Skip to content
Open
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
35 commits
Select commit Hold shift + click to select a range
abadcf6
Add design doc for HuggingFace model zoo migration
avantikalal Mar 3, 2026
8b35d25
Add implementation plan for HuggingFace migration
avantikalal Mar 3, 2026
6d7b4db
feat: add huggingface_hub dependency
avantikalal Mar 3, 2026
571ae03
refactor: extract shared utils to resources/utils.py
avantikalal Mar 3, 2026
e3e7c75
refactor: move wandb functions to resources/wandb.py
avantikalal Mar 3, 2026
91c4bca
test: add failing tests for HuggingFace resource functions
avantikalal Mar 3, 2026
38d0d36
feat: implement HuggingFace API for model zoo access
avantikalal Mar 3, 2026
fc293ce
feat: update pretrained models to download from HuggingFace
avantikalal Mar 3, 2026
c2b9e3f
test: mark wandb tests with pytest marker, skip by default
avantikalal Mar 3, 2026
17ef096
docs: add breaking changes notice for HuggingFace migration
avantikalal Mar 3, 2026
b17e15d
docs: rewrite model zoo tutorial for HuggingFace API
avantikalal Mar 3, 2026
adc7bec
docs: update tutorials for new HuggingFace API
avantikalal Mar 3, 2026
8ef94c8
Add design doc for deprecation messages
avantikalal Mar 3, 2026
c502ae2
Add implementation plan for deprecation messages
avantikalal Mar 3, 2026
76d7783
test: add failing tests for deprecation error messages
avantikalal Mar 3, 2026
6c6e9e1
feat: add deprecation stubs for removed wandb functions
avantikalal Mar 3, 2026
ee57811
feat: add deprecation detection to load_model() for old kwargs
avantikalal Mar 3, 2026
e2e49c7
fix: specify filename for borzoi model in tutorial 1
avantikalal Mar 3, 2026
2d9de4b
fix: handle strand formats in plot_tracks and fix download_dataset us…
avantikalal Mar 3, 2026
a1733e4
docs: update tutorial 1 with successful execution outputs
avantikalal Mar 3, 2026
30e79a7
docs: change version to v1.1.0 in README
avantikalal Mar 4, 2026
5df3d36
docs: add link to HuggingFace model zoo in README
avantikalal Mar 4, 2026
0214d3f
fix: update HuggingFace collection ID and disable token for public ac…
avantikalal Mar 4, 2026
8f9dcff
feat: add files list to get_model_info and get_dataset_info
avantikalal Mar 4, 2026
63c09d4
reran tutorials
avantikalal Mar 4, 2026
8ace7f1
chore: remove planning docs from repo
avantikalal Mar 4, 2026
c0c4632
change description
avantikalal Mar 4, 2026
6c7cfd7
revert: remove visualize.py strand fix (will be separate PR)
avantikalal Mar 4, 2026
4b7c06d
docs: update test file docstring
avantikalal Mar 4, 2026
9083737
refactor: remove duplicate utility tests from test_resources_hf.py
avantikalal Mar 4, 2026
c5e1cea
test: replace mock tests with integration tests for HuggingFace API
avantikalal Mar 4, 2026
95bd8e5
fix: remove wandb dependency from test_models.py
avantikalal Mar 4, 2026
c9633eb
fix: use bundled test genome instead of downloading hg38 in CI
avantikalal Mar 4, 2026
5554981
fix: use bundled test genome for GC matching test
avantikalal Mar 5, 2026
852e480
fix: add weights_only parameter to wandb.load_model
avantikalal Mar 5, 2026
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
15 changes: 13 additions & 2 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,8 +6,19 @@ gReLU is a Python library to train, interpret, and apply deep learning models to

![Flowchart](media/flowchart.jpg)

## Notices
[02-23-2026] Due to deprecated anonymous downloads from wandb (https://github.com/wandb/wandb/pull/10909) the gReLU model zoo has been migrated to huggingface (https://huggingface.co/collections/Genentech/grelu-model-zoo). In the next update, all functions to download models and datasets will connect to huggingface instead of wandb.
## Breaking Changes in v1.1.0

**Model Zoo Migration:** The gReLU model zoo has moved from Weights & Biases to [HuggingFace](https://huggingface.co/collections/Genentech/grelu-model-zoo). The `grelu.resources` API has changed:

```python
# Old API (wandb) - still available at grelu.resources.wandb but will be removed in future
grelu.resources.load_model(project="human-atac-catlas", model_name="model")

# New API (HuggingFace)
grelu.resources.load_model(repo_id="Genentech/human-atac-catlas-model", filename="model.ckpt")
```

Browse the zoo at https://huggingface.co/collections/Genentech/grelu-model-zoo and see the [Model Zoo Tutorial](docs/tutorials/6_model_zoo.ipynb) for updated usage.

## Installation

Expand Down
368 changes: 137 additions & 231 deletions docs/tutorials/1_inference.ipynb

Large diffs are not rendered by default.

2,306 changes: 778 additions & 1,528 deletions docs/tutorials/2_finetune.ipynb

Large diffs are not rendered by default.

417 changes: 222 additions & 195 deletions docs/tutorials/3_train.ipynb

Large diffs are not rendered by default.

1,567 changes: 1,072 additions & 495 deletions docs/tutorials/4_design.ipynb

Large diffs are not rendered by default.

Loading