✨ Use ruff for Linting
#625
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shaneahmed
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Jun 22, 2023
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shaneahmed
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- Add checks for
- pydocstyle
- flake8-future-annotations
- flake8-errmsg
- pygrep-hooks
- flake8-use-pathlib
- Ruff-specific rules
- flake8-self
- flake8-type-checking
- tryceratops
- Replace flake8 with ruff Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
- Add flake8 plugins Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
- Update `pyproject.toml` Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
- Update `pyproject.toml` Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
- Fix B905 Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
- Remove `flake8` settings from `setup.cfg` Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
Codecov Report
@@ Coverage Diff @@
## develop #625 +/- ##
===========================================
+ Coverage 99.83% 99.84% +0.01%
===========================================
Files 64 64
Lines 7249 7305 +56
Branches 1408 1405 -3
===========================================
+ Hits 7237 7294 +57
Misses 4 4
+ Partials 8 7 -1
📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more |
- SIM300 [*] Yoda conditions are discouraged, use `wsi.info.mpp[0] > 0.1` instead - ERA001 [*] Found commented-out code - Fix B905 `zip()` without an explicit `strict=` parameter
- A003 Class attribute `filter` is shadowing a Python builtin - N816 Variable `rcParam` in global scope should not be mixedCase
- Fix `zip()` without an explicit `strict=` parameter - This feature is not supported in Python 3.8
…ev-use-ruff-for-linting
- Fix `zip()` without an explicit `strict=` parameter - This feature is not supported in Python 3.8
- Fix `E741` Ambiguous variable name
- Fix `E501` Line too long
- Fix `SIM108` [*] Use ternary operator
- Fix `N818` Exception name should be named with an Error suffix
- Fix `ERA001` [*] Found commented-out code - Fix `FIX002` Line contains TODO - Fix `FIX004` Line contains HACK
- Fix `ERA001` [*] Found commented-out code
…keys()` - Fix `SIM118` [*] Use `pretrained_name in pretrained_info` instead of `pretrained_name in pretrained_info.keys()`
- Use ruff in Git Workflow Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
- Fix `B904` Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
- Autofix "UP" using ruff Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
- Add complexity check Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
- Add trailing commas check Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
- Fix deepsource error Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
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Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
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Fix linter error in cli, annotation and visualization from sparkles Use ruff for Linting #625 --------- Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com>
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Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
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# Conflicts: # pyproject.toml
for more information, see https://pre-commit.ci
Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
for more information, see https://pre-commit.ci
Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
…ev-use-ruff-for-linting
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Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
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## 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 <74412979+mostafajahanifar@users.noreply.github.com> Co-authored-by: John Pocock <John-P@users.noreply.github.com> Co-authored-by: DavidBAEpstein <David.Epstein@warwick.ac.uk> Co-authored-by: David Epstein <22086916+DavidBAEpstein@users.noreply.github.com> Co-authored-by: Ruqayya Awan <18444369+ruqayya@users.noreply.github.com> Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com> Co-authored-by: adamshephard <39619155+adamshephard@users.noreply.github.com> Co-authored-by: adamshephard <adam.shephard@warwick.ac.uk> Co-authored-by: Abdol <a@fkrtech.com> Co-authored-by: Jiaqi-Lv <60471431+Jiaqi-Lv@users.noreply.github.com> Co-authored-by: Abishek <abishekraj6797@gmail.com> Co-authored-by: Dmitrii Blaginin <blaginin@mbp.lan>
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## 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
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