I found a bug

[Andymare1994]

---

ValueError Traceback (most recent call last)
Cell In[10], line 28
25 adata.layers["fit_t"] = latent_time.values * scaling[np.newaxis, :]
26 adata.var['fit_scaling'] = 1.0
---> 28 add_velovi_outputs_to_adata(adata, vae)

Cell In[10], line 25, in add_velovi_outputs_to_adata(adata, vae)
18 adata.var["fit_gamma"] = vae.get_rates()["gamma"] / scaling
19 adata.var["fit_t_"] = (
20 torch.nn.functional.softplus(vae.module.switch_time_unconstr)
21 .detach()
22 .cpu()
23 .numpy()
24 ) * scaling
---> 25 adata.layers["fit_t"] = latent_time.values * scaling[np.newaxis, :]
26 adata.var['fit_scaling'] = 1.0

File ~/miniconda3/envs/velovi/lib/python3.9/site-packages/pandas/core/series.py:1153, in Series.getitem(self, key)
1150 key = np.asarray(key, dtype=bool)
1151 return self._get_rows_with_mask(key)
-> 1153 return self._get_with(key)

File ~/miniconda3/envs/velovi/lib/python3.9/site-packages/pandas/core/series.py:1163, in Series._get_with(self, key)
1158 raise TypeError(
1159 "Indexing a Series with DataFrame is not "
1160 "supported, use the appropriate DataFrame column"
1161 )
1162 elif isinstance(key, tuple):
-> 1163 return self._get_values_tuple(key)
1165 elif not is_list_like(key):
1166 # e.g. scalars that aren't recognized by lib.is_scalar, GH#32684
1167 return self.loc[key]

File ~/miniconda3/envs/velovi/lib/python3.9/site-packages/pandas/core/series.py:1203, in Series._get_values_tuple(self, key)
1198 if com.any_none(*key):
1199 # mpl compat if we look up e.g. ser[:, np.newaxis];
1200 # see tests.series.timeseries.test_mpl_compat_hack
1201 # the asarray is needed to avoid returning a 2D DatetimeArray
1202 result = np.asarray(self._values[key])
-> 1203 disallow_ndim_indexing(result)
1204 return result
1206 if not isinstance(self.index, MultiIndex):

File ~/miniconda3/envs/velovi/lib/python3.9/site-packages/pandas/core/indexers/utils.py:341, in disallow_ndim_indexing(result)
333 """
334 Helper function to disallow multi-dimensional indexing on 1D Series/Index.
335
(...)
338 in GH#30588.
339 """
340 if np.ndim(result) > 1:
--> 341 raise ValueError(
342 "Multi-dimensional indexing (e.g. obj[:, None]) is no longer "
343 "supported. Convert to a numpy array before indexing instead."
344 )

ValueError: Multi-dimensional indexing (e.g. obj[:, None]) is no longer supported. Convert to a numpy array before indexing instead.

[Andymare1994]

add_velovi_outputs_to_adata(adata, vae)