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Better logging #60

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Better logging #60

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multimeric
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This PR builds off #47, so the diff looks enormous at the moment. I'm keeping this separate so as to not delay that PR.

This reworks logging in a few ways:

  • Converts all of the print statements into formal Python logging, meaning that it can be configured better
  • Use the Rich logger, for coloured logs
  • Log the lattice parameters for user feedback, whenever we successfully validate the class

TODO:

  • Check what the old logging configuration was doing, and if it will break anything to remove

multimeric added 30 commits July 19, 2023 17:11
@multimeric
Rename underscore modules
43cb4a2
@multimeric
Merge branch 'optional-napari' into thin-wrapper
7f35ac4
@multimeric
Clean up global variables and types in dock_widget
943fb69
@multimeric
Clean up dock_widget
7e3a78f
@multimeric
Fix missing imports in deconvolution
e3742c7
@multimeric
Merge branch 'optional-napari' of github.com:multimeric/napari_lattic…
da2a363 
…e into thin-wrapper
@multimeric
Merge branch 'master' of github.com:BioimageAnalysisCoreWEHI/napari_l…
3a9f357 
…attice into thin-wrapper
@multimeric
More dock_widget cleanup
248a645
@multimeric
Type signature tidying, and remove an unused function
695b0ea
@multimeric
Refactor workflow augmentation
9752c68
@multimeric
Object oriented system
5db9120
@multimeric
Move to Pydantic, and add field validations for LatticeData and similar
e9f3866
@multimeric
Refactor process() to return a ProcessedSlices object
ba63f39
@multimeric
Fix breaking plugin errors
c02ea40
@multimeric
Initial Restructure of GUI
eee538f
@multimeric
Finish draft of one-page GUI
48b971a
@multimeric
First pass of preview working in the GUI
2370be8
@multimeric
Implemented traffic light system for first two field sets
1e41627
@multimeric
Refactor field validation into mixin
d43bce7
@multimeric
Metaclass attempt
73f248e
@multimeric
Code cleanup, dimension stacking, use mixin for validation logic
af02a25
@multimeric
Implement "disabled", greyed-out steps, fix some bugs in the Lattice
28e62b9 
model generation
@multimeric
Add new tab icons, filter down to only images in the layer select, make
39f798b 
errors red
@multimeric
Rework the dimension merging
23224b1
@multimeric
Cleanup old code
17e10b6
@multimeric
Use pydantic-cli for CLI
df6513a
@multimeric
Refactor submodels into different files
652a6de
@multimeric
Rewrite to use typer, all in on pydantic validators
a0e4bb1
@multimeric
Clean up commented/unused code
4a91550
@multimeric
Merge branch 'master' of github.com:BioimageAnalysisCoreWEHI/napari_l…
23f2b77 
…attice into thin-wrapper
multimeric and others added 30 commits December 19, 2023 11:35
@multimeric
Add the missing suffix parameter into the GUI save function
0d7c7d3
@multimeric
Merge branch 'thin-wrapper' of github.com:multimeric/napari_lattice i…
884b6b7 
…nto thin-wrapper
@multimeric
Dynamically rescale raw input image according to pixel sizes
ef448fc
@pr4deepr
Reset view to centre the image
b33772d
@multimeric
Fix for crop + deconvolution, with a test
9adf364
@multimeric
Merge branch 'thin-wrapper' of github.com:multimeric/napari_lattice i…
298c52b 
…nto thin-wrapper
@multimeric
Fix "test_process_deconvolution"
1868666
@multimeric
Reject CropParams with an empty ROI list
6a988a6
@multimeric
Add --show-schema CLI flag, and rework the way we document CLI config
15e5d8e 
flags
@multimeric
Re-enable testing on all python versions; copy a pairwise implementation
2a2024a 
for older pythons
@multimeric
Revert workflow argument handling to the old method: only passing the
f26266f 
image as the first unfilled argument
@multimeric
Fix tests broken by previous commit
3023154
@multimeric
Undo changes to workflow example
90f3523
@multimeric
Remove some dead workflow code
9e19163
@pr4deepr
added function to return csv filepath
c6fb782
@pr4deepr
avoid overwriting of output file from workflow; fix how dataframes cr…
6f15bb4 
…eated
@pr4deepr
revert change, and use pandas series explode instead
ba51e68
@pr4deepr @multimeric
Update core/lls_core/models/output.py
b294172 
Co-authored-by: Michael Milton <[email protected]>
@pr4deepr @multimeric
take only dataframe for now
1242927 
can modify this in the future

Co-authored-by: Michael Milton <[email protected]>
@multimeric
A pixel tuple should be in the order of Z, Y, then X
2139687
@multimeric
Use AICS metadata even when GUI isn't involved
420898b
@multimeric
Override read_image validator in LatticeData to get the filename
b28e5ef
@multimeric
Only use AICS pixels if they are all defined
f064ea0
@multimeric
Remove the standard default for pixel sizes
3731a21
@multimeric
Get default pixels from another model
2fb523a
@multimeric
Always run pixel validator
d7c497e
@multimeric
Separate input and output dirs for CLI tests
0958c8a
@multimeric
User feedback: progress total and success message
2f6ddf9
@multimeric
Get output dir from lattice
371287e
@multimeric
Remove old logging config, add CLI logging config
f1c6b87
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@multimeric @pr4deepr