Major Updates and Feature Improvements

• Adds Python 3.11 support [experimental] #500
  • Python 3.11 is not fully supported by pytorch pytorch/pytorch#86566 and openslide openslide/openslide-python#188
• Removes Python 3.7 support
  • This allows upgrading all the dependencies which were dependent on an older version of Python.
• Adds Neighbourhood Querying Support To AnnotationStore #540
  • This enables easy and efficient querying of annotations within a neighbourhood of other annotations.
• Adds MultiTaskSegmentor engine #424
• Fixes an issue with stain augmentation to apply augmentation to only tissue regions.
  • #546 contributed by @navidstuv
• Filters logger output to stdout instead of stderr.
  • Fixes #255
• Allows import of some modules at higher level for improved usability
  • WSIReader can now be imported as from tiatoolbox.wsicore import WSIReader
  • WSIMeta can now be imported as from tiatoolbox.wsicore import WSIMeta
  • HoVerNet, HoVerNetPlus, IDaRS, MapDe, MicroNet, NuClick, SCCNN can now be imported as `from tiatoolbox.models import HoVerNet, HoVerNetPlus, IDaRS, MapDe, MicroNet, NuClick, SCCNN
• Improves PatchExtractor performance. Updates WSIPatchDataset to be consistent. #571
• Updates documentation for License for clarity on source code and model weights license.

Changes to API

• Updates SCCNN architecture to make it consistent with other models. #544

Bug Fixes and Other Changes

• Fixes Parsing Missing Omero Version NGFF Metadata #568
  • Fixes #535 raised by @benkamphaus
• Fixes reading of DICOM WSIs at the correct level #564
  • Fixes #529
• Fixes scipy, matplotlib, scikit-image deprecated code
• Fixes breaking changes in DICOMWSIReader to make it compatible with latest wsidicom version. #539, #580
• Updates shapely dependency to version >=2.0.0 and fixes any breaking changes.
• Fixes bug with DictionaryStore.bquery and geometry=None, i.e. only a where predicate given.
  • Partly Fixes #532 raised by @blaginin
• Fixes local tests for Windows/Linux
• Fixes flake8, deepsource errors.
• Uses logger instead of warnings and print statements to properly log runs.

Development related changes

• Upgrades dependencies which are dependent on Python 3.7
• Moves requirements*.txt files to requirements folder
• Removes tox
• Uses pyproject.toml for bdist_wheel, pytest and isort
• Adds joblib and numba as dependencies.