🔖 Release 1.6.0 (#898)

## 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

Author: shaneahmed

.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.

docs/installation.rst

@@ -109,6 +109,13 @@ After installing `Anaconda <https://docs.anaconda.com/anaconda/install/index.htm
 
     $ conda install -c conda-forge tiatoolbox
 
+or
+
+.. code-block:: console
+
+    $ mamba install tiatoolbox
+
+
 Please note that conda-forge installation support is limited on Windows as openslide binaries are not supported on official conda channels. An alternate way to install using conda on Windows could be to install it in `WSL2 with CUDA support <https://docs.microsoft.com/en-us/windows/ai/directml/gpu-cuda-in-wsl>`_. In some cases, WSL2 runs faster on Python codes and therefore we **recommend** this option.
 
 From sources