Move to 3.6.5

danifranco · danifranco · commit 551a26f81eb3 · 2025-09-06T10:22:35.000+02:00
diff --git a/biapy/__init__.py b/biapy/__init__.py
@@ -11,10 +11,10 @@
 exposing the `BiaPy` class and defining the `main` function for command-line
 execution.
 
-Version: 3.6.4
+Version: 3.6.5
 """
 
-__version__ = "3.6.4"
+__version__ = "3.6.5"
 
 import argparse
 import os
diff --git a/biapy/utils/env/conda_forge_meta.yaml b/biapy/utils/env/conda_forge_meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "biapy" %}
-{% set version = "3.6.4" %}
+{% set version = "3.6.5" %}
 {% set python_min = "3.10" %}
 
 package:
diff --git a/pyproject.toml b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "biapy"
-version = "3.6.4"
+version = "3.6.5"
 description = "BiaPy: Bioimage analysis pipelines in Python"
 readme = "README.md"
 requires-python = ">=3.10"
diff --git a/templates/classification/2d_classification.yaml b/templates/classification/2d_classification.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.6.4
+# BiaPy version: 3.6.5
 
 SYSTEM:
     NUM_CPUS: -1
diff --git a/templates/classification/2d_classification_rgb.yaml b/templates/classification/2d_classification_rgb.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.6.4
+# BiaPy version: 3.6.5
 
 SYSTEM:
     NUM_CPUS: -1
diff --git a/templates/classification/3d_classification.yaml b/templates/classification/3d_classification.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.6.4
+# BiaPy version: 3.6.5
 
 SYSTEM:
     NUM_CPUS: -1
diff --git a/templates/denoising/2d_denoising.yaml b/templates/denoising/2d_denoising.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.6.4
+# BiaPy version: 3.6.5
 # We try to mimic here N2Void project parameters 
 SYSTEM:
     NUM_CPUS: -1
diff --git a/templates/denoising/3d_denoising.yaml b/templates/denoising/3d_denoising.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.6.4
+# BiaPy version: 3.6.5
 # We try to mimic here N2Void project parameters 
 
 SYSTEM:
diff --git a/templates/detection/2d_detection.yaml b/templates/detection/2d_detection.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.6.4
+# BiaPy version: 3.6.5
 
 SYSTEM:
     NUM_CPUS: -1
diff --git a/templates/detection/3D_cell_detection_zarr_tutorial.yaml b/templates/detection/3D_cell_detection_zarr_tutorial.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.6.4                                                                                                  
+# BiaPy version: 3.6.5                                                                                                  
 
 SYSTEM:
     NUM_CPUS: -1
diff --git a/templates/detection/3d_detection.yaml b/templates/detection/3d_detection.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.6.4
+# BiaPy version: 3.6.5
 
 SYSTEM:
     NUM_CPUS: -1
diff --git a/templates/image-to-image/2d_image-to-image.yaml b/templates/image-to-image/2d_image-to-image.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.6.4
+# BiaPy version: 3.6.5
 
 SYSTEM:
     NUM_CPUS: -1
diff --git a/templates/image-to-image/3d_image-to-image.yaml b/templates/image-to-image/3d_image-to-image.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.6.4
+# BiaPy version: 3.6.5
 
 SYSTEM:
     NUM_CPUS: -1
diff --git a/templates/instance_segmentation/2d_instance_segmentation.yaml b/templates/instance_segmentation/2d_instance_segmentation.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.6.4
+# BiaPy version: 3.6.5
 
 SYSTEM:
     NUM_CPUS: -1
@@ -8,7 +8,6 @@ PROBLEM:
     NDIM: 2D
     INSTANCE_SEG:
         DATA_CHANNELS: BC
-        DATA_MW_TH_TYPE: "auto"
   
 DATA: 
     PATCH_SIZE: (256, 256, 1)  
diff --git a/templates/instance_segmentation/3d_instance_segmentation.yaml b/templates/instance_segmentation/3d_instance_segmentation.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.6.4
+# BiaPy version: 3.6.5
 
 SYSTEM:
     NUM_CPUS: -1
@@ -8,7 +8,6 @@ PROBLEM:
     NDIM: 3D
     INSTANCE_SEG:
         DATA_CHANNELS: BC
-        DATA_MW_TH_TYPE: "auto"
   
 DATA: 
     PATCH_SIZE: (20, 128, 128, 1)
diff --git a/templates/instance_segmentation/CartoCell_paper/cartocell_inference_latest.yaml b/templates/instance_segmentation/CartoCell_paper/cartocell_inference_latest.yaml
@@ -1,4 +1,4 @@
-# CartoCell inference workflow compatible with BiaPy version 3.6.4
+# CartoCell inference workflow compatible with BiaPy version 3.6.5
 
 SYSTEM:
     NUM_CPUS: -1
@@ -10,7 +10,6 @@ PROBLEM:
     NDIM: 3D                    # images are 3D
     INSTANCE_SEG:
         DATA_CHANNELS: BCM              # problem representation: binary masks + contours + foreground mask
-        DATA_MW_TH_TYPE: "auto"         # automatic calculation of threshold per each channel
         DATA_REMOVE_BEFORE_MW: True     # remove objects before watershed
         DATA_REMOVE_SMALL_OBJ_BEFORE: 5 # size of small objects to be removed before watershed
 
diff --git a/templates/instance_segmentation/CartoCell_paper/cartocell_training_latest.yaml b/templates/instance_segmentation/CartoCell_paper/cartocell_training_latest.yaml
@@ -1,4 +1,4 @@
-# CartoCell training workflow compatible with BiaPy version 3.6.4
+# CartoCell training workflow compatible with BiaPy version 3.6.5
 
 SYSTEM:
     NUM_CPUS: -1
@@ -10,7 +10,6 @@ PROBLEM:
     NDIM: 3D                    # images are 3D
     INSTANCE_SEG:
         DATA_CHANNELS: BCM              # problem representation: binary masks + contours + foreground mask
-        DATA_MW_TH_TYPE: "auto"         # automatic calculation of threshold per each channel
         DATA_REMOVE_BEFORE_MW: True     # remove objects before watershed
         DATA_REMOVE_SMALL_OBJ_BEFORE: 5 # size of small objects to be removed before watershed
 
diff --git a/templates/self-supervised/2d_self-supervised.yaml b/templates/self-supervised/2d_self-supervised.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.6.4
+# BiaPy version: 3.6.5
 
 SYSTEM:
     NUM_CPUS: -1
diff --git a/templates/self-supervised/3d_self-supervised.yaml b/templates/self-supervised/3d_self-supervised.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.6.4
+# BiaPy version: 3.6.5
 
 SYSTEM:
     NUM_CPUS: -1
diff --git a/templates/semantic_segmentation/2d_semantic_segmentation.yaml b/templates/semantic_segmentation/2d_semantic_segmentation.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.6.4
+# BiaPy version: 3.6.5
 
 SYSTEM:
     NUM_CPUS: -1
diff --git a/templates/semantic_segmentation/3d_semantic_segmentation.yaml b/templates/semantic_segmentation/3d_semantic_segmentation.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.6.4
+# BiaPy version: 3.6.5
 
 SYSTEM:
     NUM_CPUS: -1
diff --git a/templates/semantic_segmentation/wound_segmentation.yaml b/templates/semantic_segmentation/wound_segmentation.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.6.4
+# BiaPy version: 3.6.5
 
 SYSTEM:
     NUM_CPUS: -1
diff --git a/templates/super-resolution/2d_super-resolution.yaml b/templates/super-resolution/2d_super-resolution.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.6.4
+# BiaPy version: 3.6.5
 
 SYSTEM:
     NUM_CPUS: -1
diff --git a/templates/super-resolution/2d_super-resolution_rgb.yaml b/templates/super-resolution/2d_super-resolution_rgb.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.6.4
+# BiaPy version: 3.6.5
 
 SYSTEM:
     NUM_CPUS: -1
diff --git a/templates/super-resolution/3d_super-resolution.yaml b/templates/super-resolution/3d_super-resolution.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.6.4
+# BiaPy version: 3.6.5
 
 SYSTEM:
     NUM_CPUS: -1

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# BiaPy version: 3.6.4`
	`1`	`+# BiaPy version: 3.6.5`
`2`	`2`
`3`	`3`	`SYSTEM:`
`4`	`4`	`NUM_CPUS: -1`