Changelog & Release Notes

Changelog

0.10.2 (2025-07-18)

Bug Fixes

fix UCE docker image build by switching to miniforge due to conda TOS changes (#333) (998ddee)

0.10.1 (2025-07-14)

Bug Fixes

scvi hvg alignment (#290) (2c90ec8)

0.10.0 (2025-06-16)

Features

allow estimating uncertainty in task metrics via batches of random seeds (#251) (5c033ff)
Reapply “geneformer updates” (#266) (#267) (a871b57)
update result output schema (#252) (#258) (8bbb365)

Bug Fixes

use macro average for auroc, not weighted (#253) (#260) (412af37)

0.9.2 (2025-05-20)

Bug Fixes

Fix UCE docker image build failure (#244) (3acf5fa)

0.9.1 (2025-05-20)

Bug Fixes

Fix transcriptformer Dockerfile (#224) (1ebf24a)

Documentation

repo and site links update (#223) (7c27747)
tweak roadmap wording (#217) (7a6f71d)

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

fix broken links, render warnings (#212) (226d4b9)
may-14 edits from gdocs (#214) (ed8279d)
update roadmap release tags (#215) (80d1020)
VC-2557 && VC-2533 (#208) (12c6727)

0.8.0 (2025-05-10)

Features

aido all model variants (#175) (b91ebde)

Documentation

Sync up docs with XFN google docs (#203) (6504333)
VC-2547 Updated base README (#199) (49d0d28)

0.7.0 (2025-05-08)

Features

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

Bug Fixes

Set random_state for RandomForestClassifier (#197) (b175388)
use correct silhouette score (#187) (a3e06eb)

Documentation

fixes for PR feedback (#200) (8d40da1)
improve add custom model docs (#193) (7adf963)
VC-2544 Instructions for working on docs (#192) (f825c23)

0.6.1 (2025-05-02)

Bug Fixes

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

0.6.0 (2025-05-02)

Features

CLI (#148) (4cd7947)
CLI batch jobs (#161) (af0bd1a)
enable minimal model developer workflow (#163) (f552bf3)
support perturbation in CLI (#156) (e14391d)
transcriptformer (#165) (173d1e7)

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

docs based on review comments from pr-160 (#169) (5e26b84)
Nc docs structure (#158) (deaee6f)

0.5.0 (2025-04-03)

Features

random seed for clustering (#151) (a1df9f9)

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

add tag to mount dir (#144) (b9d2500)
push model images to ECR public repo (#133) (8b5b653)

0.4.3 (2025-03-31)

Bug Fixes

remove old conf line in docker (#142) (69e637a)

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

docker builder (#124) (6c0e5b5)
move model validators back into docker images (#120) (ad1cb59)

Documentation

autogenerate documentation - sphinx (#116) (94be611)

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

geneformer model updates (#103) (5fdfdff)

0.2.1 (2025-03-13)

Bug Fixes

test release (#98) (d710766)

0.2.0 (2025-03-13)

Features

perturb baselines (#86) (9fe91be)

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

pypy build (#78) (8461a23)

0.1.1 (2025-03-11)

Bug Fixes

add new trigger (#76) (fc5cc3f)

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

expand dataset path (7f3fc9a)
expand dataset path (23d065a)