Merge pull request #42 from YosefLab/read-patch

h5ad without X

CHANGELOG.md

@@ -16,6 +16,16 @@ and this project adheres to [Semantic Versioning][].
 
 ### Fixed
 
+## [0.1.2] - 2024-12-02
+
+### Added
+
+### Changed
+
+### Fixed
+
+-   Fixed `KeyError: "Unable to synchronously open object (object 'X' doesn't exist)"'` when reading h5ad without X field (#40)
+
 ## [0.1.1] - 2024-11-25
 
 ### Added

pyproject.toml

@@ -4,7 +4,7 @@ requires = ["hatchling"]
 
 [project]
 name = "treedata"
-version = "0.1.1"
+version = "0.1.2"
 description = "anndata with trees"
 readme = "README.md"
 requires-python = ">=3.10"

src/treedata/_core/read.py

@@ -76,7 +76,8 @@ def _read_tdata(f, filename, backed) -> dict:
         backed = "r"
     # Read X if not backed
     if not backed:
-        d["X"] = _read_elem(f["X"])
+        if "X" in f:
+            d["X"] = _read_elem(f["X"])
     else:
         d.update({"filename": filename, "filemode": backed})
     # Read standard elements

tests/test_readwrite.py

@@ -102,6 +102,14 @@ def test_read_anndata(X, tmp_path):
     assert tdata.obst_keys() == []
 
 
+def test_read_no_X(X, tmp_path):
+    tdata = td.TreeData(obs=pd.DataFrame(index=["0", "1", "2"]))
+    file_path = tmp_path / "test.h5ad"
+    tdata.write_h5ad(file_path)
+    tdata2 = td.read_h5ad(file_path)
+    assert tdata2.X is None
+
+
 def test_h5ad_backing(tdata, tree, tmp_path):
     tdata_copy = tdata.copy()
     assert not tdata.isbacked