Gandlf

What's Changed
* Version updated for development by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/948
* Upload code coverage only from master by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/950
* Added functionality related to DP training by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/945
* Added documentation on private model training by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/952
* Automatic set strides kernels in dynunet by benmalef in https://github.com/mlcommons/GaNDLF/pull/955
* Add Huggingface Integration by pranayasinghcsmpl in https://github.com/mlcommons/GaNDLF/pull/916
* Standardized dependency installation for GitHub actions by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/921
* Added logo by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/958
* Add support for DICOM WSI by using OpenSlide by benmalef in https://github.com/mlcommons/GaNDLF/pull/959
* Getting ready to tag new version with update dependencies by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/960


**Full Changelog**: https://github.com/mlcommons/GaNDLF/compare/0.1.0...0.1.1

What's Changed
* Entrypoints and new gandlf cli command by VukW in https://github.com/mlcommons/GaNDLF/pull/818
* Trigger tests for pull requests to all branches by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/855
* Update PyTorch dependency by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/857
* Updated CLI options for new API by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/853
* Add a new optimizer by pranayasinghcsmpl in https://github.com/mlcommons/GaNDLF/pull/874
* Minor typos removed by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/882
* Add dynunet model by benmalef in https://github.com/mlcommons/GaNDLF/pull/873
* Hardcoding pip version for workflows by benmalef in https://github.com/mlcommons/GaNDLF/pull/887
* Adding function to get augmentation transforms by szmazurek in https://github.com/mlcommons/GaNDLF/pull/889
* Cleaning setup by VukW in https://github.com/mlcommons/GaNDLF/pull/890
* Added metrics for BraTS Path challenge by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/885
* Metrics library updated to support comma separate inputs by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/900
* Added output path for optimize model by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/896
* Add logging final version by benmalef in https://github.com/mlcommons/GaNDLF/pull/893
* Adding proper parameter usage in the class constructor by szmazurek in https://github.com/mlcommons/GaNDLF/pull/908
* Updated version check for nightly builds by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/910
* Ensure all build commands are in single step by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/911
* New command line API functionality by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/845
* Added programmatic pip list by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/864
* Fix binary auroc error by VukW in https://github.com/mlcommons/GaNDLF/pull/914
* Update sample configuration for classification by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/917
* Torch version updated by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/919
* Updated GaNDLF documentation for clarity by Linardos in https://github.com/mlcommons/GaNDLF/pull/915
* Fixed bug in inference by vahluw in https://github.com/mlcommons/GaNDLF/pull/922
* Add log file parameter to cli commands by benmalef in https://github.com/mlcommons/GaNDLF/pull/912
* Updated docs for clarity by Linardos in https://github.com/mlcommons/GaNDLF/pull/927
* Changed warning message by Linardos in https://github.com/mlcommons/GaNDLF/pull/933
* Fix spurious errors in OpenFL Github Actions workflow by psfoley in https://github.com/mlcommons/GaNDLF/pull/934
* Added the ademamix optimizer by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/936
* Added itcr connectivity map by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/938
* Assert messages to flush to the log file by benmalef in https://github.com/mlcommons/GaNDLF/pull/923
* Added migration guide by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/939
* Update requests version by benmalef in https://github.com/mlcommons/GaNDLF/pull/943
* Added the option to upload coverage to codacy by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/946
* Version updated for tagging by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/947

New Contributors
* pranayasinghcsmpl made their first contribution in https://github.com/mlcommons/GaNDLF/pull/874
* Linardos made their first contribution in https://github.com/mlcommons/GaNDLF/pull/915

**Full Changelog**: https://github.com/mlcommons/GaNDLF/compare/0.0.20...0.1.0

What's Changed
* Version updated for development by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/839
* Updated version checking mechanism by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/841
* PR title regex fix by VukW in https://github.com/mlcommons/GaNDLF/pull/844
* Deprecated pkg resources by VukW in https://github.com/mlcommons/GaNDLF/pull/846
* Fixing data split logic by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/847
* Commenting out auroc by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/850
* Ensure a float tensor is passed for augmentations by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/860
* Refactor inference manager code to save correct files by Geeks-Sid in https://github.com/mlcommons/GaNDLF/pull/865
* Made train batches order same as gt by VukW in https://github.com/mlcommons/GaNDLF/pull/870
* Downgrade requests from newest version by VukW in https://github.com/mlcommons/GaNDLF/pull/871
* Update black action with specific version by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/876
* Create CODEOWNERS by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/867
* Fixed pip version for CI tests by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/898
* Corrected forward operations order by hongbozheng in https://github.com/mlcommons/GaNDLF/pull/897
* Fix train metrics by VukW in https://github.com/mlcommons/GaNDLF/pull/868
* Updated version for release by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/904

New Contributors
* hongbozheng made their first contribution in https://github.com/mlcommons/GaNDLF/pull/897

**Full Changelog**: https://github.com/mlcommons/GaNDLF/compare/0.0.19...0.0.20

What's Changed
* Version update for development by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/797
* Standardizing commenting style for major functions by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/799
* Added a script to generate information useful for debugging by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/803
* Update GitHub templates by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/804
* Version update for dependency for new Google APIs by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/809
* Add schedulers monai by Ainesh06102004 in https://github.com/mlcommons/GaNDLF/pull/807
* Add default line length for linting by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/820
* Fix html rendering by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/824
* Black trailing comma config by szmazurek in https://github.com/mlcommons/GaNDLF/pull/830
* Added readme for running tests locally by VukW in https://github.com/mlcommons/GaNDLF/pull/827
* Added black trailing comma style fix by VukW in https://github.com/mlcommons/GaNDLF/pull/832
* Fixed version dicom anonymizer by VukW in https://github.com/mlcommons/GaNDLF/pull/836
* Added ability to perform stratified data splits by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/831
* Added ability to generate split CSVs using external script by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/833
* Fix code issues reported by codacy by benmalef in https://github.com/mlcommons/GaNDLF/pull/808
* Removing double print of metrics by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/838
* Version update for tagging a new release by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/837

New Contributors
* VukW made their first contribution in https://github.com/mlcommons/GaNDLF/pull/827
* benmalef made their first contribution in https://github.com/mlcommons/GaNDLF/pull/808

**Full Changelog**: https://github.com/mlcommons/GaNDLF/compare/0.0.18...0.0.19

What's Changed
* Updated version for development by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/732
* Upgrade base python and numpy versions by szmazurek in https://github.com/mlcommons/GaNDLF/pull/730
* Updated docs for new python by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/737
* Add error handling for brain age model by 1Pravi in https://github.com/mlcommons/GaNDLF/pull/710
* Updated cosign installation by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/739
* Upgrade base pandas version by Ainesh06102004 in https://github.com/mlcommons/GaNDLF/pull/740
* Making black version static by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/744
* Revert to correct download location by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/745
* Upgrade base torchmetrics version by szmazurek in https://github.com/mlcommons/GaNDLF/pull/742
* Consistent black across the codebase by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/746
* Upgrade base PyTorch version by szmazurek in https://github.com/mlcommons/GaNDLF/pull/747
* Update installation link by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/748
* Upgrade base torchio version by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/749
* Update installation instructions by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/750
* Updated the minimum and maximum python versions by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/751
* Fixed the issue where a specific library prevents training to start by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/753
* Minor documentation updates by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/754
* Bump internal version by dependabot in https://github.com/mlcommons/GaNDLF/pull/759
* Fix for sample data download by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/766
* Added documentation for extending optimizer and schedulers by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/764
* Updated min devcontainer requirement by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/769
* Ensure pip is available in environment path for devcontainers by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/770
* Sync tests with openfl develop branch by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/772
* Updated git command for speed by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/773
* Consolidated a few checks by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/774
* Added option to bias the patch extraction for label sampler by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/771
* Added option to use different weights for sampler biasing and loss by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/777
* Added option to not apply zero plane cropping for gandlf preprocess by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/779
* Add optimizers monai by Ainesh06102004 in https://github.com/mlcommons/GaNDLF/pull/781
* Rename parseconfig for consistency by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/784
* Upgrade pytorch and torchio versions by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/786
* Added flowcharts for developers by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/789
* Added an option for backwards compatibility for parseconfig by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/791
* Updated openfl tests by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/787
* Version updated for tagging by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/796

New Contributors
* szmazurek made their first contribution in https://github.com/mlcommons/GaNDLF/pull/730
* 1Pravi made their first contribution in https://github.com/mlcommons/GaNDLF/pull/710
* Ainesh06102004 made their first contribution in https://github.com/mlcommons/GaNDLF/pull/740

**Full Changelog**: https://github.com/mlcommons/GaNDLF/compare/0.0.17...0.0.18

What's Changed
* Version update for development by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/648
* Added citation file by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/654
* Added new optimizers by AdiSir05 in https://github.com/mlcommons/GaNDLF/pull/646
* Allow histology patches to be extracted without ground truth labels by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/657
* Added metric calculation from CLI by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/663
* Added a few segmentation metrics by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/661
* Repository badges have been updated by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/667
* Added instructions on creating new tutorials by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/664
* Ensure parameters are built into the model dictionary by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/673
* Calculating penalty after all compute objects are initialized by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/675
* Add image similarity metrics by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/669
* Allow the penalty and class weights in the config to be used by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/677
* Added documentation related to OpenFL by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/683
* Add MLCube wrapper for metrics API by hasan7n in https://github.com/mlcommons/GaNDLF/pull/681
* Adding mechanism to curate each extracted patch by shubhaminnani in https://github.com/mlcommons/GaNDLF/pull/653
* Added mask to SSIM function call by FelixSteinbauer in https://github.com/mlcommons/GaNDLF/pull/685
* Removed history file by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/690
* Updated the metrics output by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/687
* Update docker image name in workflow by hasan7n in https://github.com/mlcommons/GaNDLF/pull/692
* Fixed plotting function for final stats by Geeks-Sid in https://github.com/mlcommons/GaNDLF/pull/691
* Fixed import for collect stats by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/694
* HED augmentations for digital pathology image by Geeks-Sid in https://github.com/mlcommons/GaNDLF/pull/649
* Added focal loss by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/696
* Added a temporary fix for protobuf by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/702
* Use torchmetric PSNR implementation and argument ordering by FelixSteinbauer in https://github.com/mlcommons/GaNDLF/pull/693
* Introduced percentile normalization for synthesis challenge metrics by FelixSteinbauer in https://github.com/mlcommons/GaNDLF/pull/700
* Upgrade openvino version to latest by Geeks-Sid in https://github.com/mlcommons/GaNDLF/pull/699
* Additional PSNR evaluations for the normalized synthesis case by FelixSteinbauer in https://github.com/mlcommons/GaNDLF/pull/703
* Improved formatting by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/707
* Updated checkout version and test names for clarity by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/708
* Updated default options for sgd by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/709
* Added matthews correlation coefficient loss by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/706
* Using tuples for PSNR datarange by FelixSteinbauer in https://github.com/mlcommons/GaNDLF/pull/712
* Deploy model entrypoint by hasan7n in https://github.com/mlcommons/GaNDLF/pull/711
* Added parameter to toggle NCC computation by FelixSteinbauer in https://github.com/mlcommons/GaNDLF/pull/717
* Adding second classification tutorial by vavali08 in https://github.com/mlcommons/GaNDLF/pull/698
* Minor code refactoring by tosemml in https://github.com/mlcommons/GaNDLF/pull/719
* Combined writing and temp file creation in a single step by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/720
* Update usage information for anonymizer by sanashah007 in https://github.com/mlcommons/GaNDLF/pull/716
* Move unit testing data to the mlcommons storage by sarthakpati in https://github.com/mlcommons/GaNDLF/pull/722
* Fixed model saving when git repo not found by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/729
* Removing dev from version for tagging by scap3yvt in https://github.com/mlcommons/GaNDLF/pull/731

New Contributors
* AdiSir05 made their first contribution in https://github.com/mlcommons/GaNDLF/pull/646
* shubhaminnani made their first contribution in https://github.com/mlcommons/GaNDLF/pull/653
* FelixSteinbauer made their first contribution in https://github.com/mlcommons/GaNDLF/pull/685
* vavali08 made their first contribution in https://github.com/mlcommons/GaNDLF/pull/698
* tosemml made their first contribution in https://github.com/mlcommons/GaNDLF/pull/719
* sanashah007 made their first contribution in https://github.com/mlcommons/GaNDLF/pull/716
* scap3yvt made their first contribution in https://github.com/mlcommons/GaNDLF/pull/729

**Full Changelog**: https://github.com/mlcommons/GaNDLF/compare/0.0.16...0.0.17