From 2c1f7b26ac12d5ef919a9a4d07ef9211e6428df7 Mon Sep 17 00:00:00 2001
From: Michal Klein <46717574+michalk8@users.noreply.github.com>
Date: Tue, 3 Dec 2024 01:02:26 +0100
Subject: [PATCH] Fix rtol for sciPy iterative solver, bump version

---
 pyproject.toml                        | 2 +-
 src/cellrank/_utils/_linear_solver.py | 4 +---
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index c53aadb8..1c19ff96 100644
--- 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
index a310a709..d97559ea 100644
--- 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))