Update all bioimageio.core and bioimageio.spec versions to latest

HenriquesLab · Dec 13, 2024 · 6db67de · 6db67de
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commit 6db67de
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diff --git a/Colab_notebooks/CycleGAN_ZeroCostDL4Mic.ipynb b/Colab_notebooks/CycleGAN_ZeroCostDL4Mic.ipynb
@@ -207,8 +207,8 @@
     "!pip install -q fpdf2==2.8.1\n",
     "\n",
     "# The [bioimageio] extras are installed for bioimageio model support\n",
-    "!pip install -q bioimageio.core==0.6.9\n",
-    "!pip install -q bioimageio.spec==0.5.3.2\n",
+    "!pip install -q bioimageio.core==0.7.0\n",
+    "!pip install -q bioimageio.spec==0.5.3.5\n",
     "\n",
     "# Install an older version of scikit-image\n",
     "# !pip install -q scikit-image==0.18.0\n",

diff --git a/Colab_notebooks/StarDist_2D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/StarDist_2D_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/U-Net_2D_Multilabel_ZeroCostDL4Mic.ipynb b/Colab_notebooks/U-Net_2D_Multilabel_ZeroCostDL4Mic.ipynb
@@ -165,8 +165,8 @@
     "!pip install -q fpdf2==2.8.1\n",
     "\n",
     "# The [bioimageio] extras are installed for bioimageio model support\n",
-    "!pip install -q bioimageio.core==0.6.9\n",
-    "!pip install -q bioimageio.spec==0.5.3.2\n",
+    "!pip install -q bioimageio.core==0.7.0\n",
+    "!pip install -q bioimageio.spec==0.5.3.5\n",
     "\n",
     "# Install fixed version of pydantic to avoid bugs on 2.10.0\n",
     "!pip install -q pydantic==2.9.2\n",

diff --git a/Colab_notebooks/U-Net_2D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/U-Net_2D_ZeroCostDL4Mic.ipynb
@@ -188,8 +188,8 @@
     "!pip install -q fpdf2==2.8.1\n",
     "\n",
     "# The [bioimageio] extras are installed for bioimageio model support\n",
-    "!pip install -q bioimageio.core==0.6.9\n",
-    "!pip install -q bioimageio.spec==0.5.3.2\n",
+    "!pip install -q bioimageio.core==0.7.0\n",
+    "!pip install -q bioimageio.spec==0.5.3.5\n",
     "\n",
     "# Install fixed version of pydantic to avoid bugs on 2.10.0\n",
     "!pip install -q pydantic==2.9.2\n",

diff --git a/Colab_notebooks/pix2pix_ZeroCostDL4Mic.ipynb b/Colab_notebooks/pix2pix_ZeroCostDL4Mic.ipynb
@@ -261,8 +261,8 @@
     "!pip install -q lpips==0.1.4\n",
     "\n",
     "# The [bioimageio] extras are installed for bioimageio model support\n",
-    "!pip install -q bioimageio.core==0.6.9\n",
-    "!pip install -q bioimageio.spec==0.5.3.2\n",
+    "!pip install -q bioimageio.core==0.7.0\n",
+    "!pip install -q bioimageio.spec==0.5.3.5\n",
     "\n",
     "# Install an older version of scikit-image\n",
     "# !pip install -q scikit-image==0.18.0\n",

diff --git a/requirements_files/2D_UNet_multilabel_requirements_simple.txt b/requirements_files/2D_UNet_multilabel_requirements_simple.txt
@@ -1,7 +1,7 @@
 # Requirements for U_Net_2D_Multilabel_ZeroCostDL4Mic.ipynb
 Pillow==11.0.0
-bioimageio.core==0.6.9
-bioimageio.spec==0.5.3.2
+bioimageio.core==0.7.0
+bioimageio.spec==0.5.3.5
 fpdf2==2.8.1
 future==1.0.0
 h5py==3.12.1
@@ -13,6 +13,7 @@ orbax-checkpoint==0.3.0
 pandas==2.2.2
 pathlib==1.0.1
 pip==24.1.2
+pydantic==2.9.2
 requests==2.32.3
 scikit-image==0.24.0
 scikit-learn==1.5.2

diff --git a/requirements_files/2D_UNet_requirements_simple.txt b/requirements_files/2D_UNet_requirements_simple.txt
@@ -1,7 +1,7 @@
 # Requirements for U_Net_2D_ZeroCostDL4Mic.ipynb
 Pillow==11.0.0
-bioimageio.core==0.6.9
-bioimageio.spec==0.5.3.2
+bioimageio.core==0.7.0
+bioimageio.spec==0.5.3.5
 fpdf2==2.8.1
 future==1.0.0
 h5py==3.12.1
@@ -13,6 +13,7 @@ orbax-checkpoint==0.3.0
 pandas==2.2.2
 pathlib==1.0.1
 pip==24.1.2
+pydantic==2.9.2
 requests==2.32.3
 scikit-image==0.24.0
 scikit-learn==1.5.2

diff --git a/requirements_files/3D_UNet_requirements_simple.txt b/requirements_files/3D_UNet_requirements_simple.txt
@@ -14,6 +14,7 @@ orbax-checkpoint==0.3.0
 pandas==2.2.2
 pathlib==1.0.1
 pip==24.1.2
+pydantic==2.9.2
 requests==2.32.3
 scikit-image==0.24.0
 scikit-learn==1.5.2

diff --git a/requirements_files/CycleGAN_requirements_simple.txt b/requirements_files/CycleGAN_requirements_simple.txt
@@ -1,8 +1,8 @@
 # Requirements for CycleGAN_ZeroCostDL4Mic.ipynb
 astropy==6.1.7
 Augmentor==0.2.12
-bioimageio.core==0.6.9
-bioimageio.spec==0.5.3.2
+bioimageio.core==0.7.0
+bioimageio.spec==0.5.3.5
 dominate==2.9.1
 fpdf2==2.8.1
 h5py==3.12.1

diff --git a/requirements_files/pix2pix_requirements_simple.txt b/requirements_files/pix2pix_requirements_simple.txt
@@ -1,8 +1,8 @@
 # Requirements for pix2pix_ZeroCostDL4Mic.ipynb
 astropy==6.1.7
 Augmentor==0.2.12
-bioimageio.core==0.6.9
-bioimageio.spec==0.5.3.2
+bioimageio.core==0.7.0
+bioimageio.spec==0.5.3.5
 dominate==2.9.1
 fpdf2==2.8.1
 h5py==3.12.1