Merge branch 'develop' into alert-autofix-6

Author: shaneahmed

.github/workflows/docker-publish.yml

@@ -23,11 +23,15 @@ jobs:
             mtag: py3.12-debian
           - dockerfile: ./docker/3.12/Ubuntu/Dockerfile
             mtag: py3.12-ubuntu
-          - dockerfile: ./docker/3.13/Ubuntu/Dockerfile
+          - dockerfile: ./docker/3.13/Debian/Dockerfile
             mtag: py3.13-debian
           - dockerfile: ./docker/3.13/Ubuntu/Dockerfile
             mtag: py3.13-ubuntu
-          - dockerfile: ./docker/3.13/Ubuntu/Dockerfile
+          - dockerfile: ./docker/3.14/Debian/Dockerfile
+            mtag: py3.14-debian
+          - dockerfile: ./docker/3.14/Ubuntu/Dockerfile
+            mtag: py3.14-ubuntu
+          - dockerfile: ./docker/3.14/Ubuntu/Dockerfile
             mtag: latest
     permissions:
       contents: read

.github/workflows/python-package.yml

@@ -33,7 +33,7 @@ jobs:
         sudo apt update
         sudo apt-get install -y libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
-        python -m pip install ruff==0.15.12 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.15.15 pytest pytest-cov pytest-runner
         pip install uv
         uv pip install --system torch torchvision --index-url https://download.pytorch.org/whl/cpu
         uv pip install --system -r requirements/requirements.txt

.pre-commit-config.yaml

@@ -60,7 +60,7 @@ repos:
       - id: rst-inline-touching-normal # Detect mistake of inline code touching normal text in rst.
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.15.12
+    rev: v0.15.15
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

README.md

@@ -18,8 +18,8 @@
             <img src="https://shields.io/conda/dn/conda-forge/tiatoolbox"  alt="conda-forge downloads"/>
     </a>
   <br>
-  <a href="https://tia-toolbox.readthedocs.io/en/latest/?badge=latest">
-    <img src="https://readthedocs.org/projects/tia-toolbox/badge/?version=latest" alt="Documentation Status" />
+  <a href="https://tia-toolbox.readthedocs.io/en/stable/?badge=stable">
+    <img src="https://readthedocs.org/projects/tia-toolbox/badge/?version=stable" alt="Documentation Status" />
   </a>
   <br>
   <a href="#license">

docker/3.14/Debian/Dockerfile

@@ -0,0 +1,15 @@
+FROM python:3.14-slim-trixie
+
+#get linux packages
+RUN apt-get -y update && apt-get -y install --no-install-recommends \
+    libopenjp2-7-dev libopenjp2-tools \
+    sqlite3 libsqlite3-0 \
+    libgl1 \
+    libglib2.0-0 \
+    build-essential \
+    && pip3 --no-cache-dir install tiatoolbox \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# set the entry point to bash
+ENTRYPOINT ["/bin/bash"]

docker/3.14/Ubuntu/Dockerfile

@@ -0,0 +1,29 @@
+FROM ubuntu:24.04 AS builder-image
+
+# To avoid tzdata blocking the build with frontend questions
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install python3.14
+RUN apt-get update && \
+    apt install software-properties-common -y &&\
+    add-apt-repository ppa:deadsnakes/ppa -y && apt update &&\
+    apt-get install -y --no-install-recommends python3.14-venv &&\
+    apt-get install libpython3.14-dev -y &&\
+    apt-get install python3.14-dev -y &&\
+    apt-get install build-essential -y &&\
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Add env to PATH
+RUN python3.14 -m venv /venv
+ENV PATH=/venv/bin:$PATH
+
+# install TIAToolbox and its requirements
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    libopenjp2-7-dev libopenjp2-tools \
+    sqlite3 libsqlite3-0 \
+    libgl1 \
+    && apt-get clean && rm -rf /var/lib/apt/lists/*
+RUN pip install --no-cache-dir tiatoolbox
+
+# activate virtual environment
+ENV VIRTUAL_ENV=/venv

docs/requirements.txt

@@ -3,4 +3,4 @@ myst-nb>=0.17.1
 myst-parser>=0.18.1
 sphinx-copybutton>=0.5.1
 sphinx-design>=0.3.0
-sphinx-toolbox>=3.2.0
+sphinx-toolbox>=4.2.0

requirements/requirements.txt

@@ -29,7 +29,8 @@ scikit-learn>=1.2.0
 scipy>=1.8
 shapely>=2.0.0
 SimpleITK>=2.2.1
-sphinx>=5.3.0, <9.0.0
+simsimd>=6.5.16 # required by conda-package
+sphinx>=9.0.0
 tifffile>=2025.5.21
 timm>=1.0.3
 torch>=2.5.0

requirements/requirements_dev.txt

@@ -10,7 +10,7 @@ pytest>=7.2.0
 pytest-cov>=4.0.0
 pytest-runner>=6.0
 pytest-xdist[psutil]
-ruff==0.15.12  # This will be updated by pre-commit bot to latest version
+ruff==0.15.15  # This will be updated by pre-commit bot to latest version
 toml>=0.10.2
 twine>=4.0.1
 wheel>=0.37.1

tests/engines/test_semantic_segmentor.py

@@ -124,6 +124,7 @@ def test_semantic_segmentor_patches(
         processed_predictions=processed_predictions,
         output_type="annotationstore",
         save_path=output.with_suffix(".db"),
+        class_dict=None,
     )
 
     assert output_seg[0] == track_tmp_path / "output1" / (sample_image.stem + ".db")
@@ -245,6 +246,7 @@ def test_save_annotation_store_nparray(
         patch_mode=True,
         save_dir=track_tmp_path / "output1",
         output_type="annotationstore",
+        class_dict=None,
     )
 
     assert output[0] == track_tmp_path / "output1" / "0.db"
@@ -268,6 +270,7 @@ def test_save_annotation_store_nparray(
         patch_mode=True,
         save_dir=track_tmp_path / "output2",
         output_type="annotationstore",
+        class_dict=None,
     )
 
     assert output[0] == track_tmp_path / "output2" / "0.db"