Lightning integration and large-scale metrics update

What's Changed

• Update lighting integration branch by @benmalef in #996
• Version updated for development by @scap3yvt in #1003
• Lightning integration by @szmazurek in #991
• Updated version for action by @scap3yvt in #1004
• More robust CI by @scap3yvt in #1006
• Fix for new unit test data by @scap3yvt in #1008
• Fixed path for BraTS metrics config by @scap3yvt in #1009
• Usage document formatting updates by @scap3yvt in #1011
• Added sanity check for metrics by @scap3yvt in #1012
• Added ability to customize segmentation by @scap3yvt in #1014
• Added a yaml load fallback for panoptica by @scap3yvt in #1017
• Upgrade dependency version by @neuronflow in #1018
• Panoptica updated with better logic by @scap3yvt in #1020
• Fix brats config samples by @vpchung in #1021
• Updated version for release by @scap3yvt in #1016

New Contributors

• @neuronflow made their first contribution in #1018
• @vpchung made their first contribution in #1021

Full Changelog: 0.1.3...0.1.4

Updated python versions for long term maintainance

What's Changed

• Version updated for development by @scap3yvt in #975
• Correct spelling error by @szmazurek in #977
• Update versions for ossar and codeql actions by @scap3yvt in #979
• Update cron schedule for ossar by @scap3yvt in #980
• Ensure synthesis metrics have an option to take voided image by @sarthakpati in #981
• Updated the minimum python version by @benmalef in #984
• Added profiling by @pranayasinghcsmpl in #987
• Spellchecker corrections by @szmazurek in #990
• Corrected the OpenFL link in usage documentation by @naman1303 in #989
• Dependabot update by @dependabot in #992
• Update dependency version by @payalcha in #994
• Added configuration management using pydantic by @benmalef in #986
• CI updated to new python by @scap3yvt in #1000
• Added instance wise segmentation metrics by @scap3yvt in #998
• Version updated for tagging by @scap3yvt in #1002

New Contributors

• @naman1303 made their first contribution in #989
• @payalcha made their first contribution in #994

Full Changelog: 0.1.2...0.1.3

Updated documentation, and dependencies, and new optimizers

What's Changed

• Version updated for development by @scap3yvt in #961
• Added a faq point for the version mismatch by @scap3yvt in #964
• Add documentation about the log file parameter by @benmalef in #967
• Change the default logfile by @benmalef in #966
• Refactor the code related to loss computation by @szmazurek in #965
• Updated PyTorch to newer version by @scap3yvt in #971
• Update PyTorch to previous stable by @scap3yvt in #972
• Added new optimizers by @scap3yvt in #970
• Version updated for release by @scap3yvt in #973
• Added the ability to perform automated spell checking by @szmazurek in #941

Full Changelog: 0.1.1...0.1.2

New logo, updated DICOM support for WSI, and DP

What's Changed

• Version updated for development by @scap3yvt in #948
• Upload code coverage only from master by @scap3yvt in #950
• Added functionality related to DP training by @scap3yvt in #945
• Added documentation on private model training by @scap3yvt in #952
• Automatic set strides kernels in dynunet by @benmalef in #955
• Add Huggingface Integration by @pranayasinghcsmpl in #916
• Standardized dependency installation for GitHub actions by @scap3yvt in #921
• Added logo by @sarthakpati in #958
• Add support for DICOM WSI by using OpenSlide by @benmalef in #959
• Getting ready to tag new version with update dependencies by @sarthakpati in #960

Full Changelog: 0.1.0...0.1.1

0.1.0: new version to kickstart the process of updating APIs

What's Changed

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

New Contributors

• @pranayasinghcsmpl made their first contribution in #874
• @Linardos made their first contribution in #915

Full Changelog: 0.0.20...0.1.0

Last tag with older API - no new functionality to be added after this

What's Changed

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

New Contributors

• @hongbozheng made their first contribution in #897

Full Changelog: 0.0.19...0.0.20

Tagging before major API overhaul

What's Changed

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

New Contributors

• @VukW made their first contribution in #827
• @benmalef made their first contribution in #808

Full Changelog: 0.0.18...0.0.19

A major release with multiple updated dependencies

What's Changed

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

New Contributors

• @szmazurek made their first contribution in #730
• @1Pravi made their first contribution in #710
• @Ainesh06102004 made their first contribution in #740

Full Changelog: 0.0.17...0.0.18

New version before major dependency updates

What's Changed

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

New Contributors

• @AdiSir05 made their first contribution in #646
• @shubhaminnani made their first contribution in #653
• @FelixSteinbauer made their first contribution in #685
• @vavali08 made their first contribution in #698
• @tosemml made their first contribution in #719
• @sanashah007 made their first contribution in #716
• @scap3yvt made their first contribution in #729

Full Changelog: 0.0.16...0.0.17

Major release with the paper

What's Changed

• Implemented a common copyright message for CLI and updated links & email by @sarthakpati in #512
• Change python-test.yml to pass on docs-only by @AlexanderGetka-cbica in #517
• Making the flowchart a bit more generic to showcase inference by @sarthakpati in #514
• Updated install verification logic by @sarthakpati in #520
• Updated implementation for augmentations that need std-dev by @sarthakpati in #521
• Ability to generate multiple training configurations using a specific strategy by @sarthakpati in #525
• Updated patch divisibility logic by @sarthakpati in #523
• Added sanity check for norm_type for non-vgg network architectures by @sarthakpati in #528
• Fixing requirement for SimpleITK for a problematic version by @sarthakpati in #537
• Preprocessing is now working when a random set of metadata columns are present by @sarthakpati in #535
• Added ability to combine classification inference results from different architectures by @sarthakpati in #531
• Added ability to save initial and latest models in addition to best by @sarthakpati in #539
• Latest model is now saved correctly by @sarthakpati in #546
• Consideration of scaling_factor has been moved to loss/metrics by @sarthakpati in #541
• Added ability to specify testing data csv in main cli by @sarthakpati in #545
• added more information for #529 by @sarthakpati in #549
• Add docker docs by @AlexanderGetka-cbica in #550
• Added more details to documentation specifically related to training customization by @sarthakpati in #552
• Added more details about Docker by @sarthakpati in #554
• Separate modelDir and outputDir parameters for inference to cohesiveness by @sarthakpati in #557
• The logs now include metric headers from overall_stats by @sarthakpati in #558
• Fix parseConfig separately from my other PR by @AlexanderGetka-cbica in #561

Full Changelog: 0.0.5...0.0.16