energies"], -0.2197270691e03)
         self.assertEqual(self.LabeledSystem1.get_nframes(), 1)
         self.assertEqual(self.LabeledSystem1.get_natoms(), 5)

tests/test_vasp_unconverged_outcar.py

@@ -16,7 +16,6 @@ def setUp(self):
         )
 
     def test_unconverged(self):
-
         self.assertEqual(self.LabeledSystem1["energies"], -23.94708651)
         self.assertEqual(self.LabeledSystem1.get_nframes(), 1)
         self.assertEqual(self.LabeledSystem1.get_natoms(), 5)