pySCENIC：对新 SciPy 的兼容性修复

python - <<'PY'
from pathlib import Path
SP = Path("/share/biosoft/python/Python-v3.10.10/lib/python3.10/site-packages")
def sub(path, old, new):
    s = path.read_text()
    if new in s:
        print("already patched:", path)
        return
    if old not in s:
        raise SystemExit(f"pattern not found: {path}")
    path.write_text(s.replace(old, new, 1))
    print("patched:", path)
sub(SP / "arboreto/core.py",
"""    if isinstance(target_gene_expression, scipy.sparse.spmatrix):
        target_gene_expression = target_gene_expression.A.flatten()""",
"""    if scipy.sparse.issparse(target_gene_expression):
        target_gene_expression = target_gene_expression.toarray().ravel()""")
sub(SP / "pyscenic/utils.py",
"""    # Create numpy array of idx pairs.
    return np.array(
        [
            [symbol2idx[s1], symbol2idx[s2]]
            for s1, s2 in zip(adjacencies.TF, adjacencies.target)
        ]
    )""",
"""    # Create numpy array of idx pairs (int64, C-contiguous for the numba kernel).
    pairs = [
        [symbol2idx[s1], symbol2idx[s2]]
        for s1, s2 in zip(adjacencies.TF, adjacencies.target)
    ]
    return np.ascontiguousarray(pairs, dtype=np.int64).reshape(-1, 2)""")
sub(SP / "pyscenic/utils.py",
"        rhos = masked_rho4pairs(ex_mtx.values, col_idx_pairs, 0.0)",
"""        rhos = masked_rho4pairs(
            np.ascontiguousarray(ex_mtx.values, dtype=np.float64),
            col_idx_pairs,
            0.0,
        )""")
PY