clonotype_modularity() seems not to work with schema upgraded AnnData

[riederd]

Description
When using adata which was upgraded to the new schema, clonotype_modularity() throws the following error.

/home/rieder/.conda/envs/scirpy/lib/python3.10/site-packages/scipy/optimize/_numdiff.py:576: RuntimeWarning: invalid value encountered in subtract
  df = fun(x) - f0
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[173], line 1
----> 1 ir.tl.clonotype_modularity(adata, target_col="cc_aa_alignment", connectivity_key='connectivities')

File ~/.conda/envs/scirpy/lib/python3.10/site-packages/scirpy/tl/_clonotype_modularity.py:159, in clonotype_modularity(adata, target_col, connectivity_key, permutation_test, n_permutations, key_added, inplace, fdr_correction, random_state, airr_mod)
    155 # remove the entries from previous run, should they exist
    156 # results can be inconsisten otherwise (old dangling "fdr" values when only
    157 # pvalues are calculated)
    158 for suffix in ["fdr", "pvalue"]:
--> 159     for d in [params.mdata, params.adata]:
    160         try:
    161             del d.obs[f"{key_added}_{suffix}"]

File ~/.conda/envs/scirpy/lib/python3.10/site-packages/scirpy/util/__init__.py:239, in DataHandler.mdata(self)
    237     return self._data
    238 else:
--> 239     raise AttributeError("DataHandler was initalized with only AnnData")

AttributeError: DataHandler was initalized with only AnnData

To Reproduce
Use an AnnData object created with scirpy version < 0.13.0, upgrad with scirpy.io.upgrade_schema() follow the 3k Tcell tutorial and run ir.tl.clonotype_modularity(adata, target_col="cc_aa_alignment", connectivity_key='connectivities')

Expected behaviour
function call w/o error

System

• OS: CentOS 7
• Python version 3.10
• Versions of libraries involved
  scirpy==0.13.0 scanpy==1.9.3 anndata==0.9.1 umap==0.5.3 numpy==1.23.5 scipy==1.10.1 pandas==1.5.3 scikit-learn==1.2.2 statsmodels==0.13.5 python-igraph==0.10.3 pynndescent==0.5.10

[grst]

Hi,
thanks for reporting!
Could you try the proposed fix in fix-420?

pip install git+https://github.com/scverse/scirpy.git@fix-420

[riederd]

Thanks, it seems to work