Update datasets requirement from ~=3.2.0 to >=3.2,<4.1#25

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dependabot[bot] wants to merge 125 commits intomainfrom

dependabot/pip/datasets-gte-3.2-and-lt-4.1

Commits on Nov 6, 2024

First commit.
Kevin Kaichuang Yang
committed

Commits on Nov 19, 2024

Refactor common functions to utils.py.
Kevin Kaichuang Yang
committed
Allow loading without optimizer and scheduler.
Kevin Kaichuang Yang
committed

Commits on Nov 20, 2024

Small bugfixes.
Kevin Kaichuang Yang
committed
More robust unconditional generation.
Kevin Kaichuang Yang
committed

Commits on Jan 8, 2025

Cleanup utilities and a bunch of analysis code.
Kevin Kaichuang Yang
committed

Commits on Jan 25, 2025

exploring dayhoff and hf datasets
Samir Char
committed
exploring hf custom dataset
Samir Char
committed

Commits on Jan 26, 2025

script to upload folders to HF
Samir Char
committed

Commits on Jan 27, 2025

added allow and ignore patterns
Samir Char
committed

Commits on Feb 11, 2025

Model and HF Tokenizer
Samir Char
committed
remove local-only files from tracking
Samir Char
committed

Commits on Feb 12, 2025

Make writing outputs more efficient.
Kevin Kaichuang Yang
committed

Commits on Feb 14, 2025

Merge pull request #4 from microsoft/kky/dev
samirchar
authored
Merged with new main branch.
Samir Char
committed
Keep main from train.py
Samir Char
committed
Merge pull request #5 from microsoft/samir/hf_integration
yangkky
authored

Commits on Feb 20, 2025

Working resampling for scaffolding.
Kevin Kaichuang Yang
committed

Commits on Mar 1, 2025

Working simple scaffolding for 1prw.
Kevin Kaichuang Yang
committed

Commits on Mar 6, 2025

Scaffold motif benchmark things.
Kevin Kaichuang Yang
committed

Commits on Mar 25, 2025

Commits on Mar 28, 2025

Commits on Mar 31, 2025

new hf datasets
Samir Char
committed

Commits on Apr 7, 2025

updated .gitignore
Samir Char
committed
organized branch
Samir Char
committed

Commits on Apr 10, 2025

add scaffolding stuff
sarahalamdari
committed
Handle the older things, strip out special tokens.
Kevin Kaichuang Yang
committed
Fix type hints.
Kevin Kaichuang Yang
committed
A bunch of analysis for paper.
Kevin Kaichuang Yang
committed
Make things uppercase.
Kevin Kaichuang Yang
committed
Some useful tools for computing metrics.
Kevin Kaichuang Yang
committed

Commits on Apr 14, 2025

cleaned branch
Samir Char
committed
removed files not part of feature
Samir Char
committed
modified gitignore
Samir Char
committed
added mmd analysis notebooks
Samir Char
committed
fix scaffoldig and fidelity script
sarahalamdari
committed

Commits on Apr 15, 2025

More plotting code
Kevin Kaichuang Yang
committed
Working resampling for scaffolding.
Kevin Kaichuang Yang
committed
Working simple scaffolding for 1prw.
Kevin Kaichuang Yang
committed
Scaffold motif benchmark things.
Kevin Kaichuang Yang
committed
Handle the older things, strip out special tokens.
Kevin Kaichuang Yang
committed
Fix type hints.
Kevin Kaichuang Yang
committed
A bunch of analysis for paper.
Kevin Kaichuang Yang
committed
Make things uppercase.
Kevin Kaichuang Yang
committed
Some useful tools for computing metrics.
Kevin Kaichuang Yang
committed
More plotting code
Kevin Kaichuang Yang
committed
Fix typo in lr.
Kevin Kaichuang Yang
committed
Merge branch 'kky/dev' of https://github.com/microsoft/dayhoff into kky/dev
Kevin Kaichuang Yang
committed
Merge pull request #6 from microsoft/samir/hf_datasets
yangkky
authored
Merge branch 'main' of https://github.com/microsoft/dayhoff into kky/dev
Kevin Kaichuang Yang
committed

Commits on Apr 16, 2025

Create codeql.yml
samirchar
authored

Commits on Apr 23, 2025

Merge pull request #8 from microsoft/kky/dev
samirchar
authored
More plotting code.
Kevin Kaichuang Yang
committed

Commits on Apr 28, 2025

generate from homolgs with hf
Samir Char
committed

Commits on May 1, 2025

restrucutre. Edit readme, reqs.txt and toml
Samir Char
committed
restructure
Samir Char
committed
deleted old models from hub
Samir Char
committed
edit readme. modified generate.py. included assets folder
Samir Char
committed
added intended use
Samir Char
committed
added docker, cleaned.py, edit readme
Samir Char
committed
added docker and dataset sizes
Samir Char
committed
uncommitted files
Samir Char
committed
aligned requirements.txt with toml
Samir Char
committed
updated TOC in readme
Samir Char
committed

Commits on May 2, 2025

added detail to datasets
Samir Char
committed

Commits on May 7, 2025

removed credentials
Samir Char
committed
Create dependabot.yml
samirchar
authored
dependabot.yml
Samir Char
committed
Delete .github/dependabot.yml
samirchar
authored
removed dependabot yml
Samir Char
committed
Merge branch 'main' of github.com:microsoft/dayhoff
Samir Char
committed
Create dependabot.yml
samirchar
authored
removed notebooks. replaced by .py
Samir Char
committed
cleaned
Samir Char
committed
deleted assets
Samir Char
committed

Commits on Jun 16, 2025

add scripts
sarahalamdari
committed

Commits on Jul 2, 2025

New plots for paper.
Kevin Kaichuang Yang
committed
TM score -> TM-score.
Kevin Kaichuang Yang
committed

Commits on Jul 7, 2025

Commits on Jul 10, 2025

Commits on Jul 11, 2025

Update cas9 analysis.
Kevin Kaichuang Yang
committed
Merge changes.
Kevin Kaichuang Yang
committed
Fix path.
Kevin Kaichuang Yang
committed
Merge pull request #23 from microsoft/kky/dev
sarahalamdari
authored
Edit model blurbs and script descriptions.
Kevin Kaichuang Yang
committed
Merge pull request #24 from microsoft/kky/dev
sarahalamdari
authored
ready to merge
sarahalamdari
committed
Merge branch 'main' of github.com:microsoft/dayhoff
sarahalamdari
committed
fix imports
sarahalamdari
committed

Commits on Jul 15, 2025

Commits on Jul 16, 2025

Commits on Jul 18, 2025