Releases

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

v0.1.3

This is a minor release that fixes a critical bug that affects all previous releases. Update is strongly recommended. A few quality-of-life improvements are included as well.

Bug Fixes

  • Fixed a critical issue with subsetting channels not updating internal indices lineage channels.

  • Fixed a verbiage error for subsetting error messages. Now, it is explicitly stated that integer indexing is not supported.

  • Updated documentation to fix typos.

Changes and New Features

  • Updated CI pipeline to include newest Python releases.

  • Added our logo usage policy.

  • Clarified the python version needed to run PyCytoData.

  • No new software feature added.

v0.1.2

This is a minor release that fixes a critical bug that affects all previous releases. Update is strongly recommended.

Bug Fixes

  • Fixed a critical issue with PyCytoData.load_dataset() not working due to old web source down (#3)

    • This issue stems from upstream web source, thus affecting all previous releases.

    • This update fixes the issue with a different implementation.

    • There is no implementation change.

Changes and New Features

  • No new feature added.

v0.1.1

This is a minor release with various bug fixes and documentation improvents.

Bug Fixes

  • Fixed a potential issue with loading benchmark datasets’ samples out of order (This behavior is not guaranteed, but a implementation detail)

  • Fixed an issue with DataLoader.load_dataset not recognizing downloaded datasets

  • Fixed an issue with preprocess.bead_normalization having uninitialized array (#9)

Changes and New Features

  • No new feature added

  • Improved documentations with streamlined front page and updated links

  • Added docstrings for + and += operators

  • Updated references for CytofDR paper publication in Nature Communications

v0.1.0

This is the first official release of PyCytoData with LTS.

Bug Fixes

  • Fix the default cofactor of PyCytoData.preprocess

  • Fix lineage channels for levine32 and samusik

Changes and New Features

  • PyCytoData.run_dr_methods now runs on lineage channels only

  • Add tutorials and references for documentation

  • Improve docstrings and general documentations

  • Add preprocessing options for loading benchmark datasets

  • Relax numpy dependency to >=1.20

  • Add descriptors for PyPI releases

Deprecations

  • Permanently remove FileIO.make_dir function for safety reasons

v0.0.1

  • This is the first official prerelease of the PyCytoData package.

  • We have proper support for the following workflows, including:

    • Downloading data

    • Using PyCytoData as CyTOF data analysis pipeline

    • FileIO

    • CyTOF DR Integration

  • Releases on PyPI and conda

Warning

There is a potential issue of compatibility with CytofDR on conda. If a problem occurs, try using pip instead.