update pyclesperanto dependency (#117)

* Update README.md (#114)

Fix napari-hub shield in README

Update News and Citation with eLife data

Update README.md

* remove prototype

---------

Co-authored-by: Cyril Achard <[email protected]>

Author: StRigaud

conda/napari_CellSeg3D_ARM64.yml

@@ -18,7 +18,7 @@ dependencies:
         - monai[nibabel, einops]>=0.9.0
         - tqdm
         - scikit-image
-        - pyclesperanto-prototype
+        - pyclesperanto
         - tqdm
         - matplotlib
         - napari_cellseg3d

docs/welcome.rst

@@ -168,7 +168,7 @@ This plugin additionally uses the following libraries and software:
 .. _PyTorch: https://pytorch.org/
 .. _MONAI project: https://monai.io/
 .. _on their website: https://docs.monai.io/en/stable/networks.html#nets
-.. _pyclEsperanto: https://github.com/clEsperanto/pyclesperanto_prototype
+.. _pyclEsperanto: https://github.com/clEsperanto/pyclesperanto
 .. _WNet: https://arxiv.org/abs/1711.08506
 
 .. rubric:: References

napari_cellseg3d/code_models/instance_segmentation.py

@@ -6,7 +6,7 @@
 from typing import List
 
 import numpy as np
-import pyclesperanto_prototype as cle
+import pyclesperanto as cle
 from qtpy.QtWidgets import QWidget
 from skimage.measure import label, regionprops
 from skimage.morphology import remove_small_objects
@@ -287,7 +287,7 @@ def voronoi_otsu(
     BASED ON CODE FROM : napari_pyclesperanto_assistant by Robert Haase
     https://github.com/clEsperanto/napari_pyclesperanto_assistant
     Original code at :
-    https://github.com/clEsperanto/pyclesperanto_prototype/blob/master/pyclesperanto_prototype/_tier9/_voronoi_otsu_labeling.py.
+    https://github.com/clEsperanto/pyclesperanto/blob/d1990e28b1da44a7921890b7bd809d522d3198b8/pyclesperanto/_tier7.py#L409-L448.
 
     Args:
         volume (np.ndarray): volume to segment

napari_cellseg3d/dev_scripts/sliding_window_voronoi.py

@@ -1,6 +1,6 @@
 """Test script for sliding window Voronoi-Otsu segmentation.""."""
 import numpy as np
-import pyclesperanto_prototype as cle
+import pyclesperanto as cle
 from tqdm import tqdm
 
 

notebooks/Colab_inference_demo.ipynb

@@ -42,7 +42,7 @@ dependencies = [
     "tqdm",
 #    "nibabel",
 #    "pillow",
-    "pyclesperanto-prototype",
+    "pyclesperanto",
     "tqdm",
     "matplotlib",
     "pydensecrf2",

pyproject.toml

@@ -13,7 +13,7 @@ napari[all]>=0.4.14
 QtPy
 opencv-python>=4.5.5
 pre-commit
-pyclesperanto-prototype>=0.22.0
+pyclesperanto>=0.18.3
 matplotlib>=3.4.1
 ruff
 tifffile>=2022.2.9

requirements.txt

@@ -24,7 +24,7 @@ install_requires =
     itk
     tqdm
     nibabel
-    pyclesperanto-prototype
+    pyclesperanto
     scikit-image
     pillow
     tqdm