Changelog & Release Notes

Changelog

0.9.2 (2025-05-20)

Bug Fixes

0.9.1 (2025-05-20)

Bug Fixes

Documentation

0.9.0 (2025-05-15)

Features

  • add ability to remote cache embeddings and remote upload results (#207) (4da7731)

Bug Fixes

  • fix broken help message (#216) (b3f35d0)

  • run_multi_dataset_task needs to know the model args when generating results (#209) (2472ebf)

Documentation

0.8.0 (2025-05-10)

Features

Documentation

0.7.0 (2025-05-08)

Features

  • allow CLI to specify set_baseline for perturbation task (#178) (376c833)

Bug Fixes

Documentation

0.6.1 (2025-05-02)

Bug Fixes

  • Push transcriptformer docker image to ECR (#188) (e5eea6f)

0.6.0 (2025-05-02)

Features

Bug Fixes

  • Add scGenePT / Perturbation compatibility to developer workflow (#155) (feaa4fe)

  • Make Geneformer and UCE work in interactive mode again (#181) (5128953)

  • reload dataset after caching (#166) (19ac92b)

  • use macro, not weighted F1 score (VC-2551) (#186) (11dfc05)

Documentation

0.5.0 (2025-04-03)

Features

Bug Fixes

  • add descriptive comment for pipeline.py (#110) (7e0ead3)

  • developer workflow implementation (#126) (703b5eb)

  • remove gene prefix validation from condition keys of perturbation single cell datasets (#152) (e766946)

0.4.4 (2025-04-01)

Bug Fixes

0.4.3 (2025-03-31)

Bug Fixes

0.4.2 (2025-03-31)

Bug Fixes

  • include conf dir in package structure (#140) (24e02f6)

0.4.1 (2025-03-27)

Bug Fixes

  • add conf directory to all containers (#128) (9415e3c)

0.4.0 (2025-03-26)

Features

Documentation

0.3.0 (2025-03-19)

Features

  • add back interactive mode and file mounting for container debugging (#114) (ba317e5)

Bug Fixes

  • move metrics readme to the correct dir (#112) (1dcd620)

0.2.2 (2025-03-18)

Bug Fixes

0.2.1 (2025-03-13)

Bug Fixes

0.2.0 (2025-03-13)

Features

Bug Fixes

  • Improve error message for var_names and SCVI dataset validation (#83) (ac048b0)

  • model_name to model_variant kwarg for model classes (#92) (23b525a)

  • Pass AWS credentials to container (#85) (e631c70)

  • path expansion when dataset stored in local repo (#80) (5f3333a)

  • update pip index version command in publish-pypi.yml (#82) (68b63d9)

  • update scgenept model config to use full model variant name (#94) (04057f8)

0.1.2 (2025-03-11)

Bug Fixes

0.1.1 (2025-03-11)

Bug Fixes

0.1.0 (2025-03-11)

Features

  • add auroc metric to label prediction task (#68) (0b17300)

  • add baselines for all tasks except cross species and perturbation (#69) (3e79256)

  • add de genes to perturbation task (#70) (84968e6)

  • add random forest classifier (#62) (e5d0f4c)

  • add static typing of input and output types (#34) (97a7bdf)

  • cross species integration task (#39) (f49ce0d)

  • fix strong metric results typing (#71) (30d0099)

  • fix uce and geneformer (#24) (101bc04)

  • geneformer model (#14) (8d97071)

  • implement model registry for model-specific outputs (#57) (838cf73)

  • implement model weight download and caching (9ad44c1)

  • implement model weight download and caching (5a465af)

  • metadatalabel prediction task (99803db)

  • metrics registry (#49) (3a841d1)

  • perturbation tasks (#41) (29c812c)

  • readme update and various bug fixes (5543669)

  • remove ModelRunner and consolidate into BaseModel (13e1b55)

  • remove ModelRunner and consolidate into BaseModel (ae28843)

  • scgenept (#19) (8e6cf6a)

  • separate concerns for validation and implementation (#33) (fd52d07)

  • task baselines (#58) (d12be6b)

  • update dataset handling (0b456e7)

  • update dataset handling (5b8a7b7)

  • update to support lists of datasets (#35) (2b6ef60)

Bug Fixes