Releases

Here we include our release notes for past releases in sequential order.

v0.3.1

This is a minor maintenance update of v0.3.x with updated references and documentation.

Changes and New Features

  • Updated referneces and citation information in all relavent documentaion pages

  • Removed a warning on SAUCIE’s installation documentation

Improvements

  • Update-to-date documentation and references

Deprecations

  • (Since v0.2.0) The comparison_classes parameter of the EvaluationMetrics.embedding_concordance method will no longer accept str input.

v0.3.0

This releases adds some new features along with some minor improvements and fixes.

Changes and New Features

  • Add minmax normalization option for the evaluation.EvaluationMetric.EMD method

  • Add alternative implementation of evaluation.EvaluationMetric.NPE with total variation distance (TVD)

  • Allow both min-max EMD and and TVD NPE for automatic evaluation of DR methods

Improvements

  • Docstrings and documentations reformatted for clarity

Deprecations

  • (Since v0.2.0) The comparison_classes parameter of the EvaluationMetrics.embedding_concordance method will no longer accept str input.

v0.2.2

This is a minor maintenance update of v0.2.x with updated references and documentation.

Changes and New Features

  • Updated referneces and citation information in all relavent documentaion pages

  • Removed a warning on SAUCIE’s installation documentation

Improvements

  • Update-to-date documentation and references

Deprecations

  • (Since v0.2.0) The comparison_classes parameter of the EvaluationMetrics.embedding_concordance method will no longer accept str input.

v0.2.1

This is a minor maintenance update of v0.2.x with a few improvements on documentation and docstrings.

Changes and New Features

  • Update licensing information

Improvements

  • Improve documentation and docstrings

Deprecations

  • (Since v0.2.0) The comparison_classes parameter of the EvaluationMetrics.embedding_concordance method will no longer accept str input.

v0.2.0

This releases adds some new features along with some minor improvements and fixes.

Changes and New Features

  • Add pairwise_downsample option for pairwise distance optimization in Reductions.evaluate method.

  • Add example datasets for the GitHub repo.

  • Improve docstrings for documentations.

  • Improve unit tests for coverage.

Deprecations

  • The comparison_classes parameter of the EvaluationMetrics.embedding_concordance method will no longer accept str input.

v0.1.1 (EOL)

This is a minor update of v0.1.x with a few improvements on documentation and docstrings. Given the release of v0.3.0, this version is the End-of-Life (EOL) release for v0.1.x. This version will no longer be maintained going forward. For new features and future fixes, migrate to v0.2.0 or higher, which is compatible with v0.1.x.

Changes and New Features

  • Update licensing information

Improvements

  • Improve documentation and docstrings

v0.1.0

This is the first official release of CytofDR with LTS.

Changes and New Features

  • Support for magic methods: print and [] for Reductions class

  • Add names attributes to Reductions class

  • Add custom DR evaluation

  • Add functions to save DR embeddings and evaluations

  • Improve documentation and docstrings

v0.0.1

  • This is the first offical pre-release of CytofDR.

  • Most of the pipeline is complete, including DR, evaluation, ranking, and plotting.

  • Extensive documentation and tutorial complete.

  • This release aims to aid the completion of our development and tool chain.

  • We are on conda and PyPI!

Note

This is not an official stable release. Please wait for v0.1.0 in the near future.