Fractal-tasks-core

This release includes work on Pydantic models for NGFF specs and on ROI tables.

* NGFF Pydantic models:
* Introduce Pydantic models for NGFF metadata in `lib_ngff.py` (\528).
* Extract `num_levels` and `coarsening_xy` parameters from NGFF objects, rather than from `metadata` task input (\528).
* Transform several `lib_zattrs_utils.py` functions (`get_axes_names`, `extract_zyx_pixel_sizes` and `get_acquisition_paths`) into `lib_ngff.py` methods (\528).
* Load Zarr attributes from groups, rather than from `.zattrs` files (\528).
* Regions of interest:
* Set `FOV_ROI_table` and `well_ROI_table` ZYX origin to zero (\524).
* Remove heuristics to determine whether to reset origin, in `cellpose_segmentation` task (\524).
* Remove obsolete `reset_origin` argument from `convert_ROI_table_to_indices` function (\524).
* Remove redundant `reset_origin` call from `apply_registration_to_ROI_tables` task (\524).
* Add check on non-negative ROI indices (\534).
* Add check on ROI indices not starting at `(0,0,0)`, to highlight v0.12/v0.11 incompatibility (\534).
* Fix bug in creation of bounding-box ROIs when `cellpose_segmentation` loops of FOVs (\524).
* Update type of `metadata` parameter of `prepare_FOV_ROI_table` and `prepare_well_ROI_table` functions (\524).
* Fix `reset_origin` so that it returns an updated copy of its input (\524).
* Dependencies:
* Relax `fsspec<=2023.6` constraint into `fsspec!=2023.9.0` (\539).

* Tasks:
* **(major)** Introduce new tasks for registration of multiplexing cycles: `calculate_registration_image_based`, `apply_registration_to_ROI_tables`, `apply_registration_to_image` (\487).
* **(major)** Introduce new `overwrite` argument for tasks `create_ome_zarr`, `create_ome_zarr_multiplex`, `yokogawa_to_ome_zarr`, `copy_ome_zarr`, `maximum_intensity_projection`, `cellpose_segmentation`, `napari_workflows_wrapper` (\499).
* **(major)** Rename `illumination_correction` parameter from `overwrite` to `overwrite_input` (\499).
* Fix plate-selection bug in `copy_ome_zarr` task (\513).
* Fix bug in definition of `metadata["plate"]` in `create_ome_zarr_multiplex` task (\513).
* Introduce new helper functions `write_table`, `prepare_label_group` and `open_zarr_group_with_overwrite` (\499).
* Introduce new helper functions `are_ROI_table_columns_valid`, `convert_indices_to_regions`, `reset_origin`, `is_standard_roi_table`, `get_acquisition_paths`, `get_table_path_dict`, `get_axes_names`, `add_zero_translation_columns`, `calculate_min_max_across_dfs`, `apply_registration_to_single_ROI_table`, `write_registered_zarr`, `calculate_physical_shifts`, `get_ROI_table_with_translation` (\487).
* Testing:
* Add tests for `overwrite`-related task behaviors (\499).
* Introduce mock-up of `napari_skimage_regionprops` package, for testing of
`napari_workflows_wrapper` task (\499).
* Dependencies:
* Require `fsspec` version to be `<=2023.6` (\509).

* Tasks:
* Improve validation for `OmeroChannel.color` field (\488).
* Include `image-label/source/image` OME-NGFF attribute when creating labels (\478).
* Update default values for tolerance (`tol`) in `lib_ROI_overlaps.py` functions (\466).
* Development tools:
* Include `docs_info` and `docs_link` attributes in manifest tasks (\486).
* Rename and revamp scripts to update/check the manifest (\486).
* Improve logging and error-handling in tools for args-schema creation (\469).
* Documentation:
* Convert docstrings to Google style (\473, \479).
* Switch from sphinx to mkdocs for documentation (\479).
* Update generic type hints (\462, \479).
* Align examples to recent package version, and mention them in the documentation (\470).
* Testing:
* Improve coverage of core library (\459, \467, \468).
* Update Zenodo datasets used in tests (\454).
* Run tests both for the poetry-installed and pip-installed package (\455).
* Dependencies:
* Relax `numpy` required version to `<2` (\477).
* Relax `dask` required version to `>=2023.1.0` (\455).
* Relax `zarr` required version to `>=2.13.6,<3` (\455).
* Relax `pandas` required version to `>=1.2.0,<2` (\455).
* Relax `Pillow` required version to `>=9.1.1,<10.0.0` (\455).
* Full update of `poetry.lock` file (mutiple PRs, e.g. \472).
* Include `requests` and `wget` in the `dev` poetry dependency group (\455).

* Restructure the package and repository:
* Move tasks to `tasks` subpackage (\390)
* Create new `dev` subpackage (\384).
* Make tasks-related dependencies optional, and installable via `fractal-tasks` extra (\390).
* Remove `tools` package extra (\384), and split the subpackage content into `lib_ROI_overlaps` and `examples` (\390).
* **(major)** Modify task arguments
* Add Pydantic model `lib_channels.OmeroChannel` (\410, \422);
* Add Pydantic model `tasks._input_models.Channel` (\422);
* Add Pydantic model `tasks._input_models.NapariWorkflowsInput` (\422);
* Add Pydantic model `tasks._input_models.NapariWorkflowsOutput` (\422);
* Move all Pydantic models to main package (\438).
* Modify arguments of `illumination_correction` task (\431);
* Modify arguments of `create_ome_zarr` and `create_ome_zarr_multiplex` (\433).
* Modify argument default for `ROI_table_names`, in `copy_ome_zarr` (\449).
* Remove the delete option from yokogawa to ome zarr (\443).
* Reorder task inputs (\451).
* JSON Schemas for task arguments:
* Add JSON Schemas for task arguments in the package manifest (\369, \384).
* Add JSON Schemas for attributes of custom task-argument Pydantic models (\436).
* Make schema-generation tools more general, when handling custom Pydantic models (\445).
* Include titles for custom-model-typed arguments and argument attributes (\447).
* Remove `TaskArguments` models and switch to Pydantic V1 `validate_arguments` (\369).
* Make coercing&validating task arguments required, rather than optional (\408).
* Remove `default_args` from manifest (\379, \393).
* Other:
* Make pydantic dependency required for running tasks, and pin it to V1 (\408).
* Remove legacy executor definitions from manifest (\361).
* Add GitHub action for testing `pip install` with/without `fractal-tasks` extra (\390).
* Remove `sqlmodel` from dev dependencies (\374).
* Relax constraint on torch version, from `==1.12.1` to `<=2.0.0` (\406).
* Review task docstrings and improve documentation (\413, \416).
* Update `anndata` dependency requirements (from `^0.8.0` to `>=0.8.0,<=0.9.1`), and replace `anndata.experimental.write_elem` with `anndata._io.specs.write_elem` (\428).

* Relax constraint on `scikit-image` version, by only requiring a version `>=0.19` (\367).

* For labeling tasks (`cellpose_segmentation` or `napari_worfklows_wrapper`), allow empty ROI tables as input or output (\365).
* Relax constraint related to the presence of channels in `create_zarr_structure_multiplex` task (\365).