🔖 Release 1.4.0 (#599)

## 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.

Author: shaneahmed

.deepsource.toml

@@ -7,7 +7,7 @@ exclude_patterns = ["docs/*.py", "**/__init__.py"]
 [[analyzers]]
 name = "python"
 enabled = true
-dependency_file_paths = ["requirements_dev.txt"]
+dependency_file_paths = ["requirements/requirements_dev.txt"]
 
   [analyzers.meta]
   runtime_version = "3.x.x"

.github/workflows/conda-env-create.yml

@@ -4,9 +4,9 @@ name: Solve Conda Environment
 
 on:
   push:
-    paths: [ "requirements*.yml", "conda-env-create.yml", "requirement*.txt"]
+    paths: [ "requirements/requirements*.yml", "conda-env-create.yml", "requirement*.txt"]
   pull_request:
-    paths: [ "requirements*.yml", "conda-env-create.yml", "requirement*.txt"]
+    paths: [ "requirements/requirements*.yml", "conda-env-create.yml", "requirement*.txt"]
   schedule: # Run on the 1st of every month at midnight
     - cron: "0 0 1 * *"
 
@@ -20,24 +20,24 @@ jobs:
         include:
           - os: ubuntu-latest
             kind: prod
-            requirements: requirements.conda.yml
+            requirements: requirements/requirements.conda.yml
           - os: ubuntu-latest
             kind: dev
-            requirements: requirements.dev.conda.yml
+            requirements: requirements/requirements.dev.conda.yml
           - os: windows-latest
             kind: prod
-            requirements: requirements.win64.conda.yml
+            requirements: requirements/requirements.win64.conda.yml
           - os: windows-latest
             kind: dev
-            requirements: requirements.win64.dev.conda.yml
+            requirements: requirements/requirements.win64.dev.conda.yml
     runs-on: ${{ matrix.os }}
     timeout-minutes: 20
     steps:
       - uses: actions/checkout@v2
       - name: Copy requirements files
         shell: bash
         run: |
-          cp ./requirements*.txt /tmp/
+          cp ./requirements/requirements*.txt /tmp/
           mkdir /tmp/docs/
           cp ./docs/requirements*.txt /tmp/docs/
       - uses: mamba-org/provision-with-micromamba@main

.github/workflows/docker-publish.yml

@@ -6,7 +6,7 @@ env:
   REGISTRY: ghcr.io
   IMAGE_NAME: TissueImageAnalytics/tiatoolbox
   image: ghcr.io/tissueimageanalytics/tiatoolbox
-  TOOLBOX_VER: 1.3.3
+  TOOLBOX_VER: 1.4.0
 
 jobs:
   build-and-push-image:
@@ -15,8 +15,6 @@ jobs:
       fail-fast: true
       matrix:
         include:
-          - dockerfile: ./docker/3.7/Debian/Dockerfile
-            mtag: py3.7-debian
           - dockerfile: ./docker/3.8/Debian/Dockerfile
             mtag: py3.8-debian
           - dockerfile: ./docker/3.9/Debian/Dockerfile

.github/workflows/pip-install.yml

@@ -4,15 +4,15 @@ name: pip Install
 
 on:
     push:
-        paths: [ "requirements*.yml", "conda-env-create.yml", "requirement*.txt", "setup*py", "setup*cfg", "pytproject*toml", "MANIFEST*in"]
+        paths: [ "requirements*.yml", "conda-env-create.yml", "requirements/requirement*.txt", "setup*py", "setup*cfg", "pytproject*toml", "MANIFEST*in"]
 
 jobs:
   build:
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: true
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
         os: [ubuntu-22.04, windows-latest, macos-latest]
     steps:
     - name: Set up Python ${{ matrix.python-version }}

.github/workflows/python-package.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v3
@@ -31,7 +31,7 @@ jobs:
         sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest pytest-cov pytest-runner
-        pip install -r requirements.txt
+        pip install -r requirements/requirements.txt
     - name: Print Version Information
       run: |
         echo "---SQlite---"
@@ -93,7 +93,7 @@ jobs:
       run: |
         sudo apt-get install -y libopenslide-dev libopenjp2-7
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
+        pip install -r requirements/requirements.txt
         pip install build
     - name: Build package
       run: python -m build

.gitignore

@@ -39,7 +39,6 @@ pip-delete-this-directory.txt
 
 # Unit test / coverage reports
 htmlcov/
-.tox/
 .coverage
 .coverage.*
 .cache

.pre-commit-config.yaml

@@ -1,3 +1,7 @@
+ci:
+  autofix_prs: true
+  autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+  autoupdate_schedule: 'weekly'
 repos:
   - repo: local
     hooks:
@@ -32,7 +36,7 @@ repos:
       - mdformat-gfm  # GitHub flavoured markdown
       - mdformat-black  # Black formatting for python verbatim blocks
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.4.0
     hooks:
       - id: check-ast               # Simply checks whether the files parse as valid Python.
       - id: fix-byte-order-marker   # Removes utf-8 byte order marker.
@@ -54,20 +58,20 @@ repos:
       - id: debug-statements        # Checks for debugger imports and py37+ `breakpoint()` calls in python source.
       - id: pretty-format-json      # Sets a standard for formatting JSON files.
   - repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.9.0
+    rev: v1.10.0
     hooks:
       - id: rst-backticks           # Detect common mistake of using single backticks when writing rst.
       - id: rst-directive-colons    # Detect mistake of rst directive not ending with double colon.
       - id: rst-inline-touching-normal # Detect mistake of inline code touching normal text in rst.
   - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort
   - repo: https://github.com/psf/black
-    rev: 22.10.0 # Replace with any tag/version: https://github.com/psf/black/tags
+    rev: 23.3.0 # Replace with any tag/version: https://github.com/psf/black/tags
     hooks:
       - id: black
-        language_version: python3 # Should be a command that runs python3.7+
+        language_version: python3 # Should be a command that runs python3.+
         additional_dependencies: ['click==8.0.4']  # Currently >8.0.4 breaks black
       - id: black-jupyter
         language: python

.readthedocs.yml

@@ -26,5 +26,5 @@ formats:
 # Optionally set the version of Python and requirements required to build your docs
 python:
   install:
-      - requirements: requirements.txt
+      - requirements: requirements/requirements.txt
       - requirements: docs/requirements.txt

CITATION.cff

@@ -44,7 +44,7 @@ authors:
   given-names: "Shan E Ahmed"
   orcid: "https://orcid.org/0000-0002-1097-1738"
 title: "TIAToolbox as an end-to-end library for advanced tissue image analytics"
-version: 1.3.3  # TIAToolbox version
+version: 1.4.0  # TIAToolbox version
 doi: 10.5281/zenodo.5802442
 date-released: 2022-10-20
 url: "https://github.com/TissueImageAnalytics/tiatoolbox"

CONTRIBUTING.rst

@@ -77,13 +77,12 @@ Ready to contribute? Here's how to set up ``tiatoolbox`` for local development.
    Now you can make your changes locally.
 
 5. When you're done making changes, check that your changes pass flake8 and the
-   tests, including testing other Python versions with tox::
+   tests::
 
     $ flake8 tiatoolbox tests
     $ python setup.py test or pytest
-    $ tox
 
-   To get flake8 and tox, just pip install them into your virtualenv.
+   To get flake8, just pip install them into your virtualenv.
 
 6. Commit your changes and push your branch to GitHub::
 
@@ -102,7 +101,7 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
-3. The pull request should work for Python 3.7, 3.8, 3.9 and 3.10, and for PyPy. Check
+3. The pull request should work for Python 3.8, 3.9 and 3.10, and for PyPy. Check
    https://travis-ci.com/tialab/tiatoolbox/pull_requests
    and make sure that the tests pass for all supported Python versions.