a

Author: hutaobo

README.md

@@ -2,40 +2,61 @@
 
 A toy Python package for analyzing 10x Xenium data.
 
+## Installation
+
+```bash
+pip install -U "pyXenium>=0.2.0"
+```
+
 ## Quickstart
- ## Installation
-
--```bash
--pip install pyXenium
--```
-+```bash
-+pip install -U "pyXenium>=0.2.0"
-+```
-
- ## Quickstart
-
-+### Load a partial Xenium dataset from Hugging Face
-+The snippet below uses the public demo dataset and the v2 loader that supports `base_url`.
-+
-+```python
-+from pyXenium.io.partial_xenium_loader import load_anndata_from_partial
-+
-+BASE = "https://huggingface.co/datasets/hutaobo/pyxenium-gsm9116572/resolve/main"
-+
-+adata = load_anndata_from_partial(
-+    base_url=BASE,
-+    analysis_name="analysis.zarr.zip",
-+    cells_name="cells.zarr.zip",
-+    transcripts_name="transcripts.zarr.zip",
-+    # Optional: if you uploaded a 10x MEX triplet under BASE/mex/
-+    # mex_dir=BASE + "/mex",
-+    # mex_matrix_name="matrix.mtx.gz",
-+    # mex_features_name="features.tsv.gz",
-+    # mex_barcodes_name="barcodes.tsv.gz",
-+    build_counts_if_missing=True,
-+)
-+print(adata)
-+```
-+
-+> **Note:** Requires `pyXenium>=0.2.0`. The dataset used above is hosted at:
-+> - Hugging Face Datasets: `hutaobo/pyxenium-gsm9116572`
+
+### Load a partial Xenium dataset from Hugging Face
+
+The snippet below uses the **public demo dataset** and the **v2 loader** that supports `base_url`.
+
+```python
+from pyXenium.io.partial_xenium_loader import load_anndata_from_partial
+
+BASE = "https://huggingface.co/datasets/hutaobo/pyxenium-gsm9116572/resolve/main"
+
+adata = load_anndata_from_partial(
+    base_url=BASE,
+    analysis_name="analysis.zarr.zip",
+    cells_name="cells.zarr.zip",
+    transcripts_name="transcripts.zarr.zip",
+    # Optional: if you uploaded a 10x MEX triplet under BASE/mex/
+    # mex_dir=BASE + "/mex",
+    # mex_matrix_name="matrix.mtx.gz",
+    # mex_features_name="features.tsv.gz",
+    # mex_barcodes_name="barcodes.tsv.gz",
+    build_counts_if_missing=True,
+)
+print(adata)
+```
+
+> **Note:** Requires `pyXenium>=0.2.0`.
+> The demo dataset is hosted at:
+> - Hugging Face Datasets: [hutaobo/pyxenium-gsm9116572](https://huggingface.co/datasets/hutaobo/pyxenium-gsm9116572)
+
+---
+
+## Development
+
+To install with development dependencies (testing, docs, etc.):
+
+```bash
+pip install -e ".[dev]"
+pytest
+```
+
+---
+
+## Links
+
+- 📦 PyPI: [pyXenium](https://pypi.org/project/pyXenium/)
+- 📖 Documentation: [Read the Docs](https://pyxenium.readthedocs.io/en/latest/)
+- 💻 Source code: [GitHub](https://github.com/hutaobo/pyXenium)
+
+## License
+
+MIT