add isort to sort imports

.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):

dpgen/auto_test/VASP.py

@@ -1,13 +1,15 @@
 import os
-from dpgen import dlog
-from dpgen.util import sepline
-import dpgen.auto_test.lib.vasp as vasp
-from dpgen.auto_test.Task import Task
-from dpgen.generator.lib.vasp import incar_upper
+
 from dpdata import LabeledSystem
 from monty.serialization import dumpfn
-from pymatgen.io.vasp import Incar, Kpoints
 from pymatgen.core.structure import Structure
+from pymatgen.io.vasp import Incar, Kpoints
+
+import dpgen.auto_test.lib.vasp as vasp
+from dpgen import dlog
+from dpgen.auto_test.Task import Task
+from dpgen.generator.lib.vasp import incar_upper
+from dpgen.util import sepline
 
 
 class VASP(Task):

dpgen/auto_test/Vacancy.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 VacancyGenerator
 from pymatgen.core.structure import Structure
 
+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.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 Vacancy(Property):

dpgen/auto_test/calculator.py

@@ -1,6 +1,6 @@
-from dpgen.auto_test.VASP import VASP
 from dpgen.auto_test.ABACUS import ABACUS
 from dpgen.auto_test.Lammps import Lammps
+from dpgen.auto_test.VASP import VASP
 
 
 def make_calculator(inter_parameter, path_to_poscar):

dpgen/auto_test/common_equi.py

@@ -2,19 +2,20 @@
 import os
 import shutil
 import warnings
-from monty.serialization import dumpfn
 from multiprocessing import Pool
 
+from monty.serialization import dumpfn
+from packaging.version import Version
+
+import dpgen.auto_test.lib.abacus as abacus
 import dpgen.auto_test.lib.crys as crys
 import dpgen.auto_test.lib.util as util
-import dpgen.auto_test.lib.abacus as abacus
 from dpgen import dlog
 from dpgen.auto_test.calculator import make_calculator
+from dpgen.auto_test.lib.utils import create_path
 from dpgen.auto_test.mpdb import get_structure
-from packaging.version import Version
 from dpgen.dispatcher.Dispatcher import make_submission
 from dpgen.remote.decide_machine import convert_mdata
-from dpgen.auto_test.lib.utils import create_path
 
 lammps_task_type = ["deepmd", "meam", "eam_fs", "eam_alloy"]
 

dpgen/auto_test/common_prop.py

@@ -1,21 +1,23 @@
-from packaging.version import Version
 import glob
 import os
 import warnings
 from multiprocessing import Pool
+
+from packaging.version import Version
+
 import dpgen.auto_test.lib.util as util
 from dpgen import dlog
-from dpgen.util import sepline
-from dpgen.auto_test.EOS import EOS
+from dpgen.auto_test.calculator import make_calculator
 from dpgen.auto_test.Elastic import Elastic
+from dpgen.auto_test.EOS import EOS
+from dpgen.auto_test.Gamma import Gamma
 from dpgen.auto_test.Interstitial import Interstitial
+from dpgen.auto_test.lib.utils import create_path
 from dpgen.auto_test.Surface import Surface
 from dpgen.auto_test.Vacancy import Vacancy
-from dpgen.auto_test.Gamma import Gamma
-from dpgen.auto_test.calculator import make_calculator
 from dpgen.dispatcher.Dispatcher import make_submission
 from dpgen.remote.decide_machine import convert_mdata
-from dpgen.auto_test.lib.utils import create_path
+from dpgen.util import sepline
 
 lammps_task_type = ["deepmd", "meam", "eam_fs", "eam_alloy"]
 

dpgen/auto_test/gen_confs.py

@@ -1,9 +1,13 @@
 #!/usr/bin/env python3
 
-import os, re, argparse
-import dpgen.auto_test.lib.crys as crys
-from pymatgen.ext.matproj import MPRester, Composition
+import argparse
+import os
+import re
+
 from pymatgen.analysis.structure_matcher import StructureMatcher
+from pymatgen.ext.matproj import Composition, MPRester
+
+import dpgen.auto_test.lib.crys as crys
 
 global_std_crystal = {
     "fcc": crys.fcc,

dpgen/auto_test/lib/abacus.py

@@ -1,11 +1,14 @@
 #!/usr/bin/python3
-import os, sys
+import os
+import sys
 from unicodedata import numeric
+
 import dpdata
-import dpgen.generator.lib.abacus_scf as abacus_scf
 import numpy as np
 from pymatgen.core.structure import Structure
 
+import dpgen.generator.lib.abacus_scf as abacus_scf
+
 A2BOHR = 1.8897261254578281
 MASS_DICT = {
     "H": 1.0079,

dpgen/auto_test/lib/lammps.py

@@ -1,11 +1,15 @@
 #!/usr/bin/env python3
 
-import random, os, sys
-import dpdata
+import os
+import random
 import subprocess as sp
-import dpgen.auto_test.lib.util as util
-from packaging.version import Version
+import sys
+
+import dpdata
 from dpdata.periodic_table import Element
+from packaging.version import Version
+
+import dpgen.auto_test.lib.util as util
 
 
 def cvt_lammps_conf(fin, fout, type_map, ofmt="lammps/data"):