Adding training runner, various fixes and extensions

What's Changed

• Add utils and attention layers by @mebristo in #170
• Make improvements to report tool by @mebristo in #173
• Fixing checkpoint downloader by @vale-salvatelli in #174
• Updated augmentations for histology images by @maxilse in #179
• First version of runner by @mebristo in #178
• Copy histopathology folder into hi-ml by @mebristo in #181
• Add mean pooling layer by @dccastro in #187
• Add inference to runner by @mebristo in #186
• Bump pillow from 8.3.2 to 9.0.0 by @dependabot in #184
• Bump node-fetch from 2.6.2 to 2.6.7 in /.github/actions/format_coverage by @dependabot in #182
• update DeepSMILE models by @maxilse in #188
• Fix DeepMIL metrics bug by @dccastro in #195
• Adding transformation adaptor by @vale-salvatelli in #193
• Show workspace name in error message by @fepegar in #196
• Adding cross-validation to the hi-ml runner by @ant0nsc in #198
• Retire the manual changelog by @ant0nsc in #216
• Switch autodoc format to be without types by @ant0nsc in #217
• FIX: Output directories of multi-GPU DDP can be wrong by @ant0nsc in #221
• FIX: Config loader fails when using relative directories by @ant0nsc in #220
• FIX: update base_module to avoid cache being reused when cachemode is None by @vale-salvatelli in #222
• ENH: Enforce prefixes for PR titles by @ant0nsc in #224
• Migrate DeepMIL fine-tuning, dropout, subsampling, FP/TN by @dccastro in #219
• ENH: Add transformer pooling by @maxilse in #227
• DOC: Fix some Sphinx warnings by @fepegar in #232
• ENH: Multiclass AUROC, metrics test, and max pooling in DeepMIL by @harshita-s in #233
• ENH: Add cross-validation reports for DeepMIL by @dccastro in #229
• DOC: Better onboarding instructions in Readme files by @ant0nsc in #223
• BUG: Invalid commandline args should raise an error by @ant0nsc in #242
• ENH: Dataset mounting is now configurable by @ant0nsc in #241
• BUG: Added tolerance to test by @maxilse in #246
• ENH: Runner specifies docker image size, prints defaults by @ant0nsc in #243
• ENH: Adding tag argument to specify display name by @ant0nsc in #245
• BUG: Pass cycle mode to the trainer for SSL, Crossval_index check by @ant0nsc in #248
• ENH: Enable DeepMIL validation outputs via outputs handler by @dccastro in #244
• BUG: Pin package versions for histopathology by @ant0nsc in #253
• ENH: Linearly scale the learning rate of ssl models by @maxilse in #254
• BUG: Perform validation and test on full slide by @harshita-s in #256
• BUG: Fix renaming of outputs folders in Azure ML by @dccastro in #258
• DOC: Hide checklist in PR template by @fepegar in #255
• ENH: Better handling of duplicates when merging conda envs by @mebristo in #257
• BUG: Move cross validation function from innereye-dl to himl by @maxilse in #262
• BUG: Enable outputs handler to work in DDP by @dccastro in #261
• BUG: Pin jinja2 to avoid bug in latest version by @mebristo in #266
• BUG: Correct pythonpath separator character in VS code settings file by @mebristo in #267
• BUG: Fix spurious test errors by @ant0nsc in #270
• BUG: Conda environment file merging should also split on semicolons by @mebristo in #272
• ENH: Add dataloader kwargs in tiles data modules, including num_workers by @dccastro in #268
• BUG: Hotfix for breaking changes in Pytorch Lightning 1.6.0 by @ant0nsc in #278
• ENH: Add colors to the VSCode window by @ant0nsc in #277
• ENH: Using default workspace datastore when datastore name is missing by @ant0nsc in #275
• BUG: Params pl_limit_train(/val)_batches should accept float by @mebristo in #279
• BUG: Workaround to avoid saving a dataframe as a hyperparameter by @kenza-bouzid in #282
• BUG: Remove outdated SDK usage by @ant0nsc in #287
• ENH: Added histo ssl configs by @maxilse in #264
• ENH: Add step for GPU tests on the histo folder by @ant0nsc in #273
• ENH: Add validation results to crossval report by @dccastro in #286
• ENH: Add slide dataloader by @kenza-bouzid in #285
• ENH: Add regression test framework to runner by @ant0nsc in #289
• BUG: Mitigate DeepMIL GPU memory leak in results dict by @dccastro in #293
• STYLE: Fix mypy misconfiguration for histopathology by @dccastro in #294
• BUG: Fix SSL encoder setup and pin versions to support A100 GPUs by @dccastro in #295
• BUG: Resolve multiple values for keyword argument 'pin_memory' by @harshita-s in #296
• ENH: Add support for model and metadata serialization by @ant0nsc in #252
• BUG: MyPy error showing in CI by @ant0nsc in #297
• BUG: Collate gathered DeepMIL outputs on CPU by @dccastro in #291
• BUG: Pin torchvision to install alongside PyTorch and CUDA toolkit by @dccastro in #302
• ENH: Unit test for current deepmil pipeline with mock data by @kenza-bouzid in #300
• BUG: HOTFIX skip pathmnist tests by @kenza-bouzid in #307
• ENH: Add is_caching parameter in DeepMIL container by @harshita-s in #303

New Contributors

• @vale-salvatelli made their first contribution in #174
• @maxilse made their first contribution in #179
• @dccastro made their first contribution in #187
• @dependabot made their first contribution in #184
• @fepegar made their first contribution in #196
• @harshita-s made their first contribution in #233
• @kenza-bouzid made their first contribution in #282

Full Changelog: 0.1.13...v0.2.0