Cleaning

src/amrex/ArrayOfStructs.py

@@ -5,7 +5,6 @@
 Authors: Axel Huebl
 License: BSD-3-Clause-LBNL
 """
-from collections import namedtuple
 
 
 def aos_to_numpy(self, copy=False):
@@ -65,10 +64,6 @@ def aos_to_cupy(self, copy=False):
     """
     import cupy as cp
 
-    SoA_cp = namedtuple(type(self).__name__ + "_cp", ["real", "int"])
-
-    soa_view = SoA_cp([], [])
-
     if self.size() == 0:
         raise ValueError("AoS is empty.")
 

src/amrex/StructOfArrays.py

@@ -25,8 +25,6 @@ def soa_to_numpy(self, copy=False):
         A tuple with real and int components that are each lists
         of 1D numpy arrays.
     """
-    import numpy as np
-
     SoA_np = namedtuple(type(self).__name__ + "_np", ["real", "int"])
 
     soa_view = SoA_np([], [])
@@ -65,8 +63,6 @@ def soa_to_cupy(self, copy=False):
     ImportError
         Raises an exception if cupy is not installed
     """
-    import cupy as cp
-
     SoA_cp = namedtuple(type(self).__name__ + "_cp", ["real", "int"])
 
     soa_view = SoA_cp([], [])

src/amrex/space1d/__init__.py

@@ -37,10 +37,10 @@ def d_decl(x, y, z):
 
 def Print(*args, **kwargs):
     """Wrap amrex::Print() - only the IO processor writes"""
-    if not initialized():
+    if not initialized():  # noqa
         print("warning: Print all - AMReX not initialized")
         print(*args, **kwargs)
-    elif ParallelDescriptor.IOProcessor():
+    elif ParallelDescriptor.IOProcessor():  # noqa
         print(*args, **kwargs)
 
 

src/amrex/space2d/__init__.py

@@ -37,10 +37,10 @@ def d_decl(x, y, z):
 
 def Print(*args, **kwargs):
     """Wrap amrex::Print() - only the IO processor writes"""
-    if not initialized():
+    if not initialized():  # noqa
         print("warning: Print all - AMReX not initialized")
         print(*args, **kwargs)
-    elif ParallelDescriptor.IOProcessor():
+    elif ParallelDescriptor.IOProcessor():  # noqa
         print(*args, **kwargs)
 
 

src/amrex/space3d/__init__.py

@@ -37,10 +37,10 @@ def d_decl(x, y, z):
 
 def Print(*args, **kwargs):
     """Wrap amrex::Print() - only the IO processor writes"""
-    if not initialized():
+    if not initialized():  # noqa
         print("warning: Print all - AMReX not initialized")
         print(*args, **kwargs)
-    elif ParallelDescriptor.IOProcessor():
+    elif ParallelDescriptor.IOProcessor():  # noqa
         print(*args, **kwargs)
 
 

tests/conftest.py

@@ -16,8 +16,9 @@
         except ImportError:
             raise ImportError("AMReX: No 1D, 2D or 3D module found!")
 
+# Import calls MPI_Initialize, if not called already
 if amr.Config.have_mpi:
-    from mpi4py import MPI
+    from mpi4py import MPI  # noqa
 
 # base path for input files
 basepath = os.getcwd()

tests/test_aos.py

@@ -1,7 +1,6 @@
 # -*- coding: utf-8 -*-
 
 import numpy as np
-import pytest
 
 import amrex.space3d as amr
 
@@ -85,6 +84,9 @@ def test_array_interface():
     print(arr)
     print(aos[0], aos[1])
     print("-------")
+    aos[0] = p4
+    assert aos[0].x == 0
+    assert aos[0].y == -5
     aos[0] = p3
     print("array:", arr)
     print("aos[0]:", aos[0], "aos[1]:", aos[1])

tests/test_array4.py

@@ -87,8 +87,10 @@ def test_array4_numba():
     )  # type: numpy.ndarray
 
     # host-to-device copy
-    x_numba = cuda.to_device(x)  # type: numba.cuda.cudadrv.devicearray.DeviceNDArray
-    # x_cupy = cupy.asarray(x_numba)      # type: cupy.ndarray
+    x_numba = cuda.to_device(x)  # noqa
+    #   type is numba.cuda.cudadrv.devicearray.DeviceNDArray
+    # x_cupy = cupy.asarray(x_numba)
+    #   type is cupy.ndarray
 
     # TODO: Implement __cuda_array_interface__ or DLPack in Array4 constructor
     # x_arr = amr.Array4_double(x_numba)  # type: amr.Array4_double

tests/test_basefab.py

@@ -6,7 +6,7 @@
 
 
 def test_basefab():
-    bf = amr.BaseFab_Real()
+    bf = amr.BaseFab_Real()  # noqa
 
 
 def test_basefab_to_host():

tests/test_coordsys.py

@@ -1,8 +1,5 @@
 # -*- coding: utf-8 -*-
 
-import numpy as np
-import pytest
-
 import amrex.space3d as amr
 
 # import amrex.space3d as amr.CoordSys.CoordType as CoordType

tests/test_dim3.py

@@ -1,7 +1,6 @@
 # -*- coding: utf-8 -*-
 
 import numpy as np
-import pytest
 
 import amrex.space3d as amr
 

tests/test_farraybox.py

@@ -4,11 +4,11 @@
 
 
 def test_farraybox():
-    fab = amr.FArrayBox()
+    fab = amr.FArrayBox()  # noqa
 
 
 def test_farraybox_io():
-    fab = amr.FArrayBox()
+    fab = amr.FArrayBox()  # noqa
 
     # https://docs.python.org/3/library/io.html
     # https://gist.github.com/asford/544323a5da7dddad2c9174490eb5ed06#file-test_ostream_example-py

tests/test_geometry.py

@@ -115,7 +115,7 @@ def test_periodic_queries(box, real_box):
     is_periodic = [0, 0, 1]
     gm = Gm(box, real_box, coord, is_periodic)
 
-    pdcity = gm.periodicity()
+    pdcity = gm.periodicity()  # noqa
 
     assert gm.isAnyPeriodic()
     assert not gm.isPeriodic(0) and not gm.isPeriodic(1) and gm.isPeriodic(2)

tests/test_multifab.py

@@ -175,7 +175,7 @@ def set_to_three(array):
 
     # assign 3: loop through boxes and launch kernels
     for mfi in mfab_device:
-        bx = mfi.tilebox().grow(ngv)
+        bx = mfi.tilebox().grow(ngv)  # noqa
         marr = mfab_device.array(mfi)
         marr_numba = cuda.as_cuda_array(marr)
 
@@ -208,7 +208,7 @@ def test_mfab_ops_cuda_cupy(make_mfab_device):
     # assign 3
     with cupyx.profiler.time_range("assign 3 [()]", color_id=0):
         for mfi in mfab_device:
-            bx = mfi.tilebox().grow(ngv)
+            bx = mfi.tilebox().grow(ngv)  # noqa
             marr_cupy = mfab_device.array(mfi).to_cupy(order="C")
             # print(marr_cupy.shape)  # 1, 32, 32, 32
             # print(marr_cupy.dtype)  # float64
@@ -243,7 +243,7 @@ def set_to_five(mm):
             return mm
 
         for mfi in mfab_device:
-            bx = mfi.tilebox().grow(ngv)
+            bx = mfi.tilebox().grow(ngv)  # noqa
             marr_cupy = mfab_device.array(mfi).to_cupy(order="F")
             # print(marr_cupy.shape)  # 32, 32, 32, 1
             # print(marr_cupy.dtype)  # float64
@@ -268,7 +268,7 @@ def set_to_seven(x):
             x[...] = 7.0
 
         for mfi in mfab_device:
-            bx = mfi.tilebox().grow(ngv)
+            bx = mfi.tilebox().grow(ngv)  # noqa
             marr_cupy = mfab_device.array(mfi).to_cupy(order="C")
 
             # write and read into the marr_cupy
@@ -306,7 +306,7 @@ def test_mfab_ops_cuda_pytorch(make_mfab_device):
     amr.Config.gpu_backend != "CUDA", reason="Requires AMReX_GPU_BACKEND=CUDA"
 )
 def test_mfab_ops_cuda_cuml(make_mfab_device):
-    mfab_device = make_mfab_device()
+    mfab_device = make_mfab_device()  # noqa
     # https://github.com/rapidsai/cuml
     # https://github.com/rapidsai/cudf
     #   maybe better for particles as a dataframe test

tests/test_particleContainer.py

@@ -121,7 +121,7 @@ def test_pc_init():
     assert pc.TotalNumberOfParticles() == pc.NumberOfParticlesAtLevel(0) == npart
     assert pc.OK()
 
-    print(f"Finest level = ", pc.finest_level)
+    print(f"Finest level = {pc.finest_level}")
 
     print("Iterate particle boxes & set values")
     # lvl = 0

tests/test_particleTile.py

@@ -119,7 +119,7 @@ def test_ptile_soa():
 
 
 @pytest.mark.skipif(amr.Config.spacedim != 3, reason="Requires AMREX_SPACEDIM = 3")
-def test_ptile_aos():
+def test_ptile_aos_3d():
     pt = amr.ParticleTile_1_1_2_1_default()
     p1 = amr.Particle_1_1()
     p2 = amr.Particle_1_1()

tests/test_periodicity.py

@@ -1,6 +1,5 @@
 # -*- coding: utf-8 -*-
 
-import numpy as np
 import pytest
 
 import amrex.space3d as amr
@@ -19,7 +18,7 @@ def test_periodicity():
     assert obj == non_periodic
 
 
-@pytest.mark.skipif(amr.Config.spacedim == 3, reason="Requires AMREX_SPACEDIM = 3")
+@pytest.mark.skipif(amr.Config.spacedim != 3, reason="Requires AMREX_SPACEDIM = 3")
 def test_periodicity_3d():
     iv = amr.IntVect(1, 0, 1)
     obj = amr.Periodicity(iv)
@@ -32,5 +31,5 @@ def test_periodicity_3d():
 
     bx = obj.domain
     print(bx)
-    v_iv = ob.shift_IntVect
+    v_iv = obj.shift_IntVect
     print(v_iv)

tests/test_podvector.py

@@ -1,8 +1,5 @@
 # -*- coding: utf-8 -*-
 
-import numpy as np
-import pytest
-
 import amrex.space3d as amr
 
 

tests/test_realbox.py

@@ -1,8 +1,5 @@
 # -*- coding: utf-8 -*-
 
-import numpy as np
-import pytest
-
 import amrex.space3d as amr
 from amrex.space3d import RealVect as RV
 from amrex.space3d import XDim3

tests/test_soa.py

@@ -1,7 +1,6 @@
 # -*- coding: utf-8 -*-
 
 import numpy as np
-import pytest
 
 import amrex.space3d as amr