AttributeError from gene names

[galicae]

Hi Alex! very nice to see SAMap getting some love and the codebase being modernized. I was trying to run some older code, and had an issue running SAMap. My environment is on Python 3.11.14, with Numpy v2.3.5, SciPy 1.17.0 and Pandas 3.0.0.

In particular, when I call the SAMap function

sm = SAMAP(sams, f_maps = base + "aln/",)

I get the following attribute error:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[9], [line 3](vscode-notebook-cell:?execution_count=9&line=3)
      1 sams = {"afas": afas, "pdum": pdum}
----> [3](vscode-notebook-cell:?execution_count=9&line=3) sm = SAMAP(
      4         sams,
      5         f_maps = base + "aln/",
      6     )

File /opt/homebrew/Caskroom/miniforge/base/envs/samap_minimal/lib/python3.11/site-packages/samap/core/mapping.py:170, in SAMAP.__init__(self, sams, f_maps, names, keys, resolutions, gnnm, save_processed, eval_thr)
    167     sams[sid] = sam
    169 if gnnm is None:
--> 170     gnnm_matrix, gns, gns_dict = _calculate_blast_graph(
    171         ids, f_maps=f_maps, reciprocate=True, eval_thr=eval_thr
    172     )
    173     if names is not None:
    174         gnnm_matrix, gns_dict, gns = _coarsen_blast_graph(gnnm_matrix, gns, names)

File /opt/homebrew/Caskroom/miniforge/base/envs/samap_minimal/lib/python3.11/site-packages/samap/core/mapping.py:965, in _calculate_blast_graph(ids, f_maps, eval_thr, reciprocate)
    963 A.index = pd.Index(gnind[A.index].values.flatten())
    964 B.index = pd.Index(gnind[B.index].values.flatten())
--> 965 A[A.columns[0]] = gnind[A.iloc[:, 0].values.flatten()].values.flatten()
    966 B[B.columns[0]] = gnind[B.iloc[:, 0].values.flatten()].values.flatten()
    968 Arows = np.vstack((A.index, A.iloc[:, 0], A.iloc[:, i3])).T

AttributeError: 'StringArray' object has no attribute 'flatten'

I tried the offending part with the example data:

A=pd.read_csv('/path/to/repos/SAMap/example_data/maps/plsc/pl_to_sc.txt',sep='\t',index_col=0,header=None)
B=pd.read_csv('/path/to/repos/SAMap/example_data/maps/plsc/sc_to_pl.txt',sep='\t',index_col=0,header=None)
data = B.iloc[:, 0].values.flatten()

and get the same AttributeError so I think it's not a formatting issue or table reading issue on my side. Any ideas? In my environment I am getting a StringArray for B.iloc[:, 0].values, which is already one-dimensional and iterable, so I know how to fix locally, but I wonder if this is intended.