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🐛 Fix codecov Reporting #811

Merged
merged 2 commits into from
Apr 29, 2024
Merged

🐛 Fix codecov Reporting #811

merged 2 commits into from
Apr 29, 2024

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shaneahmed
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@shaneahmed shaneahmed commented Apr 29, 2024

  • Fix codecov Reporting

Fixes the following error:

[2024-04-26T13:26:38.358Z] ['error'] There was an error running the uploader: Error uploading to [https://codecov.io:](https://codecov.io/) Error: There was an error fetching the storage URL during POST: 404 - {'detail': ErrorDetail(string='Unable to locate build via Github Actions API. Please upload with the Codecov repository upload token to resolve issue.', code='not_found')}
[2024-04-26T13:26:38.358Z] ['verbose'] The error stack is: Error: Error uploading to [https://codecov.io:](https://codecov.io/) Error: There was an error fetching the storage URL during POST: 404 - {'detail': ErrorDetail(string='Unable to locate build via Github Actions API. Please upload with the Codecov repository upload token to resolve issue.', code='not_found')}
    at main (/snapshot/repo/dist/src/index.js)
    at process.processTicksAndRejections (node:internal/process/task_queues:95:5)
[2024-04-26T13:26:38.358Z] ['verbose'] End of uploader: 748 milliseconds
[2024-04-26T13:26:38.358Z] ['info'] Codecov will exit with status code 0. If you are expecting a non-zero exit code, please pass in the `-Z` flag

@shaneahmed shaneahmed self-assigned this Apr 29, 2024
@shaneahmed shaneahmed added bug Something isn't working help wanted Extra attention is needed labels Apr 29, 2024
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codecov bot commented Apr 29, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.89%. Comparing base (7b6f1ee) to head (26b100e).
Report is 3 commits behind head on develop.

Additional details and impacted files
@@           Coverage Diff            @@
##           develop     #811   +/-   ##
========================================
  Coverage    99.89%   99.89%           
========================================
  Files           69       69           
  Lines         8574     8574           
  Branches      1640     1640           
========================================
  Hits          8565     8565           
  Misses           1        1           
  Partials         8        8           

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

@shaneahmed shaneahmed added dev tools Changes/Updates in Development tools and removed help wanted Extra attention is needed labels Apr 29, 2024
@shaneahmed shaneahmed added this to the Release v1.6.0 milestone Apr 29, 2024
@shaneahmed shaneahmed merged commit f664f04 into develop Apr 29, 2024
15 checks passed
@shaneahmed shaneahmed deleted the bug-fix-codecov-reporting branch April 29, 2024 11:28
@shaneahmed shaneahmed mentioned this pull request Dec 12, 2024
shaneahmed added a commit that referenced this pull request Dec 12, 2024
## 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 <John-P@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Adam Shephard <39619155+adamshephard@users.noreply.github.com>
Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com>
Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com>
Co-authored-by: Simon Graham <20071401+simongraham@users.noreply.github.com>
Co-authored-by: Abdol A <u2271662@live.warwick.ac.uk>
Co-authored-by: Jiaqi-Lv <60471431+Jiaqi-Lv@users.noreply.github.com>
Co-authored-by: Dmitrii Blaginin <blaginin@mbp.lan>
Co-authored-by: behnazelhaminia <30952176+behnazelhaminia@users.noreply.github.com>
Co-authored-by: George Batchkala <46561186+GeorgeBatch@users.noreply.github.com>
Co-authored-by: vqdang <24943262+vqdang@users.noreply.github.com>
Co-authored-by: Jiaqi Lv <lvjiaqi9@gmail.com>
Co-authored-by: Alon Alexander <alon008@gmail.com>
@shaneahmed shaneahmed mentioned this pull request Dec 12, 2024
shaneahmed added a commit that referenced this pull request Dec 12, 2024
## 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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