Porting create_empty_zarr to iohub (#234)

* initial commit with added docs prior to refactoring to simplify the naming and functions.

* considering varying t_idx_in and out

* template for hypothesis

* Refactor NGFF module and migrate to Pydantic v2 (#233)

* unify comment format

* fix typing and docstring

* create ngff sub-package
and refactor display util file

* refactor ngff meta file

* refactor ngff

* export transformation model

* fix type hint

* bump ome-zarr target in docstring

* migrate to pydantic v2

* isort

* fix validators

* remove union type

* fix dependency

* update docstring

* typing improvements

* Update iohub/ngff/models.py

Co-authored-by: Jordão Bragantini <[email protected]>

* fix style

* update module docstring to specify their content

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Co-authored-by: Jordão Bragantini <[email protected]>

* improving docstring for functions and renaming input and output path arguments to be more intuitive.

* Fixing pyramid scaling factor (#238)

* Fixing pyramid scaling factor

* fix pyramid test

* fix test again

* Use annotation instead of field for tagged union (#244)

also removed non-standard axis

* Export `ImageArray` from the `ngff` module (#245)

* adding the ImageArray

* precommit

* black

* renaming method arguments to have consistent naming structure

* flake8

* refactor _calculate_zyx_chunk_size

* use input_store_path and output_store_path throughout

* style

* rename and clean up time indices

* update time_indices documentation

* add processing for channel indices

* fix syntax and move ngff_utils.py to ngff/utils.py

* update import

* typing

* docs typos

* fix process_single_position iterator @talonchandler @edyoshikun

* update apply_transform... docstring

* compatibility with minimal deskew w/ @edyoshikun

* pretty flat_iterable

* adding new tests

* create_empty test without testing channel names

* fixing the create_empty_zarr extra indentation

* -attempt to fix apply_transform_test. @ieivanov revert if needed

* fixed apply_transform_czyx

* debug pytest

* fixing the test for create_empty_plate pytest

* synchronize log messages

* docs improvements

* improved docs and typing for Callable func

* remove commented slurmkit fix

* delete unused function

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Co-authored-by: Ziwen Liu <[email protected]>
Co-authored-by: Jordão Bragantini <[email protected]>
Co-authored-by: Ivan Ivanov <[email protected]>
Co-authored-by: Talon Chandler <[email protected]>