CI to update the manifest versioning

.github/workflows/update_manifest_versioning.yml

@@ -0,0 +1,17 @@
+name: Update versioning on the manifest
+on:
+  workflow_dispatch:
+
+jobs:
+  update_configuration:
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout
+        uses: actions/checkout@v4
+      - name: install requirements
+        run: pip install -r requirements.txt
+      - name: update all the configurations
+        run: python3 Tools/update_manifest_versioning.py
+      - uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          commit_message: GitHub Action - Update manifest versioning

Tools/update_manifest_versioning.py

@@ -0,0 +1,80 @@
+from ruamel.yaml import YAML
+import sys
+import os
+import pandas as pd
+
+dict_ID_manifest_verseion = {
+                    'Notebook_Augmentor_ZeroCostDL4Mic': 'Augmentor' ,
+                    'Notebook_CARE_2D_ZeroCostDL4Mic': 'CARE (2D)' ,
+                    'Notebook_CARE_3D_ZeroCostDL4Mic': 'CARE (3D)' ,
+                    'Notebook_Cellpose_2D_ZeroCostDL4Mic': 'Cellpose' ,
+                    'Notebook_CycleGAN_2D_ZeroCostDL4Mic': 'CycleGAN' ,
+                    'Notebook_DFCAN_ZeroCostDL4Mic': 'DFCAN 2D' ,
+                    'Notebook_DRMIME_ZeroCostDL4Mic': 'DRMIME' ,
+                    'Notebook_DecoNoising_2D_ZeroCostDL4Mic': 'DecoNoising' ,
+                    'Notebook_Deep-STORM_2D_ZeroCostDL4Mic': 'Deep-STORM' ,
+                    'Notebook_Deep-STORM_2D_ZeroCostDL4Mic_DeepImageJ': 'Deep-STORM BioimageIO' ,
+                    'Notebook_DenoiSeg_2D_ZeroCostDL4Mic': 'DenoiSeg' ,
+                    'Notebook_Detectron2_ZeroCostDL4Mic': 'Detectron 2D' ,
+                    'Notebook_EmbedSeg_2D_ZeroCostDL4Mic': 'EmbedSeg 2D' ,
+                    'Notebook_Interactive_Segmentation_Kaibu_2D_ZeroCostDL4Mic': 'Kaibu' ,
+                    'Notebook_MaskRCNN_ZeroCostDL4Mic': 'MaskRCNN' ,
+                    'Notebook_Noise2Void_2D_ZeroCostDL4Mic': 'Noise2Void (2D)' ,
+                    'Notebook_Noise2Void_3D_ZeroCostDL4Mic': 'Noise2Void (3D)' ,
+                    'Notebook_Quality_Control_ZeroCostDL4Mic': 'Quality_control' ,
+                    'Notebook_RCAN_3D_ZeroCostDL4Mic': '3D RCAN' ,
+                    'Notebook_RetinaNet_ZeroCostDL4Mic': 'RetinaNet' ,
+                    'Notebook_SplineDist_2D_ZeroCostDL4Mic': 'SplineDist (2D)' ,
+                    'Notebook_StarDist_2D_ZeroCostDL4Mic': 'StarDist 2D' ,
+                    'Notebook_StarDist_3D_ZeroCostDL4Mic': 'StarDist 3D' ,
+                    'Notebook_U-Net_2D_ZeroCostDL4Mic': 'U-Net (2D)', 
+                    'Notebook_U-Net_2D_multilabel_ZeroCostDL4Mic': 'U-Net (2D) multilabel',
+                    'Notebook_U-Net_3D_ZeroCostDL4Mic': 'U-Net (3D)' ,
+                    'Notebook_YOLOv2_ZeroCostDL4Mic': 'YOLOv2' ,
+                    'Notebook_fnet_2D_ZeroCostDL4Mic': 'fnet (2D)' ,
+                    'Notebook_fnet_3D_ZeroCostDL4Mic': 'fnet (3D)' ,
+                    'Notebook_pix2pix_2D_ZeroCostDL4Mic': 'pix2pix' ,
+                    'WGAN_ZeroCostDL4Mic.ipynb': 'WGAN 2D' 
+                    }
+
+def main():
+    # Read the information from the manifest
+    with open('manifest.bioimage.io.yaml', 'r') as f:
+        yaml = YAML()
+        yaml.preserve_quotes = True
+        manifest_data = yaml.load(f)
+
+    # Read the versions of the notebooks
+    all_notebook_versions = pd.read_csv('Colab_notebooks/Latest_Notebook_versions.csv', dtype=str)
+
+    # List where the new collection (with versions updates) will be stored
+    new_collection = []
+
+    # We are going to check the elements in the collection from the manifest
+    for element in manifest_data['collection']:
+        new_element = element.copy()
+        # In case it is an application, we need to update the version
+        if element['type'] == 'application' and element['id'] != 'notebook_preview': 
+            # Check the version based on the ID of the notebook
+            notebook_version = all_notebook_versions[all_notebook_versions["Notebook"] == dict_ID_manifest_verseion[element['id']]]['Version'].iloc[0]
+            new_element['version'] = notebook_version
+
+        new_collection.append(new_element)
+
+    # Add the new collection to the manifest
+    manifest_data['collection'] = new_collection
+
+    # Write the new collection
+    with open('manifest.bioimage.io.yaml', 'w') as f:
+        yaml = YAML()
+        yaml.preserve_quotes = True
+        yaml.default_flow_style = False
+        yaml.indent(mapping=2, sequence=4, offset=2)
+        yaml.width = 10e10
+        yaml.dump(manifest_data, f)
+
+if __name__ == '__main__':
+    if len(sys.argv) <= 1:
+        sys.exit(main())
+    else:
+        sys.exit(1)

requirements.txt

@@ -31,6 +31,7 @@ pyasn1
 pydot
 requests
 rsa
+ruamel.yaml
 scikit-image
 scikit-learn
 scipy