Use nopython mode for all jitting (#165)

Author: dstansby

src/cellfinder_core/detect/filters/plane/tile_walker.py

@@ -1,7 +1,7 @@
 import math
 
 import numpy as np
-from numba import jit
+from numba import njit
 
 
 class TileWalker:
@@ -78,7 +78,7 @@ def mark_bright_tiles(self):
                 self.bright_tiles_mask[mask_x, mask_y] = True
 
 
-@jit
+@njit
 def is_low_average(tile: np.ndarray, threshold: float) -> bool:
     """
     Return `True` if the average value of *tile* is below *threshold*.

src/cellfinder_core/detect/filters/volume/ball_filter.py

@@ -1,5 +1,5 @@
 import numpy as np
-from numba import jit
+from numba import njit
 
 from cellfinder_core.tools.array_operations import bin_mean_3d
 from cellfinder_core.tools.geometry import make_sphere
@@ -196,7 +196,7 @@ def walk(self) -> None:  # Highly optimised because most time critical
         )
 
 
-@jit(nopython=True, cache=True)
+@njit(cache=True)
 def _cube_overlaps(
     cube: np.ndarray,
     overlap_threshold: float,
@@ -246,7 +246,7 @@ def _cube_overlaps(
     return current_overlap_value > overlap_threshold
 
 
-@jit(nopython=True)
+@njit
 def _is_tile_to_check(
     x: int,
     y: int,
@@ -263,7 +263,7 @@ def _is_tile_to_check(
     return inside_brain_tiles[x_in_mask, y_in_mask, middle_z]
 
 
-@jit(nopython=True)
+@njit
 def _walk(
     max_height: int,
     max_width: int,

src/cellfinder_core/detect/filters/volume/structure_detection.py

@@ -2,7 +2,7 @@
 from typing import List, Sequence, Tuple, Union
 
 import numpy as np
-from numba import jit
+from numba import njit
 from numba.core import types
 from numba.experimental import jitclass
 from numba.typed import Dict
@@ -16,7 +16,7 @@ class Point:
     z: int
 
 
-@jit(nopython=True)
+@njit
 def get_non_zero_dtype_min(values: np.ndarray) -> int:
     """
     Get the minimum of non-zero entries in *values*.
@@ -31,7 +31,7 @@ def get_non_zero_dtype_min(values: np.ndarray) -> int:
     return min_val
 
 
-@jit(nopython=True)
+@njit
 def traverse_dict(d: dict, a):
     """
     Traverse d, until a is not present as a key.
@@ -278,7 +278,7 @@ def structures_to_cells(self) -> List[Point]:
         return cell_centres
 
 
-@jit
+@njit
 def is_new_structure(neighbour_ids):
     for i in range(len(neighbour_ids)):
         if neighbour_ids[i] != 0: