Ehrapy

Changes

🚀 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

Changes

🚀 Features

Breaking changes

* Move information on numerical/non_numerical/encoded_non_numerical from .uns to .var (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) 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

Changes

🚀 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

Changes

🚀 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 FHIR parsing support (463) Zethson
* Add new tutorial & switch to python 3.10 (454) Zethson

:package: Dependencies

* [DEPENDABOT]: Bump pandas from 2.0.1 to 2.0.2 (535) dependabot
* [DEPENDABOT]: Bump furo from 2023.3.27 to 2023.5.20 (536) dependabot
* [DEPENDABOT]: Bump deep-translator from 1.10.1 to 1.11.1 (537) dependabot
* [DEPENDABOT]: Bump pre-commit from 3.3.1 to 3.3.2 (530) dependabot
* [DEPENDABOT]: Bump sphinx-last-updated-by-git from 0.3.4 to 0.3.5 (529) dependabot
* [DEPENDABOT]: Bump types-requests from 2.30.0.0 to 2.31.0.1 (528) dependabot
* [DEPENDABOT]: Bump requests from 2.30.0 to 2.31.0 (526) dependabot
* [DEPENDABOT]: Bump numba from 0.56.4 to 0.57.0 (520) dependabot
* [DEPENDABOT]: Bump codecov/codecov-action from 3.1.3 to 3.1.4 (519) dependabot
* [DEPENDABOT]: Bump sphinxext-opengraph from 0.8.1 to 0.8.2 (512) dependabot
* [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.8.5 to 1.8.6 (511) dependabot
* [DEPENDABOT]: Bump sphinx-copybutton from 0.5.1 to 0.5.2 (513) dependabot
* [DEPENDABOT]: Bump pyhpo from 3.1.4 to 3.1.5 (514) dependabot
* [DEPENDABOT]: Bump pandas from 1.5.3 to 2.0.0 (490) dependabot
* [DEPENDABOT]: Bump types-requests from 2.28.11.17 to 2.29.0.0 (509) dependabot
* [DEPENDABOT]: Bump pre-commit from 3.2.2 to 3.3.0 (508) dependabot
* [DEPENDABOT]: Bump pytest from 7.3.0 to 7.3.1 (507) dependabot
* [DEPENDABOT]: Bump sphinx-autodoc-typehints from 1.22 to 1.23.0 (506) dependabot
* [DEPENDABOT]: Bump codecov/codecov-action from 3.1.2 to 3.1.3 (505) dependabot
* [DEPENDABOT]: Bump anndata from 0.9.0 to 0.9.1 (501) dependabot
* [DEPENDABOT]: Bump sphinx-design from 0.3.0 to 0.4.1 (500) dependabot
* [DEPENDABOT]: Bump codecov/codecov-action from 3.1.1 to 3.1.2 (499) dependabot
* [DEPENDABOT]: Bump cvxopt from 1.3.0 to 1.3.0.1 (497) dependabot
* [DEPENDABOT]: Bump pytest from 7.2.2 to 7.3.0 (496) dependabot
* [DEPENDABOT]: Bump scikit-learn-intelex from 2023.0.2 to 2023.1.0 (491) dependabot
* [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.8.3 to 1.8.5 (489) dependabot
* [DEPENDABOT]: Bump pre-commit from 3.2.1 to 3.2.2 (492) dependabot
* [DEPENDABOT]: Bump furo from 2023.3.23 to 2023.3.27 (488) dependabot
* [DEPENDABOT]: Bump rich from 13.3.2 to 13.3.3 (487) dependabot
* [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.8.1 to 1.8.3 (485) dependabot
* [DEPENDABOT]: Bump pre-commit from 3.2.0 to 3.2.1 (486) dependabot
* [DEPENDABOT]: Bump sphinx-automodapi from 0.14.1 to 0.15.0 (478) dependabot
* [DEPENDABOT]: Bump flake8-bugbear from 23.2.13 to 23.3.12 (479) dependabot
* [DEPENDABOT]: Bump fhiry from 2.1.0 to 3.0.0 (480) dependabot
* [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.7.1 to 1.8.1 (483) dependabot
* [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.6.4 to 1.7.1 (477) dependabot
* [DEPENDABOT]: Bump sphinxcontrib-spelling from 7.7.0 to 8.0.0 (470) dependabot
* [DEPENDABOT]: Bump pytest from 7.2.1 to 7.2.2 (471) dependabot
* [DEPENDABOT]: Bump myst-parser from 0.18.1 to 0.19.1 (472) dependabot
* [DEPENDABOT]: Bump missingno from 0.5.1 to 0.5.2 (468) dependabot
* [DEPENDABOT]: Bump coverage from 7.2.0 to 7.2.1 (466) dependabot
* [DEPENDABOT]: Bump types-requests from 2.28.11.11 to 2.28.11.13 (461) dependabot
* [DEPENDABOT]: Bump deep-translator from 1.10.0 to 1.10.1 (459) dependabot
* [DEPENDABOT]: Bump scanpy from 1.9.1 to 1.9.2 (460) dependabot
* [DEPENDABOT]: Bump flake8-bugbear from 23.1.20 to 23.2.13 (455) dependabot
* [DEPENDABOT]: Bump ipython from 8.9.0 to 8.10.0 (456) dependabot
* [DEPENDABOT]: Bump sphinxext-opengraph from 0.8.0 to 0.8.1 (457) dependabot
* [DEPENDABOT]: Bump deep-translator from 1.9.3 to 1.10.0 (451) dependabot
* [DEPENDABOT]: Bump types-requests from 2.28.11.8 to 2.28.11.9 (453) dependabot
* [DEPENDABOT]: Bump mypy from 0.991 to 1.0.0 (452) dependabot
* [DEPENDABOT]: Bump pre-commit from 3.0.1 to 3.0.2 (450) dependabot
* [DEPENDABOT]: Bump sphinx-autodoc-typehints from 1.21.8 to 1.22 (449) dependabot
* [DEPENDABOT]: Bump safety from 2.3.4 to 2.3.5 (448) dependabot
* [DEPENDABOT]: Bump scikit-learn-intelex from 2023.0.1 to 2023.0.2 (445) dependabot
* [DEPENDABOT]: Bump nbsphinx from 0.8.11 to 0.8.12 (444) dependabot
* [DEPENDABOT]: Bump rich from 13.1.0 to 13.2.0 (443) dependabot
* [DEPENDABOT]: Bump pytest from 7.2.0 to 7.2.1 (442) dependabot
* [DEPENDABOT]: Bump rich from 13.0.1 to 13.1.0 (441) dependabot
* [DEPENDABOT]: Bump deep-translator from 1.9.1 to 1.9.2 (440) dependabot
* [DEPENDABOT]: Bump medcat from 1.5.0 to 1.6.0 (439) dependabot
* [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.6.1 to 1.6.4 (432) dependabot

Changes

🚀 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

:package: Dependencies

* [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.5.1 to 1.6.1 (431) dependabot
* [DEPENDABOT]: Bump mshick/add-pr-comment from 1 to 2 (417) dependabot
* [DEPENDABOT]: Bump crazy-max/ghaction-github-labeler from 4.0.0 to 4.1.0 (415) dependabot
* [DEPENDABOT]: Bump codecov/codecov-action from 3.1.0 to 3.1.1 (412) dependabot
* [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.5.0 to 1.5.1 (398) dependabot
* [DEPENDABOT]: Bump crazy-max/ghaction-github-labeler from 3.1.1 to 4.0.0 (388) dependabot
* [DEPENDABOT]: Bump actions/setup-python from 3 to 4 (390) dependabot

Changes

🚀 Features


* Important cookietemple template update 2.1.0 released! (343) Zethson
* add chronic kidney disease dataloader (301) xinyuejohn
* dataloader for diabetes dataset (292) HorlavaNastassya
* 321: 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

:package: Dependencies

* [DEPENDABOT]: Bump codecov/codecov-action from 3.0.0 to 3.1.0 (378) dependabot
* [DEPENDABOT]: Bump codecov/codecov-action from 2.1.0 to 3.0.0 (368) dependabot
* [DEPENDABOT]: Bump actions/cache from 2.1.7 to 3 (358) dependabot
* [DEPENDABOT]: Bump actions/upload-artifact from 2.3.1 to 3 (339) dependabot
* [DEPENDABOT]: Bump actions/checkout from 2 to 3 (340) dependabot
* [DEPENDABOT]: Bump actions/download-artifact from 2.1.0 to 3 (341) dependabot
* [DEPENDABOT]: Bump ipython from 7.31.1 to 7.32.0 (330) dependabot
* [DEPENDABOT]: Bump actions/setup-python from 2 to 3 (328) dependabot
* [DEPENDABOT]: Bump deepl from 1.4.1 to 1.5.0 (329) dependabot
* [DEPENDABOT]: Bump coverage from 6.3.1 to 6.3.2 (317) dependabot
* [DEPENDABOT]: Bump click from 8.0.3 to 8.0.4 (318) dependabot
* [DEPENDABOT]: Bump types-requests from 2.27.8 to 2.27.9 (311) dependabot
* [DEPENDABOT]: Bump pytest from 7.0.0 to 7.0.1 (312) dependabot
* [DEPENDABOT]: Bump sphinx-autodoc-typehints from 1.16.0 to 1.17.0 (313) dependabot