Releases · helicalAI/helical

What's Changed

Include notebook workflow by @bputzeys in #68
Include GitHub Action testing successfull runs for all Jupyter Notebooks in examples folder by @bputzeys in #70
Remove condition to only run workflow on release branch by @bputzeys in #72
Remove condition to only run workflow on release branch by @bputzeys in #73
Remove requirement to run other workflow before this. by @bputzeys in #74
Remove requirement to run other workflow before this by @bputzeys in #75
fixed typing issue for python<3.11 by @maxiallard in #77
Adjust alcs by @bputzeys in #76
changed version python by @maxiallard in #79
Fix typing issue for python<3.11 by @bputzeys in #78
Include hydra configs for each model by @bputzeys in #80
Adjust uce config by @bputzeys in #82
Improve uce memory foodprint by @bputzeys in #81
Fix data notebooks by @maxiallard in #84
fixed naming of anndata by @maxiallard in #85
Improvements UCE and Hydra introduction for configs by @maxiallard in #83
Avoid mapping ensembl ids to ensembl ids by @bputzeys in #86
Geneformer v2 by @JadSbai in #88
Basic Fine-Tuning Capabilities For All RNA Models by @mattwoodx in #90
Fix file not found issue in notebook by @mattwoodx in #92
Fix notebook errors by @JadSbai in #94
Fix Geneformer process_data by @mattwoodx in #95
Reduce train sample to stop timeout by @mattwoodx in #96
Changing to Helical Hugging Face Dataset In Repo by @mattwoodx in #97
Added Geneformer v2, Fine-Tuning for RNA models, Bug Fixes for Mapping by @maxiallard in #91
Typing fixes, refactoring and renaming by @bputzeys in #99
Include converter tests by @bputzeys in #102
Fix Weight Scrambling in scGPT by @mattwoodx in #98
Typing updates, reordering and renaming by @bputzeys in #100
Change workflow by @bputzeys in #107
Bugfix: stop execution if no genes are present by @bputzeys in #109
Change workflow to exectute tests and notebooks sequentially by @bputzeys in #108
Adding downloads where initial files might not be available anymore. by @maxiallard in #110
Change dependency strictness by @mattwoodx in #111
HyenaDNA Fine-Tuning Capabilities and Regression Head by @mattwoodx in #101
Refactor fine-tuning by @mattwoodx in #112
Raise error if download fails and include log message by @bputzeys in #113
Raise error if download fails by @bputzeys in #114
Maxiallard patch 1 by @maxiallard in #116
Merge updates in main into release by @mattwoodx in #115
Include raw counts flag by @bputzeys in #117
Include release build by @bputzeys in #118
Add missing steps by @bputzeys in #120
Include release process by @bputzeys in #119
Docker by @maxiallard in #121
Change docs to Mkdocs by @mattwoodx in #122
Use logger to show warning message by @bputzeys in #123
Fix GeneformerConfig Docstring by @mattwoodx in #124
Filter logs and warnings by @mattwoodx in #125
Filter loggging, improve README by @bputzeys in #126
Feature/helix mrna by @bputzeys in #127
Update forward of fine-tuning model by @mattwoodx in #128
Add import to the package by @mattwoodx in #130
Mamba2-mRNA and Helix-mRNA by @bputzeys in #129
Include instructions for Colab run by @bputzeys in #131
Address import issues in Colab by @bputzeys in #132
Remove causal conv 1d by @mattwoodx in #133
Add causal conv1d by @mattwoodx in #136
Fix version by @maxiallard in #135
Update HyenaDNA with new Dependencies by @mattwoodx in #137
CPU bound unit tests and GPU integration tests by @mattwoodx in #140
Modify pyproject.toml and make mamba_ssm optional. by @giogix2 in #138
Add emb_mode option to scGPT and update docs by @mattwoodx in #141
Fix mamba-ssm integration in release Pypi by @giogix2 in #144
Test models using local files by @mattwoodx in #145
Cleanup by @bputzeys in #149
Add binning seed to scGPT by @bputzeys in #148
Fix seeds v2 by @bputzeys in #151
Update versions by @bputzeys in #153
Bring back skipped tests, fix seed for reproducible results in scGPT, include updates in README by @bputzeys in #150
Cleanup scgpt and remove torchtext dependency by @bputzeys in #154
Bump torch and torchvision versions by @giogix2 in #155
Fix broken model card link by @giogix2 in #160
Remove tensorflow dependency by @bputzeys in #156
Return ensembl ID for each embedding for emb_mode="gene" by @mattwoodx in #157
Integrate Caduceus Model by @mattwoodx in #159
Bug fix: HyenaDNA variable length input sequences by @mattwoodx in #161
Transfer the benchmarking scripts to external repo by @giogix2 in #162

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