pre-commit: sort Python includes (PEP8) (openPMD#1175)

* pre-commit: sort Python includes (PEP8)

Sort Python includes according to PEP8

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

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

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

.editorconfig

@@ -30,3 +30,8 @@ trim_trailing_whitespace = false
 # TABs are part of its syntax
 indent_style = tab
 indent_size = unset
+
+
+[*.py]
+# isort config
+force_sort_within_sections = true

.pre-commit-config.yaml

@@ -55,6 +55,32 @@ repos:
 # C++ formatting
 # clang-format
 
+# Autoremoves unused Python imports
+- repo: https://github.com/hadialqattan/pycln
+  rev: v1.1.0
+  hooks:
+  - id: pycln
+    name: pycln (python)
+
+# Sorts Python imports according to PEP8
+# https://www.python.org/dev/peps/pep-0008/#imports
+- repo: https://github.com/pycqa/isort
+  rev: 5.10.1
+  hooks:
+  - id: isort
+    name: isort (python)
+
+# Python: Flake8 (checks only, does this support auto-fixes?)
+#- repo: https://github.com/PyCQA/flake8
+#  rev: 4.0.1
+#  hooks:
+#  - id: flake8
+#    additional_dependencies: &flake8_dependencies
+#      - flake8-bugbear
+#      - pep8-naming
+#    exclude: ^(docs/.*|tools/.*)$
+# Alternatively: use autopep8?
+
 # Python Formatting
 #- repo: https://github.com/psf/black
 #  rev: 21.10b0 # Keep in sync with blacken-docs

docs/source/conf.py

@@ -15,7 +15,9 @@
 #
 import os
 import subprocess
+
 from recommonmark.parser import CommonMarkParser
+
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
 

examples/10_streaming_read.py

@@ -1,8 +1,9 @@
 #!/usr/bin/env python
 import json
-import openpmd_api as io
 import sys
 
+import openpmd_api as io
+
 # pass-through for ADIOS2 engine parameters
 # https://adios2.readthedocs.io/en/latest/engines/engines.html
 config = {'adios2': {'engine': {}, 'dataset': {}}}

examples/10_streaming_write.py

@@ -1,9 +1,10 @@
 #!/usr/bin/env python
 import json
-import openpmd_api as io
-import numpy as np
 import sys
 
+import numpy as np
+import openpmd_api as io
+
 # pass-through for ADIOS2 engine parameters
 # https://adios2.readthedocs.io/en/latest/engines/engines.html
 config = {'adios2': {'engine': {}, 'dataset': {}}}

examples/11_particle_dataframe.py

@@ -6,19 +6,21 @@
 Authors: Axel Huebl, Dmitry Ganyushin
 License: LGPLv3+
 """
-import openpmd_api as io
-import numpy as np
 import sys
+
+import numpy as np
+import openpmd_api as io
+
 try:
     import pandas as pd
 except ImportError:
     print("pandas NOT found. Install pandas to run this example.")
     sys.exit()
 found_dask = False
 try:
-    from dask.delayed import delayed
-    import dask.array as da
     import dask
+    import dask.array as da
+    from dask.delayed import delayed
     found_dask = True
 except ImportError:
     print("dask NOT found. Install dask to run the 2nd example.")

examples/12_span_write.py

@@ -1,5 +1,5 @@
-import openpmd_api as io
 import numpy as np
+import openpmd_api as io
 
 
 def span_write(filename):

examples/13_write_dynamic_configuration.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 import json
-import openpmd_api as io
-import numpy as np
 
+import numpy as np
+import openpmd_api as io
 
 # This example demonstrates how to use JSON/TOML-based dynamic
 # configuration for openPMD.

examples/2_read_serial.py

@@ -8,7 +8,6 @@
 """
 import openpmd_api as io
 
-
 if __name__ == "__main__":
     series = io.Series("../samples/git-sample/data%T.h5",
                        io.Access.read_only)

examples/2a_read_thetaMode_serial.py

@@ -8,7 +8,6 @@
 """
 import openpmd_api as io
 
-
 if __name__ == "__main__":
     series = io.Series("../samples/git-sample/thetaMode/data%T.h5",
                        io.Access.read_only)

examples/3_write_serial.py

@@ -6,9 +6,8 @@
 Authors: Axel Huebl
 License: LGPLv3+
 """
-import openpmd_api as io
 import numpy as np
-
+import openpmd_api as io
 
 if __name__ == "__main__":
     # user input: size of matrix to write, default 3x3

examples/3a_write_thetaMode_serial.py

@@ -6,9 +6,8 @@
 Authors: Axel Huebl
 License: LGPLv3+
 """
-import openpmd_api as io
 import numpy as np
-
+import openpmd_api as io
 
 if __name__ == "__main__":
     # open file for writing

examples/3b_write_resizable_particles.py

@@ -6,9 +6,8 @@
 Authors: Axel Huebl
 License: LGPLv3+
 """
-import openpmd_api as io
 import numpy as np
-
+import openpmd_api as io
 
 if __name__ == "__main__":
     # open file for writing

examples/4_read_parallel.py

@@ -11,10 +11,8 @@
 # on import: calls MPI_Init_thread()
 # exit hook: calls MPI_Finalize()
 from mpi4py import MPI
-
 import openpmd_api as io
 
-
 if __name__ == "__main__":
     # also works with any other MPI communicator
     comm = MPI.COMM_WORLD

examples/5_write_parallel.py

@@ -11,10 +11,8 @@
 # on import: calls MPI_Init_thread()
 # exit hook: calls MPI_Finalize()
 from mpi4py import MPI
-
-import openpmd_api as io
 import numpy as np
-
+import openpmd_api as io
 
 if __name__ == "__main__":
     # also works with any other MPI communicator

examples/7_extended_write_serial.py

@@ -6,11 +6,11 @@
 Authors: Axel Huebl, Fabian Koller
 License: LGPLv3+
 """
-from openpmd_api import Series, Access, Dataset, Mesh_Record_Component, \
-    Unit_Dimension
 import json
-import numpy as np
 
+import numpy as np
+from openpmd_api import (Access, Dataset, Mesh_Record_Component, Series,
+                         Unit_Dimension)
 
 SCALAR = Mesh_Record_Component.SCALAR
 

examples/9_particle_write_serial.py

@@ -6,10 +6,9 @@
 Authors: Axel Huebl
 License: LGPLv3+
 """
-from openpmd_api import Series, Access, Dataset, Mesh_Record_Component, \
-    Unit_Dimension
 import numpy as np
-
+from openpmd_api import (Access, Dataset, Mesh_Record_Component, Series,
+                         Unit_Dimension)
 
 SCALAR = Mesh_Record_Component.SCALAR
 

setup.py

@@ -1,12 +1,12 @@
+from distutils.version import LooseVersion
 import os
-import re
-import sys
 import platform
+import re
 import subprocess
+import sys
 
-from setuptools import setup, Extension
+from setuptools import Extension, setup
 from setuptools.command.build_ext import build_ext
-from distutils.version import LooseVersion
 
 
 class CMakeExtension(Extension):

src/binding/python/openpmd_api/DaskArray.py

@@ -6,7 +6,9 @@
 License: LGPLv3+
 """
 import math
+
 import numpy as np
+
 try:
     from dask.array import from_array
     found_dask = True

src/binding/python/openpmd_api/DaskDataFrame.py

@@ -6,6 +6,7 @@
 License: LGPLv3+
 """
 import numpy as np
+
 try:
     import dask.dataframe as dd
     from dask.delayed import delayed

src/binding/python/openpmd_api/DataFrame.py

@@ -6,7 +6,9 @@
 License: LGPLv3+
 """
 import math
+
 import numpy as np
+
 try:
     import pandas as pd
     found_pandas = True

src/binding/python/openpmd_api/__init__.py

@@ -1,9 +1,8 @@
 from . import openpmd_api_cxx as cxx
-from .openpmd_api_cxx import *  # noqa
-from .DataFrame import particles_to_dataframe
-from .DaskDataFrame import particles_to_daskdataframe
 from .DaskArray import record_component_to_daskarray
-
+from .DaskDataFrame import particles_to_daskdataframe
+from .DataFrame import particles_to_dataframe
+from .openpmd_api_cxx import *  # noqa
 
 __version__ = cxx.__version__
 __doc__ = cxx.__doc__

src/binding/python/openpmd_api/ls/__main__.py

@@ -9,6 +9,7 @@
 License: LGPLv3+
 """
 import sys
+
 from ..openpmd_api_cxx import _ls_run
 
 

src/binding/python/openpmd_api/pipe/__main__.py

@@ -8,11 +8,12 @@
 Authors: Franz Poeschel
 License: LGPLv3+
 """
-from .. import openpmd_api_cxx as io
 import argparse
 import os  # os.path.basename
 import sys  # sys.stderr.write
 
+from .. import openpmd_api_cxx as io
+
 # MPI is an optional dependency
 try:
     from mpi4py import MPI

src/cli/pipe.py

@@ -9,9 +9,10 @@
 Authors: Franz Poeschel
 License: LGPLv3+
 """
-import openpmd_api.pipe.__main__ as pipe
 import sys
 
+import openpmd_api.pipe.__main__ as pipe
+
 if __name__ == "__main__":
     pipe.main()
     sys.exit()

test/python/unittest/API/APITest.py

@@ -6,13 +6,14 @@
 License: LGPLv3+
 """
 
-import openpmd_api as io
-
+import ctypes
 import gc
 import os
 import shutil
 import unittest
-import ctypes
+
+import openpmd_api as io
+
 try:
     import numpy as np
     found_numpy = True

test/python/unittest/Test.py

@@ -6,8 +6,8 @@
 License: LGPLv3+
 """
 
-import unittest
 import sys
+import unittest
 
 # Import suites to run.
 from API.APITest import APITest