Merge branch 'develop' of https://github.com/TissueImageAnalytics/tiatoolbox into sam-viz-fix

Author: measty

.github/workflows/docker-publish.yml

@@ -15,10 +15,6 @@ jobs:
       fail-fast: true
       matrix:
         include:
-          - dockerfile: ./docker/3.9/Debian/Dockerfile
-            mtag: py3.9-debian
-          - dockerfile: ./docker/3.9/Ubuntu/Dockerfile
-            mtag: py3.9-ubuntu
           - dockerfile: ./docker/3.10/Debian/Dockerfile
             mtag: py3.10-debian
           - dockerfile: ./docker/3.10/Ubuntu/Dockerfile
@@ -31,7 +27,11 @@ jobs:
             mtag: py3.12-debian
           - dockerfile: ./docker/3.12/Ubuntu/Dockerfile
             mtag: py3.12-ubuntu
-          - dockerfile: ./docker/3.12/Ubuntu/Dockerfile
+          - dockerfile: ./docker/3.13/Ubuntu/Dockerfile
+            mtag: py3.13-debian
+          - dockerfile: ./docker/3.13/Ubuntu/Dockerfile
+            mtag: py3.13-ubuntu
+          - dockerfile: ./docker/3.13/Ubuntu/Dockerfile
             mtag: latest
     permissions:
       contents: read

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

@@ -16,7 +16,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
 
@@ -51,3 +51,6 @@ jobs:
           tiatoolbox/models/models_abc.py \
           tiatoolbox/models/architecture/__init__.py \
           tiatoolbox/models/architecture/utils.py \
+          tiatoolbox/wsicore/__init__.py \
+          tiatoolbox/wsicore/wsimeta.py \
+          tiatoolbox/wsicore/metadata/

.github/workflows/pip-install.yml

@@ -5,30 +5,32 @@ name: pip Install
 on:
     push:
         paths: [ "requirements*.yml", "conda-env-create.yml", "requirements/requirement*.txt", "setup*py", "setup*cfg", "pytproject*toml", "MANIFEST*in"]
+    pull_request:
+        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: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
         os: [ubuntu-24.04, windows-latest, macos-latest]
     steps:
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
-    - name: 🐧 Install OpenSlide & OpenJPEG
+    - name: 🐧 Install OpenJPEG
       if: runner.os == 'Linux'
       run: |
         sudo apt update
-        sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
+        sudo apt-get install -y libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
-    - name: 🍎 Install OpenSlide & OpenJPEG
+    - name: 🍎 Install OpenJPEG
       if: runner.os == 'macOS'
       run: |
-        brew install openslide openjpeg
+        brew install openjpeg
         python -m pip install --upgrade pip
     - name: 🪟 Install OpenJPEG
       if: runner.os == 'Windows'
@@ -43,47 +45,28 @@ jobs:
         make -j4
         make install
         make clean
-    - name: 🪟 Install OpenSlide
-      if: runner.os == 'Windows'
-      run: |
-        choco install wget --no-progress
-        wget https://github.com/openslide/openslide-winbuild/releases/download/v20220811/openslide-win64-20220811.zip
-        7z x openslide-win64-20220811.zip
-        ls openslide-win64-20220811
-        # Add to PATH
-        echo "$(realpath ./openslide-win64-20220811/bin)" >> $GITHUB_PATH
-        echo "$(realpath ./openslide-win64-20220811/lib)" >> $GITHUB_PATH
-        # Install
-        mkdir "C:\Program Files\openslide"
-        Copy-Item -Path ".\openslide-win64-20220811\*" -Destination "C:\Program Files\openslide" -Recurse
-        ls "C:/Program Files/openslide"
     - name: 🪟 Install SQLite Shell
       if: runner.os == 'Windows'
       run: choco install sqlite.shell --no-progress
     - name: SQLite Version Information
       run: |
         sqlite3 --version
         sqlite3 ":memory:" -list ".output stdout" "pragma compile_options" ".exit"
-    - name: OpenSlide Version Information
-      if: runner.os == 'Linux'
-      run: openslide-quickhash1sum --version
     - name: OpenJPEG Version Information
       continue-on-error: true  # This -h option has exit code 1 for some reason
       run: opj_dump -h
     - name: pip Install From GitHub Repo on Linux and macOS
       if: runner.os != 'Windows'
-      run: python -m pip install git+https://github.com/TissueImageAnalytics/tiatoolbox@${GITHUB_REF_NAME}
+      run: python -m pip install git+https://github.com/TissueImageAnalytics/tiatoolbox@${GITHUB_SHA}
     - name: pip Install From GitHub on Windows
       if: runner.os == 'Windows'
-      run: python -m pip install git+https://github.com/TissueImageAnalytics/tiatoolbox@$env:GITHUB_REF_NAME
-    - name: Test TIAToolbox Import
+      run: python -m pip install git+https://github.com/TissueImageAnalytics/tiatoolbox@$env:GITHUB_SHA
+    - name: Test Imports
       shell: python
       run: |
-        import os
-        if hasattr(os, "add_dll_directory"):
-          # Required for Python>=3.8 on Windows
-          with os.add_dll_directory(r"D:\a\tiatoolbox\tiatoolbox\openslide-win64-20220811\bin"):
-            import tiatoolbox
-        else:
-          os.environ["PATH"] = r"D:\a\tiatoolbox\tiatoolbox\openslide-win64-20220811\bin;"
-          import tiatoolbox
+        import tiatoolbox
+        print(tiatoolbox.__version__)
+        import openslide
+        print(openslide.__version__)
+        import torch
+        print(torch.__version__)

.github/workflows/python-package.yml

@@ -17,23 +17,23 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         sudo apt update
-        sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
+        sudo apt-get install -y libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
-        python -m pip install ruff==0.11.8 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.14.3 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         key: tiatoolbox-home-static
         path: ~/.tiatoolbox
@@ -42,8 +42,6 @@ jobs:
         echo "---SQlite---"
         sqlite3 --version
         sqlite3 ":memory:" -list ".output stdout" "pragma compile_options" ".exit"
-        echo "---Openslide---"
-        openslide-quickhash1sum --version
         echo "---OpenJPEG---"
         opj_dump -h | head -n 5
         echo "---Python---"
@@ -78,6 +76,17 @@ jobs:
         coverage-file: coverage.xml
         dsn: ${{ secrets.DEEPSOURCE_DSN }}
         fail-ci-on-error: false
+    - name: List tiatoolbox contents
+      run: ls -lahR ~/.tiatoolbox
+    - name: Delete Hugging Face cache for large models
+      run: |
+        find ~/.tiatoolbox/models -type f -size +250M -exec bash -c '
+          for model_path; do
+            model_name=$(basename "$model_path")
+            cache_dir="$HOME/.tiatoolbox/models/.cache/huggingface/download"
+            rm -vf "$cache_dir/${model_name}.lock" "$cache_dir/${model_name}.metadata"
+          done
+          ' bash {} +
 
   release:
     runs-on: ubuntu-24.04
@@ -86,10 +95,10 @@ jobs:
     if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' || github.ref == 'refs/heads/pre-release' || startsWith(github.ref, 'refs/tags/v')
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python 3.10
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: '3.10'
         cache: 'pip'

.pre-commit-config.yaml

@@ -23,15 +23,15 @@ repos:
         - mdformat-black
         - mdformat-myst
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.22
+    rev: 1.0.0
     hooks:
     - id: mdformat
       # Optionally add plugins
       additional_dependencies:
       - mdformat-gfm  # GitHub flavoured markdown
       - mdformat-black  # Black formatting for python verbatim blocks
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-ast               # Simply checks whether the files parse as valid Python.
       - id: fix-byte-order-marker   # Removes utf-8 byte order marker.
@@ -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: v0.11.8
+    rev: v0.14.3
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

CONTRIBUTING.rst

@@ -98,7 +98,7 @@ Before you submit a pull request, check that it meets these guidelines:
 
 1. The pull request should include tests.
 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 pull request description.
-3. The pull request should work for Python 3.9, 3.10, 3.11, and 3.12, and for PyPy. Check https://github.com/TissueImageAnalytics/tiatoolbox/actions/workflows/python-package.yml and make sure that the tests pass for all supported Python versions.
+3. The pull request should work for Python 3.10, 3.11, 3.12 and 3.13, and for PyPy. Check https://github.com/TissueImageAnalytics/tiatoolbox/actions/workflows/python-package.yml and make sure that the tests pass for all supported Python versions.
 
 Tips
 ----

README.md

@@ -106,7 +106,7 @@ 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=3.9 # select version of your choice
+    $ conda create -n tiatoolbox-dev python=3.10 # select version of your choice
     $ conda activate tiatoolbox-dev
     $ pip install -r requirements/requirements_dev.txt
 ```

benchmarks/annotation_store.ipynb

@@ -355,7 +355,7 @@
     "        capsize=capsize,\n",
     "        **kwargs,\n",
     "    )\n",
-    "    for i, (runs, c) in enumerate(zip(experiments, color)):\n",
+    "    for i, (runs, c) in enumerate(zip(experiments, color, strict=False)):\n",
     "        plt.text(\n",
     "            i,\n",
     "            min(runs),\n",
@@ -2418,7 +2418,7 @@
     "    )\n",
     "    total = np.sum(counts)\n",
     "    frequencies = dict.fromkeys(range(256), 0)\n",
-    "    for v, x in zip(values, counts):\n",
+    "    for v, x in zip(values, counts, strict=False):\n",
     "        frequencies[v] = x / total\n",
     "    frequency_array = np.array(list(frequencies.values()))\n",
     "    epsilon = 1e-16\n",

benchmarks/annotation_store_alloc.py

@@ -141,6 +141,7 @@ def __exit__(self: memray, *args: object) -> None:
 
 import numpy as np
 import psutil
+from shapely import affinity
 from shapely.geometry import Polygon
 from tqdm import tqdm
 
@@ -188,8 +189,6 @@ def cell_polygon(
         round_coords (bool): Round coordinates to integers. Defaults to False.
 
     """
-    from shapely import affinity
-
     rand_state = np.random.default_rng().__getstate__()
     rng = np.random.default_rng(seed)
     if repeat_first: