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workflows: build wheels for all OS; python 3.11 support #188

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workflows: build wheels for all OS; python 3.11 support #188

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andreped
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@andreped andreped commented Dec 11, 2022 •
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Changes:

Note:

  • Wheels for Python 3.12 works fine for UNIX-based systems, but as Pillow don't yet support Python 3.12 on Windows (see CI build here), I only set support for Python versions 3.7-3.11.
  • In addition, it is likely more optimal to run tests on a separate virtual machine than where the binaries where built, to properly test that they work as intended, but I believe this is outside the scope of this PR.

What also should be added before merge:

  • Manulinux build

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github-actions bot commented Dec 11, 2022 •
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DCO signed off ✔️

All commits have been signed off. You have certified to the terms of the Developer Certificate of Origin, version 1.1. In particular, you certify that this contribution has not been developed using information obtained under a non-disclosure agreement or other license terms that forbid you from contributing it under the GNU Lesser General Public License, version 2.1.

@andreped andreped mentioned this pull request Dec 11, 2022
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@andreped
test build wheel on all OS and more python versions
3911c64 
Signed-off-by: André Pedersen <andrped94@gmail.com>
@andreped
forgot to install wheel
1b1b19b 
Signed-off-by: André Pedersen <andrped94@gmail.com>
@andreped
add python 3.12-alpha support
001f959 
Signed-off-by: André Pedersen <andrped94@gmail.com>
@andreped
updated setup - python 3.11 support [no ci]
e5cf08a 
Signed-off-by: André Pedersen <andrped94@gmail.com>
@andreped
removed python 3.12 due to pillow
3b3f156 
Signed-off-by: André Pedersen <andrped94@gmail.com>
@andreped
install from wheel in CI
3054fee 
Signed-off-by: André Pedersen <andrped94@gmail.com>
@andreped
revert back to old install in CI
2086b33 
Signed-off-by: André Pedersen <andrped94@gmail.com>
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revert back to original build setup
2099064 
Signed-off-by: André Pedersen <andrped94@gmail.com>
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andreped commented Dec 11, 2022 •
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As I had not signed off the DCO when making the commits originally, I rebased, signed, and force-pushed to update the commits.

@bgilbert
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We have a checklist (#189) for adding wheels for new Python releases, so I've gone ahead and added 3.11 in #190. We normally don't start building wheels for a Python release until it's out, so we shouldn't add 3.12 yet.

@shaneahmed shaneahmed mentioned this pull request Apr 17, 2023
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shaneahmed added a commit to TissueImageAnalytics/tiatoolbox that referenced this pull request May 5, 2023
@John-P @shaneahmed
🐍 Update Supported Python Versions (add 3.11 ) (#500)
591482c 
Adds support for Python 3.11 (beta)

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


Waiting on some dependencies to update:

- [x] Shapely (closed) shapely/shapely#1584
  - PyGeos pygeos/pygeos#457
- [x] PyTorch pytorch/pytorch#86566 
    - [x] PyTorch 2.0 supports Python 3.11 
    - [ ] `torch.compile` is not fully supported yet.
- [x] Scipy 1.9.2 not supported by Scikit-image scikit-image/scikit-image#6773
- [x] numba numba/numba#8304 support https://github.com/numba/numba/milestone/63
  - [x] numba/numba#8841
- [x] OpenSlide support for Python 3.11 openslide/openslide-python#189 
  - [ ] openslide/openslide-python#188

---------

Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
This was referenced May 5, 2023
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shaneahmed added a commit to TissueImageAnalytics/tiatoolbox that referenced this pull request May 5, 2023
@shaneahmed
🔖 Release 1.4.0 (#599)
5231f9d 
## 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 added a commit to TissueImageAnalytics/tiatoolbox that referenced this pull request May 5, 2023
@shaneahmed
🔖 Release 1.4.0 (#600)
b879374 
## 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.
@andreped andreped mentioned this pull request Sep 14, 2023
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bgilbert commented Nov 1, 2023

Closing in favor of #237. Thanks for the PR!

@bgilbert bgilbert closed this Nov 1, 2023
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