Merge pull request #30 from fractal-analytics-platform/29-deprecate-support-for-213-fractal-server

29 deprecate support for 213 fractal server

Author: jluethi

.github/workflows/build_and_test.yml

@@ -50,7 +50,7 @@ jobs:
           key: pooch-cache
 
       - name: Check if manifest has changed
-        run: fractal-manifest check --package fractal-helper-tasks --fractal-server-2-13
+        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
@@ -97,4 +97,4 @@ jobs:
       - uses: softprops/action-gh-release@v2
         with:
           generate_release_notes: true
-          files: './dist/*'
+          files: './dist/*'

README.md

@@ -11,7 +11,7 @@ Collection of Fractal helper tasks
 
 To create the manifest:
 ```
-fractal-manifest create --package fractal_helper_tasks --fractal-server-2-13
+fractal-manifest create --package fractal_helper_tasks
 ```
 
-Refer to the developers-guide in the [Fractal template repo](https://github.com/fractal-analytics-platform/fractal-tasks-template/blob/main/DEVELOPERS_GUIDE.md) for more detailed instructions.
+Refer to the developers-guide in the [Fractal template repo](https://github.com/fractal-analytics-platform/fractal-tasks-template/blob/main/DEVELOPERS_GUIDE.md) for more detailed instructions.

pyproject.toml

@@ -27,7 +27,7 @@ authors = [
 # Required Python version and dependencies
 requires-python = ">=3.11"
 dependencies = [
-    "ngio>=0.2.2,<0.3.0",
+    "ngio==0.2.2",
     "fractal-task-tools==0.0.12",
 ]
 

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,