Merge pull request #92 from alexdaniel654/rel/v1.1.0

Rel/v1.1.0

Author: alexdaniel654

CHANGELOG.md

@@ -1,5 +1,13 @@
 # Changelog
 
+## [1.1.0] - 2024-07-15
+
+### Added
+* Proper readthedocs documentation
+
+### Fixed
+* A lot of dependency updates
+
 ## [1.0.1] - 2023-09-05
 
 ### Fixed

CITATION.cff

@@ -5,7 +5,7 @@ authors:
   given-names: "Alexander J"
   orcid: "https://orcid.org/0000-0003-2353-3283"
 title: "Segmentation Metrics"
-version: 1.0.1
+version: 1.1.0
 doi: 10.5281/zenodo.6576199
-date-released: 2023-09-05
+date-released: 2024-07-15
 url: "https://github.com/alexdaniel654/Segmentation_Metrics"

README.md

@@ -1,6 +1,6 @@
 # Segmentation Metrics
 [![Python CI](https://github.com/alexdaniel654/Segmentation_Metrics/actions/workflows/python_ci.yml/badge.svg)](https://github.com/alexdaniel654/Segmentation_Metrics/actions/workflows/python_ci.yml) 
-[![Documentation Status](https://readthedocs.org/projects/segmentationmetrics/badge/?version=stable)](https://segmentationmetrics.readthedocs.io/en/stable/?badge=stable)
+[![Documentation Status](https://readthedocs.org/projects/segmentationmetrics/badge/?version=latest)](https://segmentationmetrics.readthedocs.io/en/latest/?badge=latest)
 [![PyPI version](https://badge.fury.io/py/segmentationmetrics.svg)](https://badge.fury.io/py/segmentationmetrics)
 [![Downloads](https://static.pepy.tech/badge/segmentationmetrics)](https://pepy.tech/project/segmentationmetrics)
 [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)

docs/conf.py

@@ -18,8 +18,8 @@
 
 project = 'Segmentation Metrics'
 copyright = f'{datetime.now().year}, Alex Daniel'
-author = 'Alex Daniel'
-release = '1.0.1'
+author = 'Alexander J Daniel'
+release = '1.1.0'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

requirements.txt

@@ -1,6 +1,6 @@
 absl-py==2.1.0
-numpy==1.26.4
+numpy==2.0.0
 pandas==2.2.2
-pytest==8.2.1
-scikit-image==0.21.0
+pytest==8.2.2
+scikit-image==0.24.0
 scipy==1.13.1

segmentationmetrics/surface_distance/metrics.py

@@ -254,13 +254,13 @@ def compute_surface_distances(mask_gt,
     distmap_gt = ndimage.morphology.distance_transform_edt(
         ~borders_gt, sampling=spacing_mm)
   else:
-    distmap_gt = np.Inf * np.ones(borders_gt.shape)
+    distmap_gt = np.inf * np.ones(borders_gt.shape)
 
   if borders_pred.any():
     distmap_pred = ndimage.morphology.distance_transform_edt(
         ~borders_pred, sampling=spacing_mm)
   else:
-    distmap_pred = np.Inf * np.ones(borders_pred.shape)
+    distmap_pred = np.inf * np.ones(borders_pred.shape)
 
   # compute the area of each surface element
   surface_area_map_gt = neighbour_code_to_surface_area[neighbour_code_map_gt]
@@ -348,7 +348,7 @@ def compute_robust_hausdorff(surface_distances, percent):
     perc_distance_gt_to_pred = distances_gt_to_pred[
         min(idx, len(distances_gt_to_pred)-1)]
   else:
-    perc_distance_gt_to_pred = np.Inf
+    perc_distance_gt_to_pred = np.inf
 
   if len(distances_pred_to_gt) > 0:  # pylint: disable=g-explicit-length-test
     surfel_areas_cum_pred = (np.cumsum(surfel_areas_pred) /
@@ -357,7 +357,7 @@ def compute_robust_hausdorff(surface_distances, percent):
     perc_distance_pred_to_gt = distances_pred_to_gt[
         min(idx, len(distances_pred_to_gt)-1)]
   else:
-    perc_distance_pred_to_gt = np.Inf
+    perc_distance_pred_to_gt = np.inf
 
   return max(perc_distance_gt_to_pred, perc_distance_pred_to_gt)
 
@@ -438,6 +438,6 @@ def compute_dice_coefficient(mask_gt, mask_pred):
   """
   volume_sum = mask_gt.sum() + mask_pred.sum()
   if volume_sum == 0:
-    return np.NaN
+    return np.nan
   volume_intersect = (mask_gt & mask_pred).sum()
   return 2*volume_intersect / volume_sum

setup.py

@@ -10,7 +10,7 @@
 
 setup(
     name="segmentationmetrics",
-    version="1.0.1",
+    version="1.1.0",
     description="Binary segmentation accuracy metrics",
     long_description=long_description,
     long_description_content_type="text/markdown",