Merge branch 'develop' into more-than-three-channels

TissueImageAnalytics · Jan 19, 2024 · 1a350c8 · 1a350c8
2 parents 5c8a7ea + 3fb5686
commit 1a350c8
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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: 1.5.1
 
 jobs:
   build-and-push-image:

diff --git a/.github/workflows/mypy-type-check.yml b/.github/workflows/mypy-type-check.yml
@@ -39,9 +39,4 @@ jobs:
           tiatoolbox/__main__.py \
           tiatoolbox/typing.py \
           tiatoolbox/tiatoolbox.py \
-          tiatoolbox/utils/__init__.py \
-          tiatoolbox/utils/env_detection.py \
-          tiatoolbox/utils/exceptions.py \
-          tiatoolbox/utils/magic.py \
-          tiatoolbox/utils/metrics.py \
-          tiatoolbox/utils/transforms.py
+          tiatoolbox/utils/*.py
diff --git a/.github/workflows/python-package.yml b/.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==0.0.286 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.1.13 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v3

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -59,7 +59,7 @@ repos:
       - 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
+    rev: 23.12.1 # Replace with any tag/version: https://github.com/psf/black/tags
     hooks:
       - id: black
         language_version: python3 # Should be a command that runs python3.+
@@ -68,7 +68,7 @@ repos:
         language: python
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.1.6
+    rev: v0.1.13
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

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: 1.5.1  # TIAToolbox version
 doi: 10.5281/zenodo.5802442
 date-released: 2022-10-20
 url: "https://github.com/TissueImageAnalytics/tiatoolbox"

diff --git a/HISTORY.md b/HISTORY.md
@@ -1,5 +1,59 @@
 # History
 
+## 1.5.1 (2023-12-16)
+
+### Development related changes
+
+- Specifies compatible Python versions
+  - Fixes `tiatoolbox-feedstock` build for conda-forge release #763
+
+**Full Changelog:** https://github.com/TissueImageAnalytics/tiatoolbox/compare/v1.5.0...v1.5.1
+
+## 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/docs/images/dual_win.png b/docs/images/dual_win.png
diff --git a/docs/images/properties_window.png b/docs/images/properties_window.png
diff --git a/docs/images/type_select.png b/docs/images/type_select.png
diff --git a/docs/images/vis_gland_cmap.png b/docs/images/vis_gland_cmap.png
diff --git a/docs/images/vis_graph.png b/docs/images/vis_graph.png
diff --git a/docs/images/visualize_interface.png b/docs/images/visualize_interface.png
diff --git a/docs/index.rst b/docs/index.rst
@@ -14,6 +14,7 @@ Welcome to TIA Toolbox's documentation!
     Pre-trained Models <pretrained.rst>
     Jupyter Notebooks <notebooks.rst>
     Algorithms <algorithms.rst>
+    Visualization <visualization.rst>
     API Reference <_autosummary/tiatoolbox>
     Contributing <contributing.rst>
     Authors <authors.rst>

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -1,5 +1,7 @@
 .. highlight:: shell
 
+.. _installation:
+
 Installation
 ************