Installation problems using a mamba/conda environment

[Maaraujo-nv]

Description
I am trying to install liana to run Mofacellular. I have tried to use the installation guidelines, but this lead to problems with decoupler 2.0.0. I have see that this is already a pull request. To solve this I have tried to use the previous version of decoupler. However, upon this I come into another error. Would it be possible to have more strict package versions, or an requirements file where all package versions are specified.

Error

Error when trying with older decoupler versions:

Traceback (most recent call last):
File "/your/project/path/analysis/mofa.py", line 39, in
mdata = li.multi.adata_to_views(adata,
File "/your/env/path/site-packages/liana/multi/to_mudata.py", line 79, in adata_to_views
padata = dc.get_pseudobulk(temp,
File "/your/env/path/site-packages/decoupler/utils_anndata.py", line 381, in get_pseudobulk
psbulk, ncells, counts, props = compute_psbulk(n_rows, n_cols, X, sample_col, groups_col, smples, groups, obs,
File "/your/env/path/site-packages/decoupler/utils_anndata.py", line 228, in compute_psbulk
profile = X[obs[sample_col] == smp]
File "/your/env/path/site-packages/scipy/sparse/_index.py", line 30, in getitem
index, new_shape = self._validate_indices(key)
File "/your/env/path/site-packages/scipy/sparse/_index.py", line 283, in _validate_indices
index.extend(ix.nonzero())
File "/your/env/path/site-packages/pandas/core/generic.py", line 6299, in getattr
return object.getattribute(self, name)
AttributeError: 'Series' object has no attribute 'nonzero'

[dbdimitrov]

Hi @Maaraujo-nv,

Thanks I'm aware of this, I will try to get to it soon. There is also a Pull Request on this: #178

In the meantime, you can try downgrade to decoupler to e.g. 1.9.2 or 1.6.0 and it should work as before.

Thanks,
Daniel