Getting the credits correct (hopefully)

diffsims/__init__.py

@@ -31,20 +31,6 @@
 
 from .sims.diffraction_simulation import DiffractionSimulation
 
-from .utils.atomic_diffraction_generator_support.probe_utils import (
-    ProbeFunction,
-    BesselProbe,
-)
-from .utils.atomic_diffraction_generator_support.fourier_transform import (
-    to_recip,
-    from_recip,
-    get_recip_points,
-    get_DFT,
-)
-from .utils.atomic_diffraction_generator_support.discretise_utils import (
-    get_discretisation,
-)
-
 from . import release_info
 
 __version__ = release_info.version

diffsims/generators/diffraction_generator.py

@@ -36,9 +36,7 @@
     get_vectorized_list_for_atomic_scattering_factors,
     is_lattice_hexagonal,
 )
-from diffsims.utils.atomic_diffraction_generator_support.fourier_transform import (
-    from_recip,
-)
+from diffsims.utils.fourier_transform import from_recip
 
 
 class DiffractionGenerator(object):
@@ -432,7 +430,7 @@ def calculate_ed_data(
         ]
 
         if mode == "kinematic":
-            from diffsims.utils import atomic_diffraction_generator_utils as simlib
+            from diffsims.utils import kinematic_simulation_utils as simlib
         else:
             raise NotImplementedError(
                 "<mode> = %s is not currently supported" % repr(mode)

diffsims/generators/rotation_list_generators.py

@@ -44,7 +44,8 @@
     "triclinic": [180, 360, 0],
 }
 
-def get_list_from_orix(grid,rounding=2):
+
+def get_list_from_orix(grid, rounding=2):
     """
     Converts an orix sample to a rotation list
 
@@ -64,12 +65,13 @@ def get_list_from_orix(grid,rounding=2):
     rotation_list = z.data.tolist()
     i = 0
     while i < len(rotation_list):
-        rotation_list[i] = tuple(np.round(rotation_list[i],decimals=rounding))
+        rotation_list[i] = tuple(np.round(rotation_list[i], decimals=rounding))
         i += 1
 
     return rotation_list
 
-def get_fundamental_zone_grid(resolution=2, point_group=None,space_group=None):
+
+def get_fundamental_zone_grid(resolution=2, point_group=None, space_group=None):
     """
     Generates an equispaced grid of rotations within a fundamental zone.
 
@@ -88,10 +90,11 @@ def get_fundamental_zone_grid(resolution=2, point_group=None,space_group=None):
         Grid of rotations lying within the specified fundamental zone
     """
 
-    orix_grid = get_sample_fundamental(resolution=resolution,space_group=space_group)
-    rotation_list = get_list_from_orix(orix_grid,rounding=2)
+    orix_grid = get_sample_fundamental(resolution=resolution, space_group=space_group)
+    rotation_list = get_list_from_orix(orix_grid, rounding=2)
     return rotation_list
 
+
 def get_local_grid(resolution=2, center=None, grid_width=10):
     """
     Generates a grid of rotations about a given rotation
@@ -112,10 +115,13 @@ def get_local_grid(resolution=2, center=None, grid_width=10):
     -------
     rotation_list : list of tuples
     """
-    orix_grid =  get_sample_local(resolution=resolution, center=center, grid_width=grid_width)
-    rotation_list = get_list_from_orix(orix_grid,rounding=2)
+    orix_grid = get_sample_local(
+        resolution=resolution, center=center, grid_width=grid_width
+    )
+    rotation_list = get_list_from_orix(orix_grid, rounding=2)
     return rotation_list
 
+
 def get_grid_around_beam_direction(beam_rotation, resolution, angular_range=(0, 360)):
     """
     Creates a rotation list of rotations for which the rotation is about given beam direction

diffsims/generators/zap_map_generator.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2019 The diffsims developers
+# Copyright 2017-2020 The diffsims developers
 #
 # This file is part of diffsims.
 #

diffsims/libraries/structure_library.py

@@ -105,7 +105,9 @@ def from_crystal_systems(
         NotImplementedError:
             "This function has been removed in version 0.3.0, in favour of creation from orientation lists"
         """
-        raise NotImplementedError("This function has been removed in version 0.3.0, in favour of creation from orientation lists")
+        raise NotImplementedError(
+            "This function has been removed in version 0.3.0, in favour of creation from orientation lists"
+        )
 
     def get_library_size(self, to_print=False):
         """

diffsims/sims/diffraction_simulation.py

@@ -148,16 +148,17 @@ def get_diffraction_pattern(self, size=512, sigma=10):
         the order of 0.5nm and a the default size and sigma are used.
         """
         side_length = np.min(np.multiply((size / 2), self.calibration))
-        mask_for_sides = np.all((np.abs(self.coordinates[:, 0:2]) < side_length), axis=1)
-
+        mask_for_sides = np.all(
+            (np.abs(self.coordinates[:, 0:2]) < side_length), axis=1
+        )
 
         spot_coords = np.add(
             self.calibrated_coordinates[mask_for_sides], size / 2
         ).astype(int)
         spot_intens = self.intensities[mask_for_sides]
         pattern = np.zeros([size, size])
-        #checks that we have some spots
-        if spot_intens.shape[0]==0:
+        # checks that we have some spots
+        if spot_intens.shape[0] == 0:
             return pattern
         else:
             pattern[spot_coords[:, 0], spot_coords[:, 1]] = spot_intens

diffsims/tests/test_generators/test_rotation_list_generator.py

@@ -22,11 +22,20 @@
     get_local_grid,
     get_grid_around_beam_direction,
     get_fundamental_zone_grid,
-    get_beam_directions_grid
-    )
+    get_beam_directions_grid,
+)
 
-@pytest.mark.parametrize("grid",[pytest.param(get_local_grid(resolution=30,center=None,grid_width=35),marks=pytest.mark.xfail(reason="Downstream bug")),
-                                 get_fundamental_zone_grid(space_group=20, resolution=20)])
+
+@pytest.mark.parametrize(
+    "grid",
+    [
+        pytest.param(
+            get_local_grid(resolution=30, center=None, grid_width=35),
+            marks=pytest.mark.xfail(reason="Downstream bug"),
+        ),
+        get_fundamental_zone_grid(space_group=20, resolution=20),
+    ],
+)
 def test_get_grid(grid):
     assert isinstance(grid, list)
     assert len(grid) > 0
@@ -40,7 +49,19 @@ def test_get_grid_around_beam_direction():
     assert isinstance(grid_simple[0], tuple)
     assert len(grid_simple) == 360
 
-@pytest.mark.parametrize("crystal_system",['cubic','hexagonal','trigonal','tetragonal','orthorhombic','monoclinic','triclinic'])
+
+@pytest.mark.parametrize(
+    "crystal_system",
+    [
+        "cubic",
+        "hexagonal",
+        "trigonal",
+        "tetragonal",
+        "orthorhombic",
+        "monoclinic",
+        "triclinic",
+    ],
+)
 def test_get_beam_directions_grid(crystal_system):
-    for equal in ["angle","area"]:
-        _  = get_beam_directions_grid(crystal_system, 5, equal=equal)
+    for equal in ["angle", "area"]:
+        _ = get_beam_directions_grid(crystal_system, 5, equal=equal)

diffsims/tests/test_generators/test_zap_map_generator.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2019 The diffsims developers
+# Copyright 2017-2020 The diffsims developers
 #
 # This file is part of diffsims.
 #

diffsims/tests/test_library/test_structure_library.py

@@ -43,12 +43,15 @@ def test_from_orientations_method():
     np.testing.assert_equal(library.struct_lib["a"], (1, 3))
     np.testing.assert_equal(library.struct_lib["b"], (2, 4))
 
+
 @pytest.mark.xfail(reason="Functionality removed")
 def test_from_systems_methods():
     identifiers = ["a", "b"]
     structures = [1, 2]
     systems = ["cubic", "hexagonal"]
-    library = StructureLibrary.from_crystal_systems(identifiers, structures, systems, resolution=2)
+    library = StructureLibrary.from_crystal_systems(
+        identifiers, structures, systems, resolution=2
+    )
 
 
 @pytest.mark.parametrize(

diffsims/tests/test_sims/test_diffraction_simulation.py

@@ -167,7 +167,7 @@ def test_assertion_free_get_diffraction_pattern(self):
         )
 
         z = short_sim.get_diffraction_pattern()
-        
+
         empty_sim = DiffractionSimulation(
             coordinates=np.asarray([[0.3, 1000, 0]]),
             intensities=np.ones(1),

diffsims/tests/test_utils/test_atomic_diffraction_generator_utils.py

@@ -1,8 +1,20 @@
-"""
-Created on 3 Nov 2019
-
-@author: Rob Tovey
-"""
+# -*- coding: utf-8 -*-
+# Copyright 2017-2020 The diffsims developers
+#
+# This file is part of diffsims.
+#
+# diffsims is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# diffsims is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with diffsims.  If not, see <http://www.gnu.org/licenses/>.
 
 import pytest
 import numpy as np

diffsims/tests/test_utils/test_discretise_utils.py

@@ -1,12 +1,24 @@
-"""
-Created on 1 Nov 2019
-
-@author: Rob Tovey
-"""
+# -*- coding: utf-8 -*-
+# Copyright 2017-2020 The diffsims developers
+#
+# This file is part of diffsims.
+#
+# diffsims is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# diffsims is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with diffsims.  If not, see <http://www.gnu.org/licenses/>.
 
 import pytest
 import numpy as np
-from diffsims.utils.atomic_diffraction_generator_support.discretise_utils import (
+from diffsims.utils.discretise_utils import (
     get_atoms,
     get_discretisation,
     _CUDA,

diffsims/tests/test_utils/test_fourier_transform.py

@@ -1,12 +1,24 @@
-"""
-Created on 2 Nov 2019
-
-@author: Rob Tovey
-"""
+# -*- coding: utf-8 -*-
+# Copyright 2017-2020 The diffsims developers
+#
+# This file is part of diffsims.
+#
+# diffsims is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# diffsims is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with diffsims.  If not, see <http://www.gnu.org/licenses/>.
 
 import pytest
 import numpy as np
-from diffsims.utils.atomic_diffraction_generator_support.fourier_transform import (
+from diffsims.utils.fourier_transform import (
     plan_fft,
     plan_ifft,
     fftn,
@@ -21,9 +33,7 @@
     get_DFT,
     convolve,
 )
-from diffsims.utils.atomic_diffraction_generator_support.discretise_utils import (
-    get_atoms,
-)
+from diffsims.utils.discretise_utils import get_atoms
 
 
 def _toMesh(x):

diffsims/tests/test_utils/test_generic_utils.py

@@ -1,11 +1,23 @@
-"""
-Created on 3 Dec 2019
-
-@author: Rob Tovey
-"""
+# -*- coding: utf-8 -*-
+# Copyright 2017-2020 The diffsims developers
+#
+# This file is part of diffsims.
+#
+# diffsims is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# diffsims is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with diffsims.  If not, see <http://www.gnu.org/licenses/>.
 
 import pytest
-from diffsims.utils.atomic_diffraction_generator_support.generic_utils import (
+from diffsims.utils.generic_utils import (
     GLOBAL_BOOL,
     get_grid,
     to_mesh,