Merge branch 'main' into ngio-projection

tcompa · tcompa · commit c8b050acc7c4 · 2024-11-26T08:46:22.000+01:00
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,6 @@
 **Note**: Numbers like (\#123) point to closed Pull Requests on the fractal-tasks-core repository.
 
+
 * Tasks:
     * Refactor projection task to use ngio
 * Dependencies:
@@ -8,8 +9,12 @@
 * CI:
     * Remove Python 3.9 from the CI matrix
 
+# 1.3.3
+
+* Add new metadata (authors, category, modality, tags) to manifest models and to tasks (\#855).
 
 # 1.3.2
+
 * Tasks:
     * Add percentile-based rescaling to calculate registration task to make it more robust (\#848)
 * Dependencies:
diff --git a/fractal_tasks_core/__FRACTAL_MANIFEST__.json b/fractal_tasks_core/__FRACTAL_MANIFEST__.json
@@ -3,6 +3,12 @@
   "task_list": [
     {
       "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": {
@@ -265,6 +271,12 @@
     },
     {
       "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": {
@@ -551,6 +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": {
@@ -672,6 +689,10 @@
       "output_types": {
         "illumination_corrected": true
       },
+      "category": "Image Processing",
+      "tags": [
+        "Preprocessing"
+      ],
       "executable_parallel": "tasks/illumination_correction.py",
       "meta_parallel": {
         "cpus_per_task": 1,
@@ -736,6 +757,12 @@
     },
     {
       "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,
@@ -1030,6 +1057,11 @@
     },
     {
       "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": {
@@ -1161,6 +1193,11 @@
     },
     {
       "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": {
@@ -1263,6 +1300,11 @@
       "output_types": {
         "registered": true
       },
+      "category": "Registration",
+      "modality": "HCS",
+      "tags": [
+        "Multiplexing"
+      ],
       "executable_parallel": "tasks/apply_registration_to_image.py",
       "meta_parallel": {
         "cpus_per_task": 1,
@@ -1378,6 +1420,7 @@
     },
     {
       "name": "Napari Workflows Wrapper",
+      "category": "Measurement",
       "executable_parallel": "tasks/napari_workflows_wrapper.py",
       "meta_parallel": {
         "cpus_per_task": 8,
@@ -1539,5 +1582,6 @@
     }
   ],
   "has_args_schemas": true,
-  "args_schema_version": "pydantic_v2"
+  "args_schema_version": "pydantic_v2",
+  "authors": "Fractal Core Team"
 }
diff --git a/fractal_tasks_core/__init__.py b/fractal_tasks_core/__init__.py
@@ -6,6 +6,6 @@
 )
 
 
-__VERSION__ = "1.3.2"
+__VERSION__ = "1.3.3"
 __OME_NGFF_VERSION__ = "0.4"
 __FRACTAL_TABLE_VERSION__ = "1"
diff --git a/fractal_tasks_core/dev/create_manifest.py b/fractal_tasks_core/dev/create_manifest.py
@@ -32,6 +32,7 @@
 
 def create_manifest(
     package: str = "fractal_tasks_core",
+    authors: Optional[str] = None,
     manifest_version: str = "2",
     has_args_schemas: bool = True,
     docs_link: Optional[str] = None,
@@ -76,6 +77,8 @@ def create_manifest(
     )
     if has_args_schemas:
         manifest["args_schema_version"] = ARGS_SCHEMA_VERSION
+    if authors is not None:
+        manifest["authors"] = authors
 
     # Prepare a default value of docs_link
     if package == "fractal_tasks_core" and docs_link is None:
@@ -148,4 +151,6 @@ def create_manifest(
 
 
 if __name__ == "__main__":
-    create_manifest()
+    PACKAGE = "fractal_tasks_core"
+    AUTHORS = "Fractal Core Team"
+    create_manifest(package=PACKAGE, authors=AUTHORS)
diff --git a/fractal_tasks_core/dev/task_list.py b/fractal_tasks_core/dev/task_list.py
@@ -22,13 +22,19 @@
         executable="tasks/cellvoyager_to_ome_zarr_compute.py",
         meta_init={"cpus_per_task": 1, "mem": 4000},
         meta={"cpus_per_task": 1, "mem": 4000},
+        category="Conversion",
+        modality="HCS",
+        tags=["Yokogawa", "Cellvoyager"],
     ),
     CompoundTask(
         name="Convert Cellvoyager Multiplexing to OME-Zarr",
         executable_init="tasks/cellvoyager_to_ome_zarr_init_multiplex.py",
         executable="tasks/cellvoyager_to_ome_zarr_compute.py",
         meta_init={"cpus_per_task": 1, "mem": 4000},
         meta={"cpus_per_task": 1, "mem": 4000},
+        category="Conversion",
+        modality="HCS",
+        tags=["Yokogawa", "Cellvoyager"],
     ),
     CompoundTask(
         name="Project Image (HCS Plate)",
@@ -38,39 +44,59 @@
         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)",
         executable_init="tasks/image_based_registration_hcs_init.py",
         executable="tasks/calculate_registration_image_based.py",
         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",
         executable_init="tasks/init_group_by_well_for_multiplexing.py",
         executable="tasks/find_registration_consensus.py",
         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",
         input_types=dict(registered=False),
         executable="tasks/apply_registration_to_image.py",
         output_types=dict(registered=True),
         meta={"cpus_per_task": 1, "mem": 4000},
+        category="Registration",
+        modality="HCS",
+        tags=["Multiplexing"],
     ),
     NonParallelTask(
         name="Import OME-Zarr",
@@ -83,5 +109,6 @@
             "cpus_per_task": 8,
             "mem": 32000,
         },
+        category="Measurement",
     ),
 ]
diff --git a/fractal_tasks_core/dev/task_models.py b/fractal_tasks_core/dev/task_models.py
@@ -19,6 +19,7 @@
 from typing import Optional
 
 from pydantic import BaseModel
+from pydantic import Field
 
 
 class _BaseTask(BaseModel):
@@ -31,6 +32,9 @@ class Config:
     meta: Optional[dict[str, Any]] = None
     input_types: Optional[dict[str, bool]] = None
     output_types: Optional[dict[str, bool]] = None
+    category: Optional[str] = None
+    modality: Optional[str] = None
+    tags: list[str] = Field(default_factory=list)
 
 
 class CompoundTask(_BaseTask):
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fractal-tasks-core"
-version = "1.3.2"
+version = "1.3.3"
 description = "Core bioimage-analysis library and tasks of the Fractal analytics platform"
 authors = [
     "Joel Lüthi  <joel.luethi@fmi.ch>",
@@ -104,7 +104,7 @@ source = ["fractal_tasks_core"]
 omit = ["tests/*", "examples/*", "fractal_tasks_core/dev/*"]
 
 [tool.bumpver]
-current_version = "1.3.2"
+current_version = "1.3.3"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

Original file line number	Diff line number	Diff line change
`@@ -6,6 +6,6 @@`
`6`	`6`	`)`
`7`	`7`
`8`	`8`
`9`		`-__VERSION__ = "1.3.2"`
	`9`	`+__VERSION__ = "1.3.3"`
`10`	`10`	`__OME_NGFF_VERSION__ = "0.4"`
`11`	`11`	`__FRACTAL_TABLE_VERSION__ = "1"`