🔖 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]>

Author: 12 people

.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:

.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

.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} \

.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]

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>
 

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"

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
 

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

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

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