🔖 Release 1.5.0 (#757)

## 1.5.0 (2023-12-15) ### Major Updates and Feature Improvements - Adds the bokeh visualization tool. #684 - The tool allows a user to launch a server on their machine to visualise whole slide images, overlay the results of deep learning algorithms or to select a patch from whole slide image and run TIAToolbox deep learning engines. - This tool powers the TIA demos server. For details please see https://tiademos.dcs.warwick.ac.uk/. - Extends Annotation to Support Init from WKB #639 - Adds `IOConfig` for NuClick in `pretrained_model.yaml` #709 - Adds functions to save the TIAToolbox Engine outputs to Zarr and AnnotationStore files. #724 - Adds Support for QuPath Annotation Imports #721 ### Changes to API - Adds `model.to(device)` and `model.load_model_from_file()` functionality to make it compatible with PyTorch API. #733 - Replaces `pretrained` with `weights` to make the engines compatible with the new PyTorch API. #621 - Adds support for high-level imports for various utility functions and classes such as `WSIReader`, `PatchPredictor` and `imread` #606, #607, - Adds `tiatoolbox.typing` for type hints. #619 - Fixes incorrect file size saved by `save_tiles`, issue with certain WSIs raised by @TomastpPereira - TissueMasker transform now returns mask instead of a list. #748 - Fixes #732 ### Bug Fixes and Other Changes - Fixes `pixman` incompability error on Colab #601 - Removes `shapely.speedups`. The module no longer has any affect in Shapely >=2.0. #622 - Fixes errors in the slidegraph example notebook #608 - Fixes bugs in WSI Registration #645, #670, #693 - Fixes the situation where PatchExtractor.get_coords() can return patch coords which lie fully outside the bounds of a slide. #712 - Fixes #710 - Fixes #738 raised by @xiachenrui ### Development related changes - Replaces `flake8` and `isort` with `ruff` #625, #666 - Adds `mypy` checks to `root` and `utils` package. This will be rolled out in phases to other modules. #723 - Adds a module to detect file types using magic number/signatures #616 - Uses `poetry` for version updates instead of `bump2version`. #638 - Removes `setup.cfg` and uses `pyproject.toml` for project configurations. - Reduces runtime for some unit tests e.g., #627, #630, #631, #629 - Reuses models and datasets in tests on GitHub actions by utilising cache #641, #644 - Set up parallel tests locally #671 **Full Changelog:** v1.4.0...v1.5.0 --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mostafajahanifar <[email protected]> Co-authored-by: John Pocock <[email protected]> Co-authored-by: DavidBAEpstein <[email protected]> Co-authored-by: David Epstein <[email protected]> Co-authored-by: Ruqayya Awan <[email protected]> Co-authored-by: Mark Eastwood <[email protected]> Co-authored-by: adamshephard <[email protected]> Co-authored-by: adamshephard <[email protected]> Co-authored-by: Abdol <[email protected]> Co-authored-by: Jiaqi-Lv <[email protected]> Co-authored-by: Abishek <[email protected]> Co-authored-by: Dmitrii Blaginin <[email protected]>
TissueImageAnalytics · Dec 15, 2023 · bba59ba · bba59ba
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diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml
@@ -6,7 +6,7 @@ env:
   REGISTRY: ghcr.io
   IMAGE_NAME: TissueImageAnalytics/tiatoolbox
   image: ghcr.io/tissueimageanalytics/tiatoolbox
-  TOOLBOX_VER: 1.4.1
+  TOOLBOX_VER: 1.5.0
 
 jobs:
   build-and-push-image:

diff --git a/.github/workflows/mypy-type-check.yml b/.github/workflows/mypy-type-check.yml
@@ -0,0 +1,42 @@
+# This workflow will perform code type checking using mypy
+
+name: mypy type checking
+
+on:
+  push:
+    branches: [ develop, pre-release, master, main ]
+  pull_request:
+    branches: [ develop, pre-release, master, main ]
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-22.04
+
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    - name: Setup mypy
+      run: |
+        pip install mypy
+
+    - name: Perform type checking
+      run: |
+        mypy --install-types --non-interactive --follow-imports=skip \
+          tiatoolbox/__init__.py \
+          tiatoolbox/__main__.py \
+          tiatoolbox/typing.py \
+          tiatoolbox/tiatoolbox.py \
+          tiatoolbox/utils/*.py
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -30,8 +30,13 @@ 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 flake8 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.0.286 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
+    - name: Cache tiatoolbox static assets
+      uses: actions/cache@v3
+      with:
+        key: tiatoolbox-home-static
+        path: ~/.tiatoolbox
     - name: Print Version Information
       run: |
         echo "---SQlite---"
@@ -46,12 +51,10 @@ jobs:
         python -c "import sqlite3; print('SQLite %s' % sqlite3.sqlite_version)"
         python -c "import numpy; print('Numpy %s' % numpy.__version__)"
         python -c "import openslide; print('OpenSlide %s' % openslide.__version__)"
-    - name: Lint with flake8
+    - name: Lint with ruff
       run: |
         # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        ruff check .
     - name: Test with pytest
       run: |
         pytest --basetemp={envtmpdir} \

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -12,11 +12,6 @@ repos:
         require_serial: true
         language: system
         stages: [push]
-      - id: notebook-check-ast
-        name: check notebook ast
-        entry: python pre-commit/notebook_check_ast.py
-        types_or: [jupyter]
-        language: python
       - id: notebook-markdown-format
         name: notebook markdown format
         entry: python pre-commit/notebook_markdown_format.py
@@ -28,15 +23,15 @@ repos:
         - mdformat-black
         - mdformat-myst
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.16
+    rev: 0.7.17
     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: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: check-ast               # Simply checks whether the files parse as valid Python.
       - id: fix-byte-order-marker   # Removes utf-8 byte order marker.
@@ -52,49 +47,29 @@ repos:
       - id: mixed-line-ending       # Replaces or checks mixed line endings.
       - id: requirements-txt-fixer  # Sorts entries in requirements.txt.
       - id: trailing-whitespace     # Trims trailing whitespace.
-        exclude: 'setup.cfg'
       - id: file-contents-sorter    # Sorts the lines in specified files (defaults to alphabetical).
         files: whitelist.txt
       - id: debug-statements        # Checks for debugger imports and py37+ `breakpoint()` calls in python source.
       - id: pretty-format-json      # Sets a standard for formatting JSON files.
+        exclude_types: [jupyter]
   - repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.10.0
     hooks:
       - 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/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
   - repo: https://github.com/psf/black
-    rev: 23.3.0 # Replace with any tag/version: https://github.com/psf/black/tags
+    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/PyCQA/flake8
-    rev: 5.0.4
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.1.7
     hooks:
-      - id: flake8
-        additional_dependencies: [
-          flake8-bugbear, # Detect potential bugs
-          flake8-builtins, # Check for built-ins being used as variables
-          flake8-cognitive-complexity, # Check max function complexity
-          flake8-comprehensions, # Suggestions for better list/set/dict comprehensions
-          flake8-eradicate, # Find dead/commented out code
-          flake8-expression-complexity, # Check max expression complexity
-          flake8-fixme, # Check for FIXME, TODO, and XXX left in comments
-          flake8-isort, # Check import ordering
-          flake8-logging-format, # Validate (lack of) logging format strings
-          flake8-mutable, # Check for mutable default arguments
-          flake8-pie, # Misc. linting rules
-          flake8-pytest-style, # Check against pytest style guide
-          flake8-return, # Check return statements
-          flake8-simplify, # Suggestions to simplify code
-          flake8-spellcheck, # Spelling checker
-          flake8-use-fstring, # Encourages use of f-strings vs old style
-          pep8-naming, # Check PEP8 class naming
-        ]
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+        types_or: [python, pyi, jupyter]
diff --git a/AUTHORS.md b/AUTHORS.md
@@ -5,15 +5,19 @@
 - TIA Centre led by Nasir Rajpoot <[email protected]>
 - Shan E Ahmed Raza \<@shaneahmed>
 - John Pocock \<@John-P>
+- Mark Eastwood \<@measty>
 - Simon Graham \<@simongraham>
 - Dang Vu \<@vqdang>
 - Mostafa Jahanifar \<@mostafajahanifar>
 - David Epstein \<@DavidBAEpstein>
-- Mark Eastwood \<@measty>
-- Srijay Deshpande \<@Srijay-lab>
-- Ruqayya Awan \<@ruqayya>
 - Adam Shephard \<@adamshephard>
+- Ruqayya Awan \<@ruqayya>
+- Abdullah Alsalemi \<@Abdol>
+- Dmitrii Blaginin \<@blaginin>
+- Srijay Deshpande \<@Srijay-lab>
+- Jiaqi Lv\<@Jiaqi-Lv>
 - George Hadjigeorgiou \<@ghadjigeorghiou>
+- Abishekraj Vinayagar Gnanasambandam \<@AbishekRajVG>
 - Wenqi Lu \<@wenqi006>
 - Saad Bashir \<@rajasaad>
 

diff --git a/CITATION.cff b/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: 1.4.1  # TIAToolbox version
+version: 1.5.0  # TIAToolbox version
 doi: 10.5281/zenodo.5802442
 date-released: 2022-10-20
 url: "https://github.com/TissueImageAnalytics/tiatoolbox"

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -120,7 +120,7 @@ A reminder for the maintainers on how to deploy.
 Make sure all your changes are committed (including an entry in HISTORY.rst).
 Then run::
 
-$ bump2version patch # possible: major / minor / patch
+$ poetry version patch # use: "poetry version --help" for other options
 $ git push
 $ git push --tags
 

diff --git a/HISTORY.md b/HISTORY.md
@@ -1,5 +1,50 @@
 # History
 
+## 1.5.0 (2023-12-15)
+
+### Major Updates and Feature Improvements
+
+- Adds the bokeh visualization tool. #684
+  - The tool allows a user to launch a server on their machine to visualise whole slide images, overlay the results of deep learning algorithms or to select a patch from whole slide image and run TIAToolbox deep learning engines.
+  - This tool powers the TIA demos server. For details please see https://tiademos.dcs.warwick.ac.uk/.
+- Extends Annotation to Support Init from WKB #639
+- Adds `IOConfig` for NuClick in `pretrained_model.yaml` #709
+- Adds functions to save the TIAToolbox Engine outputs to Zarr and AnnotationStore files. #724
+- Adds Support for QuPath Annotation Imports #721
+
+### Changes to API
+
+- Adds `model.to(device)` and `model.load_model_from_file()` functionality to make it compatible with PyTorch API. #733
+- Replaces `pretrained` with `weights` to make the engines compatible with the new PyTorch API. #621
+- Adds support for high-level imports for various utility functions and classes such as `WSIReader`, `PatchPredictor` and `imread` #606, #607,
+- Adds `tiatoolbox.typing` for type hints. #619
+- Fixes incorrect file size saved by `save_tiles`, issue with certain WSIs raised by @TomastpPereira
+- TissueMasker transform now returns mask instead of a list. #748
+  - Fixes #732
+
+### Bug Fixes and Other Changes
+
+- Fixes `pixman` incompability error on Colab #601
+- Removes `shapely.speedups`. The module no longer has any affect in Shapely >=2.0. #622
+- Fixes errors in the slidegraph example notebook #608
+- Fixes bugs in WSI Registration #645, #670, #693
+- Fixes the situation where PatchExtractor.get_coords() can return patch coords which lie fully outside the bounds of a slide. #712
+  - Fixes #710
+- Fixes #738 raised by @xiachenrui
+
+### Development related changes
+
+- Replaces `flake8` and `isort` with `ruff` #625, #666
+- Adds `mypy` checks to `root` and `utils` package. This will be rolled out in phases to other modules. #723
+- Adds a module to detect file types using magic number/signatures #616
+- Uses `poetry` for version updates instead of `bump2version`. #638
+- Removes `setup.cfg` and uses `pyproject.toml` for project configurations.
+- Reduces runtime for some unit tests e.g., #627, #630, #631, #629
+- Reuses models and datasets in tests on GitHub actions by utilising cache #641, #644
+- Set up parallel tests locally #671
+
+**Full Changelog:** https://github.com/TissueImageAnalytics/tiatoolbox/compare/v1.4.0...v1.5.0
+
 ## 1.4.1 (2023-07-25)
 
 ### Bug Fixes and Other Changes

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -7,6 +7,7 @@ include requirements/requirements.txt
 include make.bat
 include Makefile
 include conf.py
+include tiatoolbox/visualization/bokeh_app/templates/index.html
 
 recursive-include tests *
 recursive-include docs

diff --git a/Makefile b/Makefile
@@ -59,7 +59,7 @@ lint: ## check style with flake8
 	flake8 tiatoolbox tests
 
 test: ## run tests quickly with the default Python
-	pytest
+	pytest -n auto
 
 coverage: ## check code coverage quickly with the default Python
 	pytest  --cov=tiatoolbox --cov-report=term --cov-report=html --cov-report=xml

diff --git a/README.md b/README.md
@@ -29,21 +29,29 @@
   <a href="https://github.com/TissueImageAnalytics/tiatoolbox/actions/workflows/pip-install.yml">
     <img src="https://img.shields.io/pypi/pyversions/tiatoolbox.svg"  alt="Supported Python versions"/>
   </a>
- <a href="https://github.com/psf/black">
-      <img src="https://img.shields.io/badge/code%20style-black-000000.svg" alt="Code Style black"/>
-    </a>
-  <a href="https://github.com/TissueImageAnalytics/tiatoolbox/actions/workflows/python-package.yml">
+<br>
+<a href="https://github.com/TissueImageAnalytics/tiatoolbox/actions/workflows/python-package.yml">
     <img src="https://github.com/TissueImageAnalytics/tiatoolbox/actions/workflows/python-package.yml/badge.svg"  alt="GitHub Workflow passing"/>
   </a>
   <a href="https://codecov.io/gh/TissueImageAnalytics/tiatoolbox">
       <img src="https://codecov.io/gh/TissueImageAnalytics/tiatoolbox/branch/master/graph/badge.svg?token=7UZEMacQHm" alt="Code Coverage"/>
   </a>
+<br>
+<br>
+ <a href="https://github.com/psf/black">
+      <img src="https://img.shields.io/badge/code%20style-black-000000.svg" alt="Code Style black"/>
+    </a>
+<a href="https://github.com/astral-sh/ruff">
+      <img src="https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json" alt="Code Style black"/>
+    </a>
   <br><br>
   <a href="#cite-this-repository"><img src="https://img.shields.io/badge/Cite%20this%20repository-BibTeX-brightgreen" alt="DOI"></a> <a href="https://doi.org/10.1038/s43856-022-00186-5"><img src="https://img.shields.io/badge/DOI-10.1038%2Fs43856--022--00186--5-blue" alt="DOI"></a>
 <br>
 
 ## Getting Started
 
+TIAToolbox is a computational pathology toolbox developed by TIA Centre that provides an end-to-end API for pathology image analysis using best practices. It is based on **[PyTorch](https://pytorch.org/)**, a popular deep learning framework that enables efficient and flexible implementation of state-of-the-art algorithms. TIAToolbox supports many features through a command-line interface and can integrate with standard PyTorch modules. It also offers tools for data loading, pre-processing, model inference, post-processing, and visualization. Whether you are a computational, biomedical, or clinical researcher, TIAToolbox can help you get started in digital pathology with minimal effort.
+
 ### All Users
 
 This package is for those interested in digital pathology: including graduate students, medical staff, members of the TIA Centre and of PathLAKE, and anyone, anywhere, who may find it useful. We will continue to improve this package, taking account of developments in pathology, microscopy, computing and related disciplines. Please send comments and criticisms to **[[email protected]](mailto:[email protected])**.