Merge branch 'main' into lr-scheduler

Author: avantikalal

.github/workflows/pypi-publish.yml

@@ -21,6 +21,7 @@ jobs:
         run: |
           pip install --upgrade pip
           pip install -r docs/requirements.txt
+          pip install -e .
       - name: Sphinx build
         run: |
           sphinx-build docs _build

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: '^docs/conf.py'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v5.0.0
+  rev: v6.0.0
   hooks:
   - id: trailing-whitespace
   - id: check-added-large-files

README.md

@@ -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
 

docs/conf.py

@@ -10,6 +10,15 @@
 import os
 import sys
 import shutil
+from pathlib import Path
+
+# -- Path setup --------------------------------------------------------------
+# Point to the absolute path of the 'src' directory
+docs_dir = Path(__file__).parent.resolve()
+root_dir = docs_dir.parent
+src_dir = root_dir / "src"
+
+sys.path.insert(0, str(src_dir))
 
 # -- General configuration ---------------------------------------------------
 
@@ -34,8 +43,20 @@
     "autoapi.extension",
 ]
 
-autoapi_dirs = ['../src']
-autoapi_ignore = ['*.ipynb_checkpoints*/*.py']
+# -- AutoAPI configuration ---------------------------------------------------
+autoapi_type = 'python'
+autoapi_dirs = [os.path.abspath('../src/grelu')] # Point directly to the package folder
+autoapi_root = 'autoapi'
+autoapi_python_use_implicit_namespaces = True
+autoapi_options = [
+    'members',
+    'undoc-members',
+    'show-inheritance',
+    'show-module-summary',
+    'special-members',
+    'imported-members',
+]
+autoapi_ignore = ['*ipynb_checkpoints*']
 
 def linkcode_resolve(domain, info):
     if domain != 'py':

docs/index.md

@@ -7,13 +7,15 @@ This is the documentation of **gReLU**.
 ```{toctree}
 :maxdepth: 1
 Overview <readme>
-Module reference <api/modules>
+Module reference <autoapi/index>
 Tutorial: Inference <tutorials/1_inference>
 Tutorial: Fine-tuning <tutorials/2_finetune>
 Tutorial: Training <tutorials/3_train>
 Tutorial: Design <tutorials/4_design>
 Tutorial: Variant effect prediction <tutorials/5_variant>
 Tutorial: Model zoo <tutorials/6_model_zoo>
+Tutorial: Simulations <tutorials/7_simulations>
+Tutorial: Custom Model <tutorials/8_custom_models>
 contributing
 license
 authors