Code

Refactor core-library modules#631

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tcompa merged 49 commits intomainfractal-analytics-platform/fractal-tasks-core:mainfrom 600-refactor-core-library-modulesfractal-analytics-platform/fractal-tasks-core:600-refactor-core-library-modulesCopy head branch name to clipboardDec 13, 2023

+944-905

Commits

Commits on Dec 11, 2023

• Remove lib prefix from lib_channels.py

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• Remove lib prefix from `lib_tables

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• Rename lib_regions_of_interes into roi

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• Remove lib prefix from `lib_input_models.py

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• Remove lib prefix from `lib_masked_loading.py

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• Remove lib prefix from `lib_metadata_parsing.py

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• Remove lib prefix from lib_parse_filename_metadata.py

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• Remove lib prefix from lib_zattrs_utils.py

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• Remove lib prefix from lib_write.py

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• Remove lib prefix from lib_read_fractal_metadata.py

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• Remove lib prefix from lib_pyramid_creation.py

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• Remove lib prefix from lib_ngff.py

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• Remove lib prefix from lib_upscale_array.py

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• Populate ome_zarr and yokogawa subpackages

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• Fix input_models paths in dev tools

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• Fix error message

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• Remove lib prefix from lib_glob.py

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• Add missing yokogawa/glob.py file

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• Merge yokogawa modules related to filenames

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• Rename yokogawa/metadata_parsing.py into yokogawa/metadata.py

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• Rename pyramid_creation.py into pyramids.py

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• Fix docstring

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• Fill __init__.py files

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Commits on Dec 12, 2023

• Rename yokogawa subpackage to cellvoyager

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• Extract ngff from ome_zarr subpackage

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• Simplify import statement

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• Rename find_omengff_acquisition with leading underscore

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• Merge ome_zarr/read_fractal_metadata.py into ome_zarr/zattrs_utils.py

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• Extract prepare_label_group function from write.py

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• Clarify imports

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• Clarify imports and remove import *

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• Improve exports in ngff subpackage

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• Add _ prefix to open_zarr_group_with_overwrite function name

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• Move write.py to main namespace, and extract _write_elem_with_overwrite into tables/v1.py

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• Move labels.py out of ome_zarr subpackage`

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• Rename write.py into zarr.py

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• Remove deprecated use of Dict

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Commits on Dec 13, 2023

• Move napari-workflows input models to task module

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• Rename Channel into ChannelInputModel`

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• Rename zarr.py into zarr_utils.py

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• Rename zattrs_utils.py into utils.py

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• Move ChannelInputModel to channels.py

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• Remove init of ome_zarr subpackage

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• Move most relative imports to absolute imports

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• Remove ome_zarr subpackage, and move its content to main package

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• Update dev tools with new paths to models

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• Update manifest

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• Extract napari-workflows-task input models into separate module

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• Fix test

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