Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

.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:

.github/workflows/python-package.yml

@@ -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==0.8.1 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

.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: v0.8.1
+    rev: v0.8.2
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

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

@@ -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"

HISTORY.md

@@ -1,6 +1,69 @@
 # History
 
-## 1.5.1 (2023-12-16)
+## 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:** https://github.com/TissueImageAnalytics/tiatoolbox/compare/v1.5.1...v1.6.0
+
+______________________________________________________________________
+
+## TIAToolbox v1.5.1 (2023-12-16)
 
 ### Development related changes
 
@@ -9,7 +72,9 @@
 
 **Full Changelog:** https://github.com/TissueImageAnalytics/tiatoolbox/compare/v1.5.0...v1.5.1
 
-## 1.5.0 (2023-12-15)
+______________________________________________________________________
+
+## TIAToolbox v1.5.0 (2023-12-15)
 
 ### Major Updates and Feature Improvements
 
@@ -54,13 +119,17 @@
 
 **Full Changelog:** https://github.com/TissueImageAnalytics/tiatoolbox/compare/v1.4.0...v1.5.0
 
-## 1.4.1 (2023-07-25)
+______________________________________________________________________
+
+## TIAToolbox v1.4.1 (2023-07-25)
 
 ### Bug Fixes and Other Changes
 
 - Fix dictionary changed size Error #626 (#605)
 
-## 1.4.0 (2023-04-24)
+______________________________________________________________________
+
+## TIAToolbox v1.4.0 (2023-04-24)
 
 ### Major Updates and Feature Improvements
 
@@ -109,7 +178,9 @@
 - Uses `pyproject.toml` for `bdist_wheel`, `pytest` and `isort`
 - Adds `joblib` and `numba` as dependencies.
 
-## 1.3.3 (2023-03-02)
+______________________________________________________________________
+
+## TIAToolbox v1.3.3 (2023-03-02)
 
 ### Major Updates and Feature Improvements
 
@@ -127,7 +198,9 @@ None
 
 - Restricts dependency versions for compatibility
 
-## 1.3.2 (2023-02-17)
+______________________________________________________________________
+
+## TIAToolbox v1.3.2 (2023-02-17)
 
 ### Major Updates and Feature Improvements
 
@@ -145,7 +218,9 @@ None
 
 - Restricts wsidicom version to \<0.7.0 for compatibility
 
-## 1.3.1 (2022-12-20)
+______________________________________________________________________
+
+## TIAToolbox v1.3.1 (2022-12-20)
 
 ### Major Updates and Feature Improvements
 
@@ -172,7 +247,9 @@ None
 - Prevent test dumping file to root
 - Removes duplicate functions to generate parameterized test scenarios
 
-## 1.3.0 (2022-10-20)
+______________________________________________________________________
+
+## TIAToolbox v1.3.0 (2022-10-20)
 
 ### Major Updates and Feature Improvements
 
@@ -214,7 +291,9 @@ None
 - Adds pip install workflow to resolve dependencies when requirements file is updated
 - Improves tiatoolbox import using LazyLoader
 
-## 1.2.1 (2022-07-07)
+______________________________________________________________________
+
+## TIAToolbox v1.2.1 (2022-07-07)
 
 ### Major Updates and Feature Improvements
 
@@ -238,7 +317,9 @@ None
 - Adds pre-commit hooks to check requirements consistency.
 - Adds GitHub Action to resolve conda environment checks on Windows and Ubuntu.
 
-## 1.2.0 (2022-07-05)
+______________________________________________________________________
+
+## TIAToolbox v1.2.0 (2022-07-05)
 
 ### Major Updates and Feature Improvements
 
@@ -270,7 +351,9 @@ None
 - Sets up GitHub Actions Workflow.
   - Travis CI will be removed in future release.
 
-## 1.1.0 (2022-05-07)
+______________________________________________________________________
+
+## TIAToolbox v1.1.0 (2022-05-07)
 
 ### Major Updates and Feature Improvements
 
@@ -311,7 +394,9 @@ None
 - Improves CLI definitions to make it easier to integrate new functions.
 - Fixes compile options for test_annotation_stores.py
 
-## 1.0.1 (2022-01-31)
+______________________________________________________________________
+
+## TIAToolbox v1.0.1 (2022-01-31)
 
 ### Major Updates and Feature Improvements
 
@@ -332,7 +417,9 @@ None
 - Fixes flake8 linting issues and typos
 - Conditional pytest.skipif to skip GPU tests on travis while running them locally or elsewhere
 
-## 1.0.0 (2021-12-23)
+______________________________________________________________________
+
+## TIAToolbox v1.0.0 (2021-12-23)
 
 ### Major Updates and Feature Improvements
 
@@ -375,7 +462,9 @@ None
 - On demand imports for some libraries for performance
 - Improves performance of mask based patch extraction
 
-## 0.8.0 (2021-10-27)
+______________________________________________________________________
+
+## TIAToolbox v0.8.0 (2021-10-27)
 
 ### Major Updates and Feature Improvements
 
@@ -421,7 +510,9 @@ None
 - Updates to new GitHub organisation name in the repo
   - Fixes related links
 
-## 0.7.0 (2021-09-16)
+______________________________________________________________________
+
+## TIAToolbox v0.7.0 (2021-09-16)
 
 ### Major and Feature Improvements
 
@@ -455,7 +546,9 @@ None
   - Removes conda build on readthedocs build
 - Adds extra checks to pre-commit, e.g., import sorting, spellcheck etc. Detailed list can be found on this [commit](https://github.com/TissueImageAnalytics/tiatoolbox/commit/662a143e915fa55416badd992d8e7358211730a6).
 
-## 0.6.0 (2021-05-11)
+______________________________________________________________________
+
+## TIAToolbox v0.6.0 (2021-05-11)
 
 ### Major and Feature Improvements
 
@@ -481,7 +574,7 @@ None
 
 ______________________________________________________________________
 
-## 0.5.2 (2021-03-12)
+## TIAToolbox v0.5.2 (2021-03-12)
 
 ### Bug Fixes and Other Changes
 
@@ -490,7 +583,7 @@ ______________________________________________________________________
 
 ______________________________________________________________________
 
-## 0.5.1 (2020-12-31)
+## TIAToolbox v0.5.1 (2020-12-31)
 
 ### Bug Fixes and Other Changes
 
@@ -499,7 +592,7 @@ ______________________________________________________________________
 
 ______________________________________________________________________
 
-## 0.5.0 (2020-12-30)
+## TIAToolbox v0.5.0 (2020-12-30)
 
 ### Major and Feature Improvements
 
@@ -557,7 +650,7 @@ ______________________________________________________________________
 
 ______________________________________________________________________
 
-## 0.4.0 (2020-10-25)
+## TIAToolbox v0.4.0 (2020-10-25)
 
 ### Major and Feature Improvements
 
@@ -584,7 +677,7 @@ ______________________________________________________________________
 
 ______________________________________________________________________
 
-## 0.3.0 (2020-07-19)
+## TIAToolbox v0.3.0 (2020-07-19)
 
 ### Major and Feature Improvements
 
@@ -603,7 +696,7 @@ ______________________________________________________________________
 
 ______________________________________________________________________
 
-## 0.2.2 (2020-07-12)
+## TIAToolbox v0.2.2 (2020-07-12)
 
 ### Major and Feature Improvements
 
@@ -619,7 +712,7 @@ ______________________________________________________________________
 
 ______________________________________________________________________
 
-## 0.2.1 (2020-07-10)
+## TIAToolbox v0.2.1 (2020-07-10)
 
 ### Major and Feature Improvements
 
@@ -635,7 +728,7 @@ ______________________________________________________________________
 
 ______________________________________________________________________
 
-## 0.2.0 (2020-07-10)
+## TIAToolbox v0.2.0 (2020-07-10)
 
 ### Major and Feature Improvements
 
@@ -661,6 +754,6 @@ ______________________________________________________________________
 
 ______________________________________________________________________
 
-## 0.1.0 (2020-05-28)
+## TIAToolbox v0.1.0 (2020-05-28)
 
 - First release on PyPI.