🐍 Update Supported Python Versions (add 3.11 ) #500
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Add 3.11 and drop 3.7 to the GitHub Actions CI workflow.
John-P
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John-P
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John-P
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John-P
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John-P
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John-P
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Shapely does not yet support 3.11 (https://pypi.org/project/shapely/) |
Let's keep this PR as draft until we get all the dependencies supporting 3.11 |
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Shapely does have 311 wheels now. Still waiting on pygeos. |
Great! I will update this now. |
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PyTorch does not support Python 3.11 yet |
# Conflicts: # .github/workflows/pip-install.yml # .github/workflows/python-package.yml # requirements.conda.yml # requirements.dev.conda.yml # requirements.win64.conda.yml # requirements.win64.dev.conda.yml
- scikit-image supports scipy 1.9.2 scikit-image/scikit-image#6773
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Pytorch launched version 2.0.0 and officially support python3.11 now |
- Update torch requirement
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Waiting for numba release https://github.com/numba/numba/milestone/63 numba/numba#8304 support |
shaneahmed
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May 3, 2023
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@John-P I think it can be released with beta support as torch doesn't fully support 3.11 and Openslide support is not fully complete yet.
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@@ Coverage Diff @@
## develop #500 +/- ##
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Coverage 99.74% 99.74%
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Files 63 63
Lines 6744 6744
Branches 1107 1342 +235
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Hits 6727 6727
Misses 8 8
Partials 9 9 📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more |
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## 1.4.0 (2023-04-24) ### 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.
shaneahmed
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## 1.4.0 (2023-04-24) ### 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.
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Waiting on some dependencies to update:
torch.compileis not fully supported yet.