🔖 Release 1.6.0 (#895)

## TIAToolbox v1.6.0 (2024-12-12)

### Major Updates and Feature Improvements

- **Foundation Models Support via `timm` API** (#856, contributed by @GeorgeBatch)
  - Introduced `TimmBackbone` for running additional PyTorch Image Models.
  - Tested models include `UNI`, `Prov-GigaPath`, and `H-optimus-0`.
  - Added an example notebook demonstrating feature extraction with foundation models.
  - `timm` added as a dependency.
- **Performance Enhancements with `torch.compile`** (#716)
  - Improved performance on newer GPUs using `torch.compile`.
- **Multichannel Input Support in `WSIReader`** (#742)
- **AnnotationStore Filtering for Patch Extraction** (#822)
- **Python 3.12 Support**
- **Deprecation of Python 3.8 Support**
- **CLI Response Time Improvements** (#795)

### API Changes

- **Device Specification Update** (#882)
  - Replaced `has_gpu` with `device` for specifying GPU or CPU usage, aligning with PyTorch's `Model.to()` functionality.
- **Windows Compatibility Enhancement** (#769)
  - Replaced `POWER` with explicit multiplication.

### Bug Fixes and Other Changes

- **TIFFWSIReader Bound Reading Adjustment** (#777)
  - Fixed `read_bound` to use adjusted bounds.
  - Reduced code complexity in `WSIReader` (#814).
- **Annotation Rendering Fixes** (#813)
  - Corrected rendering of annotations with holes.
- **Non-Tiled TIFF Support in `WSIReader`** (#807, contributed by @GeorgeBatch)
- **HoVer-Net Documentation Update** (#751)
  - Corrected class output information.
- **Citation File Fix for `cffconvert`** (#869, contributed by @Alon-Alexander)
- **Bokeh Compatibility Updates**
  - Updated `bokeh_app` for compatibility with `bokeh>=3.5.0`.
  - Switched from `size` to `radius` for `bokeh>3.4.0` compatibility (#796).
- **JSON Extraction Fixes** (#772)
  - Restructured SQL expression construction for JSON properties with dots in keys.
- **VahadaneExtractor Warning** (#871)
  - Added warning due to changes in `scikit-learn>0.23.0` dictionary learning (#382).
- **PatchExtractor Error Message Refinement** (#883)
- **Immutable Output Fix in `WSIReader`** (#850)

### Development-Related Changes

- **Mypy Checks Added**
  - Applied to `utils`, `tools`, `data`, `annotation`, and `cli/common`.
- **ReadTheDocs PDF Build Deprecation**
- **Formatter Update**
  - Replaced `black` with `ruff-format`.
- **Dependency Removal**
  - Removed `jinja2`.
- **Test Environment Update**
  - Updated to `Ubuntu 24.04`.
- **Conda Environment Workflow Update**
  - Implemented `micromamba` setup.
- **Codecov Reporting Fix** (#811)
  **Full Changelog:** v1.5.1...v1.6.0

---------

Co-authored-by: John Pocock <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Adam Shephard <[email protected]>
Co-authored-by: Mark Eastwood <[email protected]>
Co-authored-by: Mostafa Jahanifar <[email protected]>
Co-authored-by: Simon Graham <[email protected]>
Co-authored-by: Abdol A <[email protected]>
Co-authored-by: Jiaqi-Lv <[email protected]>
Co-authored-by: Dmitrii Blaginin <[email protected]>
Co-authored-by: behnazelhaminia <[email protected]>
Co-authored-by: George Batchkala <[email protected]>
Co-authored-by: vqdang <[email protected]>
Co-authored-by: Jiaqi Lv <[email protected]>
Co-authored-by: Alon Alexander <[email protected]>

Author: 14 people

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

@@ -40,7 +40,7 @@ jobs:
           cp ./requirements/requirements*.txt /tmp/
           mkdir /tmp/docs/
           cp ./docs/requirements*.txt /tmp/docs/
-      - uses: mamba-org/provision-with-micromamba@main
+      - uses: mamba-org/setup-micromamba@v1
         with:
           environment-name: tiatoolbox
           environment-file: ${{ matrix.requirements }}

.github/workflows/docker-publish.yml

@@ -6,7 +6,7 @@ env:
   REGISTRY: ghcr.io
   IMAGE_NAME: TissueImageAnalytics/tiatoolbox
   image: ghcr.io/tissueimageanalytics/tiatoolbox
-  TOOLBOX_VER: 1.5.1
+  TOOLBOX_VER: 1.6.0
 
 jobs:
   build-and-push-image:
@@ -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

@@ -12,11 +12,11 @@ jobs:
 
   build:
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
 
@@ -28,9 +28,12 @@ jobs:
     - name: Checkout repository
       uses: actions/checkout@v3
 
-    - name: Setup mypy
+    - name: Install dependencies
       run: |
-        pip install mypy
+        sudo apt update
+        sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
+        python -m pip install --upgrade pip
+        pip install -r requirements/requirements_dev.txt
 
     - name: Perform type checking
       run: |
@@ -39,4 +42,8 @@ jobs:
           tiatoolbox/__main__.py \
           tiatoolbox/typing.py \
           tiatoolbox/tiatoolbox.py \
-          tiatoolbox/utils/*.py
+          tiatoolbox/utils \
+          tiatoolbox/tools \
+          tiatoolbox/data \
+          tiatoolbox/annotation \
+          tiatoolbox/cli/common.py

.github/workflows/pip-install.yml

@@ -12,8 +12,8 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
-        os: [ubuntu-22.04, windows-latest, macos-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        os: [ubuntu-24.04, windows-latest, macos-latest]
     steps:
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v3

.github/workflows/python-package.yml

@@ -13,11 +13,11 @@ on:
 jobs:
   build:
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     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==0.0.286 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.8.2 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v3
@@ -58,12 +58,14 @@ jobs:
     - name: Test with pytest
       run: |
         pytest --basetemp={envtmpdir} \
-           --cov=tiatoolbox --cov-report=term --cov-report=xml \
+           --cov=tiatoolbox --cov-report=term --cov-report=xml --cov-config=pyproject.toml \
            --capture=sys \
            --durations=10 --durations-min=1.0 \
            --maxfail=1
     - name: Report test coverage to Codecov
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v4
+      env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       with:
         files: coverage.xml
         fail_ci_if_error: false
@@ -78,7 +80,7 @@ jobs:
         fail-ci-on-error: false
 
   release:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     timeout-minutes: 15
     needs: build
     if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' || github.ref == 'refs/heads/pre-release' || startsWith(github.ref, 'refs/tags/v')

.gitignore

@@ -109,9 +109,13 @@ ENV/
 
 # IDE settings
 .vscode/
+.idea/
 
 # Mac generated
 .DS_Store
 
 # vim/vi generated
 *.swp
+
+# output zarr generated
+*.zarr

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 ci:
   autofix_prs: true
-  autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
-  autoupdate_schedule: 'weekly'
+  autoupdate_commit_msg: ':technologist: pre-commit autoupdate'
+  autoupdate_schedule: 'monthly'
 repos:
   - repo: local
     hooks:
@@ -11,7 +11,7 @@ repos:
         files: tests/.*\btest_\w*.py
         require_serial: true
         language: system
-        stages: [push]
+        stages: [pre-push]
       - id: notebook-markdown-format
         name: notebook markdown format
         entry: python pre-commit/notebook_markdown_format.py
@@ -23,15 +23,15 @@ repos:
         - mdformat-black
         - mdformat-myst
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.17
+    rev: 0.7.19
     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: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: check-ast               # Simply checks whether the files parse as valid Python.
       - id: fix-byte-order-marker   # Removes utf-8 byte order marker.
@@ -58,18 +58,13 @@ repos:
       - 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/psf/black
-    rev: 23.11.0 # Replace with any tag/version: https://github.com/psf/black/tags
-    hooks:
-      - id: black
-        language_version: python3 # Should be a command that runs python3.+
-        additional_dependencies: ['click==8.0.4']  # Currently >8.0.4 breaks black
-      - id: black-jupyter
-        language: python
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.1.7
+    rev: v0.8.2
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
         types_or: [python, pyi, jupyter]
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [ python, pyi, jupyter ]

.readthedocs.yml

@@ -7,7 +7,7 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
     python: "3.10"
   apt_packages:
@@ -19,10 +19,6 @@ build:
 sphinx:
   configuration: docs/conf.py
 
-# Optionally build your docs in additional formats such as PDF
-formats:
-  - pdf
-
 # Optionally set the version of Python and requirements required to build your docs
 python:
   install:

AUTHORS.md

@@ -11,18 +11,19 @@
 - Mostafa Jahanifar \<@mostafajahanifar>
 - David Epstein \<@DavidBAEpstein>
 - Adam Shephard \<@adamshephard>
-- Ruqayya Awan \<@ruqayya>
 - Abdullah Alsalemi \<@Abdol>
+- Ruqayya Awan \<@ruqayya>
+- Jiaqi Lv \<@Jiaqi-Lv>
 - Dmitrii Blaginin \<@blaginin>
 - Srijay Deshpande \<@Srijay-lab>
-- Jiaqi Lv\<@Jiaqi-Lv>
 - George Hadjigeorgiou \<@ghadjigeorghiou>
 - Abishekraj Vinayagar Gnanasambandam \<@AbishekRajVG>
 - Wenqi Lu \<@wenqi006>
 - Saad Bashir \<@rajasaad>
 
 ## Contributors
 
+- George Batchkala \<@GeorgeBatch>
 - Rob Jewsbury \<@R-J96>
 - Mohsin Bilal \<@mbhahsmi>
 - Fayyaz Minhas \<@foxtrotmike>

CITATION.cff

@@ -24,7 +24,7 @@ authors:
   orcid: "https://orcid.org/0000-0003-0969-2990"
 - family-names: "Bashir"
   given-names: "Raja Muhammad Saad"
-  orcid: "https://orcid.org/0000-0002-8984-696"
+  orcid: "https://orcid.org/0000-0002-8984-6963"
 - family-names: "Bilal"
   given-names: "Mohsin"
   orcid: "https://orcid.org/0000-0001-8632-2729"
@@ -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: 1.5.1  # TIAToolbox version
+version: 1.6.0  # TIAToolbox version
 doi: 10.5281/zenodo.5802442
 date-released: 2022-10-20
 url: "https://github.com/TissueImageAnalytics/tiatoolbox"
@@ -74,7 +74,7 @@ preferred-citation:
     orcid: "https://orcid.org/0000-0003-0969-2990"
   - family-names: "Bashir"
     given-names: "Raja Muhammad Saad"
-    orcid: "https://orcid.org/0000-0002-8984-696"
+    orcid: "https://orcid.org/0000-0002-8984-6963"
   - family-names: "Bilal"
     given-names: "Mohsin"
     orcid: "https://orcid.org/0000-0001-8632-2729"