[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

docs/conf.py

@@ -13,8 +13,8 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import os
-import sys
 import subprocess as sp
+import sys
 from datetime import date
 
 sys.path.insert(0, os.path.abspath(".."))

docs/make_format.py

@@ -1,12 +1,11 @@
 import csv
-from typing import Any
 from collections import defaultdict
+from typing import Any
 
 # ensure all plugins are loaded!
 import dpdata.plugins
+from dpdata.driver import Driver, Minimizer
 from dpdata.format import Format
-from dpdata.driver import Driver
-from dpdata.driver import Minimizer
 from dpdata.system import get_cls_name
 
 

dpdata/__init__.py

@@ -1,9 +1,5 @@
-from . import vasp
-from . import lammps
-from . import md
-from .system import System
-from .system import LabeledSystem
-from .system import MultiSystems
+from . import lammps, md, vasp
+from .system import LabeledSystem, MultiSystems, System
 
 try:
     from ._version import version as __version__

dpdata/abacus/md.py

@@ -1,17 +1,20 @@
+import os
+import re
+import sys
+import warnings
 from ast import dump
-import os, sys
+
 import numpy as np
+
 from .scf import (
-    ry2ev,
     bohr2ang,
-    kbar2evperang3,
     get_block,
-    get_geometry_in,
     get_cell,
     get_coords,
+    get_geometry_in,
+    kbar2evperang3,
+    ry2ev,
 )
-import re
-import warnings
 
 # Read in geometries from an ABACUS MD trajectory.
 # The atomic coordinates are read in from generated files in OUT.XXXX.

dpdata/abacus/relax.py

@@ -1,6 +1,9 @@
-import os, sys
+import os
+import sys
+
 import numpy as np
-from .scf import bohr2ang, kbar2evperang3, get_geometry_in, get_cell, get_coords
+
+from .scf import bohr2ang, get_cell, get_coords, get_geometry_in, kbar2evperang3
 
 # Read in geometries from an ABACUS RELAX(CELL-RELAX) trajectory in OUT.XXXX/runnning_relax/cell-relax.log.
 

dpdata/abacus/scf.py

@@ -1,7 +1,10 @@
-import os, sys
-import numpy as np
-from ..unit import EnergyConversion, PressureConversion, LengthConversion
+import os
 import re
+import sys
+
+import numpy as np
+
+from ..unit import EnergyConversion, LengthConversion, PressureConversion
 
 bohr2ang = LengthConversion("bohr", "angstrom").value()
 ry2ev = EnergyConversion("rydberg", "eV").value()

dpdata/amber/md.py

@@ -1,9 +1,12 @@
-import re
 import os
-from scipy.io import netcdf
+import re
+
 import numpy as np
+from scipy.io import netcdf
+
 from dpdata.amber.mask import pick_by_amber_mask
 from dpdata.unit import EnergyConversion
+
 from ..periodic_table import ELEMENTS
 
 kcalmol2eV = EnergyConversion("kcal_mol", "eV").value()

dpdata/amber/sqm.py

@@ -1,4 +1,5 @@
 import numpy as np
+
 from dpdata.periodic_table import ELEMENTS
 from dpdata.unit import EnergyConversion
 

dpdata/ase_calculator.py

@@ -1,12 +1,13 @@
-from typing import List, Optional, TYPE_CHECKING
+from typing import TYPE_CHECKING, List, Optional
 
 from ase.calculators.calculator import (
     Calculator,
-    all_changes,
     PropertyNotImplementedError,
+    all_changes,
 )
 
 import dpdata
+
 from .driver import Driver
 
 if TYPE_CHECKING:

dpdata/bond_order_system.py

@@ -1,12 +1,14 @@
 #%%
 # Bond Order System
-import numpy as np
-from dpdata.system import System, LabeledSystem, load_format, DataType, Axis
-import dpdata.rdkit.utils
-from dpdata.rdkit.sanitize import Sanitizer, SanitizeError
 from copy import deepcopy
+
+import numpy as np
 from rdkit.Chem import Conformer
 
+import dpdata.rdkit.utils
+from dpdata.rdkit.sanitize import SanitizeError, Sanitizer
+from dpdata.system import Axis, DataType, LabeledSystem, System, load_format
+
 # import dpdata.rdkit.mol2
 
 

dpdata/cli.py

@@ -3,7 +3,7 @@
 from typing import Optional
 
 from . import __version__
-from .system import System, LabeledSystem, MultiSystems
+from .system import LabeledSystem, MultiSystems, System
 
 
 def dpdata_parser() -> argparse.ArgumentParser:

dpdata/cp2k/cell.py

@@ -1,7 +1,8 @@
 #%%
-import numpy as np
-from collections import OrderedDict
 import re
+from collections import OrderedDict
+
+import numpy as np
 
 
 def cell_to_low_triangle(A, B, C, alpha, beta, gamma):

dpdata/cp2k/output.py

@@ -1,16 +1,17 @@
 #%%
-import numpy as np
 import re
 from collections import OrderedDict
 
+import numpy as np
 from scipy.constants import R
-from .cell import cell_to_low_triangle
+
 from ..unit import (
     EnergyConversion,
-    LengthConversion,
     ForceConversion,
+    LengthConversion,
     PressureConversion,
 )
+from .cell import cell_to_low_triangle
 
 #%%
 AU_TO_ANG = LengthConversion("bohr", "angstrom").value()

dpdata/deepmd/comp.py

@@ -1,5 +1,9 @@
-import os, glob, shutil
+import glob
+import os
+import shutil
+
 import numpy as np
+
 from .raw import load_type
 
 

dpdata/deepmd/hdf5.py

@@ -3,10 +3,8 @@
 
 import h5py
 import numpy as np
-
 from wcmatch.glob import globfilter
 
-
 __all__ = ["to_system_data", "dump"]
 
 

dpdata/deepmd/raw.py

@@ -1,4 +1,5 @@
 import os
+
 import numpy as np
 
 

dpdata/driver.py

@@ -1,7 +1,8 @@
 """Driver plugin system."""
-from typing import Callable, List, Union, TYPE_CHECKING
-from .plugin import Plugin
 from abc import ABC, abstractmethod
+from typing import TYPE_CHECKING, Callable, List, Union
+
+from .plugin import Plugin
 
 if TYPE_CHECKING:
     import ase

dpdata/fhi_aims/output.py

@@ -1,7 +1,8 @@
-import numpy as np
 import re
 import warnings
 
+import numpy as np
+
 latt_patt = "\|\s+([0-9]{1,}[.][0-9]*)\s+([0-9]{1,}[.][0-9]*)\s+([0-9]{1,}[.][0-9]*)"
 pos_patt_first = "\|\s+[0-9]{1,}[:]\s\w+\s(\w+)(\s.*[-]?[0-9]{1,}[.][0-9]*)(\s+[-]?[0-9]{1,}[.][0-9]*)(\s+[-]?[0-9]{1,}[.][0-9]*)"
 pos_patt_other = "\s+[a][t][o][m]\s+([-]?[0-9]{1,}[.][0-9]*)\s+([-]?[0-9]{1,}[.][0-9]*)\s+([-]?[0-9]{1,}[.][0-9]*)\s+(\w{1,2})"

dpdata/format.py

@@ -1,7 +1,7 @@
 """Implement the format plugin system."""
 import os
-from collections import abc
 from abc import ABC
+from collections import abc
 
 from .plugin import Plugin
 

dpdata/gaussian/gjf.py

@@ -3,10 +3,11 @@
 # under LGPL 3.0 license
 """Generate Gaussian input file."""
 
-from typing import Optional, List, Tuple, Union
-import uuid
 import itertools
+import uuid
 import warnings
+from typing import List, Optional, Tuple, Union
+
 import numpy as np
 from scipy.sparse import csr_matrix
 from scipy.sparse.csgraph import connected_components

dpdata/gaussian/log.py

@@ -1,6 +1,7 @@
 import numpy as np
-from ..unit import LengthConversion, EnergyConversion, ForceConversion
+
 from ..periodic_table import ELEMENTS
+from ..unit import EnergyConversion, ForceConversion, LengthConversion
 
 length_convert = LengthConversion("bohr", "angstrom").value()
 energy_convert = EnergyConversion("hartree", "eV").value()

dpdata/gromacs/gro.py

@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 import re
+
 import numpy as np
+
 from ..unit import LengthConversion
 
 nm2ang = LengthConversion("nm", "angstrom").value()

dpdata/lammps/dump.py

@@ -1,13 +1,16 @@
 #!/usr/bin/env python3
 
-import os, sys
+import os
+import sys
+
 import numpy as np
 
 lib_path = os.path.dirname(os.path.realpath(__file__))
 sys.path.append(lib_path)
-import lmp
 import warnings
 
+import lmp
+
 
 class UnwrapWarning(UserWarning):
     pass

dpdata/md/msd.py

@@ -1,4 +1,5 @@
 import numpy as np
+
 from .pbc import system_pbc_shift
 
 

dpdata/md/rdf.py

@@ -68,8 +68,8 @@ def _compute_rdf_1frame(box, posis, atype, sel_type=[None, None], max_r=5, nbins
     if type(sel_type[1]) is not list:
         sel_type[1] = [sel_type[1]]
     natoms = len(posis)
-    from ase import Atoms
     import ase.neighborlist
+    from ase import Atoms
 
     atoms = Atoms(positions=posis, cell=box, pbc=[1, 1, 1])
     nlist = ase.neighborlist.NeighborList(

dpdata/md/water.py

@@ -1,6 +1,6 @@
 import numpy as np
-from .pbc import posi_diff
-from .pbc import posi_shift
+
+from .pbc import posi_diff, posi_shift
 
 
 def compute_bonds(box, posis, atype, oh_sel=[0, 1], max_roh=1.3, uniq_hbond=True):
@@ -17,8 +17,8 @@ def compute_bonds(box, posis, atype, oh_sel=[0, 1], max_roh=1.3, uniq_hbond=True
 
 def compute_bonds_ase(box, posis, atype, oh_sel=[0, 1], max_roh=1.3, uniq_hbond=True):
     natoms = len(posis)
-    from ase import Atoms
     import ase.neighborlist
+    from ase import Atoms
 
     atoms = Atoms(positions=posis, cell=box, pbc=[1, 1, 1])
     nlist = ase.neighborlist.NeighborList(

dpdata/periodic_table.py

@@ -1,5 +1,6 @@
 from pathlib import Path
-from monty.serialization import loadfn, dumpfn
+
+from monty.serialization import dumpfn, loadfn
 
 fpdt = str(Path(__file__).absolute().parent / "periodic_table.json")
 _pdt = loadfn(fpdt)

dpdata/plugins/3dmol.py

@@ -1,4 +1,5 @@
 from typing import Tuple
+
 import numpy as np
 
 from dpdata.format import Format

dpdata/plugins/abacus.py

@@ -1,6 +1,6 @@
-import dpdata.abacus.scf
 import dpdata.abacus.md
 import dpdata.abacus.relax
+import dpdata.abacus.scf
 from dpdata.format import Format
 
 

dpdata/plugins/amber.py

@@ -1,11 +1,11 @@
-import tempfile
 import os
 import subprocess as sp
+import tempfile
 
 import dpdata.amber.md
 import dpdata.amber.sqm
-from dpdata.format import Format
 from dpdata.driver import Driver, Minimizer
+from dpdata.format import Format
 
 
 @Format.register("amber/md")

dpdata/plugins/ase.py

@@ -1,8 +1,10 @@
-from typing import Optional, TYPE_CHECKING, Type
-from dpdata.driver import Driver, Minimizer
-from dpdata.format import Format
+from typing import TYPE_CHECKING, Optional, Type
+
 import numpy as np
+
 import dpdata
+from dpdata.driver import Driver, Minimizer
+from dpdata.format import Format
 
 try:
     import ase.io

dpdata/plugins/cp2k.py

@@ -1,5 +1,6 @@
-import dpdata.cp2k.output
 import glob
+
+import dpdata.cp2k.output
 from dpdata.cp2k.output import Cp2kSystems
 from dpdata.format import Format