feat: prepare v1.0.0 release

- Move git dependencies (SAM2, CONCH, MUSK) out of pyproject.toml for PyPI compatibility
- Update README installation instructions with manual git install steps
- Add Hugging Face link to README

Author: Yousef Ashraf Hassan Kotb Hassan

README.md

@@ -14,13 +14,15 @@
 <p align="center">
   <a href="https://atlasanalyticslab.github.io/AtlasPatch/"><b>Project Page</b></a> |
   <a href="https://arxiv.org/abs/XXXX.XXXXX"><b>Paper</b></a> |
+  <a href="https://huggingface.co/AtlasAnalyticsLab/AtlasPatch"><b>Hugging Face</b></a> |
   <a href="https://github.com/AtlasAnalyticsLab/AtlasPatch"><b>GitHub</b></a>
 </p>
 
 ## Table of Contents
 - [Installation](#installation)
   - [Quick Install (Recommended)](#quick-install-recommended)
   - [OpenSlide Prerequisites](#openslide-prerequisites)
+  - [Optional Encoder Dependencies](#optional-encoder-dependencies)
   - [Alternative Installation Methods](#alternative-installation-methods)
 - [Usage Guide](#usage-guide)
   - [Pipeline Checkpoints](#pipeline-checkpoints)
@@ -62,7 +64,11 @@
 ### Quick Install (Recommended)
 
 ```bash
+# Install AtlasPatch
 pip install atlas-patch
+
+# Install SAM2 (required for tissue segmentation)
+pip install git+https://github.com/facebookresearch/sam2.git
 ```
 
 > **Note:** AtlasPatch requires the OpenSlide system library for WSI processing. See [OpenSlide Prerequisites](#openslide-prerequisites) below.
@@ -88,6 +94,20 @@ Before installing AtlasPatch, you need the OpenSlide system library:
 
 - **Other systems**: Visit [OpenSlide Documentation](https://openslide.org/)
 
+### Optional Encoder Dependencies
+
+Some feature extractors require additional dependencies that must be installed separately:
+
+```bash
+# For CONCH encoder (conch_v1, conch_v15)
+pip install git+https://github.com/Mahmoodlab/CONCH.git
+
+# For MUSK encoder
+pip install git+https://github.com/lilab-stanford/MUSK.git
+```
+
+These are only needed if you plan to use those specific encoders.
+
 ### Alternative Installation Methods
 
 <details>
@@ -101,8 +121,9 @@ conda activate atlas_patch
 # Install OpenSlide
 conda install -c conda-forge openslide
 
-# Install AtlasPatch
+# Install AtlasPatch and SAM2
 pip install atlas-patch
+pip install git+https://github.com/facebookresearch/sam2.git
 ```
 </details>
 
@@ -117,8 +138,9 @@ curl -LsSf https://astral.sh/uv/install.sh | sh
 uv venv
 source .venv/bin/activate  # On Windows: .venv\Scripts\activate
 
-# Install AtlasPatch
+# Install AtlasPatch and SAM2
 uv pip install atlas-patch
+uv pip install git+https://github.com/facebookresearch/sam2.git
 ```
 </details>
 

docs/release-notes/v1.0.0.md

@@ -38,15 +38,25 @@ If your encoder isn't in the list, the plugin system lets you add it without tou
 ## Installation
 
 ```bash
+# Install AtlasPatch
 pip install atlas-patch
+
+# Install SAM2 (required for tissue segmentation)
+pip install git+https://github.com/facebookresearch/sam2.git
 ```
 
-You'll need OpenSlide installed on your system. If you're using conda:
+You'll also need OpenSlide installed on your system. If you're using conda:
 
 ```bash
 conda install -c conda-forge openslide
 ```
 
+Optional encoders (install only if needed):
+```bash
+pip install git+https://github.com/Mahmoodlab/CONCH.git  # for CONCH
+pip install git+https://github.com/lilab-stanford/MUSK.git  # for MUSK
+```
+
 ## Quick start
 
 Process a directory of slides with UNI embeddings:
@@ -70,6 +80,7 @@ We are planning to add slide-level encoders (TITAN, PRISM, GigaPath slide encode
 
 - GitHub: https://github.com/AtlasAnalyticsLab/AtlasPatch
 - PyPI: https://pypi.org/project/atlas-patch/
+- Hugging Face: https://huggingface.co/AtlasAnalyticsLab/AtlasPatch
 
 ## Issues?
 

pyproject.toml

@@ -32,15 +32,12 @@ dependencies = [
     "timm>=0.9.0",
     "huggingface-hub>=0.23.0",
     "gdown>=5.2.0",
-    "conch @ git+https://github.com/Mahmoodlab/CONCH.git",
     "transformers>=4.41.0",
     "sentencepiece>=0.2.0",
     "open-clip-torch>=2.24.0",
     "fairscale>=0.4.0",
     "einops>=0.8.0",
     "einops-exts>=0.0.4",
-    "sam-2 @ git+https://github.com/facebookresearch/sam2.git",
-    "MUSK @ git+https://github.com/lilab-stanford/MUSK.git",
 ]
 
 [project.optional-dependencies]
@@ -52,6 +49,11 @@ dev = [
     "mypy>=1.0.0",
 ]
 
+# See README for installation instructions:
+#   pip install git+https://github.com/facebookresearch/sam2.git  (required)
+#   pip install git+https://github.com/Mahmoodlab/CONCH.git       (optional)
+#   pip install git+https://github.com/lilab-stanford/MUSK.git    (optional)
+
 [project.scripts]
 atlaspatch = "atlas_patch.cli:main"