What's Changed
* Include notebook workflow by bputzeys in https://github.com/helicalAI/helical/pull/68
* Include GitHub Action testing successfull runs for all Jupyter Notebooks in examples folder by bputzeys in https://github.com/helicalAI/helical/pull/70
* Remove condition to only run workflow on release branch by bputzeys in https://github.com/helicalAI/helical/pull/72
* Remove condition to only run workflow on release branch by bputzeys in https://github.com/helicalAI/helical/pull/73
* Remove requirement to run other workflow before this. by bputzeys in https://github.com/helicalAI/helical/pull/74
* Remove requirement to run other workflow before this by bputzeys in https://github.com/helicalAI/helical/pull/75
* fixed typing issue for python<3.11 by maxiallard in https://github.com/helicalAI/helical/pull/77
* Adjust alcs by bputzeys in https://github.com/helicalAI/helical/pull/76
* changed version python by maxiallard in https://github.com/helicalAI/helical/pull/79
* Fix typing issue for python<3.11 by bputzeys in https://github.com/helicalAI/helical/pull/78
* Include hydra configs for each model by bputzeys in https://github.com/helicalAI/helical/pull/80
* Adjust uce config by bputzeys in https://github.com/helicalAI/helical/pull/82
* Improve uce memory foodprint by bputzeys in https://github.com/helicalAI/helical/pull/81
* Fix data notebooks by maxiallard in https://github.com/helicalAI/helical/pull/84
* fixed naming of anndata by maxiallard in https://github.com/helicalAI/helical/pull/85
* Improvements UCE and Hydra introduction for configs by maxiallard in https://github.com/helicalAI/helical/pull/83
* Avoid mapping ensembl ids to ensembl ids by bputzeys in https://github.com/helicalAI/helical/pull/86
* Geneformer v2 by JadSbai in https://github.com/helicalAI/helical/pull/88
* Basic Fine-Tuning Capabilities For All RNA Models by mattwoodx in https://github.com/helicalAI/helical/pull/90
* Fix file not found issue in notebook by mattwoodx in https://github.com/helicalAI/helical/pull/92
* Fix notebook errors by JadSbai in https://github.com/helicalAI/helical/pull/94
* Fix Geneformer process_data by mattwoodx in https://github.com/helicalAI/helical/pull/95
* Reduce train sample to stop timeout by mattwoodx in https://github.com/helicalAI/helical/pull/96
* Changing to Helical Hugging Face Dataset In Repo by mattwoodx in https://github.com/helicalAI/helical/pull/97
* Added Geneformer v2, Fine-Tuning for RNA models, Bug Fixes for Mapping by maxiallard in https://github.com/helicalAI/helical/pull/91
* Typing fixes, refactoring and renaming by bputzeys in https://github.com/helicalAI/helical/pull/99
* Include converter tests by bputzeys in https://github.com/helicalAI/helical/pull/102
* Fix Weight Scrambling in scGPT by mattwoodx in https://github.com/helicalAI/helical/pull/98
* Typing updates, reordering and renaming by bputzeys in https://github.com/helicalAI/helical/pull/100
* Change workflow by bputzeys in https://github.com/helicalAI/helical/pull/107
* Bugfix: stop execution if no genes are present by bputzeys in https://github.com/helicalAI/helical/pull/109
* Change workflow to exectute tests and notebooks sequentially by bputzeys in https://github.com/helicalAI/helical/pull/108
* Adding downloads where initial files might not be available anymore. by maxiallard in https://github.com/helicalAI/helical/pull/110
* Change dependency strictness by mattwoodx in https://github.com/helicalAI/helical/pull/111
* HyenaDNA Fine-Tuning Capabilities and Regression Head by mattwoodx in https://github.com/helicalAI/helical/pull/101
* Refactor fine-tuning by mattwoodx in https://github.com/helicalAI/helical/pull/112
* Raise error if download fails and include log message by bputzeys in https://github.com/helicalAI/helical/pull/113
* Raise error if download fails by bputzeys in https://github.com/helicalAI/helical/pull/114
* Maxiallard patch 1 by maxiallard in https://github.com/helicalAI/helical/pull/116
* Merge updates in main into release by mattwoodx in https://github.com/helicalAI/helical/pull/115
* Include raw counts flag by bputzeys in https://github.com/helicalAI/helical/pull/117
* Include release build by bputzeys in https://github.com/helicalAI/helical/pull/118
* Add missing steps by bputzeys in https://github.com/helicalAI/helical/pull/120
* Include release process by bputzeys in https://github.com/helicalAI/helical/pull/119
* Docker by maxiallard in https://github.com/helicalAI/helical/pull/121
* Change docs to Mkdocs by mattwoodx in https://github.com/helicalAI/helical/pull/122
* Use logger to show warning message by bputzeys in https://github.com/helicalAI/helical/pull/123
* Fix GeneformerConfig Docstring by mattwoodx in https://github.com/helicalAI/helical/pull/124
* Filter logs and warnings by mattwoodx in https://github.com/helicalAI/helical/pull/125
* Filter loggging, improve README by bputzeys in https://github.com/helicalAI/helical/pull/126
* Feature/helix mrna by bputzeys in https://github.com/helicalAI/helical/pull/127
* Update forward of fine-tuning model by mattwoodx in https://github.com/helicalAI/helical/pull/128
* Add import to the package by mattwoodx in https://github.com/helicalAI/helical/pull/130
* Mamba2-mRNA and Helix-mRNA by bputzeys in https://github.com/helicalAI/helical/pull/129
* Include instructions for Colab run by bputzeys in https://github.com/helicalAI/helical/pull/131
* Address import issues in Colab by bputzeys in https://github.com/helicalAI/helical/pull/132
* Remove causal conv 1d by mattwoodx in https://github.com/helicalAI/helical/pull/133
* Add causal conv1d by mattwoodx in https://github.com/helicalAI/helical/pull/136
* Fix version by maxiallard in https://github.com/helicalAI/helical/pull/135
* Update HyenaDNA with new Dependencies by mattwoodx in https://github.com/helicalAI/helical/pull/137
* CPU bound unit tests and GPU integration tests by mattwoodx in https://github.com/helicalAI/helical/pull/140
* Modify pyproject.toml and make mamba_ssm optional. by giogix2 in https://github.com/helicalAI/helical/pull/138
* Add emb_mode option to scGPT and update docs by mattwoodx in https://github.com/helicalAI/helical/pull/141
* Fix mamba-ssm integration in release Pypi by giogix2 in https://github.com/helicalAI/helical/pull/144
* Test models using local files by mattwoodx in https://github.com/helicalAI/helical/pull/145
* Cleanup by bputzeys in https://github.com/helicalAI/helical/pull/149
* Add binning seed to scGPT by bputzeys in https://github.com/helicalAI/helical/pull/148
* Fix seeds v2 by bputzeys in https://github.com/helicalAI/helical/pull/151
* Update versions by bputzeys in https://github.com/helicalAI/helical/pull/153
* Bring back skipped tests, fix seed for reproducible results in scGPT, include updates in README by bputzeys in https://github.com/helicalAI/helical/pull/150
* Cleanup scgpt and remove torchtext dependency by bputzeys in https://github.com/helicalAI/helical/pull/154
* Bump torch and torchvision versions by giogix2 in https://github.com/helicalAI/helical/pull/155
* Fix broken model card link by giogix2 in https://github.com/helicalAI/helical/pull/160
* Remove tensorflow dependency by bputzeys in https://github.com/helicalAI/helical/pull/156
* Return ensembl ID for each embedding for emb_mode="gene" by mattwoodx in https://github.com/helicalAI/helical/pull/157
* Integrate Caduceus Model by mattwoodx in https://github.com/helicalAI/helical/pull/159
* Bug fix: HyenaDNA variable length input sequences by mattwoodx in https://github.com/helicalAI/helical/pull/161
* Transfer the benchmarking scripts to external repo by giogix2 in https://github.com/helicalAI/helical/pull/162
New Contributors
* JadSbai made their first contribution in https://github.com/helicalAI/helical/pull/88
* mattwoodx made their first contribution in https://github.com/helicalAI/helical/pull/90
* giogix2 made their first contribution in https://github.com/helicalAI/helical/pull/138
**Full Changelog**: https://github.com/helicalAI/helical/compare/0.0.1a1...v0.0.1a16