Merge branch 'develop' into enhance-torch-compile

.github/workflows/docker-publish.yml

@@ -15,8 +15,6 @@ jobs:
       fail-fast: true
       matrix:
         include:
-          - dockerfile: ./docker/3.8/Debian/Dockerfile
-            mtag: py3.8-debian
           - dockerfile: ./docker/3.9/Debian/Dockerfile
             mtag: py3.9-debian
           - dockerfile: ./docker/3.9/Ubuntu/Dockerfile
@@ -25,7 +23,15 @@ jobs:
             mtag: py3.10-debian
           - dockerfile: ./docker/3.10/Ubuntu/Dockerfile
             mtag: py3.10-ubuntu
-          - dockerfile: ./docker/3.10/Ubuntu/Dockerfile
+          - dockerfile: ./docker/3.11/Debian/Dockerfile
+            mtag: py3.11-debian
+          - dockerfile: ./docker/3.11/Ubuntu/Dockerfile
+            mtag: py3.11-ubuntu
+          - dockerfile: ./docker/3.12/Debian/Dockerfile
+            mtag: py3.12-debian
+          - dockerfile: ./docker/3.12/Ubuntu/Dockerfile
+            mtag: py3.12-ubuntu
+          - dockerfile: ./docker/3.12/Ubuntu/Dockerfile
             mtag: latest
     permissions:
       contents: read

.github/workflows/mypy-type-check.yml

@@ -16,7 +16,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
 
@@ -39,4 +39,9 @@ jobs:
           tiatoolbox/__main__.py \
           tiatoolbox/typing.py \
           tiatoolbox/tiatoolbox.py \
-          tiatoolbox/utils/*.py
+          tiatoolbox/utils/*.py \
+          tiatoolbox/tools/__init__.py \
+          tiatoolbox/tools/stainextract.py \
+          tiatoolbox/tools/pyramid.py \
+          tiatoolbox/tools/tissuemask.py \
+          tiatoolbox/tools/graph.py

.github/workflows/pip-install.yml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         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: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v3
@@ -30,7 +30,7 @@ jobs:
         sudo apt update
         sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
-        python -m pip install ruff==0.1.13 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.2.2 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v3

.pre-commit-config.yaml

@@ -59,7 +59,7 @@ repos:
       - 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/psf/black
-    rev: 24.1.1 # Replace with any tag/version: https://github.com/psf/black/tags
+    rev: 24.2.0 # Replace with any tag/version: https://github.com/psf/black/tags
     hooks:
       - id: black
         language_version: python3 # Should be a command that runs python3.+
@@ -68,7 +68,7 @@ repos:
         language: python
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.1.14
+    rev: v0.2.2
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

README.md

@@ -115,7 +115,7 @@ Prepare a computer as a convenient platform for further development of the Pytho
 5. Create virtual environment for TIAToolbox using
 
 ```sh
-    $ conda create -n tiatoolbox-dev python=3.8 # select version of your choice
+    $ conda create -n tiatoolbox-dev python=3.9 # select version of your choice
     $ conda activate tiatoolbox-dev
     $ pip install -r requirements/requirements_dev.txt
 ```

benchmarks/annotation_nquery.ipynb

@@ -71,7 +71,7 @@
     "from shapely.geometry import Polygon\n",
     "\n",
     "sys.path.append(\"..\")  # If running locally without pypi installed tiatoolbox\n",
-    "from tiatoolbox.annotation.storage import (  # noqa: E402\n",
+    "from tiatoolbox.annotation.storage import (\n",
     "    Annotation,\n",
     "    AnnotationStore,\n",
     "    DictionaryStore,\n",