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Refactor core-library modules #631

Merged
merged 49 commits into from
Dec 13, 2023
Merged

Refactor core-library modules #631

merged 49 commits into from
Dec 13, 2023

Commits on Dec 11, 2023

  1. Remove lib prefix from lib_channels.py

    @tcompa
    tcompa committed Dec 11, 2023
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  2. Remove lib prefix from `lib_tables

    @tcompa
    tcompa committed Dec 11, 2023
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  3. Rename lib_regions_of_interes into roi

    @tcompa
    tcompa committed Dec 11, 2023
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  4. Remove lib prefix from `lib_input_models.py

    @tcompa
    tcompa committed Dec 11, 2023
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  5. Remove lib prefix from `lib_masked_loading.py

    @tcompa
    tcompa committed Dec 11, 2023
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  6. Remove lib prefix from `lib_metadata_parsing.py

    @tcompa
    tcompa committed Dec 11, 2023
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  7. Remove lib prefix from lib_parse_filename_metadata.py

    @tcompa
    tcompa committed Dec 11, 2023
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  8. Remove lib prefix from lib_zattrs_utils.py

    @tcompa
    tcompa committed Dec 11, 2023
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  9. Remove lib prefix from lib_write.py

    @tcompa
    tcompa committed Dec 11, 2023
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  10. Remove lib prefix from lib_read_fractal_metadata.py

    @tcompa
    tcompa committed Dec 11, 2023
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  11. Remove lib prefix from lib_pyramid_creation.py

    @tcompa
    tcompa committed Dec 11, 2023
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  12. Remove lib prefix from lib_ngff.py

    @tcompa
    tcompa committed Dec 11, 2023
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  13. Remove lib prefix from lib_upscale_array.py

    @tcompa
    tcompa committed Dec 11, 2023
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  14. Populate ome_zarr and yokogawa subpackages

    @tcompa
    tcompa committed Dec 11, 2023
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  15. Fix input_models paths in dev tools

    @tcompa
    tcompa committed Dec 11, 2023
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  16. Fix error message

    @tcompa
    tcompa committed Dec 11, 2023
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  17. Remove lib prefix from lib_glob.py

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    tcompa committed Dec 11, 2023
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  18. Add missing yokogawa/glob.py file

    @tcompa
    tcompa committed Dec 11, 2023
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  19. Merge yokogawa modules related to filenames

    @tcompa
    tcompa committed Dec 11, 2023
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  20. Rename yokogawa/metadata_parsing.py into yokogawa/metadata.py

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    tcompa committed Dec 11, 2023
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  21. Rename pyramid_creation.py into pyramids.py

    @tcompa
    tcompa committed Dec 11, 2023
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  22. Fix docstring

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    tcompa committed Dec 11, 2023
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  23. Fill __init__.py files

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    tcompa committed Dec 11, 2023
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Commits on Dec 12, 2023

  1. Rename yokogawa subpackage to cellvoyager

    @tcompa
    tcompa committed Dec 12, 2023
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  2. Extract ngff from ome_zarr subpackage

    @tcompa
    tcompa committed Dec 12, 2023
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  3. Simplify import statement

    @tcompa
    tcompa committed Dec 12, 2023
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  4. Rename find_omengff_acquisition with leading underscore

    @tcompa
    tcompa committed Dec 12, 2023
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  5. Merge ome_zarr/read_fractal_metadata.py into `ome_zarr/zattrs_utils… 

    ….py`
    @tcompa
    tcompa committed Dec 12, 2023
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  6. Extract prepare_label_group function from write.py

    @tcompa
    tcompa committed Dec 12, 2023
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  7. Clarify imports

    @tcompa
    tcompa committed Dec 12, 2023
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  8. Clarify imports and remove import *

    @tcompa
    tcompa committed Dec 12, 2023
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  9. Improve exports in ngff subpackage

    @tcompa
    tcompa committed Dec 12, 2023
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  10. Add _ prefix to open_zarr_group_with_overwrite function name

    @tcompa
    tcompa committed Dec 12, 2023
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  11. Move write.py to main namespace, and extract `_write_elem_with_over… 

    …write` into `tables/v1.py`
    @tcompa
    tcompa committed Dec 12, 2023
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  12. Move labels.py out of ome_zarr subpackage`

    @tcompa
    tcompa committed Dec 12, 2023
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  13. Rename write.py into zarr.py

    @tcompa
    tcompa committed Dec 12, 2023
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  14. Remove deprecated use of Dict

    @tcompa
    tcompa committed Dec 12, 2023
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Commits on Dec 13, 2023

  1. Move napari-workflows input models to task module

    @tcompa
    tcompa committed Dec 13, 2023
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  2. Rename Channel into ChannelInputModel`

    @tcompa
    tcompa committed Dec 13, 2023
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  3. Rename zarr.py into zarr_utils.py

    @tcompa
    tcompa committed Dec 13, 2023
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  4. Rename zattrs_utils.py into utils.py

    @tcompa
    tcompa committed Dec 13, 2023
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  5. Move ChannelInputModel to channels.py

    @tcompa
    tcompa committed Dec 13, 2023
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  6. Remove init of ome_zarr subpackage

    @tcompa
    tcompa committed Dec 13, 2023
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  7. Move most relative imports to absolute imports

    @tcompa
    tcompa committed Dec 13, 2023
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  8. Remove ome_zarr subpackage, and move its content to main package

    @tcompa
    tcompa committed Dec 13, 2023
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  9. Update dev tools with new paths to models

    @tcompa
    tcompa committed Dec 13, 2023
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  10. Update manifest

    @tcompa
    tcompa committed Dec 13, 2023
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  11. Extract napari-workflows-task input models into separate module

    @tcompa
    tcompa committed Dec 13, 2023
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  12. Fix test

    @tcompa
    tcompa committed Dec 13, 2023
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