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♻️ Update Changes from New Engine Design #882

Merged
merged 13 commits into from
Nov 21, 2024
Merged

♻️ Update Changes from New Engine Design #882

merged 13 commits into from
Nov 21, 2024

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@shaneahmed shaneahmed commented Nov 21, 2024 •
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  • Add changes from New engine design ⚡ Improve Engine Performance and Implementation #578. This will not only simplify the PR but also keep the main repo up to date.
  • Refactor model_to to model_abc
  • Instead of on_gpu use device as an input in line with PyTorch.
  • infer_batch uses device as an input instead of on_gpu

@shaneahmed shaneahmed added the enhancement New feature or request label Nov 21, 2024
@shaneahmed shaneahmed self-assigned this Nov 21, 2024
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codecov bot commented Nov 21, 2024 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.90%. Comparing base (32cae0b) to head (f68a29f).
Report is 1 commits behind head on develop.

Additional details and impacted files 
@@             Coverage Diff             @@
##           develop     #882      +/-   ##
===========================================
+ Coverage    99.88%   99.90%   +0.02%     
===========================================
  Files           69       69              
  Lines         8717     8705      -12     
  Branches      1149     1149              
===========================================
- Hits          8707     8697      -10     
+ Misses           4        3       -1     
+ Partials         6        5       -1

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

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@shaneahmed shaneahmed merged commit ca13e7f into develop Nov 21, 2024
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@shaneahmed shaneahmed deleted the dev-add-changes-from-new-engine-design branch November 21, 2024 22:28
@shaneahmed shaneahmed mentioned this pull request Dec 12, 2024
Merged
shaneahmed added a commit that referenced this pull request Dec 12, 2024
@shaneahmed @John-P
@pre-commit-ci @adamshephard @measty @mostafajahanifar @simongraham @Jiaqi-Lv @behnazelhaminia @GeorgeBatch @vqdang @Alon-Alexander
🔖 Release 1.6.0 (#895)
e14a4fc 
## TIAToolbox v1.6.0 (2024-12-12)

### Major Updates and Feature Improvements

- **Foundation Models Support via `timm` API** (#856, contributed by @GeorgeBatch)
  - Introduced `TimmBackbone` for running additional PyTorch Image Models.
  - Tested models include `UNI`, `Prov-GigaPath`, and `H-optimus-0`.
  - Added an example notebook demonstrating feature extraction with foundation models.
  - `timm` added as a dependency.
- **Performance Enhancements with `torch.compile`** (#716)
  - Improved performance on newer GPUs using `torch.compile`.
- **Multichannel Input Support in `WSIReader`** (#742)
- **AnnotationStore Filtering for Patch Extraction** (#822)
- **Python 3.12 Support**
- **Deprecation of Python 3.8 Support**
- **CLI Response Time Improvements** (#795)

### API Changes

- **Device Specification Update** (#882)
  - Replaced `has_gpu` with `device` for specifying GPU or CPU usage, aligning with PyTorch's `Model.to()` functionality.
- **Windows Compatibility Enhancement** (#769)
  - Replaced `POWER` with explicit multiplication.

### Bug Fixes and Other Changes

- **TIFFWSIReader Bound Reading Adjustment** (#777)
  - Fixed `read_bound` to use adjusted bounds.
  - Reduced code complexity in `WSIReader` (#814).
- **Annotation Rendering Fixes** (#813)
  - Corrected rendering of annotations with holes.
- **Non-Tiled TIFF Support in `WSIReader`** (#807, contributed by @GeorgeBatch)
- **HoVer-Net Documentation Update** (#751)
  - Corrected class output information.
- **Citation File Fix for `cffconvert`** (#869, contributed by @Alon-Alexander)
- **Bokeh Compatibility Updates**
  - Updated `bokeh_app` for compatibility with `bokeh>=3.5.0`.
  - Switched from `size` to `radius` for `bokeh>3.4.0` compatibility (#796).
- **JSON Extraction Fixes** (#772)
  - Restructured SQL expression construction for JSON properties with dots in keys.
- **VahadaneExtractor Warning** (#871)
  - Added warning due to changes in `scikit-learn>0.23.0` dictionary learning (#382).
- **PatchExtractor Error Message Refinement** (#883)
- **Immutable Output Fix in `WSIReader`** (#850)

### Development-Related Changes

- **Mypy Checks Added**
  - Applied to `utils`, `tools`, `data`, `annotation`, and `cli/common`.
- **ReadTheDocs PDF Build Deprecation**
- **Formatter Update**
  - Replaced `black` with `ruff-format`.
- **Dependency Removal**
  - Removed `jinja2`.
- **Test Environment Update**
  - Updated to `Ubuntu 24.04`.
- **Conda Environment Workflow Update**
  - Implemented `micromamba` setup.
- **Codecov Reporting Fix** (#811)
  **Full Changelog:** v1.5.1...v1.6.0

---------

Co-authored-by: John Pocock <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Adam Shephard <[email protected]>
Co-authored-by: Mark Eastwood <[email protected]>
Co-authored-by: Mostafa Jahanifar <[email protected]>
Co-authored-by: Simon Graham <[email protected]>
Co-authored-by: Abdol A <[email protected]>
Co-authored-by: Jiaqi-Lv <[email protected]>
Co-authored-by: Dmitrii Blaginin <[email protected]>
Co-authored-by: behnazelhaminia <[email protected]>
Co-authored-by: George Batchkala <[email protected]>
Co-authored-by: vqdang <[email protected]>
Co-authored-by: Jiaqi Lv <[email protected]>
Co-authored-by: Alon Alexander <[email protected]>
@shaneahmed shaneahmed mentioned this pull request Dec 12, 2024
Merged
shaneahmed added a commit that referenced this pull request Dec 12, 2024
@shaneahmed
🔖 Release 1.6.0 (#898)
0ddd2b1 
## TIAToolbox v1.6.0 (2024-12-12)

### Major Updates and Feature Improvements

- **Foundation Models Support via `timm` API** (#856, contributed by @GeorgeBatch)
  - Introduced `TimmBackbone` for running additional PyTorch Image Models.
  - Tested models include `UNI`, `Prov-GigaPath`, and `H-optimus-0`.
  - Added an example notebook demonstrating feature extraction with foundation models.
  - `timm` added as a dependency.
- **Performance Enhancements with `torch.compile`** (#716)
  - Improved performance on newer GPUs using `torch.compile`.
- **Multichannel Input Support in `WSIReader`** (#742)
- **AnnotationStore Filtering for Patch Extraction** (#822)
- **Python 3.12 Support**
- **Deprecation of Python 3.8 Support**
- **CLI Response Time Improvements** (#795)

### API Changes

- **Device Specification Update** (#882)
  - Replaced `has_gpu` with `device` for specifying GPU or CPU usage, aligning with PyTorch's `Model.to()` functionality.
- **Windows Compatibility Enhancement** (#769)
  - Replaced `POWER` with explicit multiplication.

### Bug Fixes and Other Changes

- **TIFFWSIReader Bound Reading Adjustment** (#777)
  - Fixed `read_bound` to use adjusted bounds.
  - Reduced code complexity in `WSIReader` (#814).
- **Annotation Rendering Fixes** (#813)
  - Corrected rendering of annotations with holes.
- **Non-Tiled TIFF Support in `WSIReader`** (#807, contributed by @GeorgeBatch)
- **HoVer-Net Documentation Update** (#751)
  - Corrected class output information.
- **Citation File Fix for `cffconvert`** (#869, contributed by @Alon-Alexander)
- **Bokeh Compatibility Updates**
  - Updated `bokeh_app` for compatibility with `bokeh>=3.5.0`.
  - Switched from `size` to `radius` for `bokeh>3.4.0` compatibility (#796).
- **JSON Extraction Fixes** (#772)
  - Restructured SQL expression construction for JSON properties with dots in keys.
- **VahadaneExtractor Warning** (#871)
  - Added warning due to changes in `scikit-learn>0.23.0` dictionary learning (#382).
- **PatchExtractor Error Message Refinement** (#883)
- **Immutable Output Fix in `WSIReader`** (#850)

### Development-Related Changes

- **Mypy Checks Added**
  - Applied to `utils`, `tools`, `data`, `annotation`, and `cli/common`.
- **ReadTheDocs PDF Build Deprecation**
- **Formatter Update**
  - Replaced `black` with `ruff-format`.
- **Dependency Removal**
  - Removed `jinja2`.
- **Test Environment Update**
  - Updated to `Ubuntu 24.04`.
- **Conda Environment Workflow Update**
  - Implemented `micromamba` setup.
- **Codecov Reporting Fix** (#811)
  **Full Changelog:** v1.5.1...v1.6.0
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