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Update tasks to Fractal 2.0#671

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tcompa merged 131 commits intomainfractal-analytics-platform/fractal-tasks-core:mainfrom

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Apr 12, 2024

Commits

Commits on Mar 27, 2024

• Update Cellpose task to V2 API

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• Update cellpose docstring

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• Remove Cellpose task output

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• Add zarr_url type to Cellpose task

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• Update cellpose pytests to use new cellpose task API

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• Update other tests using cellpose

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• Update Cellpose manifest

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• Turn off manifest validation for now

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• Fix precommit issues

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• Skip valid manifest tests

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• Skip correct test: test_valid_args_schemas

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• Update apply_registration_to_image task

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• Update tests for apply_registration_to_image

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• Fix helper function docstring

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• Add overwrite_input=False functionality and return task output

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Commits on Mar 28, 2024

• Update illumination correction task

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• Fix workflow test for illumination correction

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• Update napari workflow wrapper to V2

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• Remove return value napari workflows

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• Update cellvoyager conversion

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• Update example 01

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• Update executable workflow

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• Update test_unit_task

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• Adapt create_ome_zarr logic in test_workflows

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• Improve create_cellvoyager_ome_zarr_init docstring

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• Update & temporarily deactivate some cellpose tests

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Commits on Apr 3, 2024

• Add parsing for is_3D to converter

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• Add test for image list output of cellvoyager converter

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Commits on Apr 4, 2024

• Add Convert Cellvoyager multiplex task & rename converter functions

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• Fix import in input model test

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• Add Plate validation model to spec, use validation models in converters & add version to plate attrs

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• Refactor copy_ome_zarr to narrower copy_ome_zarr_hcs_plate

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• precommit cleanup

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• Clean up copy_ome_zarr_hcs_plate

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• Improve new zarr_url in copy task

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• Add MIP task in new API

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• Add image_list_updates to MIP & update workflow tests

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• Remove old copy_ome_zarr.py

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• Turn off registration tests for the moment

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• Update tests for new MIP task

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• Update tests for new MIP tasks

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• Provide return types for _generate_plate_well_metadata

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• Turn off manifest test for the moment

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Commits on Apr 5, 2024

• Add draft task list

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• Update ImportOMEZarr task to 2.0 API

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• Update task list

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Commits on Apr 8, 2024

• Replace `update_manifest.py` with `create_manifest.py`

  tcompa

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• Update `create_docs_info` to handle (non-)parallel tasks

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• Update `FRACTAL_TASKS_CORE_PYDANTIC_MODELS`

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• Update manifest

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• Mark valid-manifest test as xfail

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• Remove obsolete lines from test

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• BROKEN - manually update version (to simplify fractal-containers runs)

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• Update CLI arguments of `run_fractal_task` to fractal-server v2

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• Update CLI arguments of `run_fractal_task` to fractal-server v2

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• Fix test

  tcompa

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• Use `is_3D` rather than `3D`, in `task_list.py`

  tcompa

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• For init tasks, comply with (current) task-output API

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• Update manifest

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• Rename `cellpose_segmentation` into `Cellpose Segmentation`, in task list

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• Update manifest

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• Fix test;

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• Fix test

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• Update the structure of init-task output in some tests

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• Update CLI command for task

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• Adapt cellvoyagero-to-ome-zarr-multiplex (and tests) to current task API

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Commits on Apr 10, 2024

• Move non-working examples and add TODOs

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• Merge branch 'V2_tasks' of https://github.com/fractal-analytics-platform/fractal-tasks-core into V2_tasks

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• Switch to imageio for image loading in registration tests

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• Move examples & add image_based_registration_hcs_init task

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• Add workaround for MIP for #681

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• Update calculate registration image-based to V2 API

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• Update tasks list

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• Move registration helper functions to _registration_utils

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• Add find consensus task & update tests

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• Update task list & manifest

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• Update docstrings

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• Update imports of registration utils functions

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• Remove old task functions

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Commits on Apr 11, 2024

• Update pillow in `poetry.lock` (ref #674)

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• Move `task_list.py` into `dev` folder

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• Refactor dev tools to expose a single `create_manifest` function

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• Re-order attributes in manifest

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• Include `sort_keys` in manifest

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• Improve logging

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• Re-enable manifest validation test (close #682)

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• Re-enable (broken version of) `test_valid_args_schemas.py`

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• Fix `test_task_functions_have_valid_signatures`

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• Fully update `test_valid_args_schemas.py`

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• Re-enable `test_valid_task_interface.py`

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• Enable CI for PR into `V2_tasks` branch

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• Revert "Enable CI for PR into `V2_tasks` branch"

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• Merge pull request #689 from fractal-analytics-platform/minor-changes-to-v2-branch

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• Add napari-workflow-wrapper task to task list and manifest

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• Remove use of `metadata` from `prepare_{3,2}D_zarr` helper functions in tests (close #686)

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• Fix path concatenation in test

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• Remove `zenodo_zarr_metadata` from `test_import_ome_zarr.py`

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• Remove `zenodo_zarr_metadata` from `test_workflows.py`

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• Re-enable `check_manifest.py`

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• Fix example 01

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• Fix example 02

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• Remove obsolete `create_docs_link` function

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• Add docstring

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• Minor improvements to `task_models.py`

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• Do not set `sort_keys` when dumping the manifest to a JSON file (close #691)

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• Improve plate-related ngff models:

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• Change return of `get_tables_list_v1` when there is no `tables` subgroup

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• Fix type hints and one docstring in `tables/v1.py`

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• Add type hint

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• Fix well-group attributes structure in `copy_ome_zarr_hcs_plate.py`

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• Fix well-group attributes structure in `create_well_acquisition_dict`

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• Fix docstring

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• Avoid redundant f-string casting

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• Add return type

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• Improve return type

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• Return `None` when an error takes place in cellpose task

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• Rename variable to `relative_zarrurl` for clarity

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• Improve docstring

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• Add `MultiplexingAcquisition` to list of pydantic models

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• Remove commented out function from copy_ome_zarr

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Commits on Apr 12, 2024

• Improve docstrings and type hints

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• Add `load_NgffPlateMeta` helper function

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• Minor changes to `copy_ome_zarr_hcs_plate`

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• Make variable name more precise in MIP task

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• Simplify `overwrite_input=True/False` logic in illumination-correction task

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• Minor fix to manifest

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• Use uniform style for `well` attribute (in import-ome-zarr)

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• Revert manual update of version

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• Merge branch 'main' into V2_tasks

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• Downgrade `upload-artifact` GHA to v3

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• Fix type hints [skip ci]

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