Update api and add deprecation warnings

src/scifem/eval.py

@@ -145,8 +145,10 @@ def find_cell_extrema(
     else:
         raise NotImplementedError(f"Unknown type of extrema ({kind}), expected {min} or {max}")
 
-    ud = u.ufl_domain()
-    assert ud is not None
+    uds = ufl.domain.extract_domains(u)
+    if uds is None or len(uds) != 1:
+        raise ValueError(f"Expression {u:s} must be defined on a single domain")
+    ud = uds[0]
     mesh = dolfinx.mesh.Mesh(ud.ufl_cargo(), ud)
 
     if x0 is None:
@@ -307,8 +309,10 @@ def compute_extrema(
     """
 
     # Extract DOLFINx mesh
-    ud = u.ufl_domain()
-    assert ud is not None
+    uds = ufl.domain.extract_domains(u)
+    if uds is None or len(uds) != 1:
+        raise ValueError(f"Expression {u:s} must be defined on a single domain")
+    ud = uds[0]
     mesh = dolfinx.mesh.Mesh(ud.ufl_cargo(), ud)
 
     if kind is builtins.max:

src/scifem/mesh.py

@@ -1,4 +1,10 @@
 from __future__ import annotations
+import sys
+
+if sys.version_info >= (3, 13):
+    from warnings import deprecated
+else:
+    from typing_extensions import deprecated
 
 from . import _scifem  # type: ignore
 import collections
@@ -118,6 +124,12 @@ def create_entity_markers(
     return dolfinx.mesh.meshtags(domain, dim, facets, markers[facets])
 
 
+@deprecated(
+    "This function is deprecated and will be removed in a future version. "
+    + "Please use `dolfinx.mesh.transfer_meshtags_to_submesh()` instead.",
+    category=DeprecationWarning,
+    stacklevel=2,
+)
 def transfer_meshtags_to_submesh(
     entity_tag: dolfinx.mesh.MeshTags,
     submesh: dolfinx.mesh.Mesh,

src/scifem/petsc.py

@@ -97,6 +97,9 @@ def apply_lifting_and_set_bc(
         except AssertionError:
             bcs0 = bcs
             bcs1 = bcs
+        except ValueError:  # Changed error type post https://github.com/FEniCS/dolfinx/pull/4312
+            bcs0 = bcs
+            bcs1 = bcs
 
         dolfinx.fem.petsc.apply_lifting(b, a, bcs=bcs1, x0=x, alpha=alpha)
         ghost_update(b, PETSc.InsertMode.ADD_VALUES, PETSc.ScatterMode.REVERSE)

src/scifem/solvers.py

@@ -1,7 +1,15 @@
 from __future__ import annotations
 
+import sys
 from typing import Callable
 import logging
+
+if sys.version_info >= (3, 13):
+    from warnings import deprecated
+else:
+    from typing_extensions import deprecated
+
+
 from packaging.version import parse as _v
 
 import numpy as np
@@ -23,6 +31,7 @@
     if _v(dolfinx.__version__) < _v("0.9"):
         _alpha_kw = "scale"
 
+    @deprecated("NewtonSolver is deprecated in favor of `dolfinx.fem.petsc.NonlinearProblem`.")
     class NewtonSolver:
         max_iterations: int
         _bcs: list[dolfinx.fem.DirichletBC]
@@ -307,6 +316,9 @@ def __del__(self):
             self._solver.destroy()
             self.x.destroy()
 
+    @deprecated(
+        "BlockedNewtonSolver is deprecated in favor of `dolfinx.fem.petsc.NonlinearProblem`."
+    )
     class BlockedNewtonSolver(dolfinx.cpp.nls.petsc.NewtonSolver):
         def __init__(
             self,

src/scifem/spaces.py

@@ -1,3 +1,5 @@
+from warnings import warn
+
 from mpi4py import MPI
 import dolfinx
 import basix
@@ -22,7 +24,13 @@ def create_real_functionspace(
         For scalar elements value shape is ``()``.
 
     """
-
+    if Version(dolfinx.__version__) >= Version("0.11.0"):
+        warn(
+            "`create_real_functionspace()` is deprecated and will be removed in a future version."
+            + "Please use `basix.ufl.create_real_element()` instead.",
+            category=DeprecationWarning,
+            stacklevel=2,
+        )
     dtype = mesh.geometry.x.dtype
     ufl_e = basix.ufl.element(
         "P", mesh.basix_cell(), 0, dtype=dtype, discontinuous=True, shape=value_shape