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. (#18)
• Fixed a verbiage error for subsetting error messages. Now, it is explicitly stated that integer indexing is not supported. (#17)
• Updated documentation to fix typos.

Changes and New Features

• Updated CI pipeline to include newest Python releases. (#15)
• Added our logo usage policy. (#20)
• 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 (#4 )
• Added docstrings for + and += operators
• Updated references for CytofDR paper publication in Nature Communications (#4 )

Known Issues

• Reference datasets still cannot be downloaded due to broken source links (#3 )
• data.load_expression does not report mismatched columns when loading multiple datasets (#7)

PyCytoData Datasets (Rev.1)

This release contains the three built-in datasets in PyCytoData: Levine13, Levine32, and Samusik. The datasets are originally obtained from FlowRepository (Access Number: FR-FCM-ZZPH) and distributed in accordance with the licensing terms. You do not need to manually download these datasets yourself: the updated package (starting from v0.1.2) will automatically handle the data processing.

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

Release Notes

• This is the first official pre-release 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

Known Issue

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