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