Dependency upgrades + bug fixes

What's Changed

• ENH: Add DeepSMILESlidesPandaBenchmark config by @mebristo in #385
• ENH: HTML reports for multiclass case by @harshita-s in #376
• ENH: Add utils to upload annotations to the Digital Slide Archive by @fepegar in #373
• ENH: Upload Codecov results also when tests fail by @ant0nsc in #383
• BUG: Remove padding when loading slides by @fepegar in #387
• ENH: Add visualization parameters to DSA annotations script by @fepegar in #390
• BUG: TilesPandaImageNetMIL runs hang on Azure ML by @harshita-s in #400
• STYLE: Disable pre-commit CI autofixes by @fepegar in #402
• ENH: Add Regression Tests by @mebristo in #359
• STYLE: Fix max line length in autopep8 hook by @fepegar in #403
• ENH: Select top and bottom tiles on the fly by @kenza-bouzid in #388
• BUG: Update contributing link in Readme by @kenza-bouzid in #408
• STYLE: Fix file without end line by @fepegar in #409
• ENH: PANDA SSL with tile selection enabled (random or tile occupancy) by @harshita-s in #398
• ENH: Add gpu tests coverage to codecov reports by @kenza-bouzid in #399
• DEL: Delete deprecated code from outputs utils by @kenza-bouzid in #407
• STYLE: Ensure new line at the end of JSON files by @fepegar in #410
• STYLE: Rename pl_limit_batches to pl_fast_dev_run by @kenza-bouzid in #415
• DEL: Remove TilesPANDA regression test by @mebristo in #418
• BUG: Correctly setting up encoder for SSLMIL by @harshita-s in #404
• ENH: Pin msrest to avoid missing import by @mebristo in #424
• DOC: Change outdated model name by @ant0nsc in #419
• STYLE: Set default PR title for pre-commit CI bot by @fepegar in #413
• DOC: Adding a high-level description of our software design process by @ant0nsc in #380
• ENH: Pin cloudpickle to fix warnings in Azure ML by @mebristo in #426
• BUG: Add path resolution in dataset mounting script by @kenza-bouzid in #416
• DEL: Retire the --azureml flag of the runner by @kenza-bouzid in #420
• DOC: Fix out of sync docs and typo by @kenza-bouzid in #428
• DOC: Document Histopathology Models by @ant0nsc in #429
• ENH: Simplify how we handle conda environment files in AML submissions by @ant0nsc in #414
• ENH: Add Credential Scanning Workflow by @ant0nsc in #370
• ENH: Reduce console logging noise by @ant0nsc in #430
• ENH: Add Cohen Kappa module metric to DeepMIL by @harshita-s in #422
• BUG: Stop looking for environment file if already running in AML by @mebristo in #432
• DOC: Remove retired argument names by @ant0nsc in #435
• ENH: Add unit tests for disabling top and bottom tiles by @kenza-bouzid in #439
• BUG: Default parameters in DeepSMILECRCk container by @harshita-s in #440
• ENH: Add makefile commands for smoke tests by @mebristo in #442
• ENH: Enable setting plot options in the containers config by @kenza-bouzid in #441
• BUG: Workflows time out because of using a too large test dataset by @ant0nsc in #447
• ENH: Improve mypy arguments by @fepegar in #448
• ENH: Redirect profiler traces to outputs folder and add debugging doc by @kenza-bouzid in #444
• ENH: Make building Monai-based models reproducible by @ant0nsc in #443
• ENH: Switch from azureml-sdk to azureml-core by @ant0nsc in #455
• BUG: Fix confusion matrix plots by @kenza-bouzid in #450
• ENH: Add text and image inference code for CXR multimodal by @ozan-oktay in #438
• ENH: Upgrade PyTorch Lightning to 1.6.4 by @kenza-bouzid in #453
• ENH: Remove the dependency on Lightning and Lightning Bolts by @ozan-oktay in #466
• ENH: Add Dependabot config file by @fepegar in #462
• ENH: Rename "multimodal" to "hi-ml-multimodal" by @fepegar in #467
• ENH: Enable pre-commit CI autofixes by @fepegar in #474
• ENH: Run an additional validation epoch at the end of training. by @kenza-bouzid in #465
• ENH: Add flake8 requirement to histology Conda environment by @ant0nsc in #454
• ENH: Update azureml packages versions. by @kenza-bouzid in #477

New Contributors

• @ozan-oktay made their first contribution in #438

Full Changelog: v0.2.2...v0.2.3