ehrapy 0.13.0

0.13.0 🌈

on Python PyPI

🚀 Features

• Transitioning from AnnData to EHRData
  EHRData replaces AnnData as ehrapy's core data structure to better support time-series electronic health record data.
  The key enhancement is native support for 3D tensors (observations × variables × timesteps) alongside the existing 2D matrices, enabling efficient storage of longitudinal patient data.
  A new .tem DataFrame provides time-point annotations, complementing the existing .obs and .var annotations for comprehensive temporal data description.
  While EHRData maintains full backward compatibility with AnnData's API, users can now seamlessly work with time-series data and leverage specialized methods for temporal analysis.
  Existing code using AnnData objects will continue to work, but migration to EHRData is strongly recommended to access enhanced time-series functionality.
• The preferred central data object is now EHRData (#908) @eroell
• The layers argument is now available for all functions operating on X or layers (#908) @eroell
• Update expected behaviour of io.read_fhir (#922) @eroell
• Move mimic_2, mimic_2_preprocessed, diabetes_130_raw, diabetes_130_fairlearn to ehrdata.dt (#908)
• Deprecate all ep.dt.*, refer to datasets in ehrdata (#908) @eroell
• Support Python 3.14 (#996) @Zethson
• Move kaplan_meier & cox_ph plots to holoviews (#995) @Zethson
• Longitudinal normalization (#958) @agerardy
• Add interactive ols plot (#992) @Zethson
• Longitudinal and new qc_metrics (#967) @sueoglu
• Simple Impute for timeseries (#975) @eroell
• Simple implementation of balanced sampling (#937) @sueoglu
• Add Sankey diagram visualization functions (#989) @sueoglu
• Add ep.pl.timeseries() to visualize variables over time (#994) @sueoglu
• Add GPU CI & skeleton (#998) @Zethson
• Add FAMD (#976) @Zethson
• 3D enabled implementation of ep.pp.filter_observations, ep.pp.filter_features (#953) @sueoglu
• Add time series distances (#954) @Zethson

🐛 Bug Fixes

• All green if GPU skipped (#1000) @Zethson
• Fix neighbors with timeseries (#973) @eroell
• Fix use_rep when X none (#969) @eroell
• Fix missing_values_barplot errors (#963) @sueoglu
• Fix CR notebook (#939) @Zethson

🧰 Maintenance

• Update actions (#977) @Zethson
• Cleanup simple_impute tests (#974) @eroell
• Move to ehrdata 0.0.10 (#971) @eroell
• Improved notebook CI (#959) @Zethson
• Switch to template (#960) @Zethson
• Tests for more plots (#919) @sueoglu
• Lowerbound cvxpy (#935) @Zethson
• Optimize var_metrics (#927) @Zethson
• Refactor Dask usage pattern (#926) @Zethson
• Add cover to README & remove some tokens (#923) @Zethson
• Update test coverage reporting (#918) @eroell
• Fix changelog links (#915) @Zethson
• Fixed structure of Returns in _rank_features_groups.py documentation (#911) @agerardy
• Add EHRData transition code (#897) @Zethson @eroell
• Make test that downloads dermatology dataset more robust (#906) @Zethson
• Update image source in README.md (#986) @eroell
• Fix plot docs formatting (#952) @Zethson
• Typo in the documentation of ehrapy.data.mimic_2_preprocessed (#917) @sueoglu