0.14.0 🌈

🚀 Features

• Add LOCF imputation ep.pp.locf_impute() for longitudinal (3D) data with forward fill and configurable fallback strategies (#1020) @agerardy @eroell
• Add non-negative CP decomposition ep.tl.ncp() for 3D tensor factorisation with companion plots ep.pl.ncp() and ep.pl.ncp_cluster_trajectories() (#1030, #1038) @eroell
• Add ep.pp.variable_correlations() and plotting functions ep.pl.variable_correlations() / ep.pl.variable_dependencies() (#1010) @sueoglu
• Longitudinal explicit impute ep.pp.explicit_impute() extended to enable different imputation values per timepoint (#1023) @sueoglu
• Sankey diagram state-transition colours and hover function for timeseries plots (#1019) @sueoglu
• Add longitudinal data analysis notebook (#1007) @eroell
• Add ep.tl.cox_ph_adjusted_curves() and plotting functions ep.pl.cox_ph_adjusted_curves() (#1028) @sueoglu
• Add 3D support for ep.pp.knn_impute() (#1041) @sueoglu
• Add ep.pp.missing_data_mask() to compute and apply missing-data masks for sparse, dense, and Dask arrays (#1045) @haoyu-haoyu

🧰 Maintenance

• Fix plotting CI (#1011) @sueoglu @eroell
• Continuous values don't repeat title in CohortTracker's barplot (#1021) @sueoglu
• Remove legacy code deprecated in 0.13.0, fix test warnings & adjust to future scanpy arguments (#1016) @eroell
• Update plotting ci dotplot (#1011) @sueoglu @Zethson @eroell
• Add ehrdata as submodule (#1040) @eroell
• Adapt to updated ed.infer_feature_type, discard alternative feature type inference in imputation methods (#1039) @eroell
• Upgrade tutorials (#1042, #1043, #1046) @agerardy @sueoglu @Zethson
• Remove ML with ehrapy notebook (#1048) @eroell

🐛 Bug Fixes

• ep.pp normalization functions now work when using a layer and .X is None (#1015) @agerardy @eroell
• ep.tl.rank_features_groups can use .obs regardless of what is in .X or .layers (#1015) @agerardy @eroell

⚠️ Modified

• Update qc_lab_metrics(#1025) @eroell
• remove deprecated ep.ad (moved to ehrdata): infer_feature_types, feature_type_overview, replace_feature_types, anndata_to_df, df_to_anndata, move_to_obs, move_to_x (#1016) @eroell
• remove deprecated ep.dt (moved to ehrdata) (#1016) @eroell
• remove deprecated ep.io (moved to ehrdata): df_to_anndata, read_csv, read_fhir, read_h5ad, write (#1016) @eroell