Add CellxGene Census lung Zarr dataset

README.md

@@ -197,13 +197,13 @@ sc.tl.leiden(adata, resolution=0.5)
 
 Measured locally while building this dataset:
 
-- open Zarr group: **0.0013 s**
-- read one `X[chunk]` (1000×1000): **0.0070 s**
+- open Zarr group: **0.0012 s**
+- read one `X[chunk]` (1000×1000): **0.0061 s**
 
 ```json
 {
-  "open_seconds": 0.0013324879109859467,
-  "read_chunk_seconds": 0.007030146196484566,
+  "open_seconds": 0.0011517200618982315,
+  "read_chunk_seconds": 0.006099492311477661,
   "chunk_shape": [
     1000,
     1000

build_lung_zarr.py

@@ -38,6 +38,31 @@ def _utc_now_iso() -> str:
     return _dt.datetime.now(tz=_dt.timezone.utc).isoformat()
 
 
+def _configure_hf_http_timeout(timeout_seconds: float) -> None:
+    """
+    HuggingFace Hub default HTTP read timeout is small (~10s) and can cause
+    `httpx.ReadTimeout` during large/many-file commits. Increase it by setting
+    a custom shared httpx client factory.
+    """
+    try:
+        import httpx
+        from huggingface_hub.utils import set_client_factory
+        from huggingface_hub.utils._http import hf_request_event_hook
+
+        def _factory() -> httpx.Client:
+            timeout = httpx.Timeout(timeout_seconds, write=timeout_seconds)
+            return httpx.Client(
+                event_hooks={"request": [hf_request_event_hook]},
+                follow_redirects=True,
+                timeout=timeout,
+            )
+
+        set_client_factory(_factory)
+    except Exception:
+        # Best-effort: if this fails for any reason, fall back to defaults.
+        return
+
+
 def _chunk_1d(n: int, target: int = 100_000) -> int:
     return int(min(max(1, target), max(1, n)))
 
@@ -339,6 +364,7 @@ def main() -> None:
     ap.add_argument("--seed", type=int, default=0, help="Random seed for subsampling.")
     ap.add_argument("--n-hvg", type=int, default=0, help="Select this many HVGs (0 = keep all genes).")
     ap.add_argument("--only-readme", action="store_true", help="Only (re)generate README+summary from an existing zarr store.")
+    ap.add_argument("--hf-timeout", type=float, default=600.0, help="HF Hub HTTP read/write timeout in seconds (upload only).")
     ap.add_argument("--upload", action="store_true", help="Upload folder to HuggingFace Hub (requires HF_TOKEN env var).")
     args = ap.parse_args()
 
@@ -423,6 +449,7 @@ def main() -> None:
                 raise SystemExit("HF_TOKEN env var is required for --upload.")
             from huggingface_hub import create_repo, upload_folder
 
+            _configure_hf_http_timeout(args.hf_timeout)
             print(f"[upload] ensuring dataset repo exists: {args.repo_id}", flush=True)
             create_repo(repo_id=args.repo_id, repo_type="dataset", exist_ok=True, token=token)
             print(f"[upload] uploading folder: {out_dir}", flush=True)
@@ -587,6 +614,7 @@ def main() -> None:
 
         from huggingface_hub import create_repo, upload_folder
 
+        _configure_hf_http_timeout(args.hf_timeout)
         print(f"[upload] ensuring dataset repo exists: {args.repo_id}", flush=True)
         create_repo(repo_id=args.repo_id, repo_type="dataset", exist_ok=True, token=token)
         print(f"[upload] uploading folder: {out_dir}", flush=True)

dataset_summary.json

@@ -590,8 +590,8 @@
     "ulcerative colitis"
   ],
   "benchmark": {
-    "open_seconds": 0.0013324879109859467,
-    "read_chunk_seconds": 0.007030146196484566,
+    "open_seconds": 0.0011517200618982315,
+    "read_chunk_seconds": 0.006099492311477661,
     "chunk_shape": [
       1000,
       1000