Merge pull request #3 from Imageomics/feature/doc_use_case

Feature/doc use case

Author: NetZissou

.github/workflows/docs.yml

@@ -0,0 +1,33 @@
+name: Deploy MkDocs to GitHub Pages
+
+on:
+  push:
+    branches: [ main, master, feature/doc_use_case ]
+  workflow_dispatch:
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r docs-requirements.txt
+
+      - name: Build MkDocs site
+        run: |
+          mkdocs build --clean --strict
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./site

.gitignore

@@ -147,6 +147,7 @@ venv.bak/
 
 # mkdocs documentation
 /site
+site/
 
 # mypy
 .mypy_cache/
@@ -195,4 +196,6 @@ cython_debug/
 .cursorignore
 .cursorindexingignore
 
-jobs/
+jobs/
+
+docs/neon_beetles_data/

README.md

@@ -1,8 +1,11 @@
 
 <table width="100%">
   <tr>
-    <td align="left" width="120">
-      <img src="docs/imgs/Imageomics_logo_butterfly.png" alt="OpenCut Logo" width="100" />
+    <td align="left" width="100">
+      <img src="docs/imgs/Imageomics_logo_butterfly.png" alt="Imageomics Logo" width="100" />
+    </td>
+    <td align="left" width="100">
+      <img src="docs/imgs/full_ABC_logo_for_web_and_digital.png" alt="ABC Logo" width="100" />
     </td>
     <td align="right">
       <h1>HPC-Inference</h1>
@@ -75,6 +78,11 @@ uv pip install -e ".[all]"          # Install dependency for all use cases
 
 ### Use Cases Guide
 
+#### `ImageFolderDataset`
+For a comprehensive tutorial on using the `ImageFolderDataset` class, please see this notebook: [ImageFolderDataset Guide](docs/ImageFolderDataset_guide.ipynb). 
+
+This guide demonstrates working with the [NEON Beetle dataset](https://huggingface.co/datasets/imageomics/2018-NEON-beetles) and covers basic usage, validation, multi-model preprocessing, distributed processing, and performance optimization. 
+
 Use case 1: 
 - Image Folder Dataset
 - Parquet Dataset
@@ -93,3 +101,7 @@ Use case 5:
 - Grid search profiling
 
 ## Project Structure
+
+## Acknowledgement
+
+This project is a joint effort between the [Imageomics Institute](https://imageomics.osu.edu/) and the [ABC Global Center](https://www.biodiversityai.org/).

docs-requirements.txt

@@ -0,0 +1,4 @@
+mkdocs>=1.5.0
+mkdocs-material>=9.0.0
+mkdocstrings[python]>=0.20.0
+pymdown-extensions>=10.0.0