Merge branch 'main' into ngio_02

Author: jluethi

.github/workflows/build_and_test.yml

@@ -42,9 +42,6 @@ jobs:
       - name: Install some testing dependencies (hard-coded)
         run: python -m pip install pytest pytest-cov devtools jsonschema requests wget pooch
 
-      - name: Regenerate the manifest
-        run: python src/fractal_helper_tasks/dev/create_manifest.py
-
       - name: Cache Pooch folder
         id: cache-pooch-folder
         uses: actions/cache@v3
@@ -53,13 +50,7 @@ jobs:
           key: pooch-cache
 
       - name: Check if manifest has changed
-        run: |
-          if [ -n "$(git diff --exit-code ./src/fractal_helper_tasks/__FRACTAL_MANIFEST__.json)" ]; then
-          echo "__FRACTAL_MANIFEST__.json has changed. Please run 'python src/fractal_helper_tasks/dev/create_manifest.py' and commit the changes."
-            exit 1
-          else
-            echo "__FRACTAL_MANIFEST__.json has not changed."
-          fi
+        run: fractal-manifest check --package fractal-helper-tasks
 
       - name: Test tasks with pytest
         run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing -s --log-cli-level debug

pyproject.toml

@@ -28,6 +28,7 @@ authors = [
 requires-python = ">=3.11"
 dependencies = [
     "ngio>=0.2.2,<0.3.0",
+    "fractal-task-tools==0.0.12",
 ]
 
 # Optional dependencies (e.g. for `pip install -e ".[dev]"`, see

src/fractal_helper_tasks/__FRACTAL_MANIFEST__.json

@@ -10,6 +10,7 @@
         "Singleton time dimension"
       ],
       "docs_info": "### Purpose\n- Removes a **singleton time (T) dimension** from an OME-Zarr image.  \n- Creates a new OME-Zarr image with updated metadata and dimensions.\n- Optionally overwrites the input image if `overwrite_input` is set to True.\n\n### Outputs\n- A **new Zarr image** without the singleton T-dimension, stored with a configurable suffix.  \n\n### Limitations\n- Only processes OME-Zarr images where the **T-axis is the first axis**.  \n- Assumes the T-dimension is **singleton**; does not process non-singleton time axes.  \n- Does not copy associated **label images** or **ROI tables** to the new Zarr structure.  ",
+      "type": "parallel",
       "executable_parallel": "drop_t_dimension.py",
       "meta_parallel": {
         "cpus_per_task": 2,
@@ -57,6 +58,7 @@
         "2D to 3D workflows"
       ],
       "docs_info": "### Purpose\n- Converts a **2D segmentation** image into a **3D segmentation** by replicating the 2D segmentation across Z-slices.  \n- Supports OME-Zarr datasets where **2D and 3D images** share the same base name but differ by suffixes.  \n- Optionally copies associated ROI tables and adjusts them to align with the replicated Z-dimensions.  \n\n### Outputs\n- A **3D segmentation label image** saved with a new name.  \n- Updated **ROI tables** adjusted for Z-dimensions (optional).  \n\n### Limitations\n- Only supports **same-base 2D and 3D Zarr names**; full flexibility in file names is not yet implemented.  \n- Assumes **2D OME-Zarr images** and corresponding 3D images are stored in the same base folder and just differ with a suffix before the .zarr.  \n",
+      "type": "parallel",
       "executable_parallel": "convert_2D_segmentation_to_3D.py",
       "meta_parallel": {
         "cpus_per_task": 2,
@@ -144,6 +146,7 @@
         "Many files"
       ],
       "docs_info": "### Purpose\n- Rechunks OME-Zarr to new chunking parameters: Changes whether the array is stored as many small files or few larger files.\n- Optionally applies the same rechunking to label images.\n\n### Outputs\n- A **new Zarr image** that is rechunked.\n",
+      "type": "parallel",
       "executable_parallel": "rechunk_zarr.py",
       "meta_parallel": {
         "cpus_per_task": 1,

src/fractal_helper_tasks/convert_2D_segmentation_to_3D.py

@@ -211,7 +211,7 @@ def convert_2D_segmentation_to_3D(
 
 
 if __name__ == "__main__":
-    from fractal_tasks_core.tasks._utils import run_fractal_task
+    from fractal_task_tools.task_wrapper import run_fractal_task
 
     run_fractal_task(
         task_function=convert_2D_segmentation_to_3D,

src/fractal_helper_tasks/dev/create_manifest.py

@@ -1,7 +1,9 @@
 """Fractal Task list for Fractal Helper Tasks."""
 
-from fractal_tasks_core.dev.task_models import ParallelTask
+from fractal_task_tools.task_models import ParallelTask
 
+AUTHORS = "Joel Luethi"
+DOCS_LINK = "https://github.com/jluethi/fractal-helper-tasks"
 TASK_LIST = [
     ParallelTask(
         name="Drop T Dimension",

src/fractal_helper_tasks/dev/task_list.py

@@ -86,7 +86,7 @@ def drop_t_dimension(
 
 
 if __name__ == "__main__":
-    from fractal_tasks_core.tasks._utils import run_fractal_task
+    from fractal_task_tools.task_wrapper import run_fractal_task
 
     run_fractal_task(
         task_function=drop_t_dimension,

src/fractal_helper_tasks/drop_t_dimension.py

@@ -163,7 +163,7 @@ def rechunk_zarr(
 
 
 if __name__ == "__main__":
-    from fractal_tasks_core.tasks._utils import run_fractal_task
+    from fractal_task_tools.task_wrapper import run_fractal_task
 
     run_fractal_task(
         task_function=rechunk_zarr,