From 5e60c7527a0d4f04d934c8cecc2b1bb8ae21b67a Mon Sep 17 00:00:00 2001 From: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Date: Fri, 15 Dec 2023 22:33:18 +0000 Subject: [PATCH 1/4] [skip ci] :memo: Update HISTORY.md Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> --- HISTORY.md | 45 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/HISTORY.md b/HISTORY.md index 55a4a0757..8a865f82b 100644 --- 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 From 464f1cf0058b889d6358064d656de2892cd8fbc7 Mon Sep 17 00:00:00 2001 From: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Date: Fri, 15 Dec 2023 22:33:41 +0000 Subject: [PATCH 2/4] [skip ci] :memo: Update HISTORY.md and AUTHORS.md Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> --- AUTHORS.md | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/AUTHORS.md b/AUTHORS.md index 8da83c9dc..5b574b01b 100644 --- a/AUTHORS.md +++ b/AUTHORS.md @@ -5,15 +5,19 @@ - TIA Centre led by Nasir Rajpoot - 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> From 612f05e9f3761f3c472ed5af8e332d2a940661f4 Mon Sep 17 00:00:00 2001 From: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Date: Fri, 15 Dec 2023 22:38:00 +0000 Subject: [PATCH 3/4] [skip ci] :memo: Update version numbers Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> --- .github/workflows/docker-publish.yml | 2 +- CITATION.cff | 2 +- pyproject.toml | 2 +- setup.py | 2 +- tiatoolbox/__init__.py | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml index da47e2827..1d29fa28b 100644 --- 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/CITATION.cff b/CITATION.cff index 4d2bcc803..f04d2f4a3 100644 --- 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/pyproject.toml b/pyproject.toml index ab7e480bb..40cd0c2c9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -47,7 +47,7 @@ [tool.poetry] name = "TIA Centre" -version = "1.4.0" +version = "1.5.0" description = "test" authors = ["TIA Centre "] diff --git a/setup.py b/setup.py index f72cac62f..784075514 100644 --- a/setup.py +++ b/setup.py @@ -63,6 +63,6 @@ test_suite="tests", tests_require=test_requirements, url="https://github.com/TissueImageAnalytics/tiatoolbox", - version="1.4.1", + version="1.5.0", zip_safe=False, ) diff --git a/tiatoolbox/__init__.py b/tiatoolbox/__init__.py index 333252032..9c009a1ac 100644 --- a/tiatoolbox/__init__.py +++ b/tiatoolbox/__init__.py @@ -20,7 +20,7 @@ __author__ = """TIA Centre""" __email__ = "tialab@dcs.warwick.ac.uk" -__version__ = "1.4.1" +__version__ = "1.5.0" # This will set the tiatoolbox external data # default to be the user home folder, should work on both Window and Unix/Linux From ed2cfa07336542811d1a9d2d10bd4792cb4df53e Mon Sep 17 00:00:00 2001 From: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Date: Fri, 15 Dec 2023 22:40:13 +0000 Subject: [PATCH 4/4] [skip ci] :bug: Fix deepsource errors Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> --- tiatoolbox/annotation/storage.py | 1 + 1 file changed, 1 insertion(+) diff --git a/tiatoolbox/annotation/storage.py b/tiatoolbox/annotation/storage.py index dbfe7e1b3..59388777b 100644 --- a/tiatoolbox/annotation/storage.py +++ b/tiatoolbox/annotation/storage.py @@ -2377,6 +2377,7 @@ def _unpack_wkb( cx: float, cy: float, ) -> bytes: + """Unpack WKB data.""" return ( self._decompress_data(data) if data