Merge branch '853-include-new-task-metadata-in-manifest' of github.com:fractal-analytics-platform/fractal-tasks-core into 853-include-new-task-metadata-in-manifest

Author: tcompa

fractal_tasks_core/__FRACTAL_MANIFEST__.json

@@ -5,6 +5,10 @@
       "name": "Convert Cellvoyager to OME-Zarr",
       "category": "Conversion",
       "modality": "HCS",
+      "tags": [
+        "Yokogawa",
+        "Cellvoyager"
+      ],
       "executable_non_parallel": "tasks/cellvoyager_to_ome_zarr_init.py",
       "executable_parallel": "tasks/cellvoyager_to_ome_zarr_compute.py",
       "meta_non_parallel": {
@@ -269,6 +273,10 @@
       "name": "Convert Cellvoyager Multiplexing to OME-Zarr",
       "category": "Conversion",
       "modality": "HCS",
+      "tags": [
+        "Yokogawa",
+        "Cellvoyager"
+      ],
       "executable_non_parallel": "tasks/cellvoyager_to_ome_zarr_init_multiplex.py",
       "executable_parallel": "tasks/cellvoyager_to_ome_zarr_compute.py",
       "meta_non_parallel": {
@@ -555,6 +563,11 @@
       "output_types": {
         "is_3D": false
       },
+      "category": "Image Processing",
+      "modality": "HCS",
+      "tags": [
+        "Preprocessing"
+      ],
       "executable_non_parallel": "tasks/copy_ome_zarr_hcs_plate.py",
       "executable_parallel": "tasks/projection.py",
       "meta_non_parallel": {
@@ -676,6 +689,10 @@
       "output_types": {
         "illumination_corrected": true
       },
+      "category": "Image Processing",
+      "tags": [
+        "Preprocessing"
+      ],
       "executable_parallel": "tasks/illumination_correction.py",
       "meta_parallel": {
         "cpus_per_task": 1,
@@ -741,6 +758,11 @@
     {
       "name": "Cellpose Segmentation",
       "category": "Segmentation",
+      "tags": [
+        "Deep Learning",
+        "Convolutional Neural Network",
+        "Instance Segmentation"
+      ],
       "executable_parallel": "tasks/cellpose_segmentation.py",
       "meta_parallel": {
         "cpus_per_task": 4,
@@ -1036,6 +1058,10 @@
     {
       "name": "Calculate Registration (image-based)",
       "category": "Registration",
+      "modality": "HCS",
+      "tags": [
+        "Multiplexing"
+      ],
       "executable_non_parallel": "tasks/image_based_registration_hcs_init.py",
       "executable_parallel": "tasks/calculate_registration_image_based.py",
       "meta_non_parallel": {
@@ -1168,6 +1194,10 @@
     {
       "name": "Find Registration Consensus",
       "category": "Registration",
+      "modality": "HCS",
+      "tags": [
+        "Multiplexing"
+      ],
       "executable_non_parallel": "tasks/init_group_by_well_for_multiplexing.py",
       "executable_parallel": "tasks/find_registration_consensus.py",
       "meta_non_parallel": {
@@ -1271,6 +1301,10 @@
         "registered": true
       },
       "category": "Registration",
+      "modality": "HCS",
+      "tags": [
+        "Multiplexing"
+      ],
       "executable_parallel": "tasks/apply_registration_to_image.py",
       "meta_parallel": {
         "cpus_per_task": 1,
@@ -1386,6 +1420,7 @@
     },
     {
       "name": "Napari Workflows Wrapper",
+      "category": "Measurement",
       "executable_parallel": "tasks/napari_workflows_wrapper.py",
       "meta_parallel": {
         "cpus_per_task": 8,
@@ -1548,5 +1583,5 @@
   ],
   "has_args_schemas": true,
   "args_schema_version": "pydantic_v2",
-  "authors": "Name FIXME, Name FIXME, Name FIXME"
+  "authors": "Fractal Core Team"
 }

fractal_tasks_core/dev/create_manifest.py

@@ -152,5 +152,5 @@ def create_manifest(
 
 if __name__ == "__main__":
     PACKAGE = "fractal_tasks_core"
-    AUTHORS = "Name FIXME, Name FIXME, Name FIXME"
+    AUTHORS = "Fractal Core Team"
     create_manifest(package=PACKAGE, authors=AUTHORS)

fractal_tasks_core/dev/task_list.py

@@ -24,6 +24,7 @@
         meta={"cpus_per_task": 1, "mem": 4000},
         category="Conversion",
         modality="HCS",
+        tags=["Yokogawa", "Cellvoyager"],
     ),
     CompoundTask(
         name="Convert Cellvoyager Multiplexing to OME-Zarr",
@@ -33,6 +34,7 @@
         meta={"cpus_per_task": 1, "mem": 4000},
         category="Conversion",
         modality="HCS",
+        tags=["Yokogawa", "Cellvoyager"],
     ),
     CompoundTask(
         name="Project Image (HCS Plate)",
@@ -42,19 +44,29 @@
         output_types={"is_3D": False},
         meta_init={"cpus_per_task": 1, "mem": 4000},
         meta={"cpus_per_task": 1, "mem": 4000},
+        category="Image Processing",
+        modality="HCS",
+        tags=["Preprocessing"],
     ),
     ParallelTask(
         name="Illumination Correction",
         input_types=dict(illumination_corrected=False),
         executable="tasks/illumination_correction.py",
         output_types=dict(illumination_corrected=True),
         meta={"cpus_per_task": 1, "mem": 4000},
+        category="Image Processing",
+        tags=["Preprocessing"],
     ),
     ParallelTask(
         name="Cellpose Segmentation",
         executable="tasks/cellpose_segmentation.py",
         meta={"cpus_per_task": 4, "mem": 16000, "needs_gpu": True},
         category="Segmentation",
+        tags=[
+            "Deep Learning",
+            "Convolutional Neural Network",
+            "Instance Segmentation",
+        ],
     ),
     CompoundTask(
         name="Calculate Registration (image-based)",
@@ -63,6 +75,8 @@
         meta_init={"cpus_per_task": 1, "mem": 1000},
         meta={"cpus_per_task": 1, "mem": 8000},
         category="Registration",
+        modality="HCS",
+        tags=["Multiplexing"],
     ),
     CompoundTask(
         name="Find Registration Consensus",
@@ -71,6 +85,8 @@
         meta_init={"cpus_per_task": 1, "mem": 1000},
         meta={"cpus_per_task": 1, "mem": 1000},
         category="Registration",
+        modality="HCS",
+        tags=["Multiplexing"],
     ),
     ParallelTask(
         name="Apply Registration to Image",
@@ -79,6 +95,8 @@
         output_types=dict(registered=True),
         meta={"cpus_per_task": 1, "mem": 4000},
         category="Registration",
+        modality="HCS",
+        tags=["Multiplexing"],
     ),
     NonParallelTask(
         name="Import OME-Zarr",
@@ -91,5 +109,6 @@
             "cpus_per_task": 8,
             "mem": 32000,
         },
+        category="Measurement",
     ),
 ]