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Changelog

Early versions of this toolbox used a manually created changelog. As of March 2022, we have switched to using Github's auto-generated changelog. If you would like to view the changelog for a particular release, you can do so on the Releases page: Each release contains a link for "Full Changelog"

Changelog for Versions before March 2022

0.1.14

Added

  • (#227) Add TransformerPooling.
  • (#179) Add GaussianBlur and RotationByMultiplesOf90 augmentations. Added torchvision and opencv to the environment file since it is necessary for the augmentations.
  • (#193) Add transformation adaptor to hi-ml-histopathology.
  • (#178) Add runner script for running ML experiments.
  • (#181) Add computational pathology tools in hi-ml-histopathology folder.
  • (#187) Add mean pooling layer for MIL.
  • (#186) Add inference to hi-ml runner.
  • (#198) Add cross-validation to hi-ml runner.
  • (#198) Improved editor setup for VSCode.

Changed

  • (#227) Pooling constructor is outside of DeepMIL and inside of BaseMIL now.

  • (#198) Model config loader is now more flexible, can accept fully qualified class name or just top-level module name and class (like histopathology.DeepSMILECrck)

  • (#198) Runner raises an error when Conda environment file contains a pip include (-r) statement

  • (#196) Show current workspace name in error message.

Fixed

  • ([#267]microsoft#267)) Correct PYTHONPATH for Windows in VS Code settings
  • ([#266]microsoft#266)) Pin jinja2 package to avoid 'No attribute Markup' bug in version 3.1.0
  • (#246) Added tolerance to test_attentionlayers.py.
  • (#198) Dependencies for histopathology folder are no longer specified in test_requirements.txt, but correctly in the histopathology Conda environment.
  • (#188) Updated DeepSMILES models. Now they are uptodate with innereye-dl.
  • (#179) HEDJitter was jittering the D channel as well. StainNormalization was relying on skimage.
  • (#195) Fix DeepMIL metrics bug whereby hard labels were used instead of probabilities.

Removed

Deprecated

0.1.13

Added

  • (#170) Add utils including bag sampling, bounding boxes, HEDJitter, StainNormalisation and add attention layers

Changed

  • (#173) Improve report tool: allow lists of tables, option for zipping report folder, option for base64 encoding images

Fixed

  • (#169) Fix a test that was failing occasionally

Removed

Deprecated

0.1.12

Added

  • (#159) Add profiling for loading png image files as numpy arrays.
  • (#152) Add a custom HTML reporting tool
  • (#167) Ability to log to an AzureML run when outside of AzureML

Changed

  • (164) Look in more locations for std out from AzureML run.
  • (#167) The AzureMLLogger has one mandatory argument now, that controls whether it should log to AzureML also when running on a VM.

Fixed

  • (#161) Empty string as target folder for a dataset creates an invalid mounting path for the dataset in AzureML (fixes #160)
  • (#167) Fix bugs in logging hyperparameters: logging as name/value table, rather than one column per hyperparameter. Use string logging for all hyperparameters
  • (#174) Fix bugs in returned local_checkpoint_path when downloading checkpoints from AML run

Removed

Deprecated

0.1.11

Added

  • (#145) Add ability to mount datasets when running locally.
  • (#149) Add a k-fold cross validation wrapper around HyperDrive
  • (#132) Profile methods for loading png image files.

Changed

Fixed

  • (#156 AzureML Runs should use registered environment after retrieval)

Removed

Deprecated

0.1.10

Added

  • (#142) Adding AzureML progress bar and diagnostics for batch loading
  • (#138) Guidelines and profiling for whole slide images.

Changed

  • ([#129])microsoft#129)) Refactor command line tools' arguments. Refactor health_azure.utils' various get_run functions. Replace argparsing with parametrized classes.

Fixed

Removed

Deprecated

0.1.9 (2021-10-20)

Added

  • (#133) PyTorch Lightning logger for AzureML. Helper functions for consistent logging
  • (#136) Documentation for using low priority nodes

Changed

  • (#133) Made large breaking changes to module names, from health.azure to health_azure.
  • ([#141])(microsoft#141)) Update changelog for release and increase scope of test_register_environment to ensure that by default environments are registered with a version number

Fixed

  • (#134) Fixed repo references and added pyright to enforce global checking
  • (#139 Fix register_environment, which was ignoring existing environemnts previously. Also ensure that the environment is given version 1 by default instead of "autosave")

0.1.8 (2021-10-06)

Added

  • (#123) Add helper function to download checkpoint files
  • (#128) When downloading files in a distributed PyTorch job, a barrier is used to synchronize the processes.

Changed

  • (#127) The field is_running_in_azure of AzureRunInfo has been renamed to is_running_in_azure_ml

Fixed

  • (#127) Fixing bug #126: get_workspace was assuming it runs in AzureML, when it was running on a plain Azure build agent.

0.1.7 (2021-10-04)

Added

  • (#111) Adding changelog. Displaying changelog in sphinx docu. Ensure changelog is updated.

Changed

  • (#112) Update himl_tensorboard to work with files not in 'logs' directory
  • (#106) Split into two packages. Most of existing package renamed to hi-ml-azure, remained remains hi-ml.
  • (#113) Add helper function to download files from AML Run, tidied up some command line args, and moved some functions from himl.py to azure_util.py
  • (#122) Add helper functions to upload to and download from AML Datastores

Fixed

  • (#117) Bug fix: Config.json file was expected to be present, even if workspace was provided explicitly.
  • (#119) Bug fix: Code coverage wasn't formatted correctly.

0.1.4 (2021-09-15)

  • This is the baseline release.