Read AnnData object directly from .h5ad (#128)

* Read AnnData object directly from .h5ad

* Only import anndata if read_h5ad is called

* Bump version

Author: sminot

cirro/sdk/file.py

@@ -4,6 +4,10 @@
 
 import pandas as pd
 
+from typing import TYPE_CHECKING
+if TYPE_CHECKING:
+    import anndata
+
 from cirro.cirro_client import CirroApi
 from cirro.models.file import File
 from cirro.sdk.asset import DataPortalAssets, DataPortalAsset
@@ -124,6 +128,19 @@ def read_csv(self, compression='infer', encoding='utf-8', **kwargs) -> pd.DataFr
         handle.close()
         return df
 
+    def read_h5ad(self) -> 'anndata.AnnData':
+        """Read an AnnData object from a file."""
+        # Import the anndata library, and raise an error if it is not available
+        try:
+            import anndata as ad # noqa
+        except ImportError:
+            raise ImportError("The anndata library is required to read AnnData files. "
+                              "Please install it using 'pip install anndata'.")
+
+        # Download the file to a temporary file handle and parse the contents
+        with BytesIO(self._get()) as handle:
+            return ad.read_h5ad(handle)
+
     def readlines(self, encoding='utf-8', compression=None) -> List[str]:
         """Read the file contents as a list of lines."""
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cirro"
-version = "1.2.7"
+version = "1.2.8"
 description = "CLI tool and SDK for interacting with the Cirro platform"
 authors = ["Cirro Bio <[email protected]>"]
 license = "MIT"