diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 9ca30f7a2..0624240e6 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -21,6 +21,11 @@ repos:
     rev: 22.12.0
     hooks:
     -   id: black-jupyter
+-   repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
+    hooks:
+    - id: isort
+    files: \.py$
 # Python inside docs
 -   repo: https://github.com/asottile/blacken-docs
     rev: 1.13.0
diff --git a/docs/conf.py b/docs/conf.py
index eabf1c845..d09cf3fd5 100644
--- a/docs/conf.py
+++ b/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(".."))
diff --git a/docs/make_format.py b/docs/make_format.py
index 801e08308..a7962208b 100644
--- a/docs/make_format.py
+++ b/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
 
 
diff --git a/dpdata/__init__.py b/dpdata/__init__.py
index f426b7903..d160717c3 100644
--- a/dpdata/__init__.py
+++ b/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__
diff --git a/dpdata/abacus/md.py b/dpdata/abacus/md.py
index be6bee47d..7532b7b2f 100644
--- a/dpdata/abacus/md.py
+++ b/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.
diff --git a/dpdata/abacus/relax.py b/dpdata/abacus/relax.py
index 6b5521749..7d0da0fa7 100644
--- a/dpdata/abacus/relax.py
+++ b/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.
 
diff --git a/dpdata/abacus/scf.py b/dpdata/abacus/scf.py
index 4bbd7091b..e82089ad1 100644
--- a/dpdata/abacus/scf.py
+++ b/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()
diff --git a/dpdata/amber/md.py b/dpdata/amber/md.py
index 0d178104a..f477efab4 100644
--- a/dpdata/amber/md.py
+++ b/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()
diff --git a/dpdata/amber/sqm.py b/dpdata/amber/sqm.py
index 7826d2018..9b4505017 100644
--- a/dpdata/amber/sqm.py
+++ b/dpdata/amber/sqm.py
@@ -1,4 +1,5 @@
 import numpy as np
+
 from dpdata.periodic_table import ELEMENTS
 from dpdata.unit import EnergyConversion
 
diff --git a/dpdata/ase_calculator.py b/dpdata/ase_calculator.py
index ea5e50094..65a462a52 100644
--- a/dpdata/ase_calculator.py
+++ b/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:
diff --git a/dpdata/bond_order_system.py b/dpdata/bond_order_system.py
index 6cb834d47..124a6faa5 100644
--- a/dpdata/bond_order_system.py
+++ b/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
 
 
diff --git a/dpdata/cli.py b/dpdata/cli.py
index 88e49ba5d..c80de99c2 100644
--- a/dpdata/cli.py
+++ b/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:
diff --git a/dpdata/cp2k/cell.py b/dpdata/cp2k/cell.py
index 3fd8b6c5e..33e566371 100644
--- a/dpdata/cp2k/cell.py
+++ b/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):
diff --git a/dpdata/cp2k/output.py b/dpdata/cp2k/output.py
index 965d06567..f7b94f252 100644
--- a/dpdata/cp2k/output.py
+++ b/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()
diff --git a/dpdata/deepmd/comp.py b/dpdata/deepmd/comp.py
index a5eb73349..66bf4ee66 100644
--- a/dpdata/deepmd/comp.py
+++ b/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
 
 
diff --git a/dpdata/deepmd/hdf5.py b/dpdata/deepmd/hdf5.py
index 1e44b7902..69b993abd 100644
--- a/dpdata/deepmd/hdf5.py
+++ b/dpdata/deepmd/hdf5.py
@@ -3,10 +3,8 @@
 
 import h5py
 import numpy as np
-
 from wcmatch.glob import globfilter
 
-
 __all__ = ["to_system_data", "dump"]
 
 
diff --git a/dpdata/deepmd/raw.py b/dpdata/deepmd/raw.py
index 7de14baab..2f2021d44 100644
--- a/dpdata/deepmd/raw.py
+++ b/dpdata/deepmd/raw.py
@@ -1,4 +1,5 @@
 import os
+
 import numpy as np
 
 
diff --git a/dpdata/driver.py b/dpdata/driver.py
index 2d66ae41c..8f952984b 100644
--- a/dpdata/driver.py
+++ b/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
diff --git a/dpdata/fhi_aims/output.py b/dpdata/fhi_aims/output.py
index 423957b7c..9706b91a8 100755
--- a/dpdata/fhi_aims/output.py
+++ b/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})"
diff --git a/dpdata/format.py b/dpdata/format.py
index 84813c760..e40ad1903 100644
--- a/dpdata/format.py
+++ b/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
 
diff --git a/dpdata/gaussian/gjf.py b/dpdata/gaussian/gjf.py
index be089e246..354187f01 100644
--- a/dpdata/gaussian/gjf.py
+++ b/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
diff --git a/dpdata/gaussian/log.py b/dpdata/gaussian/log.py
index 54bc1d518..73ae693d1 100644
--- a/dpdata/gaussian/log.py
+++ b/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()
diff --git a/dpdata/gromacs/gro.py b/dpdata/gromacs/gro.py
index b9930f2bf..b643eea86 100644
--- a/dpdata/gromacs/gro.py
+++ b/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()
diff --git a/dpdata/lammps/dump.py b/dpdata/lammps/dump.py
index 85b87ba80..2e4dd5611 100644
--- a/dpdata/lammps/dump.py
+++ b/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
diff --git a/dpdata/md/msd.py b/dpdata/md/msd.py
index eebc72963..cfb446dde 100644
--- a/dpdata/md/msd.py
+++ b/dpdata/md/msd.py
@@ -1,4 +1,5 @@
 import numpy as np
+
 from .pbc import system_pbc_shift
 
 
diff --git a/dpdata/md/rdf.py b/dpdata/md/rdf.py
index 220bdcb03..16f6baccb 100644
--- a/dpdata/md/rdf.py
+++ b/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(
diff --git a/dpdata/md/water.py b/dpdata/md/water.py
index b9ab833b6..42e27243b 100644
--- a/dpdata/md/water.py
+++ b/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(
diff --git a/dpdata/periodic_table.py b/dpdata/periodic_table.py
index dc64d40ad..30ffb1be9 100644
--- a/dpdata/periodic_table.py
+++ b/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)
diff --git a/dpdata/plugins/3dmol.py b/dpdata/plugins/3dmol.py
index fa9f02aa2..3b463abb3 100644
--- a/dpdata/plugins/3dmol.py
+++ b/dpdata/plugins/3dmol.py
@@ -1,4 +1,5 @@
 from typing import Tuple
+
 import numpy as np
 
 from dpdata.format import Format
diff --git a/dpdata/plugins/abacus.py b/dpdata/plugins/abacus.py
index a9c82b059..43abf3188 100644
--- a/dpdata/plugins/abacus.py
+++ b/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
 
 
diff --git a/dpdata/plugins/amber.py b/dpdata/plugins/amber.py
index cf2df3ca6..4d6a22290 100644
--- a/dpdata/plugins/amber.py
+++ b/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")
diff --git a/dpdata/plugins/ase.py b/dpdata/plugins/ase.py
index b6e0fcb70..9a626be8e 100644
--- a/dpdata/plugins/ase.py
+++ b/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
diff --git a/dpdata/plugins/cp2k.py b/dpdata/plugins/cp2k.py
index 143c1821b..e1df43e58 100644
--- a/dpdata/plugins/cp2k.py
+++ b/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
 
diff --git a/dpdata/plugins/deepmd.py b/dpdata/plugins/deepmd.py
index 2e8850091..d16b86a52 100644
--- a/dpdata/plugins/deepmd.py
+++ b/dpdata/plugins/deepmd.py
@@ -1,13 +1,14 @@
-from typing import Optional, Union, List
+from typing import List, Optional, Union
+
+import h5py
+import numpy as np
 
 import dpdata
-import dpdata.deepmd.raw
 import dpdata.deepmd.comp
 import dpdata.deepmd.hdf5
-import numpy as np
-import h5py
-from dpdata.format import Format
+import dpdata.deepmd.raw
 from dpdata.driver import Driver
+from dpdata.format import Format
 
 
 @Format.register("deepmd")
diff --git a/dpdata/plugins/gaussian.py b/dpdata/plugins/gaussian.py
index 37a5ee8bb..416c61ad0 100644
--- a/dpdata/plugins/gaussian.py
+++ b/dpdata/plugins/gaussian.py
@@ -1,11 +1,11 @@
 import os
-import tempfile
 import subprocess as sp
+import tempfile
 
-import dpdata.gaussian.log
 import dpdata.gaussian.gjf
-from dpdata.format import Format
+import dpdata.gaussian.log
 from dpdata.driver import Driver
+from dpdata.format import Format
 
 
 @Format.register("gaussian/log")
diff --git a/dpdata/plugins/lammps.py b/dpdata/plugins/lammps.py
index d4bce01b4..300bd4efd 100644
--- a/dpdata/plugins/lammps.py
+++ b/dpdata/plugins/lammps.py
@@ -1,5 +1,5 @@
-import dpdata.lammps.lmp
 import dpdata.lammps.dump
+import dpdata.lammps.lmp
 from dpdata.format import Format
 
 
diff --git a/dpdata/plugins/list.py b/dpdata/plugins/list.py
index 99ac6d4a7..f7880fa08 100644
--- a/dpdata/plugins/list.py
+++ b/dpdata/plugins/list.py
@@ -7,7 +7,7 @@ def to_system(self, data, **kwargs):
         """
         convert system to list, usefull for data collection
         """
-        from dpdata import System, LabeledSystem
+        from dpdata import LabeledSystem, System
 
         if "forces" in data:
             system = LabeledSystem(data=data)
diff --git a/dpdata/plugins/pwmat.py b/dpdata/plugins/pwmat.py
index baa415d6b..4d123f1e8 100644
--- a/dpdata/plugins/pwmat.py
+++ b/dpdata/plugins/pwmat.py
@@ -1,6 +1,7 @@
-import dpdata.pwmat.movement
-import dpdata.pwmat.atomconfig
 import numpy as np
+
+import dpdata.pwmat.atomconfig
+import dpdata.pwmat.movement
 from dpdata.format import Format
 
 
diff --git a/dpdata/plugins/pymatgen.py b/dpdata/plugins/pymatgen.py
index 514b8d76c..36efc12cf 100644
--- a/dpdata/plugins/pymatgen.py
+++ b/dpdata/plugins/pymatgen.py
@@ -1,7 +1,8 @@
-from dpdata.format import Format
-import dpdata.pymatgen.molecule
 import numpy as np
 
+import dpdata.pymatgen.molecule
+from dpdata.format import Format
+
 
 @Format.register("pymatgen/structure")
 class PyMatgenStructureFormat(Format):
diff --git a/dpdata/plugins/qe.py b/dpdata/plugins/qe.py
index 1b95a6d4e..d524462f6 100644
--- a/dpdata/plugins/qe.py
+++ b/dpdata/plugins/qe.py
@@ -1,6 +1,6 @@
-import dpdata.qe.traj
-import dpdata.qe.scf
 import dpdata.md.pbc
+import dpdata.qe.scf
+import dpdata.qe.traj
 from dpdata.format import Format
 
 
diff --git a/dpdata/plugins/rdkit.py b/dpdata/plugins/rdkit.py
index 043fad1e6..64a2f343d 100644
--- a/dpdata/plugins/rdkit.py
+++ b/dpdata/plugins/rdkit.py
@@ -2,6 +2,7 @@
 
 try:
     import rdkit.Chem
+
     import dpdata.rdkit.utils
 except ModuleNotFoundError:
     pass
diff --git a/dpdata/plugins/siesta.py b/dpdata/plugins/siesta.py
index 5b38e8b2a..662b5c0e0 100644
--- a/dpdata/plugins/siesta.py
+++ b/dpdata/plugins/siesta.py
@@ -1,5 +1,5 @@
-import dpdata.siesta.output
 import dpdata.siesta.aiMD_output
+import dpdata.siesta.output
 from dpdata.format import Format
 
 
diff --git a/dpdata/plugins/vasp.py b/dpdata/plugins/vasp.py
index 5b151f807..6e2fe5f0a 100644
--- a/dpdata/plugins/vasp.py
+++ b/dpdata/plugins/vasp.py
@@ -1,7 +1,8 @@
+import numpy as np
+
+import dpdata.vasp.outcar
 import dpdata.vasp.poscar
 import dpdata.vasp.xml
-import dpdata.vasp.outcar
-import numpy as np
 from dpdata.format import Format
 from dpdata.utils import sort_atom_names, uniq_atom_names
 
diff --git a/dpdata/plugins/xyz.py b/dpdata/plugins/xyz.py
index 4db722e3e..69cca61b4 100644
--- a/dpdata/plugins/xyz.py
+++ b/dpdata/plugins/xyz.py
@@ -1,8 +1,8 @@
 import numpy as np
 
+from dpdata.format import Format
 from dpdata.xyz.quip_gap_xyz import QuipGapxyzSystems
 from dpdata.xyz.xyz import coord_to_xyz, xyz_to_coord
-from dpdata.format import Format
 
 
 @Format.register("xyz")
diff --git a/dpdata/pwmat/atomconfig.py b/dpdata/pwmat/atomconfig.py
index 5e953c472..28cfaebcf 100644
--- a/dpdata/pwmat/atomconfig.py
+++ b/dpdata/pwmat/atomconfig.py
@@ -1,7 +1,8 @@
 #!/usr/bin/python3
-from ..periodic_table import ELEMENTS
 import numpy as np
 
+from ..periodic_table import ELEMENTS
+
 
 def _to_system_data_lower(lines):
     system = {}
diff --git a/dpdata/pwmat/movement.py b/dpdata/pwmat/movement.py
index c2e0bf3a7..2440641e5 100644
--- a/dpdata/pwmat/movement.py
+++ b/dpdata/pwmat/movement.py
@@ -1,6 +1,8 @@
+import warnings
+
 import numpy as np
+
 from ..periodic_table import ELEMENTS
-import warnings
 
 
 def system_info(lines, type_idx_zero=False):
diff --git a/dpdata/pymatgen/molecule.py b/dpdata/pymatgen/molecule.py
index c2559bef2..25e13c29f 100644
--- a/dpdata/pymatgen/molecule.py
+++ b/dpdata/pymatgen/molecule.py
@@ -5,6 +5,7 @@
 except ImportError:
     pass
 from collections import Counter
+
 import dpdata
 
 
diff --git a/dpdata/qe/scf.py b/dpdata/qe/scf.py
index afdb6ae12..f78be7cb3 100755
--- a/dpdata/qe/scf.py
+++ b/dpdata/qe/scf.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 
-import os, sys
+import os
+import sys
+
 import numpy as np
 
 ry2ev = 13.605693009
diff --git a/dpdata/qe/traj.py b/dpdata/qe/traj.py
index 1bdacab3e..700f2ebcf 100644
--- a/dpdata/qe/traj.py
+++ b/dpdata/qe/traj.py
@@ -1,10 +1,14 @@
 #!/usr/bin/python3
+import warnings
+
 import numpy as np
-import dpdata, warnings
+
+import dpdata
+
 from ..unit import (
     EnergyConversion,
-    LengthConversion,
     ForceConversion,
+    LengthConversion,
     PressureConversion,
 )
 
diff --git a/dpdata/rdkit/sanitize.py b/dpdata/rdkit/sanitize.py
index f3b1690eb..6a5a1c34e 100644
--- a/dpdata/rdkit/sanitize.py
+++ b/dpdata/rdkit/sanitize.py
@@ -1,8 +1,9 @@
-from copy import deepcopy
-from rdkit import Chem
-from rdkit.Chem.rdchem import Atom, Bond, Mol, BondType
 import os
 import time
+from copy import deepcopy
+
+from rdkit import Chem
+from rdkit.Chem.rdchem import Atom, Bond, BondType, Mol
 
 # openbabel
 try:
diff --git a/dpdata/system.py b/dpdata/system.py
index f7ad7b5f8..5a985e041 100644
--- a/dpdata/system.py
+++ b/dpdata/system.py
@@ -1,30 +1,26 @@
 #%%
-import os
 import glob
 import inspect
-import numpy as np
-import dpdata.md.pbc
+import os
 from copy import deepcopy
 from enum import Enum, unique
 from typing import Any, Tuple, Union
+
+import numpy as np
 from monty.json import MSONable
-from monty.serialization import loadfn, dumpfn
-from dpdata.periodic_table import Element
-from dpdata.amber.mask import pick_by_amber_mask, load_param_file
+from monty.serialization import dumpfn, loadfn
+
 import dpdata
+import dpdata.md.pbc
 
 # ensure all plugins are loaded!
 import dpdata.plugins
-from dpdata.plugin import Plugin
-from dpdata.format import Format
+from dpdata.amber.mask import load_param_file, pick_by_amber_mask
 from dpdata.driver import Driver, Minimizer
-
-from dpdata.utils import (
-    elements_index_map,
-    remove_pbc,
-    sort_atom_names,
-    add_atom_names,
-)
+from dpdata.format import Format
+from dpdata.periodic_table import Element
+from dpdata.plugin import Plugin
+from dpdata.utils import add_atom_names, elements_index_map, remove_pbc, sort_atom_names
 
 
 def load_format(fmt):
diff --git a/dpdata/unit.py b/dpdata/unit.py
index a1dc1c7bf..1c7255cce 100644
--- a/dpdata/unit.py
+++ b/dpdata/unit.py
@@ -1,4 +1,5 @@
 from abc import ABC
+
 from scipy import constants
 
 AVOGADRO = constants.Avogadro  # Avagadro constant
diff --git a/dpdata/utils.py b/dpdata/utils.py
index 90fef137d..c461d8c09 100644
--- a/dpdata/utils.py
+++ b/dpdata/utils.py
@@ -1,4 +1,5 @@
 import numpy as np
+
 from dpdata.periodic_table import Element
 
 
diff --git a/dpdata/vasp/outcar.py b/dpdata/vasp/outcar.py
index ec26a1812..e8280d056 100644
--- a/dpdata/vasp/outcar.py
+++ b/dpdata/vasp/outcar.py
@@ -1,7 +1,8 @@
-import numpy as np
 import re
 import warnings
 
+import numpy as np
+
 
 def system_info(lines, type_idx_zero=False):
     atom_names = []
diff --git a/dpdata/vasp/xml.py b/dpdata/vasp/xml.py
index f87b57168..9d4cb8033 100755
--- a/dpdata/vasp/xml.py
+++ b/dpdata/vasp/xml.py
@@ -1,6 +1,7 @@
 #!/usr/bin/env python3
 
 import xml.etree.ElementTree as ET
+
 import numpy as np
 
 
diff --git a/dpdata/xyz/quip_gap_xyz.py b/dpdata/xyz/quip_gap_xyz.py
index ea2d9a776..a0b9fd4a7 100644
--- a/dpdata/xyz/quip_gap_xyz.py
+++ b/dpdata/xyz/quip_gap_xyz.py
@@ -1,8 +1,9 @@
 #!/usr/bin/env python3
 #%%
-import numpy as np
-from collections import OrderedDict
 import re
+from collections import OrderedDict
+
+import numpy as np
 
 
 class QuipGapxyzSystems(object):
diff --git a/plugin_example/dpdata_random/__init__.py b/plugin_example/dpdata_random/__init__.py
index 8e1450c9e..22820e0fa 100644
--- a/plugin_example/dpdata_random/__init__.py
+++ b/plugin_example/dpdata_random/__init__.py
@@ -1,6 +1,7 @@
-from dpdata.format import Format
 import numpy as np
 
+from dpdata.format import Format
+
 
 @Format.register("random")
 class RandomFormat(Format):
diff --git a/pyproject.toml b/pyproject.toml
index 8c1dac023..cdb7a25d1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -64,3 +64,6 @@ dpdata = ['*.json']
 
 [tool.setuptools_scm]
 write_to = "dpdata/_version.py"
+
+[tool.isort]
+profile = "black"
diff --git a/tests/context.py b/tests/context.py
index e305ff0fe..10348a8d6 100644
--- a/tests/context.py
+++ b/tests/context.py
@@ -1,9 +1,10 @@
-import sys, os
+import os
+import sys
 
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..")))
 import dpdata
-import dpdata.md.water
-import dpdata.md.msd
 import dpdata.gaussian.gjf
-import dpdata.system
+import dpdata.md.msd
+import dpdata.md.water
 import dpdata.stat
+import dpdata.system
diff --git a/tests/poscars/test_lammps_dump_s_su.py b/tests/poscars/test_lammps_dump_s_su.py
index 5e914ea5f..4b40cf35b 100644
--- a/tests/poscars/test_lammps_dump_s_su.py
+++ b/tests/poscars/test_lammps_dump_s_su.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 from poscars.poscar_ref_oh import TestPOSCARoh
 
diff --git a/tests/test_abacus_md.py b/tests/test_abacus_md.py
index 89df93b65..f2b80295c 100644
--- a/tests/test_abacus_md.py
+++ b/tests/test_abacus_md.py
@@ -1,7 +1,9 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
+
 from dpdata.unit import LengthConversion
 
 bohr2ang = LengthConversion("bohr", "angstrom").value()
diff --git a/tests/test_abacus_pw_scf.py b/tests/test_abacus_pw_scf.py
index 6ada7736f..eb712fbeb 100644
--- a/tests/test_abacus_pw_scf.py
+++ b/tests/test_abacus_pw_scf.py
@@ -1,7 +1,10 @@
 import os
+import shutil
+import unittest
+
 import numpy as np
-import unittest, shutil
 from context import dpdata
+
 from dpdata.unit import LengthConversion
 
 bohr2ang = LengthConversion("bohr", "angstrom").value()
diff --git a/tests/test_abacus_relax.py b/tests/test_abacus_relax.py
index a39249bd7..ed9b77dd0 100644
--- a/tests/test_abacus_relax.py
+++ b/tests/test_abacus_relax.py
@@ -1,7 +1,10 @@
-import os, shutil
-import numpy as np
+import os
+import shutil
 import unittest
+
+import numpy as np
 from context import dpdata
+
 from dpdata.unit import LengthConversion
 
 bohr2ang = LengthConversion("bohr", "angstrom").value()
diff --git a/tests/test_abacus_stru_dump.py b/tests/test_abacus_stru_dump.py
index 6d6dbeea8..78fcd0880 100644
--- a/tests/test_abacus_stru_dump.py
+++ b/tests/test_abacus_stru_dump.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 from test_vasp_poscar_dump import myfilecmp
 
diff --git a/tests/test_amber_md.py b/tests/test_amber_md.py
index 5a9cded81..8d8304ccd 100644
--- a/tests/test_amber_md.py
+++ b/tests/test_amber_md.py
@@ -1,8 +1,9 @@
 import os
-import unittest
 import shutil
-from context import dpdata
+import unittest
+
 from comp_sys import CompLabeledSys, IsPBC
+from context import dpdata
 
 try:
     import parmed
diff --git a/tests/test_amber_sqm.py b/tests/test_amber_sqm.py
index f9ca80f8d..99c1a2857 100644
--- a/tests/test_amber_sqm.py
+++ b/tests/test_amber_sqm.py
@@ -1,8 +1,9 @@
 import os
-import unittest
 import shutil
+import unittest
+
+from comp_sys import CompLabeledSys, CompSys, IsNoPBC
 from context import dpdata
-from comp_sys import CompSys, CompLabeledSys, IsNoPBC
 
 try:
     from dpdata import BondOrderSystem
diff --git a/tests/test_ase_traj.py b/tests/test_ase_traj.py
index 6f957f848..2a3e92679 100644
--- a/tests/test_ase_traj.py
+++ b/tests/test_ase_traj.py
@@ -1,8 +1,9 @@
 import os
-import numpy as np
 import unittest
-from context import dpdata
+
+import numpy as np
 from comp_sys import CompLabeledSys, IsPBC
+from context import dpdata
 
 try:
     import ase
diff --git a/tests/test_bond_order_system.py b/tests/test_bond_order_system.py
index d0b8fbd07..52f259efa 100644
--- a/tests/test_bond_order_system.py
+++ b/tests/test_bond_order_system.py
@@ -1,11 +1,13 @@
+import glob
 import os
 import unittest
+
 from context import dpdata
-import glob
 
 try:
     from rdkit import Chem
     from rdkit.Chem import AllChem
+
     from dpdata import BondOrderSystem
 except ImportError:
     skip_bond_order_system = True
@@ -13,9 +15,10 @@
     skip_bond_order_system = False
 
 import shutil
-import numpy as np
 from copy import deepcopy
 
+import numpy as np
+
 
 @unittest.skipIf(
     skip_bond_order_system,
diff --git a/tests/test_cell_to_low_triangle.py b/tests/test_cell_to_low_triangle.py
index 6696e1710..d3121e38e 100644
--- a/tests/test_cell_to_low_triangle.py
+++ b/tests/test_cell_to_low_triangle.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 7275237a7..423b8896a 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -1,7 +1,8 @@
+import subprocess as sp
 import unittest
+
 from context import dpdata
 from poscars.poscar_ref_oh import TestPOSCARoh
-import subprocess as sp
 
 
 class TestCli(unittest.TestCase, TestPOSCARoh):
diff --git a/tests/test_corr.py b/tests/test_corr.py
index 74fb2a103..3224c950c 100644
--- a/tests/test_corr.py
+++ b/tests/test_corr.py
@@ -1,7 +1,7 @@
 import unittest
+
+from comp_sys import CompLabeledSys, IsPBC
 from context import dpdata
-from comp_sys import CompLabeledSys
-from comp_sys import IsPBC
 
 
 class TestCorr(unittest.TestCase, CompLabeledSys, IsPBC):
diff --git a/tests/test_cp2k_aimd_output.py b/tests/test_cp2k_aimd_output.py
index 471153b10..f87804267 100644
--- a/tests/test_cp2k_aimd_output.py
+++ b/tests/test_cp2k_aimd_output.py
@@ -1,9 +1,11 @@
 #%%
 import os
-import numpy as np
 import unittest
-from context import dpdata
+
+import numpy as np
 from comp_sys import CompLabeledSys
+from context import dpdata
+
 
 #%%
 class TestCp2kAimdOutput(unittest.TestCase, CompLabeledSys):
diff --git a/tests/test_cp2k_output.py b/tests/test_cp2k_output.py
index 37c639c60..a7af46969 100644
--- a/tests/test_cp2k_output.py
+++ b/tests/test_cp2k_output.py
@@ -1,8 +1,9 @@
 import os
-import numpy as np
 import unittest
-from context import dpdata
+
+import numpy as np
 from comp_sys import CompLabeledSys
+from context import dpdata
 
 
 class TestCp2kNormalOutput(unittest.TestCase, CompLabeledSys):
diff --git a/tests/test_deepmd_comp.py b/tests/test_deepmd_comp.py
index 3b8068597..616caa468 100644
--- a/tests/test_deepmd_comp.py
+++ b/tests/test_deepmd_comp.py
@@ -1,8 +1,10 @@
-import os, shutil
-import numpy as np
+import os
+import shutil
 import unittest
-from context import dpdata
+
+import numpy as np
 from comp_sys import CompLabeledSys, CompSys, IsPBC
+from context import dpdata
 
 
 class TestDeepmdLoadDumpComp(unittest.TestCase, CompLabeledSys, IsPBC):
diff --git a/tests/test_deepmd_hdf5.py b/tests/test_deepmd_hdf5.py
index 24ed4f0dd..20d16c370 100644
--- a/tests/test_deepmd_hdf5.py
+++ b/tests/test_deepmd_hdf5.py
@@ -1,8 +1,9 @@
 import os
-import numpy as np
 import unittest
-from context import dpdata
+
+import numpy as np
 from comp_sys import CompLabeledSys, CompSys, IsNoPBC, IsPBC, MultiSystems
+from context import dpdata
 
 
 class TestDeepmdLoadDumpHDF5(unittest.TestCase, CompLabeledSys, IsPBC):
diff --git a/tests/test_deepmd_raw.py b/tests/test_deepmd_raw.py
index 5ba54877d..1b0567260 100644
--- a/tests/test_deepmd_raw.py
+++ b/tests/test_deepmd_raw.py
@@ -1,8 +1,10 @@
-import os, shutil
-import numpy as np
+import os
+import shutil
 import unittest
-from context import dpdata
+
+import numpy as np
 from comp_sys import CompLabeledSys, CompSys, IsPBC
+from context import dpdata
 
 
 class TestDeepmdLoadRaw(unittest.TestCase, CompLabeledSys, IsPBC):
diff --git a/tests/test_elements_index.py b/tests/test_elements_index.py
index 6b924548b..17a7ea91f 100644
--- a/tests/test_elements_index.py
+++ b/tests/test_elements_index.py
@@ -1,6 +1,8 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
+
 from dpdata.system import elements_index_map
 
 
diff --git a/tests/test_empty.py b/tests/test_empty.py
index 0fd84ca0f..3892ab3b1 100644
--- a/tests/test_empty.py
+++ b/tests/test_empty.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 
diff --git a/tests/test_fhi_md_multi_elem_output.py b/tests/test_fhi_md_multi_elem_output.py
index dc4cbfcf2..a20c45bdd 100644
--- a/tests/test_fhi_md_multi_elem_output.py
+++ b/tests/test_fhi_md_multi_elem_output.py
@@ -1,5 +1,6 @@
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 
diff --git a/tests/test_fhi_md_output.py b/tests/test_fhi_md_output.py
index 3f945b318..d205e3911 100644
--- a/tests/test_fhi_md_output.py
+++ b/tests/test_fhi_md_output.py
@@ -1,5 +1,6 @@
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 
diff --git a/tests/test_fhi_output.py b/tests/test_fhi_output.py
index 7c8307ea1..acbe2aac9 100644
--- a/tests/test_fhi_output.py
+++ b/tests/test_fhi_output.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 
diff --git a/tests/test_gaussian_driver.py b/tests/test_gaussian_driver.py
index f1029ec11..07150bc7b 100644
--- a/tests/test_gaussian_driver.py
+++ b/tests/test_gaussian_driver.py
@@ -1,11 +1,11 @@
-import unittest
-import shutil
 import importlib
 import os
+import shutil
+import unittest
 
 import numpy as np
-from context import dpdata
 from comp_sys import CompSys, IsNoPBC
+from context import dpdata
 
 
 @unittest.skipIf(shutil.which("g16") is None, "g16 is not installed")
diff --git a/tests/test_gaussian_gjf.py b/tests/test_gaussian_gjf.py
index 24cb56bd8..861eae287 100644
--- a/tests/test_gaussian_gjf.py
+++ b/tests/test_gaussian_gjf.py
@@ -1,5 +1,5 @@
-import unittest
 import os
+import unittest
 
 from context import dpdata
 
diff --git a/tests/test_gaussian_log.py b/tests/test_gaussian_log.py
index 8d7bec818..67e13910e 100644
--- a/tests/test_gaussian_log.py
+++ b/tests/test_gaussian_log.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 
diff --git a/tests/test_gromacs_gro.py b/tests/test_gromacs_gro.py
index d2553809d..27d2742ef 100644
--- a/tests/test_gromacs_gro.py
+++ b/tests/test_gromacs_gro.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 
diff --git a/tests/test_json.py b/tests/test_json.py
index 7337d6820..09fc46dd7 100644
--- a/tests/test_json.py
+++ b/tests/test_json.py
@@ -1,8 +1,9 @@
 import os
-import numpy as np
 import unittest
-from context import dpdata
+
+import numpy as np
 from comp_sys import CompLabeledSys, IsPBC
+from context import dpdata
 
 
 class TestJsonLoad(unittest.TestCase, CompLabeledSys, IsPBC):
diff --git a/tests/test_lammps_dump_idx.py b/tests/test_lammps_dump_idx.py
index 110f4bc64..272cc222e 100644
--- a/tests/test_lammps_dump_idx.py
+++ b/tests/test_lammps_dump_idx.py
@@ -1,8 +1,9 @@
 # The index should map to that in the dump file
 
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 
diff --git a/tests/test_lammps_dump_shift_origin.py b/tests/test_lammps_dump_shift_origin.py
index eec6b4f32..60eb94c04 100644
--- a/tests/test_lammps_dump_shift_origin.py
+++ b/tests/test_lammps_dump_shift_origin.py
@@ -1,8 +1,9 @@
 import os
-import numpy as np
 import unittest
-from context import dpdata
+
+import numpy as np
 from comp_sys import CompSys, IsPBC
+from context import dpdata
 
 
 class TestLammpsDumpShiftOrigin(unittest.TestCase, CompSys, IsPBC):
diff --git a/tests/test_lammps_dump_skipload.py b/tests/test_lammps_dump_skipload.py
index d604607a4..224ec6d1f 100644
--- a/tests/test_lammps_dump_skipload.py
+++ b/tests/test_lammps_dump_skipload.py
@@ -1,8 +1,9 @@
 import os
-import numpy as np
 import unittest
-from context import dpdata
+
+import numpy as np
 from comp_sys import CompSys, IsPBC
+from context import dpdata
 
 
 class TestLmpDumpSkip(unittest.TestCase, CompSys, IsPBC):
diff --git a/tests/test_lammps_dump_to_system.py b/tests/test_lammps_dump_to_system.py
index 739f4e439..b2061c099 100644
--- a/tests/test_lammps_dump_to_system.py
+++ b/tests/test_lammps_dump_to_system.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 from poscars.poscar_ref_oh import TestPOSCARoh
 
diff --git a/tests/test_lammps_dump_unfold.py b/tests/test_lammps_dump_unfold.py
index bce95f7ba..3e5ca47db 100644
--- a/tests/test_lammps_dump_unfold.py
+++ b/tests/test_lammps_dump_unfold.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 from poscars.poscar_ref_oh import TestPOSCARoh
 
diff --git a/tests/test_lammps_lmp_dump.py b/tests/test_lammps_lmp_dump.py
index 2ded5e448..e083fc8db 100644
--- a/tests/test_lammps_lmp_dump.py
+++ b/tests/test_lammps_lmp_dump.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 from poscars.poscar_ref_oh import TestPOSCARoh
 
diff --git a/tests/test_lammps_lmp_to_system.py b/tests/test_lammps_lmp_to_system.py
index ea8d21574..80909def7 100644
--- a/tests/test_lammps_lmp_to_system.py
+++ b/tests/test_lammps_lmp_to_system.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 from poscars.poscar_ref_oh import TestPOSCARoh
 
diff --git a/tests/test_lammps_read_from_trajs.py b/tests/test_lammps_read_from_trajs.py
index 128aedb71..f1e5afdd1 100644
--- a/tests/test_lammps_read_from_trajs.py
+++ b/tests/test_lammps_read_from_trajs.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 
diff --git a/tests/test_msd.py b/tests/test_msd.py
index fd62d13c1..f102ea9db 100644
--- a/tests/test_msd.py
+++ b/tests/test_msd.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 
diff --git a/tests/test_multisystems.py b/tests/test_multisystems.py
index 689b1a869..3df15192b 100644
--- a/tests/test_multisystems.py
+++ b/tests/test_multisystems.py
@@ -1,13 +1,11 @@
 import os
-import numpy as np
 import unittest
-from context import dpdata
-from comp_sys import CompSys
-from comp_sys import CompLabeledSys
-from comp_sys import MultiSystems
-from comp_sys import IsNoPBC
 from itertools import permutations
 
+import numpy as np
+from comp_sys import CompLabeledSys, CompSys, IsNoPBC, MultiSystems
+from context import dpdata
+
 
 class TestMultiSystems(unittest.TestCase, CompLabeledSys, MultiSystems, IsNoPBC):
     def setUp(self):
diff --git a/tests/test_periodic_table.py b/tests/test_periodic_table.py
index 40a29a1c1..6b856e913 100644
--- a/tests/test_periodic_table.py
+++ b/tests/test_periodic_table.py
@@ -1,4 +1,5 @@
 import unittest
+
 from context import dpdata
 
 data = {
diff --git a/tests/test_perturb.py b/tests/test_perturb.py
index c047dfa4d..162f17280 100644
--- a/tests/test_perturb.py
+++ b/tests/test_perturb.py
@@ -1,11 +1,10 @@
 import os
-import numpy as np
 import unittest
-from context import dpdata
-from comp_sys import CompSys, IsPBC
+from unittest.mock import MagicMock, Mock, patch
 
-from unittest.mock import Mock
-from unittest.mock import patch, MagicMock
+import numpy as np
+from comp_sys import CompSys, IsPBC
+from context import dpdata
 
 
 class NormalGenerator(object):
diff --git a/tests/test_pick_atom_idx.py b/tests/test_pick_atom_idx.py
index 37be5d8fe..1de7ad321 100644
--- a/tests/test_pick_atom_idx.py
+++ b/tests/test_pick_atom_idx.py
@@ -1,7 +1,8 @@
-import numpy as np
 import unittest
-from context import dpdata
+
+import numpy as np
 from comp_sys import CompSys, IsNoPBC
+from context import dpdata
 
 try:
     import parmed
diff --git a/tests/test_predict.py b/tests/test_predict.py
index 2176bf74e..1de04d895 100644
--- a/tests/test_predict.py
+++ b/tests/test_predict.py
@@ -1,6 +1,6 @@
 import unittest
-import numpy as np
 
+import numpy as np
 from comp_sys import CompLabeledSys, IsPBC
 from context import dpdata
 
diff --git a/tests/test_pwmat_config_dump.py b/tests/test_pwmat_config_dump.py
index 32c6ee529..db79a923f 100644
--- a/tests/test_pwmat_config_dump.py
+++ b/tests/test_pwmat_config_dump.py
@@ -1,9 +1,11 @@
 import os
-import numpy as np
 import unittest
-import dpdata
+
+import numpy as np
 from pwmat.config_ref_oh import Testconfigoh
 
+import dpdata
+
 
 def myfilecmp(test, f0, f1):
     with open(f0) as fp0:
diff --git a/tests/test_pwmat_config_to_system.py b/tests/test_pwmat_config_to_system.py
index 3ff43b66e..0956f9569 100644
--- a/tests/test_pwmat_config_to_system.py
+++ b/tests/test_pwmat_config_to_system.py
@@ -1,9 +1,11 @@
 import os
-import numpy as np
 import unittest
-import dpdata
+
+import numpy as np
 from pwmat.config_ref_ch4 import Testconfigch4
 
+import dpdata
+
 
 class Testconfig(unittest.TestCase, Testconfigch4):
     def setUp(self):
diff --git a/tests/test_pwmat_mlmd.py b/tests/test_pwmat_mlmd.py
index f35ef42b2..ae2d1334e 100644
--- a/tests/test_pwmat_mlmd.py
+++ b/tests/test_pwmat_mlmd.py
@@ -1,6 +1,8 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
+
 import dpdata
 
 
diff --git a/tests/test_pwmat_movement.py b/tests/test_pwmat_movement.py
index e188c7462..bba4f2cae 100644
--- a/tests/test_pwmat_movement.py
+++ b/tests/test_pwmat_movement.py
@@ -1,6 +1,8 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
+
 import dpdata
 
 
diff --git a/tests/test_pymatgen_molecule.py b/tests/test_pymatgen_molecule.py
index 8c3e72b66..4000480a0 100644
--- a/tests/test_pymatgen_molecule.py
+++ b/tests/test_pymatgen_molecule.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 try:
diff --git a/tests/test_qe_cp_traj.py b/tests/test_qe_cp_traj.py
index 2cb982cee..e947a0f46 100644
--- a/tests/test_qe_cp_traj.py
+++ b/tests/test_qe_cp_traj.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 bohr2ang = dpdata.unit.LengthConversion("bohr", "angstrom").value()
diff --git a/tests/test_qe_cp_traj_skipload.py b/tests/test_qe_cp_traj_skipload.py
index e8cc84bf1..2964e716b 100644
--- a/tests/test_qe_cp_traj_skipload.py
+++ b/tests/test_qe_cp_traj_skipload.py
@@ -1,10 +1,9 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
+from comp_sys import CompLabeledSys, CompSys, IsPBC
 from context import dpdata
-from comp_sys import CompSys
-from comp_sys import CompLabeledSys
-from comp_sys import IsPBC
 
 bohr2ang = dpdata.unit.LengthConversion("bohr", "angstrom").value()
 
diff --git a/tests/test_qe_pw_scf.py b/tests/test_qe_pw_scf.py
index 4cb78cbdb..4d3032da4 100644
--- a/tests/test_qe_pw_scf.py
+++ b/tests/test_qe_pw_scf.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 
diff --git a/tests/test_qe_pw_scf_crystal_atomic_positions.py b/tests/test_qe_pw_scf_crystal_atomic_positions.py
index 19dc7b59c..e335c51ad 100644
--- a/tests/test_qe_pw_scf_crystal_atomic_positions.py
+++ b/tests/test_qe_pw_scf_crystal_atomic_positions.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 
diff --git a/tests/test_qe_pw_scf_energy_bug.py b/tests/test_qe_pw_scf_energy_bug.py
index 85d793552..49ff0e34f 100644
--- a/tests/test_qe_pw_scf_energy_bug.py
+++ b/tests/test_qe_pw_scf_energy_bug.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 
diff --git a/tests/test_quip_gap_xyz.py b/tests/test_quip_gap_xyz.py
index 272856067..03f69d955 100644
--- a/tests/test_quip_gap_xyz.py
+++ b/tests/test_quip_gap_xyz.py
@@ -1,8 +1,9 @@
 import os
-import numpy as np
 import unittest
-from context import dpdata
+
+import numpy as np
 from comp_sys import CompLabeledSys, IsPBC
+from context import dpdata
 
 
 class TestQuipGapxyz1(unittest.TestCase, CompLabeledSys, IsPBC):
diff --git a/tests/test_remove_atom_names.py b/tests/test_remove_atom_names.py
index 4d4e23ec8..d2d4abc7e 100644
--- a/tests/test_remove_atom_names.py
+++ b/tests/test_remove_atom_names.py
@@ -1,7 +1,7 @@
 import unittest
+
+from comp_sys import CompLabeledSys, IsNoPBC
 from context import dpdata
-from comp_sys import CompLabeledSys
-from comp_sys import IsNoPBC
 
 
 class TestRemove(unittest.TestCase, CompLabeledSys, IsNoPBC):
diff --git a/tests/test_remove_pbc.py b/tests/test_remove_pbc.py
index 558587b06..28310088d 100644
--- a/tests/test_remove_pbc.py
+++ b/tests/test_remove_pbc.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 
diff --git a/tests/test_replace.py b/tests/test_replace.py
index f0f4430f5..eaef289ca 100644
--- a/tests/test_replace.py
+++ b/tests/test_replace.py
@@ -1,11 +1,10 @@
 import os
-import numpy as np
 import unittest
-from context import dpdata
-from comp_sys import CompSys, IsPBC
+from unittest.mock import MagicMock, Mock, patch
 
-from unittest.mock import Mock
-from unittest.mock import patch, MagicMock
+import numpy as np
+from comp_sys import CompSys, IsPBC
+from context import dpdata
 
 
 class ConstGenerator(object):
diff --git a/tests/test_replicate.py b/tests/test_replicate.py
index 1a7590b6b..fc41e62d9 100644
--- a/tests/test_replicate.py
+++ b/tests/test_replicate.py
@@ -1,8 +1,9 @@
 import os
-import numpy as np
 import unittest
-from context import dpdata
+
+import numpy as np
 from comp_sys import CompSys, IsPBC
+from context import dpdata
 
 
 class TestReplicate123(unittest.TestCase, CompSys, IsPBC):
diff --git a/tests/test_shuffle.py b/tests/test_shuffle.py
index 8acbb42ae..9c4622143 100644
--- a/tests/test_shuffle.py
+++ b/tests/test_shuffle.py
@@ -1,6 +1,7 @@
 import unittest
-from context import dpdata
+
 from comp_sys import CompLabeledSys, IsPBC
+from context import dpdata
 
 
 class TestDeepmdLoadRaw(unittest.TestCase, CompLabeledSys, IsPBC):
diff --git a/tests/test_siesta_aiMD_output.py b/tests/test_siesta_aiMD_output.py
index 8ea4be359..e7f61641c 100644
--- a/tests/test_siesta_aiMD_output.py
+++ b/tests/test_siesta_aiMD_output.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 
diff --git a/tests/test_siesta_output.py b/tests/test_siesta_output.py
index 2539173d6..0c51ae21d 100644
--- a/tests/test_siesta_output.py
+++ b/tests/test_siesta_output.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 
diff --git a/tests/test_sqm_driver.py b/tests/test_sqm_driver.py
index b06ab26ce..3dbc6df4a 100644
--- a/tests/test_sqm_driver.py
+++ b/tests/test_sqm_driver.py
@@ -1,9 +1,9 @@
-import unittest
 import shutil
+import unittest
 
 import numpy as np
-from context import dpdata
 from comp_sys import CompSys, IsNoPBC
+from context import dpdata
 
 
 @unittest.skipIf(shutil.which("sqm") is None, "sqm is not installed")
diff --git a/tests/test_stat.py b/tests/test_stat.py
index 62d045f43..9ae8a175b 100644
--- a/tests/test_stat.py
+++ b/tests/test_stat.py
@@ -1,7 +1,7 @@
-from context import dpdata
-
 import unittest
 
+from context import dpdata
+
 
 class TestStat(unittest.TestCase):
     def test_errors(self):
diff --git a/tests/test_system_append.py b/tests/test_system_append.py
index 698832476..32107a4c4 100644
--- a/tests/test_system_append.py
+++ b/tests/test_system_append.py
@@ -1,10 +1,9 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
+from comp_sys import CompLabeledSys, CompSys, IsNoPBC, IsPBC
 from context import dpdata
-from comp_sys import CompSys
-from comp_sys import CompLabeledSys
-from comp_sys import IsPBC, IsNoPBC
 
 
 class TestFailedAppend(unittest.TestCase):
diff --git a/tests/test_system_apply_pbc.py b/tests/test_system_apply_pbc.py
index 96b06989f..c9f14d924 100644
--- a/tests/test_system_apply_pbc.py
+++ b/tests/test_system_apply_pbc.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 
diff --git a/tests/test_system_set_type.py b/tests/test_system_set_type.py
index 27e0da97f..edcddc646 100644
--- a/tests/test_system_set_type.py
+++ b/tests/test_system_set_type.py
@@ -1,9 +1,8 @@
 import os
-import numpy as np
 import unittest
-from context import dpdata
 
 import numpy as np
+from context import dpdata
 
 
 class TestSetAtomTypes(unittest.TestCase):
diff --git a/tests/test_to_ase.py b/tests/test_to_ase.py
index 187d8907b..2440962c2 100644
--- a/tests/test_to_ase.py
+++ b/tests/test_to_ase.py
@@ -1,8 +1,9 @@
 import os
-import numpy as np
 import unittest
-from context import dpdata
+
+import numpy as np
 from comp_sys import CompSys, IsPBC
+from context import dpdata
 
 try:
     from ase import Atoms
diff --git a/tests/test_to_list.py b/tests/test_to_list.py
index 4aa90885d..68c98bf61 100644
--- a/tests/test_to_list.py
+++ b/tests/test_to_list.py
@@ -1,8 +1,9 @@
 import os
-import numpy as np
 import unittest
-from context import dpdata
+
+import numpy as np
 from comp_sys import CompLabeledSys, IsPBC
+from context import dpdata
 
 
 class TestToList(unittest.TestCase, CompLabeledSys, IsPBC):
diff --git a/tests/test_to_pymatgen.py b/tests/test_to_pymatgen.py
index abe251502..e2b91e24d 100644
--- a/tests/test_to_pymatgen.py
+++ b/tests/test_to_pymatgen.py
@@ -1,8 +1,9 @@
 import os
-import numpy as np
 import unittest
-from context import dpdata
+
+import numpy as np
 from comp_sys import CompSys, IsPBC
+from context import dpdata
 
 try:
     from pymatgen import Structure
diff --git a/tests/test_to_pymatgen_entry.py b/tests/test_to_pymatgen_entry.py
index 1cad9c174..9510224b1 100644
--- a/tests/test_to_pymatgen_entry.py
+++ b/tests/test_to_pymatgen_entry.py
@@ -1,8 +1,9 @@
 import os
-import numpy as np
 import unittest
-from context import dpdata
+
+import numpy as np
 from comp_sys import CompSys, IsPBC
+from context import dpdata
 from monty.serialization import loadfn
 
 try:
diff --git a/tests/test_type_map.py b/tests/test_type_map.py
index 4d98aa7a8..2cc508654 100644
--- a/tests/test_type_map.py
+++ b/tests/test_type_map.py
@@ -1,7 +1,8 @@
 import unittest
-from context import dpdata
 from itertools import permutations
 
+from context import dpdata
+
 
 class TestTypeMap:
     def test_check_type_map(self):
diff --git a/tests/test_vasp_outcar.py b/tests/test_vasp_outcar.py
index 2fcaa0a1b..d7e38867e 100644
--- a/tests/test_vasp_outcar.py
+++ b/tests/test_vasp_outcar.py
@@ -1,8 +1,10 @@
 import os
-import numpy as np
 import unittest
-from context import dpdata
+
+import numpy as np
 from comp_sys import CompLabeledSys, IsPBC
+from context import dpdata
+
 from dpdata.utils import uniq_atom_names
 
 
diff --git a/tests/test_vasp_poscar_dump.py b/tests/test_vasp_poscar_dump.py
index f83e208ca..c67f42fcb 100644
--- a/tests/test_vasp_poscar_dump.py
+++ b/tests/test_vasp_poscar_dump.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 from poscars.poscar_ref_oh import TestPOSCARoh
 
diff --git a/tests/test_vasp_poscar_to_system.py b/tests/test_vasp_poscar_to_system.py
index 7eea37577..dcb83bfdf 100644
--- a/tests/test_vasp_poscar_to_system.py
+++ b/tests/test_vasp_poscar_to_system.py
@@ -1,8 +1,9 @@
 import os
-import numpy as np
 import unittest
-from context import dpdata
+
+import numpy as np
 from comp_sys import CompSys, IsPBC
+from context import dpdata
 from poscars.poscar_ref_oh import TestPOSCARoh
 
 
diff --git a/tests/test_vasp_unconverged_outcar.py b/tests/test_vasp_unconverged_outcar.py
index 579edf09f..97318223c 100644
--- a/tests/test_vasp_unconverged_outcar.py
+++ b/tests/test_vasp_unconverged_outcar.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 
diff --git a/tests/test_vasp_xml.py b/tests/test_vasp_xml.py
index a3cd90d03..d5df49dad 100644
--- a/tests/test_vasp_xml.py
+++ b/tests/test_vasp_xml.py
@@ -1,10 +1,9 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
+from comp_sys import CompLabeledSys, CompSys, IsPBC
 from context import dpdata
-from comp_sys import CompSys
-from comp_sys import CompLabeledSys
-from comp_sys import IsPBC
 
 
 class TestVaspXml(unittest.TestCase, CompSys, IsPBC):
diff --git a/tests/test_water_ions.py b/tests/test_water_ions.py
index 98b3838b5..8b70dc736 100644
--- a/tests/test_water_ions.py
+++ b/tests/test_water_ions.py
@@ -1,6 +1,7 @@
 import os
-import numpy as np
 import unittest
+
+import numpy as np
 from context import dpdata
 
 try:
diff --git a/tests/test_xyz.py b/tests/test_xyz.py
index 8f0779b31..a84ad28bc 100644
--- a/tests/test_xyz.py
+++ b/tests/test_xyz.py
@@ -1,8 +1,9 @@
+import tempfile
 import unittest
+
 import numpy as np
-import tempfile
-from context import dpdata
 from comp_sys import CompSys, IsNoPBC
+from context import dpdata
 
 
 class TestToXYZ(unittest.TestCase):