Changelog

Changelog#

This project adheres to Semantic Versioning.

v0.13.0#

🚀 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

v0.12.1#

🚀 Features#

  • Make dowhy optional & remove medcat (#903) @Zethson

  • Add about page & improve citations (#902) @Zethson

  • Overhaul doc structure (#895) @Zethson

  • Move to biome & improve CI & reenable CR (#890) @Zethson

  • Clean up Round - cut down anndata extension functionality (#880) @eroell

v0.12.0#

🚀 Features#

  • Improved KM plot data depth and functionality (#853) @aGuyLearning

  • New Feature: Forestplot for CoxPH model (#838) @aGuyLearning

  • Datatype Support in Quality Control and Impute (#865) @aGuyLearning

  • Revamp survival analysis interface (#842) @aGuyLearning

  • Improve submodule documentation (#859) @Zethson

  • Update Kaplan Meier plots in survival analysis notebook (#864) @aGuyLearning

🐛 Bug Fixes#

  • Pass all non-nan features along desired var_names to impute (KNN) (#867) @nicolassidoux

  • Remove Syntax warnings (#869) @Zethson

  • Fix test_norm_power_group (#862) @Zethson

🧰 Maintenance#

  • Fix a typo in pl.paga_compare: pos -> pos, (#846) @VladimirShitov

v0.11.0#

✨ Features#

  • Add array type handling for normalization (#835) @eroell @Zethson

🐛 Bug Fixes#

  • Fix scipy array support (#844) @Zethson

  • Fix casting to float when assigning numeric values; fixes normalization of integer arrays (#837) @eroell

v0.9.0 & 0.10.0#

🚀 Features#

  • Make all imputation methods consistent in regard to encoding requirements (#827) @nicolassidoux

  • Add approximate KNN backend (#791) @nicolassidoux

  • Improve survival analysis interface (#825) @aGuyLearning

  • Python 3.12 support (#794) @Lilly-May

  • Python 3.10+ & use uv for docs & fix RTD & support numpy 2 (#830) @Zethson

🐛 Bug Fixes#

  • move_to_x: Fix name of non-implemented argument “copy” to “copy_x”, implement & test (#832) @eroell

  • Contributing typo fix (#821) @aGuyLearning

  • Fix miceforest (#800) @Zethson

  • style: == to is for type comparison (#774) @eroell

v0.8.0#

🚀 Features#

  • remove pyyaml & explicit scikit-learn (#729) @Zethson

  • Remove fancyimpute (#728) @Zethson

  • Unify feature type detection (#724) @Lilly-May

  • catplot (#721) @eroell

  • Simplify ehrapy (#719) @Zethson

  • Use all (#715) @Zethson

  • Add bias detection to preprocessing (#690) @Lilly-May

  • Use lamin logger (#707) @Zethson

  • Add faiss backend for KNN imputation (#704) @Zethson

  • Build RTD docs with uv (#700) @Zethson

  • Refactor feature importance ranking (#698) @Zethson

  • Simplify CI (#694) @Zethson

  • Refactor outliers and IQR (#692) @Zethson

  • Calculation of feature importances in a supervised setting (#677) @Lilly-May

  • Speed up winsorize (#681) @Zethson

  • Remove notebook prefix in tutorial URLs (#679) @Zethson

  • Add cohort tracking notebook (#678) @Zethson

  • Switch to uv (#674) @Zethson

  • Style: typing of _scale_func_group (#727) @eroell

  • Improved support of encoded features in detect_bias (#725) @Lilly-May

  • Enable Synchronous dataloader write (#722) @wxicu

  • Feature scaling on training set when computing feature importances (#716) @Lilly-May

  • add batch-wise normalization argument (#711) @eroell

  • add functools.wraps to type check (#705) @eroell

  • add bias notebook to list of notebooks (#696) @eroell

  • basic sampling (#686) @eroell

  • add options for subitles in legend of cohorttrackers barplot (#688) @eroell

  • doc fix imputation: 70 instead of 30 (#683) @eroell

🐛 Bug Fixes#

  • Encoded dtype to float32 instead of np.number (#714) @Zethson

  • Fix feature importance warnings (#708) @Zethson

  • Remove notebook prefix in tutorial URLs (#679) @Zethson

  • fix name of log_rogistic_aft to log_logistic_aft (#676) @eroell

🧰 Maintenance#

  • Remove notebook prefix in tutorial URLs (#679) @Zethson

  • Add cohort tracking notebook (#678) @Zethson

  • knni amendments (#706) @eroell

v0.7.0#

🚀 Features#

  • Cohort Tracker (#658) @eroell

  • change diabetes-130 datasets which are provided (#672) @eroell

  • More sa functions (#664) @fatisati

  • Coxphfitter (#643) @fatisati

  • Implement little’s test (#667) @Zethson

  • Improve test design (#651) @Zethson

  • Improve QC docstring (#639) @Zethson

  • Refactor _missing_values calculation (#638) @Zethson

🐛 Bug Fixes#

  • Fix one-hot encoding tests (#644) @Zethson

v0.6.0#

🚀 Features#

Breaking changes#

  • Move information on numerical/non_numerical/encoded_non_numerical from .uns to .var (#630) @eroell

Make older AnnData objects compatible using

def move_type_info_from_uns_to_var(adata, copy=False):
    """Move type information from adata.uns to adata.var['ehrapy_column_type'].

    The latter is the current, updated flavor used by ehrapy.
    """
    if copy:
        adata = adata.copy()

    adata.var['ehrapy_column_type'] = 'unknown'

    if 'numerical_columns' in adata.uns.keys():
        for key in adata.uns['numerical_columns']:
            adata.var.loc[key, 'ehrapy_column_type'] = 'numeric'
    if 'non_numerical_columns' in adata.uns.keys():
        for key in adata.uns['non_numerical_columns']:
            adata.var.loc[key, 'ehrapy_column_type'] = 'non_numeric'
    if 'encoded_non_numerical_columns' in adata.uns.keys():
        for key in adata.uns['encoded_non_numerical_columns']:
            adata.var.loc[key, 'ehrapy_column_type'] = 'non_numeric_encoded'

    if copy:
        return adata

New features#

  • Medcat refresh (#623) @eroell

  • Rank features groups obs (#622) @eroell

  • Add FHIR tutorial and simplify code (#626) @Zethson

  • Add input checks for imputers (#625) @Zethson

  • Removed unused dependencies (#615) @Zethson

  • Refactor encoding (#588) @Zethson

🐛 Bug Fixes#

  • Use fixtures for preprocessing tests (#577) @Zethson

🧰 Maintenance#

  • Refactoring (#627) @Zethson

  • Add FHIR tutorial and simplify code (#626) @Zethson

  • pre-commit (#587) @Zethson

  • Small edits (#599) @eroell

v0.5.0#

🚀 Features#

  • Add g-tests for rank features group (#546) @VladimirShitov

  • Causal Inference with dowhy (#502) @timtreis

  • Remove MuData support (#545) @Zethson

🐛 Bug Fixes#

  • Fixed reading format warnings (#569) @namsaraeva

  • Fixed inability to normalize AnnData that does not require encoding (#568) @namsaraeva

  • Fixed adata.uns[“non_numericlal_columns”] being empty in mimic_2 dataset (#567) @namsaraeva

v0.4.0#

🚀 Features#

  • Add Synthea dataset (#510) @namsaraeva

  • Added tiny examples to every function (#498) @namsaraeva

  • add a title parameter (#494) @xinyuejohn

  • Changed the hue of grey (#493) @namsaraeva

  • Logger info message when writing to .h5ad files (#458) @namsaraeva

  • Modified docstrings (#533) @namsaraeva

  • Added examples to missing modules (#531) @namsaraeva

  • Allow Python 3.11 (#523) @Zethson

  • Add test_kmf_logrank (#516) @Zethson

  • Add scget functions (#484) @Zethson

  • Add FHIR parsing support (#463) @Zethson

  • Add new tutorial & switch to python 3.10 (#454) @Zethson

  • Add docs group (#437) @Zethson

  • Add thefuzz (#434) @Zethson

🐛 Bug Fixes#

  • Fix CI (#524) @Zethson

  • Error message and minor fixes, issue #447 (#504) @namsaraeva

  • fix quality control (#495) @xinyuejohn

  • Fix MacOS CI (#435) @Zethson

🧰 Maintenance#

  • Add test_kmf_logrank (#516) @Zethson

  • Add scget functions (#484) @Zethson

  • Add new tutorial & switch to python 3.10 (#454) @Zethson

v0.3.0#

🚀 Features#

  • Add winsorize, clip quantiles and filter quantiles (#418) @Zethson

  • Remove PDF support (#430) @Zethson

  • Logging instance, issue #246 (#426) @namsaraeva

  • Negative values offset (#420) @Zethson

  • Missing values visualization, ref issue #271 (#419) @namsaraeva

  • Add copy_obs parameter to move_to_obs (#404) @namsaraeva

  • add anova_glm function (#400) @xinyuejohn

  • issue #397 “check for neighbors run before UMAP” fixed (#401) @namsaraeva

  • add more tutorials to CI (#382) @Zethson

  • add support for reading multiple files into Pandas DFs & adapted MIMIC-III Demo (#386) @Zethson

  • #321: Add X_only option for reading (#380) @Imipenem

🐛 Bug Fixes#

  • KeyError fix issue #423 (#428) @namsaraeva

  • fix qc_metrics bug (#425) @xinyuejohn

  • df_to_anndata logical XOR to OR, issue #422 (#429) @namsaraeva

  • Fix docs CI (#392) @Zethson

  • small fix in the qc_metrics() example (#407) @namsaraeva

🧰 Maintenance#

  • Add winsorize, clip quantiles and filter quantiles (#418) @Zethson

  • Remove PDF support (#430) @Zethson

  • Negative values offset (#420) @Zethson

  • Missing values visualization, ref issue #271 (#419) @namsaraeva

  • Fix docs CI (#392) @Zethson

v0.2.0#

🚀 Features#

  • Important cookietemple template update 2.1.0 released! (#343) @Zethson

  • add chronic kidney disease dataloader (#301) @xinyuejohn

  • dataloader for diabetes dataset (#292) @HorlavaNastassya

  • Add X_only option for reading (#380) @Imipenem

  • MedCAT API improvements & function renaming (#381) @Zethson

  • minor changes (#379) @xinyuejohn

  • add functions related to survival analysis (#371) @xinyuejohn

  • MedCat [#101]: extract biomedical concepts/entities from (free) text (#367) @Imipenem

  • Add heart dataset to docs (#377) @xinyuejohn

  • add heart disease data set to ehrapy (#376) @xinyuejohn

  • add highly_variable_features (#364) @xinyuejohn

  • add SoftImpute and IterativeSVD to imputation (#353) @xinyuejohn

  • (#307) Improve KNN with n_neighbours parameter (#365) @Imipenem

  • add furo theme & switch to markdown (#359) @Zethson

  • add several datasets and change Docstring examples (#355) @xinyuejohn

  • Add ability to compare laboratory measurements to reference values (#352) @Zethson

  • (Feature) New read API #263 (#351) @Imipenem

  • (Feature) Set index column #305 (#350) @Imipenem

  • Add encoded parameter to all new datasets amd fix import (#336) @xinyuejohn

  • (FEATURE) #314: Autodetect binary (0,1) columns (#327) @Imipenem

  • (FEATURE) Display QC metrics of var #239 (#323) @Imipenem

  • Add several dataset loaders (#322) @xinyuejohn

  • (FEATURE) Improve type_overview #306 (#308) @Imipenem

  • Feature/deep translator integration (#303) @MxMstrmn

  • remove CLI module (#298) @Zethson

  • Improve missforest interface (#284) @Zethson

  • Add example calls and preview images to all plotting functions (#289) @xinyuejohn

  • add heart failure dataloader (#291) @Zethson

  • add highly_variable_features (#364) @xinyuejohn

  • add SoftImpute and IterativeSVD to imputation (#353) @xinyuejohn

  • add furo theme & switch to markdown (#359) @Zethson

🐛 Bug Fixes#

  • (FIX) #255: Encode mutates input adata object (#348) @Imipenem

  • (FIX) Write .h5ad files (#347) @Imipenem

  • Fix #331: Improved autodetect docs (#344) @Imipenem

  • Add encoded parameter to all new datasets amd fix import (#336) @xinyuejohn

  • (FIX) Autodetect encode + specify encode mode for autodetect (#310) @Imipenem

🧰 Maintenance#

  • MedCAT API improvements & function renaming (#381) @Zethson

  • add functions related to survival analysis (#371) @xinyuejohn

  • MedCat [#101]: extract biomedical concepts/entities from (free) text (#367) @Imipenem

  • Add heart dataset to docs (#377) @xinyuejohn

  • remove CLI module (#298) @Zethson

v0.1.0#

🚀 Features#

  • Input and output of CSVs, PDFs, h5ad files

  • Several encoding modes (one-hot, label, …)

  • Several imputation methods (simple, KNN, MissForest, …)

  • Several normalization methods (log, scale, …)

  • Full Scanpy API support

  • Initial MedCAT integration

  • DeepL & Google Translator support

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