spatial/tangram_scvi_tools.ipynb is not running to some logic issue with mudata:
---------------------------------------------------------------------------
InvalidIndexError Traceback (most recent call last)
Cell In[12], line 8
6 mdata.mod["sp_train"] = mdata.mod["sp"][:, genes].copy()
7 mdata.mod["sc_train"] = mdata.mod["sc"][:, genes].copy()
----> 8 mdata.update()
File /usr/local/lib/python3.12/site-packages/mudata/_core/mudata.py:1725, in MuData.update(self)
1719 def update(self):
1720 """
1721 Update both .obs and .var indices of MuData with the data from all the modalities
1722
1723 NOTE: From v0.4, it will not pull columns from modalities by default.
1724 """
-> 1725 self.update_var()
1726 self.update_obs()
File /usr/local/lib/python3.12/site-packages/mudata/_core/mudata.py:1531, in MuData.update_var(self)
1527 """
1528 Update global .var_names according to the .var_names of all the modalities.
1529 """
1530 join_common = self.axis == 0
-> 1531 self._update_attr("var",axis=0,join_common=join_common)
File /usr/local/lib/python3.12/site-packages/mudata/_core/mudata.py:579, in MuData._update_attr(self, attr, axis, **kwargs)
577 if "join_common" in kwargs:
578 join_common = kwargs.pop("join_common")
--> 579 self._update_attr_legacy(attr,axis,join_common,**kwargs)
580 return
582 prev_index = getattr(self, attr).index
File /usr/local/lib/python3.12/site-packages/mudata/_core/mudata.py:1273, in MuData._update_attr_legacy(self, attr, axis, join_common, **kwargs)
1270 prev_index = pd.Index(prev_values)
1271 now_index = pd.Index(now_values)
-> 1273 index_order = prev_index.get_indexer(now_index)
1275 for mx_key, mx in attrm.items():
12[76](https://github.com/scverse/scvi-tutorials/actions/runs/10981118176/job/30487753331#step:5:77) if mx_key not in self.mod.keys(): # not a modality name
File /usr/local/lib/python3.12/site-packages/pandas/core/indexes/base.py:3885, in Index.get_indexer(self, target, method, limit, tolerance)
38[82](https://github.com/scverse/scvi-tutorials/actions/runs/10981118176/job/30487753331#step:5:83) self._check_indexing_method(method, limit, tolerance)
3884 if not self._index_as_unique:
-> 3885 raise InvalidIndexError(self._requires_unique_msg)
3887 if len(target) == 0:
3888 return np.array([], dtype=np.intp)
InvalidIndexError: Reindexing only valid with uniquely valued Index objects
spatial/tangram_scvi_tools.ipynb is not running to some logic issue with mudata:
Versions:
1.2