ValueError: could not convert integer scalar

[alexlenail]

File ~/.conda/envs/py39/lib/python3.9/site-packages/muon/_atac/preproc.py:77, in tfidf(data, log_tf, log_idf, log_tfidf, scale_factor)
     74 if log_tfidf:
     75     tf_idf = np.log1p(tf_idf)
---> 77 adata.X = np.nan_to_num(tf_idf, 0)

File ~/.conda/envs/py39/lib/python3.9/site-packages/anndata/_core/anndata.py:688, in AnnData.X(self, value)
    684     if sparse.issparse(self._adata_ref._X) and isinstance(
    685         value, np.ndarray
    686     ):
    687         value = sparse.coo_matrix(value)
--> 688     self._adata_ref._X[oidx, vidx] = value
    689 else:
    690     self._X = value

File ~/.conda/envs/py39/lib/python3.9/site-packages/scipy/sparse/_index.py:137, in IndexMixin.__setitem__(self, key, x)
    135     x = x.tocoo(copy=True)
    136     x.sum_duplicates()
--> 137     self._set_arrayXarray_sparse(i, j, x)
    138 else:
    139     # Make x and i into the same shape
    140     x = np.asarray(x, dtype=self.dtype)

File ~/.conda/envs/py39/lib/python3.9/site-packages/scipy/sparse/_compressed.py:827, in _cs_matrix._set_arrayXarray_sparse(self, row, col, x)
    825 def _set_arrayXarray_sparse(self, row, col, x):
    826     # clear entries that will be overwritten
--> 827     self._zero_many(*self._swap((row, col)))
    829     M, N = row.shape  # matches col.shape
    830     broadcast_row = M != 1 and x.shape[0] == 1

File ~/.conda/envs/py39/lib/python3.9/site-packages/scipy/sparse/_compressed.py:947, in _cs_matrix._zero_many(self, i, j)
    945 n_samples = len(i)
    946 offsets = np.empty(n_samples, dtype=self.indices.dtype)
--> 947 ret = csr_sample_offsets(M, N, self.indptr, self.indices, n_samples,
    948                          i, j, offsets)
    949 if ret == 1:
    950     # rinse and repeat
    951     self.sum_duplicates()

ValueError: could not convert integer scalar

Saw scverse/anndata#339

Trying .copy()

If that works, shouldn't muon catch this error rather than computing the entire tf_idf matrix before failing?

[gtca]

Thanks, @alexlenail!

Do you know how to reproduce this error? Is the modified modality a view?

[alexlenail]

hippo_atac = adata_atac[adata_atac.obs.index.isin(hippo_cells)]
ac.pp.tfidf(hippo_atac)

==> ValueError: could not convert integer scalar

hippo_atac = adata_atac[adata_atac.obs.index.isin(hippo_cells)].copy()
ac.pp.tfidf(hippo_atac)

==> works

[gtca]

I believe this is an issue that this particular preprocessing method doesn't handle views correctly. By convention, it should copy the data.
I'll mark this to be fixed for the next release, thank you!