Adding a registry to have the hashes of datasets

src/squidpy/datasets/_10x_datasets.py

@@ -9,6 +9,7 @@
 from scanpy import settings
 
 from squidpy._constants._constants import TenxVersions
+from squidpy.datasets._hash_registry import KNOWN_HASHES
 from squidpy.datasets._utils import DEFAULT_CACHE_DIR, PathLike, _get_zipped_dataset, download_file
 
 __all__ = ["visium"]
@@ -163,4 +164,5 @@ def visium_hne_sdata(folderpath: Path | str | None = None) -> sd.SpatialData:
         folderpath=folderpath,
         dataset_name=DATASET_NAME,
         figshare_id=FIGSHARE_ID,
+        known_hash=KNOWN_HASHES.get(f"https://ndownloader.figshare.com/files/{FIGSHARE_ID}"),
     )

src/squidpy/datasets/_hash_registry.py

@@ -0,0 +1,25 @@
+from __future__ import annotations
+
+__all__ = ["KNOWN_HASHES"]
+
+
+KNOWN_HASHES: dict[str, str] = {
+    # 10x V1 – V1_Mouse_Kidney
+    "https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/V1_Mouse_Kidney/V1_Mouse_Kidney_filtered_feature_bc_matrix.h5": "sha256:5e0b1d1c51c4e8759cd623d212573e1c28daf95d66e0d25a8e4488f6bed3831a",
+    "https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/V1_Mouse_Kidney/V1_Mouse_Kidney_spatial.tar.gz": "sha256:91570548eae3d2bcf738af45e9dc463547a01669841db43ff20afb41b7cc0539",
+    # 10x V1 – V1_Adult_Mouse_Brain
+    "https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/V1_Adult_Mouse_Brain/V1_Adult_Mouse_Brain_filtered_feature_bc_matrix.h5": "sha256:eb78379e02dcf48036abf05b67233e73ecb0d880787feb82f76ff16f6ce01eb3",
+    "https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/V1_Adult_Mouse_Brain/V1_Adult_Mouse_Brain_image.tif": "sha256:39d0a85a7cecb0bde9ad2566260d571bb49834d26fc443cb32b96475f30668b2",
+    "https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/V1_Adult_Mouse_Brain/V1_Adult_Mouse_Brain_spatial.tar.gz": "sha256:46d6b05ba740f232d6bf4b27b9a8846815851e000985fb878f1364bab04e5bd4",
+    # 10x V2 - Parent_Visium_Human_Cerebellum
+    "https://cf.10xgenomics.com/samples/spatial-exp/1.2.0/Parent_Visium_Human_Cerebellum/Parent_Visium_Human_Cerebellum_filtered_feature_bc_matrix.h5": "sha256:05c137dd74623e748558c60a99d8e19749cbd073d070ce827aec73cee899f1d0",
+    "https://cf.10xgenomics.com/samples/spatial-exp/1.2.0/Parent_Visium_Human_Cerebellum/Parent_Visium_Human_Cerebellum_spatial.tar.gz": "sha256:7a8a42ad53d93776b7b21b31c3727d76a8ed6c332e2f39b6b056b52ef41eeea0",
+    # 10x V3 - Visium_FFPE_Mouse_Brain
+    "https://cf.10xgenomics.com/samples/spatial-exp/1.3.0/Visium_FFPE_Mouse_Brain/Visium_FFPE_Mouse_Brain_filtered_feature_bc_matrix.h5": "sha256:f5a5d0fafeab6259ded1c4883b255ef57557b81f32774513594e23a49e8352ce",
+    "https://cf.10xgenomics.com/samples/spatial-exp/1.3.0/Visium_FFPE_Mouse_Brain/Visium_FFPE_Mouse_Brain_spatial.tar.gz": "sha256:e4e1b845fd078946c6f8b61bd8d1927c0ce2395c3730f602cd80ef439d4a9d73",
+    # figshare
+    "https://ndownloader.figshare.com/files/26098124": "sha256:39d0a85a7cecb0bde9ad2566260d571bb49834d26fc443cb32b96475f30668b2",
+    "https://ndownloader.figshare.com/files/26098328": "sha256:56d379d96da859ea963c4349bbc8de07da9b68ce133839ebef5fe1b033c9e7bb",
+    "https://ndownloader.figshare.com/files/26098364": "sha256:2929fdd06e32fa25b38493e67f301fc5b22b1a32bfbe48ab7237d8d85fe8982d",
+    "https://ndownloader.figshare.com/files/52370645": "sha256:6f88b1624d072a362cb2b40a12f86b7649d3d2f2cc762dd6be23a078ac3093b6",
+}

src/squidpy/datasets/_utils.py

@@ -182,7 +182,9 @@ def _extension(self) -> str:
         return ".tiff"
 
 
-def _get_zipped_dataset(folderpath: Path, dataset_name: str, figshare_id: str) -> sd.SpatialData:
+def _get_zipped_dataset(
+    folderpath: Path, dataset_name: str, figshare_id: str, known_hash: str | None = None
+) -> sd.SpatialData:
     """Returns a specific dataset as SpatialData object. If the file is not present on disk, it will be downloaded and extracted."""
 
     # Create directory if it doesn't exist
@@ -204,7 +206,11 @@ def _get_zipped_dataset(folderpath: Path, dataset_name: str, figshare_id: str) -
     if not download_zip.exists():
         logg.info(f"Downloading Visium H&E SpatialData to {download_zip}")
         try:
-            download_file(filename=download_zip, backup_url=f"https://ndownloader.figshare.com/files/{figshare_id}")
+            download_file(
+                filename=download_zip,
+                backup_url=f"https://ndownloader.figshare.com/files/{figshare_id}",
+                known_hash=known_hash,
+            )
         except Exception as e:
             raise RuntimeError(f"Failed to download dataset: {e}") from e
 
@@ -222,14 +228,14 @@ def _get_zipped_dataset(folderpath: Path, dataset_name: str, figshare_id: str) -
     return sd.read_zarr(extracted_path)
 
 
-def download_file(filename: PathLike, backup_url: str) -> None:
+def download_file(filename: PathLike, backup_url: str, known_hash: str | None = None) -> None:
     """
     Replacement for scanpy._utils.check_presence_download using Pooch.
     Saves to the exact local path specified in 'filename'.
     """
     pooch.retrieve(
         url=backup_url,
-        known_hash=None,
+        known_hash=known_hash,
         fname=os.path.basename(filename),
         path=os.path.dirname(filename) or ".",  # Handles current dir if no folder
     )