0.9.4 🌈

Changes

• Update _datasets.py (#649) @tessadgreen

🧰 Maintenance

• Fix docs rendering for classes using lazy import (#651) @Lilly-May

0.9.3 🌈

Changes

🚀 Features

• Python 3.12 support (#644) @Lilly-May
• Add lazy loading for deferred modules (#647) and (#648) @Zethson
• Support for scipy 1.14 (#646) @andr-kun

0.8.0 🌈

Changes

🚀 Features

• Add hagai dataloader (#627) @Zethson
• Add more informative error if not every cell type is represented in e… (#620) @Zethson
• Add typehints_defaults (#619) @Zethson
• Add metadata notebook (#609) @Zethson
• Add multicondition analysis (differential gene expression interface) (#607) @Zethson
• Add zhang 2021 dataloader (#602) @Zethson
• Speed up tests (#601) (#599) @Zethson
• Use all (#588) @Zethson
• Use lamin logger (#586) @Zethson
• Add two distance metrics, three-way comparison and bootstrapping (#608) @wxicu
• Metadata GDSC annotation improvements (#625) @Lilly-May
• Add file lock during downloading (#590) @wxicu

🐛 Bug Fixes

• Fix CI (#637) @Zethson
• Fix layer handling in Mixscape.mixscape to resolve errors with adata.raw (#636) @Lilly-May
• Fix from_scanpy (#596) @Zethson
• • Fix volcano plot y-axis being cut-off (#622) @pakiessling

0.7.0 🌈

Pertpy release 0.7.0

Due to a lack of release notes for 0.6.0, this release may contain the some of the changes of 0.6.0 as well.

Note that the syntax for plotting for most tools changed. We removed the pt.pl modules in favor of moving all plots with plot_ prefixes to the respective tools. We hope that this will make the documentation easier to navigate.

We are now slowly maturing the API, but there will still be some changes for the upcoming release. We are especially looking to reduce the number of required dependencies and move some to be optional.

Changes

🚀 Features

• Silence pandas groupby() warning when running Augur predict (#573) @namsaraeva
• Added milo beeswarm example plot (#552) @namsaraeva
• Lazily metadata loading (#544) @wxicu
• Added tasccoda example plots (#527) @namsaraeva
• Add examples to plotting functions (#511) @namsaraeva
• Replace plotnine implementation of barplot with seaborn/matplotlib (#441) @kcArtemis
• Cinemaot dataset loader (#424) @Lilly-May
• Add classifiers (#427) @Zethson
• Remove remotezip (#401) @wxicu
• Add new distances (#304) @mojtababahrami
• wasserstein distance return type float (#386) @eroell
• Implementation of CINEMA-OT for pertpy - follow up (#379) @MingzeDong
• Implementation of CINEMA-OT for pertpy (#377) @MingzeDong
• Update cell line meta data class (#539) @wxicu
• Add dgidb and pharmgkb for drug annotation (#575) @wxicu
• Add sciplex-GxE dataloader (#576) @namsaraeva
• Harmonize plots (#574) @namsaraeva
• Compute method for MLPClassifierSpace (#565) @Lilly-May
• uv for CI (#569) @Zethson
• Logistic regression support for the Discriminator Classifier (#560) @Lilly-May
• Allow saving of CODA plots (#559) @namsaraeva
• Order plot functions last (#555) @Zethson
• Sparse guide RNA plot (#554) @Zethson
• Rename cmap to palette (#553) @Zethson
• Expand load for sccoda docstrings (#543) @Zethson
• Pseudobulk improvements (#529) @Lilly-May
• Add more detailed tool explanations (#528) @Zethson
• Add knn imputation (#517) @Zethson
• Add combosciplex (#512) @Zethson
• Add DE set comparisons (#489) @Zethson
• More informative images in tutorial gallery (#488) @Lilly-May
• Add perturbation space tutorial (#487) @Lilly-May
• Add enrichment (#482) @Zethson
• Save perturbation and clustering labels as categorical (#481) @Lilly-May
• Optimize from_scanpy (#473) @Zethson
• Add Drug metadata from chembl (#480) @Zethson
• Add DE filtering (#477) @Zethson
• PertSpace docs improvements (#471) @Lilly-May
• Add moa and compound annotation (#444) @wxicu
• Docs improvements for perturbation space (#465) @Lilly-May
• Make dialogue's load protected (#464) @Lilly-May
• New plotting API (#456) @Zethson
• Added smillie_2019 dataloader and renamed smillie dataset to tasccoda_example (#450) @Lilly-May
• Docs examples for CINEMA-OT (#433) @Lilly-May
• Removing dependencies (#426) @Zethson
• Added example for pt.pl.milo.nhood_graph (#423) @Lilly-May
• scope imports of ete3 in tasccoda (#422) @Zethson
• Add cinemaot nb (#419) @Zethson
• DIALOGUE attribution (#371) @Zethson
• DIALOGUE extensions and plots (#368) @tessadgreen
• Set run nuts random key to 0 by default. (#363) @Zethson
• Remove statsannotations (#362) @Zethson
• Refactoring (#354) @Zethson
• Add combosciplex (#512) @Zethson

🐛 Bug Fixes

• Fix stephenson 2021 and refactor (#374) @Zethson
• fix: double plot issue related to barplot (#460) @kcArtemis
• Small fixes to milo.plot_da_beeswarm (#551) @emdann
• Check and fix plotting functions (#579) @namsaraeva
• Fix jax config (#550) @Zethson
• fixed augur runtime (#547) @zzheng18
• Fix Distance docstring rendering (#537) @Zethson
• Address some Jax random key issues (#531) @Zethson
• Fixed Augur bug (#533) @namsaraeva
• Fix discriminator classifier nn dimensions (#475) @Lilly-May
• bug fixes, implementation tweaks, and additional distances (#397) @yugeji
• Fix subsetting of milo.plot_da_beeswarm (#472) @Lilly-May
• CentroidSpace AnnData Annotations (#455) @Lilly-May
• DiscriminatorClassifier compatibility with sparse matrices (#453) @Lilly-May
• Fix code coverage (#432) @flying-sheep
• Fixed set_fdr for tascCODA models (#411) @Lilly-May
• Small bug fixes and docs improvements (#409) @Lilly-May
• Move to new numpy.random.Generator (#396) @Lilly-May
• Fix cinema OT test (#392) @Zethson
• fix naming of example data in doc examples (#387) @eroell
• Fix stephenson 2021 and refactor (#374) @Zethson
• scCODA: add low/high acceptance probability warnings (#366) @johannesostner
• actually use neighbors_key in milo (#418) @maarten-devries
• Fixed some bugs (due to inconsistencies during migration) and typos in CINEMA-OT (#413) @MingzeDong
• fix Implicit modification warnings in cellline tests (#404) @wxicu

🧰 Maintenance

• Update README.md (#572) @namsaraeva
• Add more detailed tool explanations (#528) @Zethson
• Added links to tutorials (#505) @namsaraeva
• Add DE set comparisons (#489) @Zethson
• Add enrichment (#482) @Zethson
• Removed scGen batch removal tutorial from gallery (#443) @Lilly-May
• Add cinemaot nb (#419) @Zethson
• Fixed set_fdr for tascCODA models (#411) @Lilly-May
• Move to new numpy.random.Generator (#396) @Lilly-May
• Speed up tests by subsampling (#398) @Lilly-May
• Installation Apple Silicon (#393) @Lilly-May
• Fixture for Augur tests (#406) @Lilly-May
• Documentation examples (#391) @Lilly-May
• Speed up tests by subsampling (#398) @Lilly-May
• old codecov config (#431) @Zethson

0.5.0 🌈

Changes

🚀 Features

• Perturbation space - add/subtract (#328) @AlejandroTL
• Perturbation space - pseudobulk, discriminative classifier, clustering (#316) @AlejandroTL
• add n_jobs support for pairwise distance computation (#305) @XinmingTu

🐛 Bug Fixes

• fix initial MCMC values (#302) @johannesostner
• Fix docs CI (#303) @Zethson
• fixed the output_file_name of frangieh_2021_raw (#321) @XinmingTu

📦 Dependencies

• [DEPENDABOT]: Bump rich from 13.5.1 to 13.5.2 (#329) @dependabot
• [DEPENDABOT]: Bump ipywidgets from 8.0.7 to 8.1.0 (#330) @dependabot
• [DEPENDABOT]: Bump sphinx from 7.1.1 to 7.1.2 (#331) @dependabot
• [DEPENDABOT]: Bump pyupgrade from 3.9.0 to 3.10.1 (#324) @dependabot
• [DEPENDABOT]: Bump furo from 2023.5.20 to 2023.7.26 (#325) @dependabot
• [DEPENDABOT]: Bump flake8 from 6.0.0 to 6.1.0 (#326) @dependabot
• [DEPENDABOT]: Bump plotnine from 0.12.1 to 0.12.2 (#319) @dependabot
• [DEPENDABOT]: Bump types-requests from 2.31.0.1 to 2.31.0.2 (#320) @dependabot
• [DEPENDABOT]: Bump arviz from 0.15.1 to 0.16.0 (#318) @dependabot
• [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.8.7 to 1.8.8 (#317) @dependabot
• [DEPENDABOT]: Bump pyupgrade from 3.8.0 to 3.9.0 (#313) @dependabot
• [DEPENDABOT]: Bump scvi-tools from 1.0.0 to 1.0.2 (#314) @dependabot
• [DEPENDABOT]: Bump ott-jax from 0.4.1 to 0.4.2 (#315) @dependabot
• [DEPENDABOT]: Bump scipy from 1.11.0 to 1.11.1 (#308) @dependabot
• [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.8.6 to 1.8.7 (#306) @dependabot
• [DEPENDABOT]: Bump pyupgrade from 3.7.0 to 3.8.0 (#307) @dependabot
• [DEPENDABOT]: Bump mypy from 1.4.0 to 1.4.1 (#299) @dependabot
• [DEPENDABOT]: Bump scipy from 1.10.1 to 1.11.0 (#298) @dependabot
• [DEPENDABOT]: Bump scvi-tools from 0.20.3 to 1.0.0 (#293) @dependabot
• [DEPENDABOT]: Bump pyupgrade from 3.6.0 to 3.7.0 (#292) @dependabot
• [DEPENDABOT]: Bump pyupgrade from 3.4.0 to 3.6.0 (#280) @dependabot
• [DEPENDABOT]: Bump rich from 13.3.5 to 13.4.1 (#281) @dependabot
• [DEPENDABOT]: Bump decoupler from 1.3.4 to 1.4.0 (#282) @dependabot
• [DEPENDABOT]: Bump sphinx-last-updated-by-git from 0.3.4 to 0.3.5 (#276) @dependabot
• [DEPENDABOT]: Bump requests from 2.30.0 to 2.31.0 (#275) @dependabot
• [DEPENDABOT]: Bump numpyro from 0.11.0 to 0.12.1 (#278) @dependabot
• [DEPENDABOT]: Bump pre-commit from 3.3.1 to 3.3.2 (#272) @dependabot
• [DEPENDABOT]: Bump codecov/codecov-action from 3.1.3 to 3.1.4 (#273) @dependabot
• [DEPENDABOT]: Bump furo from 2023.3.27 to 2023.5.20 (#271) @dependabot
• [DEPENDABOT]: Bump scvi-tools from 0.19.0 to 0.20.3 (#270) @dependabot
• [DEPENDABOT]: Bump typeguard from 3.0.2 to 4.0.0 (#265) @dependabot
• [DEPENDABOT]: Bump plotnine from 0.10.1 to 0.12.1 (#263) @dependabot
• [DEPENDABOT]: Bump mypy from 1.2.0 to 1.3.0 (#264) @dependabot
• [DEPENDABOT]: Bump numba from 0.56.4 to 0.57.0 (#259) @dependabot
• [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.8.5 to 1.8.6 (#257) @dependabot
• [DEPENDABOT]: Bump safety from 2.3.4 to 2.3.5 (#258) @dependabot
• [DEPENDABOT]: Bump protobuf from 4.22.3 to 4.22.4 (#260) @dependabot
• [DEPENDABOT]: Bump protobuf from 3.20.1 to 4.22.3 (#250) @dependabot
• [DEPENDABOT]: Bump rich from 13.3.4 to 13.3.5 (#251) @dependabot
• [DEPENDABOT]: Bump coverage from 7.2.3 to 7.2.5 (#252) @dependabot
• [DEPENDABOT]: Bump codecov/codecov-action from 3.1.2 to 3.1.3 (#246) @dependabot
• [DEPENDABOT]: Bump sphinx from 6.1.3 to 6.2.0 (#248) @dependabot
• [DEPENDABOT]: Bump pygments from 2.15.0 to 2.15.1 (#247) @dependabot
• [DEPENDABOT]: Bump safety from 2.3.4 to 2.3.5 (#249) @dependabot
• [DEPENDABOT]: Bump sphinx-gallery from 0.10.1 to 0.13.0 (#241) @dependabot
• [DEPENDABOT]: Bump scikit-misc from 0.1.4 to 0.2.0 (#242) @dependabot
• [DEPENDABOT]: Bump codecov/codecov-action from 3.1.1 to 3.1.2 (#239) @dependabot
• [DEPENDABOT]: Bump adjusttext from 0.7.3 to 0.8 (#243) @dependabot

0.4.0 🌈

Changes

🚀 Features

• Guide assignment (#194) @moinfar
• Distances (#217) @Zethson
• Add initial DIALOGUE (#199) @Zethson
• Add Jax ScGen (#183) @Zethson
• Guide assignment (#194) @moinfar
• Add cell line annotation (#187) @wxicu

🐛 Bug Fixes

• docstring enhancement for sample identifiers (#237) @johannesostner
• improve mixscape documentation & fix a bug (#222) @xinyuejohn
• Fix docs ete3 (#206) @Zethson
• Update _dialogue.py (#203) @tessadgreen
• scCODA bugfix: duplicates in covariate_obs (#198) @Zethson
• Fix #211 (#212) @Moomboh
• fix #207 ete3 warning masks other ImportErrors (#208) @Moomboh

📦 Dependencies

• [DEPENDABOT]: Bump pytest from 7.2.2 to 7.3.0 (#236) @dependabot
• [DEPENDABOT]: Bump numpyro from 0.10.1 to 0.11.0 (#235) @dependabot
• [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.8.4 to 1.8.5 (#234) @dependabot
• [DEPENDABOT]: Bump safety from 2.3.4 to 2.3.5 (#229) @dependabot
• [DEPENDABOT]: Bump arviz from 0.14.0 to 0.15.1 (#228) @dependabot
• [DEPENDABOT]: Bump adjusttext from 0.7.3 to 0.8 (#227) @dependabot
• [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.8.3 to 1.8.4 (#225) @dependabot
• [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.8.1 to 1.8.3 (#223) @dependabot
• [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.7.1 to 1.8.1 (#221) @dependabot
• [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.6.4 to 1.7.1 (#218) @dependabot

0.3.0 🌈

Changes

• Solve pre-commit prettier and isort version incompatibility issues (#193) @moinfar
• Add scperturb datasets (#182) @wxicu
• Added subsampled Stephenson2021 COVID19 dataset (#179) @emdann

🚀 Features

• added list option for sample_identifier in load (#190) @Zethson
• integrate scCODA and tascCODA (#188) @xinyuejohn
• add milopy (#165) @xinyuejohn

🐛 Bug Fixes

• changes default settings of coda and milo (#196) @xinyuejohn
• fix mixscape default setting of layer (#195) @xinyuejohn

🧰 Maintenance

• integrate scCODA and tascCODA (#188) @xinyuejohn
• add milopy (#165) @xinyuejohn

📦 Dependencies

• [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.6.1 to 1.6.4 (#186) @dependabot
• [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.5.1 to 1.6.1 (#185) @dependabot
• [DEPENDABOT]: Bump mshick/add-pr-comment from 1 to 2 (#174) @dependabot
• [DEPENDABOT]: Bump crazy-max/ghaction-github-labeler from 4.0.0 to 4.1.0 (#168) @dependabot
• [DEPENDABOT]: Bump codecov/codecov-action from 3.1.0 to 3.1.1 (#166) @dependabot

0.2.0 🌈

Changes

• Solve pre-commit prettier and isort version incompatibility issues (#193) @moinfar
• Add scperturb datasets (#182) @wxicu
• Added subsampled Stephenson2021 COVID19 dataset (#179) @emdann

🚀 Features

• added list option for sample_identifier in load (#190) @Zethson
• integrate scCODA and tascCODA (#188) @xinyuejohn
• add milopy (#165) @xinyuejohn

🐛 Bug Fixes

• changes default settings of coda and milo (#196) @xinyuejohn
• fix mixscape default setting of layer (#195) @xinyuejohn

🧰 Maintenance

• integrate scCODA and tascCODA (#188) @xinyuejohn
• add milopy (#165) @xinyuejohn

📦 Dependencies

• [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.6.1 to 1.6.4 (#186) @dependabot
• [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.5.1 to 1.6.1 (#185) @dependabot
• [DEPENDABOT]: Bump mshick/add-pr-comment from 1 to 2 (#174) @dependabot
• [DEPENDABOT]: Bump crazy-max/ghaction-github-labeler from 4.0.0 to 4.1.0 (#168) @dependabot
• [DEPENDABOT]: Bump codecov/codecov-action from 3.1.0 to 3.1.1 (#166) @dependabot

0.1.0 🌈

Changes

🚀 Features

• Augurpy refactoring (#148) @Zethson
• add kang dataset (#146) @antschum
• add inits for plots, fix error messages and output, tutorial version (#144) @antschum
• Feature/furo md (#141) @Zethson
• add augurpy (#135) @antschum
• add better data draft (#71) @Zethson
• Documentation structure (#23) @Zethson
• add pypi-latest & architecture (#22) @Zethson

🐛 Bug Fixes

• add inits for plots, fix error messages and output, tutorial version (#144) @antschum

🧰 Maintenance

• Augurpy refactoring (#148) @Zethson
• Feature/furo md (#141) @Zethson
• add pypi-latest & architecture (#22) @Zethson