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

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>

## 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.

## 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.