Code

Porting create_empty_zarr to iohub#234

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ieivanov merged 38 commits intomainczbiohub-sf/iohub:mainfrom mp_utils_portczbiohub-sf/iohub:mp_utils_portCopy head branch name to clipboardSep 27, 2024

+1,047

Commits

Commits on Jul 16, 2024

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

  edyoshikun

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• considering varying t_idx_in and out

  edyoshikun

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Commits on Jul 17, 2024

• template for hypothesis

  edyoshikun

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Commits on Jul 31, 2024

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

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  2 peopleauthored and

  edyoshikun

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

  edyoshikun

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Commits on Sep 17, 2024

• Fixing pyramid scaling factor (#238)

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  JoOkuma

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  edyoshikun

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

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  ziw-liu

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  edyoshikun

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• Export ImageArray from the ngff module (#245)

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  edyoshikun

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• renaming method arguments to have consistent naming structure

  edyoshikun

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• flake8

  edyoshikun

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Commits on Sep 19, 2024

• Merge branch 'main' into mp_utils_port

  ieivanov

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Commits on Sep 20, 2024

• refactor _calculate_zyx_chunk_size

  ieivanov

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• use input_store_path and output_store_path throughout

  ieivanov

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• style

  ieivanov

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• rename and clean up time indices

  ieivanov

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• update time_indices documentation

  ieivanov

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• add processing for channel indices

  ieivanov

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

  talonchandler

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• update import

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• typing

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• docs typos

  talonchandler

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• fix process_single_position iterator @talonchandler @edyoshikun

  ieivanov

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• update apply_transform... docstring

  ieivanov

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• compatibility with minimal deskew w/ @edyoshikun

  talonchandler

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• pretty flat_iterable

  ieivanov

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Commits on Sep 21, 2024

• adding new tests

  edyoshikun

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• create_empty test without testing channel names

  edyoshikun

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• fixing the create_empty_zarr extra indentation

  edyoshikun

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Commits on Sep 23, 2024

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

  edyoshikun

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• fixed apply_transform_czyx

  edyoshikun

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• debug pytest

  ieivanov

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Commits on Sep 24, 2024

• fixing the test for create_empty_plate pytest

  edyoshikun

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Commits on Sep 25, 2024

• synchronize log messages

  talonchandler

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Commits on Sep 26, 2024

• docs improvements

  talonchandler

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• improved docs and typing for Callable func

  talonchandler

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• remove commented slurmkit fix

  talonchandler

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• delete unused function

  talonchandler

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• Merge branch 'main' into mp_utils_port

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