Move to 3.5.4 version

BiaPyX · Oct 10, 2024 · 4cb6490 · 4cb6490
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Showing 26 changed files with 29 additions and 30 deletions.
diff --git a/biapy/__init__.py b/biapy/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "3.5.3"
+__version__ = "3.5.4"
 
 import argparse
 import os

diff --git a/biapy/utils/env/Dockerfile b/biapy/utils/env/Dockerfile
@@ -31,14 +31,14 @@ RUN conda update -qy conda \
 SHELL ["conda", "run", "-n", "BiaPy_env", "/bin/bash", "-c"]
 
 # Install BiaPy
-RUN pip install biapy==3.5.3
+RUN pip install biapy==3.5.4
 
 # Install Pytorch 2.2.0 + CUDA 11.8
 RUN pip install torch==2.4.0 torchvision==0.19.0 torchaudio==2.4.0 --index-url https://download.pytorch.org/whl/cu118 
 RUN pip install timm pytorch-msssim torchmetrics[image]
 
 # Clone BiaPy, as running it with python -c "" stops the container with no error after a few seconds running 
- RUN git clone --depth 1 https://github.com/BiaPyX/BiaPy.git  --branch v3.5.3 /installations/BiaPy
+ RUN git clone --depth 1 https://github.com/BiaPyX/BiaPy.git  --branch v3.5.4 /installations/BiaPy
 
 # This time clone the last commit (25729c ; v3.5.2) as some minor bugs were solved but not created a new release yet
 #RUN git clone --depth 1 https://github.com/BiaPyX/BiaPy.git /installations/BiaPy

diff --git a/biapy/utils/env/Dockerfile_CUDA10.2 b/biapy/utils/env/Dockerfile_CUDA10.2
@@ -32,14 +32,14 @@ RUN conda update -qy conda \
 SHELL ["conda", "run", "-n", "BiaPy_env", "/bin/bash", "-c"]
 
 # Install BiaPy
-RUN pip install biapy==3.5.3
+RUN pip install biapy==3.5.4
 
 # Install Pytorch 1.12.1 + CUDA 10.2
 RUN conda install pytorch==1.12.1 torchvision==0.13.1 torchaudio==0.12.1 cudatoolkit=10.2 -c pytorch
 RUN pip install timm pytorch-msssim torchmetrics[image]
 
 # Clone BiaPy, as running it with python -c "" stops the container with no error after a few seconds running
-RUN git clone --depth 1 https://github.com/BiaPyX/BiaPy.git  --branch v3.5.3 /installations/BiaPy
+RUN git clone --depth 1 https://github.com/BiaPyX/BiaPy.git  --branch v3.5.4 /installations/BiaPy
 # This time clone the last commit (25729c ; v3.5.2) as some minor bugs were solved but not created a new release yet
 # RUN git clone --depth 1 https://github.com/BiaPyX/BiaPy.git /installations/BiaPy
 

diff --git a/biapy/utils/scripts/export_bmz_test.py b/biapy/utils/scripts/export_bmz_test.py
@@ -1,4 +1,3 @@
-import os
 import sys
 import argparse
 
@@ -34,7 +33,7 @@
 
 # import pdb; pdb.set_trace()
 if args["reuse_original_bmz_config"]:
-    biapy.export_model_to_bmz("/data/dfranco/bmz_check", reuse_original_bmz_config=True)
+    biapy.export_model_to_bmz(args["bmz_folder"], reuse_original_bmz_config=True)
 else:
     # Create a dict with all BMZ requirements
     bmz_cfg = {}

diff --git a/biapy/utils/scripts/run_checks.py b/biapy/utils/scripts/run_checks.py
@@ -75,9 +75,9 @@
     "yaml": "test_5.yaml",
     "internal_checks": [
         {"type": "DatasetMatching", "pattern": "DatasetMatching(criterion='iou', thresh=0.3,", "nApparition": 1, "metric": "f1",
-            "gt": True, "value": 0.6},
+            "gt": True, "value": 0.55},
         {"type": "DatasetMatching", "pattern": "DatasetMatching(criterion='iou', thresh=0.3,", "nApparition": 2, "metric": "f1",
-            "gt": True, "value": 0.6}, # Post-processing
+            "gt": True, "value": 0.55}, # Post-processing
     ]
 }
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "biapy"
-version = "3.5.3"
+version = "3.5.4"
 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: 3.5.3
+# BiaPy version: 3.5.4
 
 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: 3.5.3
+# BiaPy version: 3.5.4
 
 SYSTEM:
     NUM_CPUS: -1

diff --git a/templates/classification/3d_classification.yaml b/templates/classification/3d_classification.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.5.3
+# BiaPy version: 3.5.4
 
 SYSTEM:
     NUM_CPUS: -1

diff --git a/templates/denoising/2d_denoising.yaml b/templates/denoising/2d_denoising.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.5.3
+# BiaPy version: 3.5.4
 # 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: 3.5.3
+# BiaPy version: 3.5.4
 # 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: 3.5.3
+# BiaPy version: 3.5.4
 
 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: 3.5.3                                                                                                  
+# BiaPy version: 3.5.4                                                                                                  
 
 SYSTEM:
     NUM_CPUS: -1

diff --git a/templates/detection/3d_detection.yaml b/templates/detection/3d_detection.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.5.3
+# BiaPy version: 3.5.4
 
 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: 3.5.3
+# BiaPy version: 3.5.4
 
 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: 3.5.3
+# BiaPy version: 3.5.4
 
 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: 3.5.3
+# BiaPy version: 3.5.4
 
 SYSTEM:
     NUM_CPUS: -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: 3.5.3
+# BiaPy version: 3.5.4
 
 SYSTEM:
     NUM_CPUS: -1

diff --git a/templates/self-supervised/2d_self-supervised.yaml b/templates/self-supervised/2d_self-supervised.yaml
@@ -1,4 +1,4 @@
-# BiaPy version: 3.5.3
+# BiaPy version: 3.5.4
 
 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: 3.5.3
+# BiaPy version: 3.5.4
 
 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: 3.5.3
+# BiaPy version: 3.5.4
 
 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: 3.5.3
+# BiaPy version: 3.5.4
 
 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: 3.5.3
+# BiaPy version: 3.5.4
 
 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: 3.5.3
+# BiaPy version: 3.5.4
 
 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: 3.5.3
+# BiaPy version: 3.5.4
 
 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: 3.5.3
+# BiaPy version: 3.5.4
 
 SYSTEM:
     NUM_CPUS: -1