first-pass at full flexibility with prelim tests (accordance with pre…

pyproject.toml

@@ -17,14 +17,16 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Bio-Informatics",    
     "Typing :: Typed",
 ]
+include = ["examples"]
 
 [tool.poetry.dependencies]
 # These are the main runtime dependencies.
-python = "^3.10.0"
+python = ">= 3.10.0, < 3.13"
 numpy = [
     {version = "^1.24.2", python = "<3.12"},
     {version = "^1.25", python = ">=3.12"}
 ]
+numpydoc_decorator = { git = "https://github.com/alimanfoo/numpydoc_decorator.git", branch = "main" }
 pandas = "^1.5.3"
 scikit-image = "^0.20.0"
 scipy = "^1.10.1"

spotfishing/__init__.py

@@ -4,12 +4,14 @@
 from ._exceptions import *
 from .detection_result import DetectionResult
 from .detectors import detect_spots_dog, detect_spots_int
+from .dog_transform import DifferenceOfGaussiansTransformation
 
 __author__ = "Vince Reuter"
 __credits__ = ["Vince Reuter", "Kai Sandoval Beckwith"]
 
 __all__ = [
     "ROI_MEAN_INTENSITY_KEY",
+    "DifferenceOfGaussiansTransformation",
     "DimensionalityError",
     "DetectionResult",
     "detect_spots_dog",

spotfishing/_exceptions.py

@@ -3,6 +3,10 @@
 __author__ = "Vince Reuter"
 __credits__ = ["Vince Reuter"]
 
+__all__ = [
+    "DimensionalityError",
+]
+
 
 class DimensionalityError(Exception):
     """Error subtype when dimensionality of something isn't as expected"""

spotfishing/_numeric_types.py

@@ -9,6 +9,6 @@
 
 __all__ = ["NumpyInt", "NumpyFloat", "PixelValue"]
 
-NumpyInt = Union[np.int8, np.int16, np.int32, np.int64]
 NumpyFloat = Union[np.float16, np.float32, np.float64]
+NumpyInt = Union[np.int8, np.int16, np.int32, np.int64]
 PixelValue = Union[np.int8, np.int16]

spotfishing/detection_result.py

@@ -1,8 +1,10 @@
 """Abstraction over the result of application of a spot detection procedure to an input image"""
 
-import dataclasses
+from dataclasses import dataclass
 from typing import TYPE_CHECKING, Iterable
 
+from numpydoc_decorator import doc  # type: ignore[import-untyped]
+
 if TYPE_CHECKING:
     import numpy.typing as npt
     import pandas as pd
@@ -39,21 +41,16 @@
 ]
 
 
-@dataclasses.dataclass(frozen=True)
+@doc(
+    summary="The result of applying spot detection to an input image",
+    parameters=dict(
+        table="A table of detected spot coordinates and measurements",
+        image="The image (after possibly some preprocessing) that was actually used in detection",
+        labels="Array of the same size/shape as the image, with nonnegative integer entries; a zero indicates that the pixel isn't in an ROI, and a nonzero indicates the index of the ROI to which the pixel's been assigned",
+    ),
+)
+@dataclass(frozen=True, kw_only=True)
 class DetectionResult:
-    """
-    The result of applying spot detection to an input image
-
-    Parameters
-    ----------
-    table : pd.DataFrame
-        The table of detected spot coordinates and measurements
-    image : np.ndarray
-        The image (after possibly some preprocessing) that was actually used in detection
-    labels : np.ndarray
-        Array of the same size/shape as the image, with nonnegative integer entries; a zero indicates that the pixel isn't in an ROI, and a nonzero indicates the index of the ROI to which the pixel's been assigned
-    """
-
     table: "pd.DataFrame"
     image: "npt.NDArray[PixelValue]"
     labels: "npt.NDArray[NumpyInt]"