Refactor packaging, part I

Relates to #75 (closed).

Move all project info to pyproject.toml.

Tasks:

• Static Project Info
• Register and run versioneer
• Register Cython extension modules
• Clean up package data files & manifest
• Remove quicktest action from setup.py and realize quicktests some other way -> introduced quicktest.py

Notes:

• The quicktest command in setup.py uses the distutils command interface, but distutils is deprecated since Python 3.10. We must find some other way to realize quicktests.

pystencils/boundaries/createindexlist.py

@@ -2,26 +2,22 @@ import warnings
 
 import numpy as np
 
+
 try:
-    # Try to import right away - assume compiled code is available
-    # compile with: python setup.py build_ext --inplace --use-cython
-    from pystencils.boundaries.createindexlistcython import create_boundary_neighbor_index_list_2d, \
-        create_boundary_neighbor_index_list_3d, create_boundary_cell_index_list_2d, create_boundary_cell_index_list_3d
+    import pyximport
 
+    pyximport.install(language_level=3)
     cython_funcs_available = True
 except ImportError:
-    try:
-        # If not, try development mode and import via pyximport
-        import pyximport
-
-        pyximport.install(language_level=3)
-        cython_funcs_available = True
-    except ImportError:
-        cython_funcs_available = False
-    if cython_funcs_available:
-        from pystencils.boundaries.createindexlistcython import create_boundary_neighbor_index_list_2d, \
-            create_boundary_neighbor_index_list_3d, create_boundary_cell_index_list_2d, \
-            create_boundary_cell_index_list_3d
+    cython_funcs_available = False
+
+if cython_funcs_available:
+    from pystencils.boundaries.createindexlistcython import (
+        create_boundary_neighbor_index_list_2d,
+        create_boundary_neighbor_index_list_3d,
+        create_boundary_cell_index_list_2d,
+        create_boundary_cell_index_list_3d,
+    )
 
 boundary_index_array_coordinate_names = ["x", "y", "z"]
 direction_member_name = "dir"
@@ -30,40 +26,59 @@ default_index_array_dtype = np.int32
 
 def numpy_data_type_for_boundary_object(boundary_object, dim):
     coordinate_names = boundary_index_array_coordinate_names[:dim]
-    return np.dtype([(name, default_index_array_dtype) for name in coordinate_names]
-                    + [(direction_member_name, default_index_array_dtype)]
-                    + [(i[0], i[1].numpy_dtype) for i in boundary_object.additional_data], align=True)
-
-
-def _create_index_list_python(flag_field_arr, boundary_mask,
-                              fluid_mask, stencil, single_link, inner_or_boundary=False, nr_of_ghost_layers=None):
-
+    return np.dtype(
+        [(name, default_index_array_dtype) for name in coordinate_names]
+        + [(direction_member_name, default_index_array_dtype)]
+        + [(i[0], i[1].numpy_dtype) for i in boundary_object.additional_data],
+        align=True,
+    )
+
+
+def _create_index_list_python(
+    flag_field_arr,
+    boundary_mask,
+    fluid_mask,
+    stencil,
+    single_link,
+    inner_or_boundary=False,
+    nr_of_ghost_layers=None,
+):
     if inner_or_boundary and nr_of_ghost_layers is None:
-        raise ValueError("If inner_or_boundary is set True the number of ghost layers "
-                         "around the inner domain has to be specified")
+        raise ValueError(
+            "If inner_or_boundary is set True the number of ghost layers "
+            "around the inner domain has to be specified"
+        )
 
     if nr_of_ghost_layers is None:
         nr_of_ghost_layers = 0
 
-    coordinate_names = boundary_index_array_coordinate_names[:len(flag_field_arr.shape)]
-    index_arr_dtype = np.dtype([(name, default_index_array_dtype) for name in coordinate_names]
-                               + [(direction_member_name, default_index_array_dtype)])
+    coordinate_names = boundary_index_array_coordinate_names[
+        : len(flag_field_arr.shape)
+    ]
+    index_arr_dtype = np.dtype(
+        [(name, default_index_array_dtype) for name in coordinate_names]
+        + [(direction_member_name, default_index_array_dtype)]
+    )
 
     # boundary cells are extracted via np.where. To ensure continous memory access in the compute kernel these cells
     # have to be sorted.
     boundary_cells = np.transpose(np.nonzero(flag_field_arr == boundary_mask))
     for i in range(len(flag_field_arr.shape)):
-        boundary_cells = boundary_cells[boundary_cells[:, i].argsort(kind='mergesort')]
+        boundary_cells = boundary_cells[boundary_cells[:, i].argsort(kind="mergesort")]
 
     # First a set is created to save all fluid cells which are near boundary
     fluid_cells = set()
     for cell in boundary_cells:
         cell = tuple(cell)
         for dir_idx, direction in enumerate(stencil):
-            neighbor_cell = tuple([cell_i + dir_i for cell_i, dir_i in zip(cell, direction)])
+            neighbor_cell = tuple(
+                [cell_i + dir_i for cell_i, dir_i in zip(cell, direction)]
+            )
             # prevent out ouf bounds access. If boundary cell is at the border, some stencil directions would be out.
-            if any(not 0 + nr_of_ghost_layers <= e < upper - nr_of_ghost_layers
-                   for e, upper in zip(neighbor_cell, flag_field_arr.shape)):
+            if any(
+                not 0 + nr_of_ghost_layers <= e < upper - nr_of_ghost_layers
+                for e, upper in zip(neighbor_cell, flag_field_arr.shape)
+            ):
                 continue
             if flag_field_arr[neighbor_cell] & fluid_mask:
                 fluid_cells.add(neighbor_cell)
@@ -83,9 +98,14 @@ def _create_index_list_python(flag_field_arr, boundary_mask,
         cell = tuple(cell)
         sum_cells = np.zeros(len(cell))
         for dir_idx, direction in enumerate(stencil):
-            neighbor_cell = tuple([cell_i + dir_i for cell_i, dir_i in zip(cell, direction)])
+            neighbor_cell = tuple(
+                [cell_i + dir_i for cell_i, dir_i in zip(cell, direction)]
+            )
             # prevent out ouf bounds access. If boundary cell is at the border, some stencil directions would be out.
-            if any(not 0 <= e < upper for e, upper in zip(neighbor_cell, flag_field_arr.shape)):
+            if any(
+                not 0 <= e < upper
+                for e, upper in zip(neighbor_cell, flag_field_arr.shape)
+            ):
                 continue
             if flag_field_arr[neighbor_cell] & checkmask:
                 if single_link:
@@ -101,8 +121,15 @@ def _create_index_list_python(flag_field_arr, boundary_mask,
     return np.array(result, dtype=index_arr_dtype)
 
 
-def create_boundary_index_list(flag_field, stencil, boundary_mask, fluid_mask,
-                               nr_of_ghost_layers=1, inner_or_boundary=True, single_link=False):
+def create_boundary_index_list(
+    flag_field,
+    stencil,
+    boundary_mask,
+    fluid_mask,
+    nr_of_ghost_layers=1,
+    inner_or_boundary=True,
+    single_link=False,
+):
     """Creates a numpy array storing links (connections) between domain cells and boundary cells.
 
     Args:
@@ -119,11 +146,20 @@ def create_boundary_index_list(flag_field, stencil, boundary_mask, fluid_mask,
     """
     dim = len(flag_field.shape)
     coordinate_names = boundary_index_array_coordinate_names[:dim]
-    index_arr_dtype = np.dtype([(name, default_index_array_dtype) for name in coordinate_names]
-                               + [(direction_member_name, default_index_array_dtype)])
+    index_arr_dtype = np.dtype(
+        [(name, default_index_array_dtype) for name in coordinate_names]
+        + [(direction_member_name, default_index_array_dtype)]
+    )
 
     stencil = np.array(stencil, dtype=default_index_array_dtype)
-    args = (flag_field, nr_of_ghost_layers, boundary_mask, fluid_mask, stencil, single_link)
+    args = (
+        flag_field,
+        nr_of_ghost_layers,
+        boundary_mask,
+        fluid_mask,
+        stencil,
+        single_link,
+    )
     args_no_gl = (flag_field, boundary_mask, fluid_mask, stencil, single_link)
 
     if cython_funcs_available:
@@ -142,22 +178,42 @@ def create_boundary_index_list(flag_field, stencil, boundary_mask, fluid_mask,
         return np.array(idx_list, dtype=index_arr_dtype)
     else:
         if flag_field.size > 1e6:
-            warnings.warn("Boundary setup may take very long! Consider installing cython to speed it up")
-        return _create_index_list_python(*args_no_gl, inner_or_boundary=inner_or_boundary,
-                                         nr_of_ghost_layers=nr_of_ghost_layers)
-
-
-def create_boundary_index_array(flag_field, stencil, boundary_mask, fluid_mask, boundary_object,
-                                nr_of_ghost_layers=1, inner_or_boundary=True, single_link=False):
-    idx_array = create_boundary_index_list(flag_field, stencil, boundary_mask, fluid_mask,
-                                           nr_of_ghost_layers, inner_or_boundary, single_link)
+            warnings.warn(
+                "Boundary setup may take very long! Consider installing cython to speed it up"
+            )
+        return _create_index_list_python(
+            *args_no_gl,
+            inner_or_boundary=inner_or_boundary,
+            nr_of_ghost_layers=nr_of_ghost_layers,
+        )
+
+
+def create_boundary_index_array(
+    flag_field,
+    stencil,
+    boundary_mask,
+    fluid_mask,
+    boundary_object,
+    nr_of_ghost_layers=1,
+    inner_or_boundary=True,
+    single_link=False,
+):
+    idx_array = create_boundary_index_list(
+        flag_field,
+        stencil,
+        boundary_mask,
+        fluid_mask,
+        nr_of_ghost_layers,
+        inner_or_boundary,
+        single_link,
+    )
     dim = len(flag_field.shape)
 
     if boundary_object.additional_data:
         coordinate_names = boundary_index_array_coordinate_names[:dim]
         index_arr_dtype = numpy_data_type_for_boundary_object(boundary_object, dim)
         extended_idx_field = np.empty(len(idx_array), dtype=index_arr_dtype)
-        for prop in coordinate_names + ['dir']:
+        for prop in coordinate_names + ["dir"]:
             extended_idx_field[prop] = idx_array[prop]
 
         idx_array = extended_idx_field