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Better logging#60

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multimeric wants to merge 148 commits intoBioimageAnalysisCoreWEHI:masterBioimageAnalysisCoreWEHI/napari_lattice:masterfrom multimeric:better-loggingmultimeric/napari_lattice:better-loggingCopy head branch name to clipboard

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Commits on Jul 19, 2023

• Rename underscore modules

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Commits on Jul 21, 2023

• Merge branch 'optional-napari' into thin-wrapper

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• Clean up global variables and types in dock_widget

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Commits on Jul 26, 2023

• Clean up dock_widget

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Commits on Jul 27, 2023

• Fix missing imports in deconvolution

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• Merge branch 'optional-napari' of github.com:multimeric/napari_lattice into thin-wrapper

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Commits on Jul 28, 2023

• Merge branch 'master' of github.com:BioimageAnalysisCoreWEHI/napari_lattice into thin-wrapper

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• More dock_widget cleanup

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Commits on Aug 2, 2023

• Type signature tidying, and remove an unused function

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Commits on Aug 4, 2023

• Refactor workflow augmentation

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• Object oriented system

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Commits on Aug 10, 2023

• Move to Pydantic, and add field validations for LatticeData and similar

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• Refactor process() to return a ProcessedSlices object

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Commits on Aug 11, 2023

• Fix breaking plugin errors

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Commits on Aug 16, 2023

• Initial Restructure of GUI

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Commits on Aug 17, 2023

• Finish draft of one-page GUI

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Commits on Aug 21, 2023

• First pass of preview working in the GUI

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Commits on Sep 1, 2023

• Implemented traffic light system for first two field sets

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Commits on Sep 4, 2023

• Refactor field validation into mixin

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Commits on Sep 5, 2023

• Metaclass attempt

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• Code cleanup, dimension stacking, use mixin for validation logic

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Commits on Sep 6, 2023

• Implement "disabled", greyed-out steps, fix some bugs in the Lattice

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Commits on Sep 7, 2023

• Add new tab icons, filter down to only images in the layer select, make

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Commits on Sep 11, 2023

• Rework the dimension merging

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• Cleanup old code

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Commits on Sep 12, 2023

• Use pydantic-cli for CLI

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Commits on Sep 14, 2023

• Refactor submodels into different files

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• Rewrite to use typer, all in on pydantic validators

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• Clean up commented/unused code

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Commits on Sep 15, 2023

• Merge branch 'master' of github.com:BioimageAnalysisCoreWEHI/napari_lattice into thin-wrapper

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• Fix missing imports

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• pydantic-numpy

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• Use older pydantic-numpy

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• Remove pydantic-numpy

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• Pyright settings in the pyproject.toml

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• Rework workflow handling, move sample data into package

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  1b0b0f3

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• Add pkg_resources dependency

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• GUI fixes

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• Fix type errors

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• Fix dependency issues

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  57f9a2c

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• Cartesian product tests

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• Fix some tests, add comprehensive LatticeData tests

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Commits on Sep 16, 2023

• Skip validations when image is missing

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• invoke() test utility, forbid extra fields, ignore_keyerror() utility

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Commits on Sep 17, 2023

• Add formal click depenedency

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Commits on Sep 20, 2023

• Refactor CLI to use None default values, add JSON config help, throw

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• Fix GUI bugs, fix some CLI tests to use subcommands

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• Fix cli tests, use click argument panels, clean up CLI code

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• Fix CLI tests

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• Clean up LatticeData tests

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Commits on Sep 21, 2023

• Implement pixel data source selection

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• Copy the args before modifying them

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Commits on Sep 22, 2023

• Improvements to workflow handling

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• Missing test files

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• More missing files, disable cropping test until we have ROIs

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• Add missing params.py

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• Fix test_process_workflow test suite

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Commits on Sep 25, 2023

• Removed plugin preview

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  6b856c4

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• Clean up GUI code, and fix tests

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  4202b58

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• Fix ROI handling, add ROI class, fix plugin linting

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  2e750d1

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• Fix for when crop is None

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• Add missing ROI test data

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• Stop using static methods

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Commits on Oct 2, 2023

• Remove commented crop test

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• Fix enable_if documentation

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• Fix tab naming

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• Pretty print LatticeData in GUI

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• Stop re-running validations when napari layers change

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• Fix for crop enabling, ADD_RECTANGLE for cropping, fix for ROI selection

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• Add more checks before we load the workflow modules

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• Add save completed notification

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• Add rich as formal plugin dependency

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Commits on Oct 3, 2023

• Show CLI help by default

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• Pretty print table of validation errors in CLI

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• Add rich as formal CLI dependency

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Commits on Oct 4, 2023

• Always print help when no argumeunts provided

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• Fix tests after subcommands were removed

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  cb65609

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• Rename image to input_image, and fix the CLI validation error display

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• Fix for the confusing "time_range │ 'NoneType' object is not iterable"

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  98c435d

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• Add roi_subset parameter

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  16b28fe

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• Fix workflow test

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Commits on Oct 10, 2023

• Infer the output dir correctly, separate validation and process tests

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• Workflow loads from YAML in CLI

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  4483693

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• Fix broken CLI tests

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Commits on Oct 13, 2023

• Create test_cli test suite

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• Fix save directory selection

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Commits on Oct 27, 2023

• Workflow processing into data frames

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Commits on Oct 30, 2023

• Document the new IO modules, remove the old io.py

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• Apply feedback to plugin, change save suffix behaviour

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• Add test suite for GUI saving

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  e757779

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• Fix type import errors

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Commits on Oct 31, 2023

• Fix CLI tests that now need an output directory

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• Only run all the tests on one version, to avoid using excessive CPU hours

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• ${{ }} notation

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• Single quotes?

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• Use public API for finding the tab widget

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• Magicgui dependency bound

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Commits on Nov 3, 2023

• Fix for missing output directory for previewing; add make() method for

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• Add validation for z range, and loosen the GUI restrictions

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Commits on Nov 10, 2023

• Dynamically update the maximum range values

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• Clean up code

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Commits on Nov 15, 2023

• Remove the z cropping fields from the GUI

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Commits on Nov 17, 2023

• Fix for cropping by treating roi as floats

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• Revert "Remove the z cropping fields from the GUI"

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• Tests for float ROIs

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Commits on Nov 20, 2023

• Rework Z-range handling to use deskewed max, and to update automatically

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• Fix broken GUI tests

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Commits on Nov 23, 2023

• Fix deskew vol usage

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Commits on Dec 6, 2023

• Minimal test images

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• Add progress bars more consistently

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Commits on Dec 7, 2023

• Add tool tip for PSFs

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Commits on Dec 8, 2023

• Add working parent_connect implementation

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Commits on Dec 11, 2023

• Use TupleEdit for PSFs

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Commits on Dec 13, 2023

• Fix negative crop excess

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• GUI cropping improvements; remove PLACEHOLDER

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Commits on Dec 14, 2023

• Fix for array parameters such as time_range in the CLI

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Commits on Dec 18, 2023

• Don't compute the dask array when calculating deskewed shape

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• fix voxel_size_z for cropping

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Commits on Dec 19, 2023

• Add the missing suffix parameter into the GUI save function

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• Merge branch 'thin-wrapper' of github.com:multimeric/napari_lattice into thin-wrapper

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• Dynamically rescale raw input image according to pixel sizes

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• Reset view to centre the image

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• Fix for crop + deconvolution, with a test

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• Merge branch 'thin-wrapper' of github.com:multimeric/napari_lattice into thin-wrapper

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• Fix "test_process_deconvolution"

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Commits on Dec 20, 2023

• Reject CropParams with an empty ROI list

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• Add --show-schema CLI flag, and rework the way we document CLI config

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• Re-enable testing on all python versions; copy a pairwise implementation

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Commits on Dec 21, 2023

• Revert workflow argument handling to the old method: only passing the

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• Fix tests broken by previous commit

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• Undo changes to workflow example

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Commits on Jan 11, 2024

• Remove some dead workflow code

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Commits on Jan 15, 2024

• added function to return csv filepath

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Commits on Jan 16, 2024

• avoid overwriting of output file from workflow; fix how dataframes created

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Commits on Jan 17, 2024

• revert change, and use pandas series explode instead

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Commits on Jan 18, 2024

• Update core/lls_core/models/output.py

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• take only dataframe for now

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Commits on Aug 1, 2024

• A pixel tuple should be in the order of Z, Y, then X

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• Use AICS metadata even when GUI isn't involved

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Commits on Aug 2, 2024

• Override read_image validator in LatticeData to get the filename

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• Only use AICS pixels if they are all defined

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• Remove the standard default for pixel sizes

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• Get default pixels from another model

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• Always run pixel validator

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Commits on Aug 6, 2024

• Separate input and output dirs for CLI tests

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• User feedback: progress total and success message

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• Get output dir from lattice

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Commits on Aug 8, 2024

• Remove old logging config, add CLI logging config

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