Fix rtol for sciPy iterative solver, bump version

theislab · Dec 3, 2024 · 2c1f7b2 · 2c1f7b2
1 parent 82248b2
commit 2c1f7b2
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Showing 2 changed files with 2 additions and 4 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -57,7 +57,7 @@ dependencies = [
     "pygpcca>=1.0.4",
     "scanpy>=1.7.2",
     "scikit-learn>=0.24.0",
-    "scipy>=1.2.0",
+    "scipy>=1.12.0",
     "scvelo>=0.2.5",
     "seaborn>=0.10.0",
     "wrapt>=1.12.1",

diff --git a/src/cellrank/_utils/_linear_solver.py b/src/cellrank/_utils/_linear_solver.py
@@ -223,11 +223,9 @@ def _solve_many_sparse_problems(
     """
     # initialise solution list and info list
     x_list, n_converged = [], 0
-    kwargs = {} if solver is not sp.linalg.gmres else {"atol": "legacy"}  # get rid of the warning
-
     for b in mat_b:
         # actually call the solver for the current sub-problem
-        x, info = solver(mat_a, b.toarray().flatten(), tol=tol, x0=None, **kwargs)
+        x, info = solver(mat_a, b.toarray().flatten(), rtol=tol, x0=None)
 
         # append solution and info
         x_list.append(np.atleast_1d(x))