🔖 Release 1.5.0

[shaneahmed]

1.5.0 (2023-12-15)

Major Updates and Feature Improvements

• Adds the bokeh visualization tool. #684
  • The tool allows a user to launch a server on their machine to visualise whole slide images, overlay the results of deep learning algorithms or to select a patch from whole slide image and run TIAToolbox deep learning engines.
  • This tool powers the TIA demos server. For details please see https://tiademos.dcs.warwick.ac.uk/.
• Extends Annotation to Support Init from WKB #639
• Adds IOConfig for NuClick in pretrained_model.yaml #709
• Adds functions to save the TIAToolbox Engine outputs to Zarr and AnnotationStore files. #724
• Adds Support for QuPath Annotation Imports #721

Changes to API

• Adds model.to(device) and model.load_model_from_file() functionality to make it compatible with PyTorch API. #733
• Replaces pretrained with weights to make the engines compatible with the new PyTorch API. #621
• Adds support for high-level imports for various utility functions and classes such as WSIReader, PatchPredictor and imread #606, #607,
• Adds tiatoolbox.typing for type hints. #619
• Fixes incorrect file size saved by save_tiles, issue with certain WSIs raised by @TomastpPereira
• TissueMasker transform now returns mask instead of a list. #748
  • Fixes #732

Bug Fixes and Other Changes

• Fixes pixman incompability error on Colab #601
• Removes shapely.speedups. The module no longer has any affect in Shapely >=2.0. #622
• Fixes errors in the slidegraph example notebook #608
• Fixes bugs in WSI Registration #645, #670, #693
• Fixes the situation where PatchExtractor.get_coords() can return patch coords which lie fully outside the bounds of a slide. #712
  • Fixes #710
• Fixes #738 raised by @xiachenrui

Development related changes

• Replaces flake8 and isort with ruff #625, #666
• Adds mypy checks to root and utils package. This will be rolled out in phases to other modules. #723
• Adds a module to detect file types using magic number/signatures #616
• Uses poetry for version updates instead of bump2version. #638
• Removes setup.cfg and uses pyproject.toml for project configurations.
• Reduces runtime for some unit tests e.g., #627, #630, #631, #629
• Reuses models and datasets in tests on GitHub actions by utilising cache #641, #644
• Set up parallel tests locally #671

Full Changelog: https://github.com/TissueImageAnalytics/tiatoolbox/compare/v1.4.0...v1.5.0

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All modified and coverable lines are covered by tests :white_check_mark:

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```diff @@ Coverage Diff @@ ## master #757 +/- ## ========================================== + Coverage 99.77% 99.91% +0.13% ========================================== Files 63 69 +6 Lines 6782 8518 +1736 Branches 1352 1637 +285 ========================================== + Hits 6767 8511 +1744 + Misses 7 0 -7 + Partials 8 7 -1 ```

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