preserve modality index names in names_make_unique()

closes #146

Author: ilia-kats

CHANGELOG.md

@@ -8,14 +8,11 @@ and this project adheres to [Semantic Versioning][].
 [keep a changelog]: https://keepachangelog.com/en/1.1.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
-## [0.4.0] (unreleased)
+## [0.3.9] (Unreleased)
 
-### Changed
+### Fixed
 
-- `update()` no longer automatically pulls obs/var columns from individual modalities by default. Set `mudata.set_options(pull_on_update=true)`
-  to restore the old behavior. Use `pull_obs/pull_var` and `push_obs/push_var` for more flexibility.
-- The settings API has changed. Use e.g. `mudata.settings.pull_on_update = True` instead of `mudata.set_options(pull_on_update=True)` and use
-  `mudata.settings.override` as context manager for local settings overrides.
+- `make_obs_names_unique` and `make_var_names_unique` now preserve the `.obs.index.name` / `.var.index.name` of each modality and of the MuData object.
 
 ## [0.3.8]
 
@@ -180,7 +177,7 @@ To copy the annotations explicitly, you will need to use `pull_obs()` and/or `pu
 
 Initial `mudata` release with `MuData`, previously a part of the `muon` framework.
 
-[0.4.0]: https://github.com/scverse/mudata/releases/tag/v0.4.0
+[0.3.9]: https://github.com/scverse/mudata/releases/tag/v0.3.9
 [0.3.8]: https://github.com/scverse/mudata/releases/tag/v0.3.8
 [0.3.7]: https://github.com/scverse/mudata/releases/tag/v0.3.7
 [0.3.6]: https://github.com/scverse/mudata/releases/tag/v0.3.6

src/mudata/_core/mudata.py

@@ -1299,14 +1299,19 @@ def _names_make_unique(self, attr: Literal["obs", "var"]):
                     kj = mods[j]
                     if len(getattr(self._mod[ki], namesattr).intersection(getattr(self._mod[kj], namesattr))) > 0:
                         warnings.warn(
-                            "Modality names will be prepended to obs_names since there are identical obs_names in different modalities.",
+                            f"Modality names will be prepended to {namesattr} since there are identical {namesattr} in different modalities.",
                             stacklevel=1,
                         )
                         for m, mod in self._mod.items():
                             setattr(mod, namesattr, m + ":" + getattr(mod, namesattr).astype(str))
                         raise StopIteration()  # break out of both loops
 
-        setattr(self, namesattr, pd.Index([]).append([getattr(mod, namesattr) for mod in self._mod.values()]))
+        attrval = getattr(self, attr)
+
+        # self._set_names replaces the names of each modality. Unnecessary here, since the names are coming directly from the modalities
+        attrval.index = pd.Index([], name=attrval.index.name).append(
+            [getattr(mod, namesattr) for mod in self._mod.values()]
+        )
 
     def obs_names_make_unique(self):
         """

tests/conftest.py

@@ -60,6 +60,8 @@ def mdata(rng: np.random.Generator, request: pytest.FixtureRequest) -> MuData:
             [f"{attr}_{i}" for i in rng.choice(mod.shape[axis], size=mod.shape[axis], replace=False)],
         )
         setattr(mod, f"{oattr}_names", [f"{modname}_{oattr}_{i}" for i in range(mod.shape[1 - axis])])
+    mod1.obs.index.name = "fizz"
+    mod2.var.index.name = "buzz"
     mdata = MuData(mods, axis=axis)
     mdata.obs["arange"] = np.arange(mdata.n_obs)
     return mdata

tests/test_obs_var.py

@@ -105,24 +105,30 @@ def test_names_make_unique(mdata: md.MuData):
     namesfun = getattr(mdata, f"{oattr}_names_make_unique")
 
     mods = mdata.mod_names
-    names = getattr(mdata.mod[mods[0]], namesattr).to_list()
-    names[1] = names[0]
-    setattr(mdata.mod[mods[0]], namesattr, names)
+    names = getattr(mdata.mod[mods[0]], namesattr)
+    nameslist = names.to_list()
+    nameslist[1] = nameslist[0]
+    setattr(mdata.mod[mods[0]], namesattr, pd.Index(nameslist, name=names.name))
     namesfun()
     assert mdata.shape[1 - mdata.axis] == sum(mod.shape[1 - mdata.axis] for mod in mdata.mod.values())
     assert getattr(mdata, namesattr).is_unique
+    assert getattr(mdata.mod[mods[0]], namesattr).name == names.name
 
+    modality_index_names = {}
     for mod in mods[:2]:
-        names = getattr(mdata.mod[mod], namesattr).to_list()
-        names[1] = names[0] = "testname"
-        setattr(mdata.mod[mod], namesattr, names)
+        names = getattr(mdata.mod[mod], namesattr)
+        nameslist = names.to_list()
+        nameslist[1] = nameslist[0] = "testname"
+        setattr(mdata.mod[mod], namesattr, pd.Index(nameslist, name=names.name))
+        modality_index_names[mod] = names.name
     with pytest.warns(UserWarning, match="Modality names will be prepended"):
         namesfun()
     assert mdata.shape[1 - mdata.axis] == sum(mod.shape[1 - mdata.axis] for mod in mdata.mod.values())
     assert getattr(mdata, namesattr).is_unique
     for m, mod in mdata.mod.items():
         assert getattr(mod, namesattr).is_unique
         assert (getattr(mod, namesattr).str[: len(m) + 1] == f"{m}:").all()
+        assert getattr(mod, namesattr).name == modality_index_names[m]
 
     with pytest.raises(TypeError, match="axis="):
         getattr(mdata, f"{attr}_names_make_unique")()