add isort to sort imports (#1133)

This is an automatic tool to format and sort imports. See
https://github.com/PyCQA/isort for details.

---------

Signed-off-by: Jinzhe Zeng <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: njzjz

.pre-commit-config.yaml

@@ -23,6 +23,11 @@ repos:
     rev: 22.12.0
     hooks:
     -   id: black-jupyter
+-   repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.253
+    hooks:
+    - id: ruff
+      args: ["--fix"]
 # numpydoc
 -   repo: https://github.com/Carreau/velin
     rev: 0.0.12

doc/conf.py

@@ -11,15 +11,14 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import os
-import sys
 import subprocess
+import sys
 from datetime import date
 
 # import sys
 import recommonmark
 from recommonmark.transform import AutoStructify
 
-
 # -- Project information -----------------------------------------------------
 
 project = "DP-GEN"

dpgen/__init__.py

@@ -1,8 +1,8 @@
-from __future__ import unicode_literals, print_function
+from __future__ import print_function, unicode_literals
+
 import logging
 import os
 
-
 ROOT_PATH = __path__[0]
 NAME = "dpgen"
 SHORT_CMD = "dpgen"

dpgen/auto_test/ABACUS.py

@@ -1,13 +1,14 @@
 import os
-from dpgen import dlog
-from dpgen.util import sepline
-import dpgen.auto_test.lib.abacus as abacus
-import dpgen.generator.lib.abacus_scf as abacus_scf
-from dpgen.auto_test.Task import Task
 
+import numpy as np
 from dpdata import LabeledSystem
 from monty.serialization import dumpfn
-import numpy as np
+
+import dpgen.auto_test.lib.abacus as abacus
+import dpgen.generator.lib.abacus_scf as abacus_scf
+from dpgen import dlog
+from dpgen.auto_test.Task import Task
+from dpgen.util import sepline
 
 
 class ABACUS(Task):

dpgen/auto_test/EOS.py

@@ -4,17 +4,15 @@
 import re
 
 import numpy as np
-from monty.serialization import loadfn, dumpfn
+from monty.serialization import dumpfn, loadfn
 
+import dpgen.auto_test.lib.abacus as abacus
 import dpgen.auto_test.lib.vasp as vasp
+import dpgen.generator.lib.abacus_scf as abacus_scf
 from dpgen import dlog
 from dpgen.auto_test.Property import Property
 from dpgen.auto_test.refine import make_refine
-from dpgen.auto_test.reproduce import make_repro
-from dpgen.auto_test.reproduce import post_repro
-
-import dpgen.generator.lib.abacus_scf as abacus_scf
-import dpgen.auto_test.lib.abacus as abacus
+from dpgen.auto_test.reproduce import make_repro, post_repro
 
 
 class EOS(Property):

dpgen/auto_test/Elastic.py

@@ -1,24 +1,23 @@
 import glob
 import os
-from shutil import copyfile
 import re
+from shutil import copyfile
 
-from monty.serialization import loadfn, dumpfn
+from monty.serialization import dumpfn, loadfn
 from pymatgen.analysis.elasticity.elastic import ElasticTensor
 from pymatgen.analysis.elasticity.strain import DeformedStructureSet, Strain
 from pymatgen.analysis.elasticity.stress import Stress
 from pymatgen.core.structure import Structure
 from pymatgen.io.vasp import Incar, Kpoints
 
+import dpgen.auto_test.lib.abacus as abacus
 import dpgen.auto_test.lib.vasp as vasp
+import dpgen.generator.lib.abacus_scf as abacus_scf
 from dpgen import dlog
 from dpgen.auto_test.Property import Property
 from dpgen.auto_test.refine import make_refine
 from dpgen.generator.lib.vasp import incar_upper
 
-import dpgen.auto_test.lib.abacus as abacus
-import dpgen.generator.lib.abacus_scf as abacus_scf
-
 
 class Elastic(Property):
     def __init__(self, parameter, inter_param=None):

dpgen/auto_test/Gamma.py

@@ -5,22 +5,20 @@
 
 import dpdata
 import numpy as np
-from monty.serialization import loadfn, dumpfn
-from pymatgen.core.structure import Structure
-from pymatgen.core.surface import SlabGenerator
-from pymatgen.io.ase import AseAtomsAdaptor
 from ase.lattice.cubic import BodyCenteredCubic as bcc
 from ase.lattice.cubic import FaceCenteredCubic as fcc
 from ase.lattice.hexagonal import HexagonalClosedPacked as hcp
+from monty.serialization import dumpfn, loadfn
+from pymatgen.core.structure import Structure
+from pymatgen.core.surface import SlabGenerator
+from pymatgen.io.ase import AseAtomsAdaptor
 
+import dpgen.auto_test.lib.abacus as abacus
 import dpgen.auto_test.lib.vasp as vasp
 from dpgen import dlog
 from dpgen.auto_test.Property import Property
 from dpgen.auto_test.refine import make_refine
-from dpgen.auto_test.reproduce import make_repro
-from dpgen.auto_test.reproduce import post_repro
-
-import dpgen.auto_test.lib.abacus as abacus
+from dpgen.auto_test.reproduce import make_repro, post_repro
 
 
 class Gamma(Property):

dpgen/auto_test/Interstitial.py

@@ -2,20 +2,18 @@
 import json
 import os
 import re
-import numpy as np
 
-from monty.serialization import loadfn, dumpfn
+import numpy as np
+from monty.serialization import dumpfn, loadfn
 from pymatgen.analysis.defects.generators import InterstitialGenerator
 from pymatgen.core.structure import Structure
 
+import dpgen.auto_test.lib.abacus as abacus
 import dpgen.auto_test.lib.lammps as lammps
+import dpgen.generator.lib.abacus_scf as abacus_scf
 from dpgen.auto_test.Property import Property
 from dpgen.auto_test.refine import make_refine
-from dpgen.auto_test.reproduce import make_repro
-from dpgen.auto_test.reproduce import post_repro
-
-import dpgen.auto_test.lib.abacus as abacus
-import dpgen.generator.lib.abacus_scf as abacus_scf
+from dpgen.auto_test.reproduce import make_repro, post_repro
 
 
 class Interstitial(Property):

dpgen/auto_test/Lammps.py

@@ -1,15 +1,17 @@
 import os
 import warnings
+
+from monty.serialization import dumpfn, loadfn
+
 import dpgen.auto_test.lib.lammps as lammps
 from dpgen import dlog
-from monty.serialization import loadfn, dumpfn
-from dpgen.auto_test.Task import Task
 from dpgen.auto_test.lib.lammps import (
     inter_deepmd,
-    inter_meam,
-    inter_eam_fs,
     inter_eam_alloy,
+    inter_eam_fs,
+    inter_meam,
 )
+from dpgen.auto_test.Task import Task
 
 supported_inter = ["deepmd", "meam", "eam_fs", "eam_alloy"]
 

dpgen/auto_test/Surface.py

@@ -5,19 +5,17 @@
 
 import dpdata
 import numpy as np
-from monty.serialization import loadfn, dumpfn
+from monty.serialization import dumpfn, loadfn
 from pymatgen.core.structure import Structure
 from pymatgen.core.surface import generate_all_slabs
 
+import dpgen.auto_test.lib.abacus as abacus
 import dpgen.auto_test.lib.vasp as vasp
+import dpgen.generator.lib.abacus_scf as abacus_scf
 from dpgen import dlog
 from dpgen.auto_test.Property import Property
 from dpgen.auto_test.refine import make_refine
-from dpgen.auto_test.reproduce import make_repro
-from dpgen.auto_test.reproduce import post_repro
-
-import dpgen.auto_test.lib.abacus as abacus
-import dpgen.generator.lib.abacus_scf as abacus_scf
+from dpgen.auto_test.reproduce import make_repro, post_repro
 
 
 class Surface(Property):