# Changelog

This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## v0.12.1

### 🚀 Features

* Make dowhy optional & remove medcat [#903](https://github.com/theislab/ehrapy/pull/903) @Zethson
* Add about page & improve citations [#902](https://github.com/theislab/ehrapy/pull/902) @Zethson
* Overhaul doc structure [#895](https://github.com/theislab/ehrapy/pull/895) @Zethson
* Move to biome & improve CI & reenable CR [#890](https://github.com/theislab/ehrapy/pull/890) @Zethson
* Clean up Round - cut down anndata extension functionality [#880](https://github.com/theislab/ehrapy/pull/880) @eroell

## v0.12.0

### 🚀 Features

* Improved KM plot data depth and functionality [#853](https://github.com/theislab/ehrapy/pull/853) @aGuyLearning
* New Feature: Forestplot for CoxPH model [#838](https://github.com/theislab/ehrapy/pull/838) @aGuyLearning
* Datatype Support in Quality Control and Impute [#865](https://github.com/theislab/ehrapy/pull/865) @aGuyLearning
* Revamp survival analysis interface [#842](https://github.com/theislab/ehrapy/pull/842) @aGuyLearning
* Improve submodule documentation [#859](https://github.com/theislab/ehrapy/pull/859) @Zethson
* Update Kaplan Meier plots in survival analysis notebook [#864](https://github.com/theislab/ehrapy/pull/864) @aGuyLearning

### 🐛 Bug Fixes

* Pass all non-nan features along desired var_names to impute (KNN) [#867](https://github.com/theislab/ehrapy/pull/867) @nicolassidoux
* Remove Syntax warnings [#869](https://github.com/theislab/ehrapy/pull/869) @Zethson
* Fix test_norm_power_group [#862](https://github.com/theislab/ehrapy/pull/862) @Zethson

### 🧰 Maintenance

* Fix a typo in `pl.paga_compare`: `pos` -> `pos,` [#846](https://github.com/theislab/ehrapy/pull/846) @VladimirShitov

## v0.11.0

### ✨ Features

* Add array type handling for normalization [#835](https://github.com/theislab/ehrapy/pull/835) @eroell @Zethson

### 🐛 Bug Fixes

* Fix scipy array support [#844](https://github.com/theislab/ehrapy/pull/844) @Zethson
* Fix casting to float when assigning numeric values; fixes normalization of integer arrays [#837](https://github.com/theislab/ehrapy/pull/837) @eroell

## v0.9.0 & 0.10.0

### 🚀 Features

* Make all imputation methods consistent in regard to encoding requirements [#827](https://github.com/theislab/ehrapy/pull/827) @nicolassidoux
* Add approximate KNN backend [#791](https://github.com/theislab/ehrapy/pull/791) @nicolassidoux
* Improve survival analysis interface [#825](https://github.com/theislab/ehrapy/pull/825) @aGuyLearning
* Python 3.12 support [#794](https://github.com/theislab/ehrapy/pull/794) @Lilly-May
* Python 3.10+ & use uv for docs & fix RTD & support numpy 2 [#830](https://github.com/theislab/ehrapy/pull/830) @Zethson

### 🐛 Bug Fixes

* move_to_x: Fix name of non-implemented argument "copy" to "copy_x", implement & test [#832](https://github.com/theislab/ehrapy/pull/832) @eroell
* Contributing typo fix [#821](https://github.com/theislab/ehrapy/pull/821) @aGuyLearning
* Fix miceforest [#800](https://github.com/theislab/ehrapy/pull/800) @Zethson
* style: == to is for type comparison [#774](https://github.com/theislab/ehrapy/pull/774) @eroell

## v0.8.0

### 🚀 Features

* remove pyyaml & explicit scikit-learn [#729](https://github.com/theislab/ehrapy/pull/729) @Zethson
* Remove fancyimpute [#728](https://github.com/theislab/ehrapy/pull/728) @Zethson
* Unify feature type detection [#724](https://github.com/theislab/ehrapy/pull/724) @Lilly-May
* catplot [#721](https://github.com/theislab/ehrapy/pull/721) @eroell
* Simplify ehrapy [#719](https://github.com/theislab/ehrapy/pull/719) @Zethson
* Use __all__ [#715](https://github.com/theislab/ehrapy/pull/715) @Zethson
* Add bias detection to preprocessing [#690](https://github.com/theislab/ehrapy/pull/690) @Lilly-May
* Use lamin logger [#707](https://github.com/theislab/ehrapy/pull/707) @Zethson
* Add faiss backend for KNN imputation [#704](https://github.com/theislab/ehrapy/pull/704) @Zethson
* Build RTD docs with uv [#700](https://github.com/theislab/ehrapy/pull/700) @Zethson
* Refactor feature importance ranking [#698](https://github.com/theislab/ehrapy/pull/698) @Zethson
* Simplify CI [#694](https://github.com/theislab/ehrapy/pull/694) @Zethson
* Refactor outliers and IQR [#692](https://github.com/theislab/ehrapy/pull/692) @Zethson
* Calculation of feature importances in a supervised setting [#677](https://github.com/theislab/ehrapy/pull/677) @Lilly-May
* Speed up winsorize [#681](https://github.com/theislab/ehrapy/pull/681) @Zethson
* Remove notebook prefix in tutorial URLs [#679](https://github.com/theislab/ehrapy/pull/679) @Zethson
* Add cohort tracking notebook [#678](https://github.com/theislab/ehrapy/pull/678) @Zethson
* Switch to uv [#674](https://github.com/theislab/ehrapy/pull/674) @Zethson
* Style: typing of _scale_func_group [#727](https://github.com/theislab/ehrapy/pull/727) @eroell
* Improved support of encoded features in detect_bias [#725](https://github.com/theislab/ehrapy/pull/725) @Lilly-May
* Enable Synchronous dataloader write [#722](https://github.com/theislab/ehrapy/pull/722) @wxicu
* Feature scaling on training set when computing feature importances [#716](https://github.com/theislab/ehrapy/pull/716) @Lilly-May
* add batch-wise normalization argument [#711](https://github.com/theislab/ehrapy/pull/711) @eroell
* add functools.wraps to type check [#705](https://github.com/theislab/ehrapy/pull/705) @eroell
* add bias notebook to list of notebooks [#696](https://github.com/theislab/ehrapy/pull/696) @eroell
* basic sampling [#686](https://github.com/theislab/ehrapy/pull/686) @eroell
* add options for subitles in legend of cohorttrackers barplot [#688](https://github.com/theislab/ehrapy/pull/688) @eroell
* doc fix imputation: 70 instead of 30 [#683](https://github.com/theislab/ehrapy/pull/683) @eroell

### 🐛 Bug Fixes

* Encoded dtype to float32 instead of np.number [#714](https://github.com/theislab/ehrapy/pull/714) @Zethson
* Fix feature importance warnings [#708](https://github.com/theislab/ehrapy/pull/708) @Zethson
* Remove notebook prefix in tutorial URLs [#679](https://github.com/theislab/ehrapy/pull/679) @Zethson
* fix name of log_rogistic_aft to log_logistic_aft [#676](https://github.com/theislab/ehrapy/pull/676) @eroell

### 🧰 Maintenance

* Remove notebook prefix in tutorial URLs [#679](https://github.com/theislab/ehrapy/pull/679) @Zethson
* Add cohort tracking notebook [#678](https://github.com/theislab/ehrapy/pull/678) @Zethson
* knni amendments [#706](https://github.com/theislab/ehrapy/pull/706) @eroell

## v0.7.0

### 🚀 Features

* Cohort Tracker [#658](https://github.com/theislab/ehrapy/pull/658) @eroell
* change diabetes-130 datasets which are provided [#672](https://github.com/theislab/ehrapy/pull/672) @eroell
* More sa functions [#664](https://github.com/theislab/ehrapy/pull/664) @fatisati
* Coxphfitter [#643](https://github.com/theislab/ehrapy/pull/643) @fatisati
* Implement little's test [#667](https://github.com/theislab/ehrapy/pull/667) @Zethson
* Improve test design [#651](https://github.com/theislab/ehrapy/pull/651) @Zethson
* Improve QC docstring [#639](https://github.com/theislab/ehrapy/pull/639) @Zethson
* Refactor _missing_values calculation [#638](https://github.com/theislab/ehrapy/pull/638) @Zethson

### 🐛 Bug Fixes

* Fix one-hot encoding tests [#644](https://github.com/theislab/ehrapy/pull/644) @Zethson

## v0.6.0

### 🚀 Features

#### Breaking changes

* Move information on numerical/non_numerical/encoded_non_numerical from .uns to .var [#630](https://github.com/theislab/ehrapy/pull/630) @eroell

Make older AnnData objects compatible using

```python
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](https://github.com/theislab/ehrapy/pull/623) @eroell
* Rank features groups obs [#622](https://github.com/theislab/ehrapy/pull/622) @eroell
* Add FHIR tutorial and simplify code [#626](https://github.com/theislab/ehrapy/pull/626) @Zethson
* Add input checks for imputers [#625](https://github.com/theislab/ehrapy/pull/625) @Zethson
* Removed unused dependencies [#615](https://github.com/theislab/ehrapy/pull/615) @Zethson
* Refactor encoding [#588](https://github.com/theislab/ehrapy/pull/588) @Zethson

### 🐛 Bug Fixes

* Use fixtures for preprocessing tests [#577](https://github.com/theislab/ehrapy/pull/577) @Zethson

### 🧰 Maintenance

* Refactoring [#627](https://github.com/theislab/ehrapy/pull/627) @Zethson
* Add FHIR tutorial and simplify code [#626](https://github.com/theislab/ehrapy/pull/626) @Zethson
* pre-commit [#587](https://github.com/theislab/ehrapy/pull/587) @Zethson
* Small edits [#599](https://github.com/theislab/ehrapy/pull/599) @eroell

## v0.5.0

### 🚀 Features

* Add g-tests for rank features group [#546](https://github.com/theislab/ehrapy/pull/546) @VladimirShitov
* Causal Inference with dowhy [#502](https://github.com/theislab/ehrapy/pull/502) @timtreis
* Remove MuData support [#545](https://github.com/theislab/ehrapy/pull/545) @Zethson

### 🐛 Bug Fixes

* Fixed reading format warnings  [#569](https://github.com/theislab/ehrapy/pull/569) @namsaraeva
* Fixed inability to normalize AnnData that does not require encoding  [#568](https://github.com/theislab/ehrapy/pull/568) @namsaraeva
* Fixed adata.uns["non_numericlal_columns"] being empty in mimic_2 dataset [#567](https://github.com/theislab/ehrapy/pull/567) @namsaraeva

## v0.4.0

### 🚀 Features

* Add Synthea dataset [#510](https://github.com/theislab/ehrapy/pull/510) @namsaraeva
* Added tiny examples to every function [#498](https://github.com/theislab/ehrapy/pull/498) @namsaraeva
* add a title parameter [#494](https://github.com/theislab/ehrapy/pull/494) @xinyuejohn
* Changed the hue of grey [#493](https://github.com/theislab/ehrapy/pull/493) @namsaraeva
* Logger info message when writing to .h5ad files [#458](https://github.com/theislab/ehrapy/pull/458) @namsaraeva
* Modified docstrings [#533](https://github.com/theislab/ehrapy/pull/533) @namsaraeva
* Added examples to missing modules [#531](https://github.com/theislab/ehrapy/pull/531) @namsaraeva
* Allow Python 3.11 [#523](https://github.com/theislab/ehrapy/pull/523) @Zethson
* Add test_kmf_logrank [#516](https://github.com/theislab/ehrapy/pull/516) @Zethson
* Add scget functions [#484](https://github.com/theislab/ehrapy/pull/484) @Zethson
* Add FHIR parsing support [#463](https://github.com/theislab/ehrapy/pull/463) @Zethson
* Add new tutorial & switch to python 3.10 [#454](https://github.com/theislab/ehrapy/pull/454) @Zethson
* Add docs group [#437](https://github.com/theislab/ehrapy/pull/437) @Zethson
* Add thefuzz [#434](https://github.com/theislab/ehrapy/pull/434) @Zethson

### 🐛 Bug Fixes

* Fix CI [#524](https://github.com/theislab/ehrapy/pull/524) @Zethson
* Error message and minor fixes, issue #447 [#504](https://github.com/theislab/ehrapy/pull/504) @namsaraeva
* fix quality control [#495](https://github.com/theislab/ehrapy/pull/495) @xinyuejohn
* Fix MacOS CI [#435](https://github.com/theislab/ehrapy/pull/435) @Zethson

### 🧰 Maintenance

* Add test_kmf_logrank [#516](https://github.com/theislab/ehrapy/pull/516) @Zethson
* Add scget functions [#484](https://github.com/theislab/ehrapy/pull/484) @Zethson
* Add new tutorial & switch to python 3.10 [#454](https://github.com/theislab/ehrapy/pull/454) @Zethson

## v0.3.0

### 🚀 Features

* Add winsorize, clip quantiles and filter quantiles [#418](https://github.com/theislab/ehrapy/pull/418) @Zethson
* Remove PDF support [#430](https://github.com/theislab/ehrapy/pull/430) @Zethson
* Logging instance, issue #246 [#426](https://github.com/theislab/ehrapy/pull/426) @namsaraeva
* Negative values offset [#420](https://github.com/theislab/ehrapy/pull/420) @Zethson
* Missing values visualization, ref issue #271 [#419](https://github.com/theislab/ehrapy/pull/419) @namsaraeva
* Add copy_obs parameter to move_to_obs [#404](https://github.com/theislab/ehrapy/pull/404) @namsaraeva
* add anova_glm function [#400](https://github.com/theislab/ehrapy/pull/400) @xinyuejohn
* issue #397 "check for neighbors run before UMAP" fixed [#401](https://github.com/theislab/ehrapy/pull/401) @namsaraeva
* add more tutorials to CI [#382](https://github.com/theislab/ehrapy/pull/382) @Zethson
* add support for reading multiple files into Pandas DFs & adapted MIMIC-III Demo [#386](https://github.com/theislab/ehrapy/pull/386) @Zethson
* #321: Add X_only option for reading [#380](https://github.com/theislab/ehrapy/pull/380) @Imipenem

### 🐛 Bug Fixes

* KeyError fix issue #423 [#428](https://github.com/theislab/ehrapy/pull/428) @namsaraeva
* fix qc_metrics bug [#425](https://github.com/theislab/ehrapy/pull/425) @xinyuejohn
* df_to_anndata logical XOR to OR, issue #422 [#429](https://github.com/theislab/ehrapy/pull/429) @namsaraeva
* Fix docs CI [#392](https://github.com/theislab/ehrapy/pull/392) @Zethson
* small fix in the qc_metrics() example [#407](https://github.com/theislab/ehrapy/pull/407) @namsaraeva

### 🧰 Maintenance

* Add winsorize, clip quantiles and filter quantiles [#418](https://github.com/theislab/ehrapy/pull/418) @Zethson
* Remove PDF support [#430](https://github.com/theislab/ehrapy/pull/430) @Zethson
* Negative values offset [#420](https://github.com/theislab/ehrapy/pull/420) @Zethson
* Missing values visualization, ref issue #271 [#419](https://github.com/theislab/ehrapy/pull/419) @namsaraeva
* Fix docs CI [#392](https://github.com/theislab/ehrapy/pull/392) @Zethson

## v0.2.0

### 🚀 Features

* Important cookietemple template update 2.1.0 released! [#343](https://github.com/theislab/ehrapy/pull/343) @Zethson
* add chronic kidney disease dataloader [#301](https://github.com/theislab/ehrapy/pull/301) @xinyuejohn
* dataloader for diabetes dataset [#292](https://github.com/theislab/ehrapy/pull/292) @HorlavaNastassya
* Add X_only option for reading [#380](https://github.com/theislab/ehrapy/pull/380) @Imipenem
* MedCAT API improvements & function renaming [#381](https://github.com/theislab/ehrapy/pull/381) @Zethson
* minor changes [#379](https://github.com/theislab/ehrapy/pull/379) @xinyuejohn
* add functions related to survival analysis [#371](https://github.com/theislab/ehrapy/pull/371) @xinyuejohn
* MedCat [#101]: extract biomedical concepts/entities from (free) text [#367](https://github.com/theislab/ehrapy/pull/367) @Imipenem
* Add heart dataset to docs [#377](https://github.com/theislab/ehrapy/pull/377) @xinyuejohn
* add heart disease data set to ehrapy [#376](https://github.com/theislab/ehrapy/pull/376) @xinyuejohn
* add highly_variable_features [#364](https://github.com/theislab/ehrapy/pull/364) @xinyuejohn
* add SoftImpute and IterativeSVD to imputation [#353](https://github.com/theislab/ehrapy/pull/353) @xinyuejohn
* [#307] Improve KNN with n_neighbours parameter [#365](https://github.com/theislab/ehrapy/pull/365) @Imipenem
* add furo theme & switch to markdown [#359](https://github.com/theislab/ehrapy/pull/359) @Zethson
* add several datasets and change Docstring examples [#355](https://github.com/theislab/ehrapy/pull/355) @xinyuejohn
* Add ability to compare laboratory measurements to reference values [#352](https://github.com/theislab/ehrapy/pull/352) @Zethson
* [Feature] New read API #263 [#351](https://github.com/theislab/ehrapy/pull/351) @Imipenem
* [Feature] Set index column #305 [#350](https://github.com/theislab/ehrapy/pull/350) @Imipenem
* Add encoded parameter to all new datasets amd fix import [#336](https://github.com/theislab/ehrapy/pull/336) @xinyuejohn
* [FEATURE] #314: Autodetect binary (0,1) columns [#327](https://github.com/theislab/ehrapy/pull/327) @Imipenem
* [FEATURE] Display QC metrics of var #239 [#323](https://github.com/theislab/ehrapy/pull/323) @Imipenem
* Add several dataset loaders [#322](https://github.com/theislab/ehrapy/pull/322) @xinyuejohn
* [FEATURE] Improve type_overview #306 [#308](https://github.com/theislab/ehrapy/pull/308) @Imipenem
* Feature/deep translator integration [#303](https://github.com/theislab/ehrapy/pull/303) @MxMstrmn
* remove CLI module [#298](https://github.com/theislab/ehrapy/pull/298) @Zethson
* Improve missforest interface [#284](https://github.com/theislab/ehrapy/pull/284) @Zethson
* Add example calls and preview images to all plotting functions [#289](https://github.com/theislab/ehrapy/pull/289) @xinyuejohn
* add heart failure dataloader [#291](https://github.com/theislab/ehrapy/pull/291) @Zethson
* add highly_variable_features [#364](https://github.com/theislab/ehrapy/pull/364) @xinyuejohn
* add SoftImpute and IterativeSVD to imputation [#353](https://github.com/theislab/ehrapy/pull/353) @xinyuejohn
* add furo theme & switch to markdown [#359](https://github.com/theislab/ehrapy/pull/359) @Zethson

### 🐛 Bug Fixes

* [FIX] #255: Encode mutates input adata object [#348](https://github.com/theislab/ehrapy/pull/348) @Imipenem
* [FIX] Write .h5ad files [#347](https://github.com/theislab/ehrapy/pull/347) @Imipenem
* Fix #331: Improved autodetect docs [#344](https://github.com/theislab/ehrapy/pull/344) @Imipenem
* Add encoded parameter to all new datasets amd fix import [#336](https://github.com/theislab/ehrapy/pull/336) @xinyuejohn
* [FIX] Autodetect encode + specify encode mode for autodetect [#310](https://github.com/theislab/ehrapy/pull/310) @Imipenem

### 🧰 Maintenance

* MedCAT API improvements & function renaming [#381](https://github.com/theislab/ehrapy/pull/381) @Zethson
* add functions related to survival analysis [#371](https://github.com/theislab/ehrapy/pull/371) @xinyuejohn
* MedCat [#101]: extract biomedical concepts/entities from (free) text [#367](https://github.com/theislab/ehrapy/pull/367) @Imipenem
* Add heart dataset to docs [#377](https://github.com/theislab/ehrapy/pull/377) @xinyuejohn
* remove CLI module [#298](https://github.com/theislab/ehrapy/pull/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