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CHANGELOG.md

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Changelog

1.1.*

  • Adds lionheart --version command to CLI.

1.1.5

  • Fixes package specification in pyproject.toml

Future note: An upcoming version will contain completely recomputed resource files with changed bin-coordinates to reduce RAM usage of the mosdepth coverage extraction. At the same time, we will be updating the exclusion bin index files to fix a small discrepency between the shared features and the features extracted with the current lionheart version. Stay tuned for updates in the coming month(s).

1.1.4

  • Adds project URLs to package to list them on the pypi site.

1.1.2

  • Fixes writing of README in lionheart predict_sample. Thanks to @LauraAndersen for detecting the problem.
  • Improvements to installation guide in repository README.
  • Workflow example improvements.

1.1.1

  • Improves CLI documentation for some commands (in --help pages).

1.1.0

This release adds multiple CLI commands that:

  1. allow reproducing results from the article and seeing the effect of adding your own datasets:
  • Adds lionheart cross_validate command. Perform nested leave-one-dataset-out cross-validation on your dataset(s) and/or the included features.
  • Adds lionheart validate command. Validate a model on the included external dataset or a custom dataset.
  • Adds lionheart evaluate_univariates command. Evaluate each feature (cell-type) separately on your dataset(s) and/or the included features.
  1. expands what you can do with your own data:
  • Adds lionheart customize_thresholds command. Calculate the ROC curve and probability densities (for deciding probability thresholds) on your data and/or the included features for a custom model or an included model. Allows using probability thresholds suited to your own data when using lionheart predict_sample and lionheart validate.
  • Adds --custom_threshold_dirs argument in lionheart predict_sample. Allows passing the ROC curves and probability densities extracted with lionheart customize_thresholds.

Also:

  • Adds matplotlib as dependency.
  • Bumps generalize dependency requirement to 0.2.1.
  • Bumps utipy dependency requirement to 1.0.3.

1.0.2

  • Fixes bug when training model on a single dataset.
  • Adds tests for a subset of the CLI tools.

1.0.1

  • Fixed model name.