maint: bump siibra-python veresion

maint: fix deploy script

.github/workflows/deploy-worker-helm-v4.yml

@@ -30,6 +30,10 @@ on:
       WORKER_PATH:
         default: "api.worker.app"
         type: string
+
+      PULL_POLICY:
+        default: IfNotPresent
+        type: string
 
     secrets:
       KUBECONFIG:
@@ -73,6 +77,7 @@ jobs:
             --set sapi.flavor=${{ inputs.FALVOR }} \
             --set sapi.queue=${{ inputs.QUEUE }} \
             --set image.tag=${{ inputs.IMAGE_TAG }} \
+            --set image.pullPolicy=${{ input.PULL_POLICY }} \
             --set sapi.worker=${{ inputs.WORKER_PATH }} \
             --set sapi.resources.flavor=${{ inputs.RESOURCE }} \
             --reuse-values \
@@ -85,6 +90,7 @@ jobs:
             --set sapi.flavor=${{ inputs.FALVOR }} \
             --set sapi.queue=${{ inputs.QUEUE }} \
             --set image.tag=${{ inputs.IMAGE_TAG }} \
+            --set image.pullPolicy=${{ input.PULL_POLICY }} \
             --set sapi.worker=${{ inputs.WORKER_PATH }} \
             --set sapi.resources.flavor=${{ inputs.RESOURCE }} \
             ${{ inputs.DEPLOYMENT_NAME }} \

.github/workflows/docker-img.yml

@@ -208,7 +208,7 @@ jobs:
         - queue: "compounds"
           resource: "low"
         include:
-        - queue: "comopunds"
+        - queue: "compounds"
           resource: 'high'
 
     if:  ${{ github.event_name == 'release' && contains(github.ref, 'rc') }}
@@ -220,6 +220,7 @@ jobs:
       QUEUE: ${{ needs.setup-envvar.outputs.version }}.rc.${{ matrix.queue }}
       IMAGE_TAG: rc-worker
       RESOURCE: ${{ matrix.resource }}
+      PULL_POLICY: Always
     secrets:
       KUBECONFIG: ${{ secrets.KUBECONFIG }}
 
@@ -237,6 +238,7 @@ jobs:
       QUEUE: celery
       IMAGE_TAG: rc-worker-v4
       WORKER_PATH: new_api.worker.app
+      PULL_POLICY: Always
     secrets:
       KUBECONFIG: ${{ secrets.KUBECONFIG }}
 

.helm/siibra-api-v4-worker/Chart.yaml

@@ -21,4 +21,4 @@ version: 0.1.0
 # incremented each time you make changes to the application. Versions are not expected to
 # follow Semantic Versioning. They should reflect the version the application is using.
 # It is recommended to use it with quotes.
-appVersion: "0.3.21-rc3"
+appVersion: "0.3.21-rc3-real"

api/common/data_handlers/compounds/download.py

@@ -84,19 +84,45 @@ def write_model(filename, obj, **kwargs):
                 zipfile.writestr(filename, instance_to_model(obj, **kwargs).json(indent=2))
             except Exception as e:
                 zipfile.writestr(f"{filename}.error.txt", str(e))
-        
+
         def write_desc(filename, obj, **kwargs):
-            if isinstance(obj, _concept.AtlasConcept):
-                try:
+            try:
+                if isinstance(obj, siibra.core.parcellation.region.Region):
+                    space = kwargs.get("space")
+                    assert isinstance(space, _space.Space)
+                    mp = siibra.get_map(obj.parcellation, space, "statistical")
+                    volidx = mp.get_index(obj)
+                    vol = mp.volumes[volidx.volume]
+                    publications = "\n\n".join([
+                        f"[{url.get('citation', 'url')}]({url.get('url')})"
+                        for ds in vol.datasets
+                        for url in ds.urls
+                    ])
+                    desc = "\n\n".join([ds.description for ds in vol.datasets])
+                    license_list = []
+                    for ds in vol.datasets:
+                        if isinstance(ds.LICENSE, list):
+                            license_list.extend(ds.LICENSE)
+                        if isinstance(ds.LICENSE, str):
+                            license_list.append(ds.LICENSE)
+
+                    license = "\n\n".join(license_list)
+                    desc_str = DESC.format(name=f"Statistical map of {obj.name} in {space.name}",
+                                           description=desc,
+                                           citations=publications,
+                                           license=license)
+                    zipfile.writestr(filename, desc_str)
+                    return
+                if isinstance(obj, _concept.AtlasConcept):
                     publications = "\n\n".join([f"[{p.get('citation', 'url')}]({p.get('url')})"
                                                 if p.get('url')
                                                 else p.get("citation", "CITATION")
                                                 for p in obj.publications])
                     desc_str = DESC.format(name=obj.name, description=obj.description, citations=publications, license=obj.LICENSE)
                     zipfile.writestr(filename, desc_str)
-                except Exception as e:
-                    zipfile.writestr(f"{filename}.error.txt", str(e))
-
+                    return
+            except Exception as e:
+                zipfile.writestr(f"{filename}.error.txt", str(e))
 
         readme_txt = README.format(siibra_api_version=__version__,
                                    timestamp=str(datetime.now()),
@@ -150,7 +176,7 @@ def write_desc(filename, obj, **kwargs):
                 region_filename = f"{region.key}.nii.gz"
                 regional_map = region.fetch_regional_map(space, siibra.MapType.STATISTICAL)
                 zipfile.writestr(region_filename, gzip.compress(regional_map.to_bytes()))
-                write_desc(f'{region_filename}.info.md', region)
+                write_desc(f'{region_filename}.info.md', region, space=space)
             except Exception as e:
                 zipfile.writestr(f"{region_filename or 'UNKNOWN_REGION'}.error.txt", str(e))
 

requirements/siibra.txt

@@ -1,2 +1,2 @@
-siibra==0.4a82
+siibra==0.4a83
 plotly