Fix: Test for legacy mudata .h5mu files

src/mudata/_core/mudata.py

@@ -204,16 +204,20 @@ def __init__(
             if isinstance(self._var, abc.Mapping) or self._var is None:
                 self._var = pd.DataFrame(self._var)
 
+            # Replace missing/None with empty dictionaries
+            for attr in ("obsm", "varm", "obsp", "varp", "obsmap", "varmap"):
+                if kwargs.get(attr, None) is None:
+                    kwargs[attr] = {}
             # Get global obsm
-            self._obsm = MuAxisArrays(self, axis=0, store=kwargs.get("obsm", {}))
+            self._obsm = MuAxisArrays(self, axis=0, store=kwargs.get("obsm"))
             # Get global varm
-            self._varm = MuAxisArrays(self, axis=1, store=kwargs.get("varm", {}))
+            self._varm = MuAxisArrays(self, axis=1, store=kwargs.get("varm"))
 
-            self._obsp = PairwiseArrays(self, axis=0, store=kwargs.get("obsp", {}))
-            self._varp = PairwiseArrays(self, axis=1, store=kwargs.get("varp", {}))
+            self._obsp = PairwiseArrays(self, axis=0, store=kwargs.get("obsp"))
+            self._varp = PairwiseArrays(self, axis=1, store=kwargs.get("varp"))
 
-            self._obsmap = MuAxisArrays(self, axis=0, store=kwargs.get("obsmap", {}))
-            self._varmap = MuAxisArrays(self, axis=1, store=kwargs.get("varmap", {}))
+            self._obsmap = MuAxisArrays(self, axis=0, store=kwargs.get("obsmap"))
+            self._varmap = MuAxisArrays(self, axis=1, store=kwargs.get("varmap"))
 
             self._axis = kwargs.get("axis") or 0
 

tests/data/archives/v0.1.2/create_testfiles.py

@@ -0,0 +1,45 @@
+# /// script
+# requires-python = ">=3.10"
+# dependencies = [
+#     "mudata==0.1.2",
+#     "numpy==1.*", # required as numpy 2 raises errors
+# ]
+# ///
+import os
+
+import numpy as np
+from anndata import AnnData
+
+from mudata import MuData
+
+
+def create_mudata() -> MuData:
+    """Create a mudata testfile
+
+    Returns:
+        MuData: MuData object with two AnnData objects
+    """
+    return MuData(
+        {
+            "mod1": AnnData(np.arange(0, 100, 0.1).reshape(-1, 10)),
+            "mod2": AnnData(np.arange(101, 2101, 1).reshape(-1, 20)),
+        }
+    )
+
+
+def write_h5mu_testfile(mdata: MuData, filepath_h5mu: str | os.PathLike) -> None:
+    """Write a MuData object to a file
+
+    Args:
+        mdata (MuData): MuData object to write
+        filepath_h5mu (str | os.PathLike): Path to write the MuData object
+
+    Returns:
+        None
+    """
+    mdata.write(filepath_h5mu)
+
+
+if __name__ == "__main__":
+    mdata = create_mudata()
+    write_h5mu_testfile(mdata, "mudata.h5mu")

tests/test_io_backwards_compat.py

@@ -0,0 +1,35 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+import numpy as np
+import pytest
+from anndata import AnnData
+from anndata.tests.helpers import assert_equal
+
+from mudata import MuData, read_h5mu
+
+ARCHIVE_PTH = Path(__file__).parent / "data/archives"
+
+
+@pytest.fixture(params=list(ARCHIVE_PTH.glob("v*")), ids=lambda x: x.name)
+def archive_dir(request):
+    return request.param
+
+
+@pytest.fixture
+def mdata():
+    return MuData(
+        {
+            "mod1": AnnData(np.arange(0, 100, 0.1).reshape(-1, 10)),
+            "mod2": AnnData(np.arange(101, 2101, 1).reshape(-1, 20)),
+        }
+    )
+
+
+class TestLegacyMuData:
+    def test_legacy_files(self, archive_dir, mdata):
+        from_h5mu = read_h5mu(archive_dir / "mudata.h5mu")
+
+        for mod in mdata.mod:
+            assert_equal(from_h5mu.mod[mod].X, mdata.mod[mod].X, exact=False)