add isort to sort imports (#418)

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

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: njzjz

.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

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: