Merge pull request #106 from boutproject/fix-format-ci

Fix formatting CI

.github/workflows/formatting.yml

@@ -1,7 +1,6 @@
 name: Formatting (black & isort)
 on:
   push:
-    branches: master
     paths:
       - '**.py'
 
@@ -27,12 +26,12 @@ jobs:
         python --version
         black --version
         isort --version
-    - name: Run black
-      run: |
-        black boututils
     - name: Run isort
       run: |
-        isort boututils
+        isort src
+    - name: Run black
+      run: |
+        black src
     - uses: stefanzweifel/git-auto-commit-action@v4
       with:
         commit_message: "[skip ci] Apply black/isort changes"

src/boutdata/__init__.py

@@ -1,18 +1,17 @@
 """ Routines for exchanging data to/from BOUT++ """
 
-from boutdata.collect import collect, attributes
+from boutdata.collect import attributes, collect
 from boututils.boutarray import BoutArray
 from boututils.boutwarnings import alwayswarn
 from boututils.run_wrapper import (
+    build_and_log,
+    determineNumberOfCPUs,
     launch,
     launch_safe,
     shell,
     shell_safe,
-    determineNumberOfCPUs,
-    build_and_log,
 )
 
-
 __all__ = [
     "attributes",
     "collect",
@@ -31,18 +30,19 @@
 __name__ = "boutdata"
 
 try:
-    from importlib.metadata import version, PackageNotFoundError
+    from importlib.metadata import PackageNotFoundError, version
 except ModuleNotFoundError:
-    from importlib_metadata import version, PackageNotFoundError
+    from importlib_metadata import PackageNotFoundError, version
 try:
     # This gives the version if the boutdata package was installed
     __version__ = version(__name__)
 except PackageNotFoundError:
     # This branch handles the case when boutdata is used from the git repo
     try:
-        from setuptools_scm import get_version
         from pathlib import Path
 
+        from setuptools_scm import get_version
+
         path = Path(__file__).resolve()
         __version__ = get_version(root="..", relative_to=path)
     except (ModuleNotFoundError, LookupError):

src/boutdata/collect.py

@@ -1,11 +1,11 @@
+import glob
 import os
 import sys
-import glob
 
 import numpy as np
 
-from boututils.datafile import DataFile
 from boututils.boutarray import BoutArray
+from boututils.datafile import DataFile
 
 
 def findVar(varname, varlist):

src/boutdata/data.py

@@ -4,61 +4,44 @@
 
 """
 
-from collections import OrderedDict
 import copy
 import glob
 import io
-import numpy
 import os
 import re
+from collections import OrderedDict, UserDict
+from multiprocessing import Pipe, Process, RawArray
 
-from multiprocessing import Process, Pipe, RawArray
+import numpy
+
+# These are imported to be used by 'eval' in
+# BoutOptions.evaluate_scalar() and BoutOptionsFile.evaluate().
+# Change the names to match those used by C++/BOUT++
+from numpy import abs as abs  # noqa: F401
+from numpy import arccos as acos  # noqa: F401
+from numpy import arccosh as acosh  # noqa: F401
+from numpy import arcsin as asin  # noqa: F401
+from numpy import arcsinh as asinh  # noqa: F401
+from numpy import arctan as atan  # noqa: F401
+from numpy import arctan2 as atan2  # noqa: F401
+from numpy import arctanh as atanh  # noqa: F401
+from numpy import ceil, cos, cosh, exp, floor, log, log10, pi  # noqa: F401
+from numpy import power as pow  # noqa: F401
+from numpy import round, sin, sinh, sqrt, tan, tanh  # noqa: F401
 
 from boutdata.collect import (
-    collect,
-    create_cache,
-    findVar,
     _check_fieldperp_attributes,
     _collect_from_one_proc,
     _get_grid_info,
+    collect,
+    create_cache,
+    findVar,
 )
 from boututils.boutarray import BoutArray
 from boututils.boutwarnings import alwayswarn
 from boututils.datafile import DataFile
 from boututils.run_wrapper import determineNumberOfCPUs
 
-# These are imported to be used by 'eval' in
-# BoutOptions.evaluate_scalar() and BoutOptionsFile.evaluate().
-# Change the names to match those used by C++/BOUT++
-from numpy import (  # noqa: F401
-    pi,
-    sin,
-    cos,
-    tan,
-    arccos as acos,
-    arcsin as asin,
-    arctan as atan,
-    arctan2 as atan2,
-    sinh,
-    cosh,
-    tanh,
-    arcsinh as asinh,
-    arccosh as acosh,
-    arctanh as atanh,
-    exp,
-    log,
-    log10,
-    power as pow,
-    sqrt,
-    ceil,
-    floor,
-    round,
-    abs,
-)
-
-
-from collections import UserDict
-
 
 class CaseInsensitiveDict(UserDict):
     def __missing__(self, key):
@@ -1345,11 +1328,12 @@ def redistribute(self, npes, nxpe=None, mxg=2, myg=2, include_restarts=True):
             redistribute the restart files also (default: True)
 
         """
+        from os import mkdir, path, rename
+
         from boutdata.processor_rearrange import (
-            get_processor_layout,
             create_processor_layout,
+            get_processor_layout,
         )
-        from os import rename, path, mkdir
 
         # use get_processor_layout to get nx, ny
         old_processor_layout = get_processor_layout(
@@ -1490,9 +1474,10 @@ def redistribute(self, npes, nxpe=None, mxg=2, myg=2, include_restarts=True):
 
         if include_restarts:
             print("processing restarts")
-            from boutdata import restart
             from glob import glob
 
+            from boutdata import restart
+
             restart_prefix = "BOUT.restart"
             restarts_list = glob(path.join(self._path, restart_prefix + "*"))
 

src/boutdata/griddata.py

@@ -2,9 +2,9 @@
 
 """
 
-from numpy import ndarray, zeros, concatenate, linspace, amin, amax
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
+from numpy import amax, amin, concatenate, linspace, ndarray, zeros
 
 from boututils.datafile import DataFile
 

src/boutdata/input.py

@@ -2,8 +2,8 @@
 
 """
 
-from numpy.fft import rfft
 from numpy import ndarray
+from numpy.fft import rfft
 
 
 def transform3D(arr):

src/boutdata/mayavi2.py

@@ -1,8 +1,7 @@
 import numpy as np
-from numpy import cos, sin, pi
-
-from enthought.tvtk.api import tvtk
 from enthought.mayavi.scripts import mayavi2
+from enthought.tvtk.api import tvtk
+from numpy import cos, pi, sin
 
 
 def aligned_points(grid, nz=1, period=1.0, maxshift=0.4):
@@ -74,8 +73,8 @@ def create_grid(grid, data, period=1):
 
 @mayavi2.standalone
 def view3d(sgrid):
+    from enthought.mayavi.modules.api import GridPlane, Outline
     from enthought.mayavi.sources.vtk_data_source import VTKDataSource
-    from enthought.mayavi.modules.api import Outline, GridPlane
 
     mayavi2.new_scene()
     src = VTKDataSource(data=sgrid)

src/boutdata/mms.py

@@ -3,9 +3,8 @@
 
 """
 
-from sympy import symbols, cos, sin, diff, sqrt, pi, simplify, trigsimp, integrate, Wild
-
 from numpy import arange, zeros
+from sympy import Wild, cos, diff, integrate, pi, simplify, sin, sqrt, symbols, trigsimp
 
 # Constants
 qe = 1.602e-19

src/boutdata/pol_slice.py

@@ -1,7 +1,8 @@
-from boututils.datafile import DataFile
 import numpy as np
 from scipy.ndimage import map_coordinates
 
+from boututils.datafile import DataFile
+
 
 def pol_slice(var3d, gridfile, n=1, zangle=0.0, nyInterp=None):
     """Takes a 3D variable, and returns a 2D slice at fixed toroidal angle

src/boutdata/processor_rearrange.py

@@ -3,8 +3,8 @@
 
 """
 
-from math import sqrt
 from collections import namedtuple
+from math import sqrt
 
 processor_layout_ = namedtuple(
     "BOUT_processor_layout",

src/boutdata/restart.py

@@ -8,23 +8,22 @@
 
 """
 
-import os
 import glob
-
-from boutdata.collect import collect, create_cache
-from boututils.datafile import DataFile
-from boututils.boutarray import BoutArray
-from boutdata.processor_rearrange import get_processor_layout, create_processor_layout
-
 import multiprocessing
-from natsort import natsorted
+import os
+
 import numpy as np
-from numpy import mean, zeros, arange
+from natsort import natsorted
+from numpy import arange, mean, zeros
 from numpy.random import normal
-
 from scipy.interpolate import interp1d
 
 from boutdata import shiftz
+from boutdata.collect import collect, create_cache
+from boutdata.processor_rearrange import create_processor_layout, get_processor_layout
+from boututils.boutarray import BoutArray
+from boututils.datafile import DataFile
+
 from . import griddata
 
 try:

src/boutdata/shiftz.py

@@ -1,5 +1,4 @@
-from numpy import ndarray, pi, cos, sin
-from numpy import fft
+from numpy import cos, fft, ndarray, pi, sin
 
 
 def shiftz(var, zangle, zperiod=1.0):

src/boutdata/squashoutput.py

@@ -110,15 +110,17 @@ def squashoutput(
         is used.
     """
     # use local imports to allow fast import for tab-completion
-    from boutdata.data import BoutOutputs
-    from boututils.datafile import DataFile
-    from boututils.boutarray import BoutArray
-    import numpy
-    import os
     import gc
-    import tempfile
-    import shutil
     import glob
+    import os
+    import shutil
+    import tempfile
+
+    import numpy
+
+    from boutdata.data import BoutOutputs
+    from boututils.boutarray import BoutArray
+    from boututils.datafile import DataFile
 
     try:
         # If we are using the netCDF4 module (the usual case) set caching to zero, since

src/boutdata/tests/make_test_data.py

@@ -1,6 +1,7 @@
 from copy import copy
-from netCDF4 import Dataset
+
 import numpy as np
+from netCDF4 import Dataset
 
 field3d_t_list = ["field3d_t_1", "field3d_t_2"]
 field3d_list = ["field3d_1", "field3d_2"]

src/boutdata/tests/test_boutoptions.py

@@ -1,7 +1,8 @@
-from boutdata.data import BoutOptions
+import textwrap
 
 import pytest
-import textwrap
+
+from boutdata.data import BoutOptions
 
 
 def test_getSection_nonexistent():