a

Author: hutaobo

.github/workflows/test.yml

@@ -0,0 +1,12 @@
+name: tests
+on: [push, pull_request]
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - run: pip install -U "pyXenium>=0.1.0" pytest
+      - run: pytest

README.md

@@ -3,7 +3,39 @@
 A toy Python package for analyzing 10x Xenium data.
 
 ## Quickstart
-```bash
-pip install pyXenium
-pyXenium demo
-```
+ ## 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`

docs/examples/partial_xenium_loader.md

@@ -0,0 +1,29 @@
+# Load a partial Xenium dataset (remote)
+
+This example loads a public demo dataset directly from Hugging Face using the v2 loader that supports `base_url`.
+
+> **Requirements**
+>
+> - `pyXenium >= 0.2.0`
+> - Internet access for the first run (files are streamed/downloaded)
+
+```python
+# doctest: +ELLIPSIS
+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 10x 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)  # doctest: +ELLIPSIS

pyproject.toml

@@ -35,3 +35,8 @@ pyXenium = ["data/**", "*.csv", "*.zarr", "*.txt"]
 
 [project.scripts]
 pyxenium-import-partial = "pyXenium.io.partial_xenium_loader:app"
+
+# pytest.ini
+[pytest]
+addopts = -q
+doctest_glob = docs/**/*.md