I've apply changes to the patch:
- updated to the latest upstream version 5.0.1
- move propagated and native inputs after arguments
- move pybind11 to native-inputs


--8<---------------cut here---------------start------------->8---
@@ -460,21 +460,21 @@ (define-public python-meshzoo
 (define-public python-pyamg
   (package
     (name "python-pyamg")
-    (version "5.0.0")
+    (version "5.0.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "pyamg" version))
               (sha256
                (base32
-                "0bm0cbqcj5zgs4k7djs5ga98pb95raxxdd674g744hv1iwi6gfga"))))
+                "0l3dliwynxyjvbgpmi2k8jqvkkw6fc00c8w69h6swhrkfh0ql12z"))))
     (build-system pyproject-build-system)
-    (propagated-inputs (list pybind11 python-numpy python-scipy))
-    (native-inputs (list python-setuptools-scm python-pytest))
     (arguments
      (list
       #:test-flags
       ;; Test installed package in order to find C++ modules.
       #~(list "--pyargs" "pyamg.tests")))
+    (native-inputs (list pybind11 python-pytest python-setuptools-scm))
+    (propagated-inputs (list python-numpy python-scipy))
     (home-page "https://github.com/pyamg/pyamg")
     (synopsis "Algebraic Multigrid Solvers in Python")
     (description "PyAMG is a Python library of Algebraic Multigrid
@@ -489,8 +489,7 @@ (define-public python-pyamg
 @item Krylov methods such as CG, GMRES, FGMRES, BiCGStab, MINRES, etc.
 @end itemize
 PyAMG is primarily written in Python with supporting C++ code for
-performance critical operations.
-")
+performance critical operations.")
     (license license:expat)))

 (define-public python-tspex
--8<---------------cut here---------------end--------------->8---

Pushe as 5f93aa182a32e4baecc6238c21d2538af0b18ad3

Thanks,
Oleg