🐍 Update Supported Python Versions (add 3.11 ) by John-P · Pull Request #500 · TissueImageAnalytics/tiatoolbox

John-P · 2022-10-28T09:48:57Z

Add 3.11 to the GitHub Actions CI workflow.
Add 3.11 to setup.py
Update pip install workflow.
Update conda requirements python versions.

Waiting on some dependencies to update:

Shapely (closed) Pygeos installation with python 3.11 doesn't work shapely/shapely#1584
- PyGeos Pygeos installation doesn't work with python 3.11 pygeos/pygeos#457
PyTorch Support Python 3.11 pytorch/pytorch#86566
- PyTorch 2.0 supports Python 3.11
- torch.compile is not fully supported yet.
Scipy 1.9.2 not supported by Scikit-image Unpin scipy dependency scikit-image/scikit-image#6773
numba Python 3.11 numba/numba#8304 support https://github.com/numba/numba/milestone/63
- Numba 0.57.0rc1 Checklist numba/numba#8841
OpenSlide support for Python 3.11 Build for Python 3.11 openslide/openslide-python#189
- workflows: build wheels for all OS; python 3.11 support openslide/openslide-python#188

Add 3.11 and drop 3.7 to the GitHub Actions CI workflow.

Add 3.11, drop 3.7.

John-P · 2022-10-28T11:34:51Z

Shapely does not yet support 3.11 (https://pypi.org/project/shapely/)

shaneahmed · 2022-10-31T09:46:23Z

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

Erotemic · 2022-12-03T16:09:10Z

Shapely does have 311 wheels now. Still waiting on pygeos.

shaneahmed · 2022-12-06T10:07:40Z

Shapely does have 311 wheels now. Still waiting on pygeos.

Great! I will update this now.

shaneahmed · 2022-12-06T10:39:31Z

PyTorch does not support Python 3.11 yet

pytorch/pytorch#86566

# 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

Somiona · 2023-03-16T14:23:21Z

Pytorch launched version 2.0.0 and officially support python3.11 now

- Update torch requirement

shaneahmed · 2023-03-17T18:07:49Z

Waiting for numba release https://github.com/numba/numba/milestone/63 numba/numba#8304 support

shaneahmed

@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.

codecov · 2023-05-03T14:15:21Z

Codecov Report

Merging #500 (2be4072) into develop (bb78d2e) will not change coverage.
The diff coverage is n/a.

@@            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     
=========================================
  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

@navidstuv

## 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.

@navidstuv

## 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.

DEV: Update CI Python Versions (+3.11, -3.7)

7ea21d0

Add 3.11 and drop 3.7 to the GitHub Actions CI workflow.

John-P requested a review from shaneahmed October 28, 2022 09:49

John-P assigned John-P and shaneahmed Oct 28, 2022

DEV: Add Python 3.11 & Drop 3.7 In setup.py

6ef57f7

John-P changed the title ~~DEV: Update CI Python Versions (+3.11, -3.7)~~ DEV: Update CI Python Versions (add 3.11 & drop 3.7) Oct 28, 2022

John-P changed the title ~~DEV: Update CI Python Versions (add 3.11 & drop 3.7)~~ DEV: Update Supported Python Versions (add 3.11 & drop 3.7) Oct 28, 2022

John-P changed the title ~~DEV: Update Supported Python Versions (add 3.11 & drop 3.7)~~ 🐍 DEV: Update Supported Python Versions (add 3.11 & drop 3.7) Oct 28, 2022

John-P changed the title ~~🐍 DEV: Update Supported Python Versions (add 3.11 & drop 3.7)~~ 🐍 DEV: Update Supported Python Versions (➕ 3.11 & ➖ 3.7) Oct 28, 2022

John-P added 5 commits October 28, 2022 10:53

DEV: Update pip Workflow Python Versions

abdab19

Add 3.11, drop 3.7.

DEV: Update Conda Requirements Python Versions

4ef2433

DEV: Update Conda Dev Python Requirements Versions

31ab661

DEV: Update Conda Windows Python Versions

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DEV: Update Windows Dev Conda Python Versions

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John-P changed the title ~~🐍 DEV: Update Supported Python Versions (➕ 3.11 & ➖ 3.7)~~ 🐍 DEV: Update Supported Python Versions (➕ 3.11 ) Oct 28, 2022

John-P added 3 commits October 28, 2022 12:05

DEV: Add Back 3.7 To CI Workflow

5d5d93a

DEV: Add 3.7 Back To setup.py

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DEV: Add 3.7 Back To pip Install Workflow

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John-P changed the title ~~🐍 DEV: Update Supported Python Versions (➕ 3.11 )~~ 🐍 DEV: Update Supported Python Versions (add 3.11 ) Oct 28, 2022

shaneahmed marked this pull request as draft October 31, 2022 09:47

John-P added release dependencies Pull requests that update a dependency file labels Nov 4, 2022

John-P and others added 4 commits November 4, 2022 17:09

Merge branch 'develop' into dev-upgrade-python

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Merge branch 'develop' into dev-upgrade-python

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Merge branch 'develop' into dev-upgrade-python

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Merge branch 'develop' into dev-upgrade-python

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shaneahmed added 8 commits December 19, 2022 23:56

Merge branch 'develop' into dev-upgrade-python

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Merge remote-tracking branch 'origin/develop' into dev-upgrade-python

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# 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

Merge branch 'develop' into dev-upgrade-python

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Merge branch 'develop' into dev-upgrade-python

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Merge branch 'develop' into dev-upgrade-python

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Merge branch 'develop' into dev-upgrade-python

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Merge branch 'develop' into dev-upgrade-python

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⬆️ DEV: Unpin scipy version

01d8038

- scikit-image supports scipy 1.9.2 scikit-image/scikit-image#6773

shaneahmed added 2 commits March 16, 2023 14:53

⬆️ Update torch requirement

d32a645

- Update torch requirement

Merge branch 'develop' into dev-upgrade-python

fd16718

shaneahmed changed the title ~~🐍 DEV: Update Supported Python Versions (add 3.11 )~~ 🐍 Update Supported Python Versions (add 3.11 ) Apr 6, 2023

Merge branch 'develop' into dev-upgrade-python

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shaneahmed added this to the Release v2.0.0 milestone Apr 10, 2023

shaneahmed added 3 commits April 18, 2023 10:36

Merge branch 'develop' into dev-upgrade-python

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Merge branch 'develop' into dev-upgrade-python

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Merge branch 'develop' into dev-upgrade-python

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shaneahmed marked this pull request as ready for review May 3, 2023 14:12

shaneahmed approved these changes May 3, 2023

View reviewed changes

shaneahmed modified the milestones: Release v2.0.0, Release v1.4.0 May 5, 2023

shaneahmed merged commit 591482c into develop May 5, 2023

shaneahmed deleted the dev-upgrade-python branch May 5, 2023 10:00

This was referenced May 5, 2023

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🐍 Update Supported Python Versions (add 3.11 )#500
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