accessors: make resolving behavior match AnnData's more closely

Author: ilia-kats

src/mudata/acc/__init__.py

@@ -21,7 +21,6 @@
     MultiMapAcc,
     RefAcc,
 )
-from anndata.acc._parse_str import _check_vec
 from anndata.compat import XVariable
 from anndata.typing import InMemoryArray
 
@@ -273,30 +272,19 @@ def resolve(
 
         firstdot = spec.find(".")
         if firstdot < 0:
-            firstdot = None
+            raise ValueError(f"Cannot parse accessor {spec!r} that is not period-separated.")
         firstattr = spec[:firstdot]
         match firstattr:
             case "mod":
-                do_vec = firstdot is not None
-                if not do_vec:
-                    _check_vec(spec, vec=vec, actual=do_vec)
-                    return self.mod
-
                 modend = spec.find(".", firstdot + 1)
-                do_vec = modend >= 0
-                if not do_vec:
-                    modend = None
-                    _check_vec(spec, vec=vec, actual=do_vec)
                 mod = spec[firstdot + 1 : modend]
                 if not mod:
                     raise ValueError(f"Cannot parse accessor{spec!r} that has an empty modality.")
                 acc = self.mod[mod]
-                return super().resolve.__func__(acc, spec[modend + 1 :], strict=strict, vec=vec) if do_vec else acc
+                return super().resolve.__func__(acc, spec[modend + 1 :], strict=strict, vec=vec)
             case "obsmap" | "varmap":
-                do_vec = firstdot is not None and firstdot < len(spec)
-                _check_vec(spec, vec=vec, actual=do_vec)
-                if not do_vec:
-                    return getattr(self, firstattr)
+                if firstdot == len(spec):
+                    raise ValueError(f"Cannot parse accessor{spec!r} that has an empty modality.")
                 mod = spec[firstdot + 1 :]
                 return getattr(self, firstattr)[mod]
             case _:

tests/test_accessors.py

@@ -1,6 +1,5 @@
 import json
 from collections.abc import Mapping
-from contextlib import nullcontext
 from dataclasses import fields
 from importlib import metadata, resources
 from urllib.request import urlopen
@@ -140,31 +139,45 @@ def test_no_data():
         assert field.name not in ("X", "layers")
 
 
-@pytest.mark.parametrize("vec", [None, True, False])
-def test_resolve_vec_true(vec: bool):
-    with pytest.raises(ValueError, match="refers to a vector/") if vec is False else nullcontext():
-        assert A.resolve("mod.rna.X[:, ACT1]", vec=vec) == A.mod["rna"].X[:, "ACT1"]
-        assert A.resolve("obsmap.rna", vec=vec) == A.obsmap["rna"]
+def test_resolve():
+    assert A.resolve("mod.rna.X[:, ACT1]") == A.mod["rna"].X[:, "ACT1"]
+    assert A.resolve("obsmap.rna") == A.obsmap["rna"]
 
-
-@pytest.mark.parametrize("vec", [None, True, False])
-def test_resolve_vec_false(vec: bool):
-    with pytest.raises(ValueError, match="refers to a whole container") if vec is True else nullcontext():
-        assert A.resolve("mod.rna.X", vec=vec) == A.mod["rna"].X
-        assert A.resolve("mod.rna", vec=vec) == A.mod["rna"]
-        assert A.resolve("mod", vec=vec) == A.mod
-        assert A.resolve("obsmap", vec=vec) == A.obsmap
-
-
-def test_resolve_raises():
     with pytest.raises(ValueError, match="Unknown accessor"):
         A.resolve("rna.X[:, :]")
+
     with pytest.raises(ValueError, match="empty modality"):
         A.resolve("mod..X[:, :]")
+
     with pytest.raises(ValueError, match="period-separated"):
         A.resolve("abcd")
 
 
+@pytest.mark.parametrize("vec", [None, True])
+def test_resolve_vec_true(vec):
+    assert A.resolve("mod.rna.X[:, ACT1]", vec=vec) == A.mod["rna"].X[:, "ACT1"]
+    assert A.resolve("mod.rna.X[:, :]", vec=vec) == A.mod["rna"].X[:, :]
+    assert A.resolve("obsm.test.2", vec=vec) == A.obsm["test"][2]
+
+
+@pytest.mark.parametrize("vec", [None, False])
+def test_resolve_vec_false(vec):
+    assert A.resolve("mod.rna.X", vec=vec) == A.mod["rna"].X
+    assert A.resolve("obsm.test") == A.obsm["test"]
+
+
+def test_resolve_vec_mismatch():
+    with pytest.raises(ValueError, match="refers to a whole container"):
+        A.resolve("mod.rna.X", vec=True)
+        A.resolve("mod.rna.X[:, :]", vec=True)
+        A.resolve("obsm.test", vec=True)
+    with pytest.raises(ValueError, match="refers to a vector"):
+        A.resolve("mod.rna.X", vec=False)
+        A.resolve("mod.rna.X[:, ACT1]", vec=False)
+        A.resolve("mod.rna.X[:, :]", vec=False)
+        A.resolve("obsm.test.2", vec=False)
+
+
 @pytest.mark.parametrize("acc", [path[0] for path in PATHS if isinstance(path[0], ad.acc.AdRef)])
 def test_to_from_json(mudata_json_schema, anndata_schema_registry, acc):
     serialized = A.to_json(acc)