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ENH: Upgrade Python and other packages #910

Merged
merged 40 commits into from
Nov 9, 2023
Merged

ENH: Upgrade Python and other packages #910

merged 40 commits into from
Nov 9, 2023

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ant0nsc
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@ant0nsc ant0nsc commented Nov 1, 2023

  • Upgrade to Python 3.9 as a minimum
  • Upgrade pillow because of security alerts. This required some API changes and update of test result images
  • The behaviour of the LogCaptureFixture changed, requiring changes from logging.info to logger.info
  • Downgraded black from 23 to 22 because of version constraints
  • Changes in calls to WorkflowParams because of mypy issues that were not detected until now
  • hi-ml-azure now also has its own minimal Conda dev environment

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codecov bot commented Nov 1, 2023

Codecov Report

Merging #910 (755a4a5) into main (2d8a380) will increase coverage by 0.05%.
The diff coverage is 60.71%.

Impacted file tree graph

Flag Coverage Δ
hi-ml-azure 27.27% <50.00%> (+0.03%) ⬆️
hi-ml-cpath 76.22% <65.21%> (+0.05%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files Coverage Δ
hi-ml-cpath/src/health_cpath/models/encoders.py 95.50% <100.00%> (ø)
...-ml-cpath/src/health_cpath/utils/download_utils.py 0.00% <ø> (ø)
hi-ml-cpath/src/health_cpath/utils/viz_utils.py 87.82% <100.00%> (ø)
hi-ml-azure/src/health_azure/utils.py 29.61% <50.00%> (-0.10%) ⬇️
.../src/health_cpath/preprocessing/tiff_conversion.py 87.61% <83.33%> (+0.11%) ⬆️
hi-ml-cpath/src/health_cpath/utils/callbacks.py 95.52% <60.00%> (+0.01%) ⬆️
hi-ml-cpath/src/health_cpath/utils/montage.py 67.92% <0.00%> (ø)
hi-ml/src/health_ml/utils/common_utils.py 84.21% <33.33%> (-1.66%) ⬇️
hi-ml-cpath/src/health_cpath/utils/plots_utils.py 81.76% <57.14%> (+0.10%) ⬆️

... and 8 files with indirect coverage changes

@ant0nsc ant0nsc requested review from dccastro and fepegar November 8, 2023 23:45
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@dccastro dccastro left a comment

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Thanks for the monumental effort in handling all the version conflicts and breaking changes! I assume it's all working now based on the tests, and the code changes LGTM.

@ant0nsc ant0nsc merged commit 1cf19cc into main Nov 9, 2023
47 of 48 checks passed
@ant0nsc ant0nsc deleted the antonsc/alerts branch November 9, 2023 13:17
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3 participants