diff --git a/.github/workflows/build_and_test.yml b/.github/workflows/build_and_test.yml index c5a4107..aca5bd3 100644 --- a/.github/workflows/build_and_test.yml +++ b/.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/*' \ No newline at end of file + files: './dist/*' diff --git a/README.md b/README.md index 3faba2c..35bfc69 100644 --- a/README.md +++ b/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. \ No newline at end of file +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. diff --git a/pyproject.toml b/pyproject.toml index f5f656f..e76ae0e 100644 --- a/pyproject.toml +++ b/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", ] diff --git a/src/fractal_helper_tasks/__FRACTAL_MANIFEST__.json b/src/fractal_helper_tasks/__FRACTAL_MANIFEST__.json index 9c3ccd4..d2bd3db 100644 --- a/src/fractal_helper_tasks/__FRACTAL_MANIFEST__.json +++ b/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,