merge conflict

Author: pbrubeck

MANIFEST.in

@@ -3,10 +3,8 @@
 # the specific version, here we are more permissive. This is to catch the
 # case where users don't update their PETSc for a really long time or
 # accidentally install a too-new release that isn't yet supported.
-PETSC_SUPPORTED_VERSIONS = ">=3.24.2"
-
-# TODO RELEASE
-# PETSC_SUPPORTED_VERSIONS = ">=3.25"
+# TODO RELEASE set to ">=3.25"
+PETSC_SUPPORTED_VERSIONS = ">=3.23.0"
 
 
 def init_petsc():
@@ -78,6 +76,7 @@ def init_petsc():
 from firedrake.mg.opencascade_mh import *
 from firedrake.norms import *
 from firedrake.nullspace import *
+from firedrake.output import *
 from firedrake.parameters import *
 from firedrake.parloops import *
 from firedrake.projection import *
@@ -99,11 +98,7 @@ def init_petsc():
 set_log_handlers(comm=COMM_WORLD)
 
 # Moved functionality
-from firedrake._deprecation import plot, File  # noqa: F401
-# Once `File` is deprecated update the above line removing `File` and add
-#   from firedrake._deprecation import output
-#   sys.modules["firedrake.output"] = output
-from firedrake.output import *
+from firedrake._deprecation import plot  # noqa: F401
 import sys
 sys.modules["firedrake.plot"] = plot
 from firedrake.plot import *

firedrake/__init__.py

@@ -2,8 +2,6 @@
 """
 import importlib
 
-from warnings import warn
-
 
 class _fake_module:
     """ Object which behaves like a module
@@ -47,28 +45,6 @@ def __call__(*args, **kwargs):
         return __call__
 
 
-# Deprecate output.File in the global namespace
-output = _fake_module(
-    "firedrake.output",
-    ["File", ],
-    ["VTKFile", ]
-)
-
-
-# I hate it
-def File(*args, **kwargs):
-    """Deprecated File constructor.
-
-    Use `VTKFile` from `firedrake.output` instead
-    """
-    from .output import VTKFile
-    warn(
-        "The use of `File` for output is deprecated, please update your "
-        "code to use `VTKFile` from `firedrake.output`."
-    )
-    return VTKFile(*args, **kwargs)
-
-
 # Deprecate plotting in the global namespace
 plot = _fake_module(
     "firedrake.pyplot",

firedrake/_deprecation.py

@@ -176,28 +176,6 @@ def is_dg_space(space: WithGeometry) -> bool:
     return e.is_dg()
 
 
-def dg_space(space: WithGeometry) -> WithGeometry:
-    """Construct a DG space containing a given function space as a subspace.
-
-    Parameters
-    ----------
-
-    space
-        A function space.
-
-    Returns
-    -------
-
-    firedrake.functionspaceimpl.WithGeometry
-        A DG space containing `space` as a subspace. May be `space`.
-    """
-
-    if is_dg_space(space):
-        return space
-    else:
-        return fd.FunctionSpace(space.mesh(), finat.ufl.BrokenElement(space.ufl_element()))
-
-
 class L2TransformedFunctional(AbstractReducedFunctional):
     r"""Represents the functional
 
@@ -265,7 +243,8 @@ def __init__(self, functional: pyadjoint.OverloadedType, controls: Union[Control
         self._space_D = Enlist(space_D)
         if len(self._space_D) != len(self._space):
             raise ValueError("Invalid length")
-        self._space_D = tuple(dg_space(space) if space_D is None else space_D
+        self._space_D = tuple((space if is_dg_space(space) else space.broken_space())
+                              if space_D is None else space_D
                               for space, space_D in zip(self._space, self._space_D))
 
         self._controls = tuple(Control(fd.Function(space_D), riesz_map="l2")

firedrake/adjoint/transformed_functional.py

@@ -3906,7 +3906,7 @@ def submesh_correct_entity_classes(PETSc.DM dm,
         DMLabel lbl_core, lbl_owned, lbl_ghost
         PetscBool has
 
-    if dm.comm.size == 1:
+    if subdm.comm.size == 1:
         return
     CHKERR(DMPlexGetChart(dm.dm, &pStart, &pEnd))
     CHKERR(DMPlexGetChart(subdm.dm, &subpStart, &subpEnd))

firedrake/cython/dmcommon.pyx

@@ -93,7 +93,7 @@ class Term(object):
 
     __slots__ = ["form", "labels"]
 
-    def __init__(self, form: ufl.BaseForm, label_dict: Mapping = None):
+    def __init__(self, form: ufl.Form, label_dict: Mapping = None):
         """
 
         Parameters
@@ -216,9 +216,6 @@ def __mul__(
 
     __rmul__ = __mul__
 
-    def __neg__(self):
-        return -1 * self
-
     def __truediv__(
         self,
         other: Union[float, Constant, ufl.algebra.Product]
@@ -277,7 +274,7 @@ def __init__(self, *terms: Sequence[Term]):
 
     def __add__(
         self,
-        other: Union[ufl.BaseForm, Term, "LabelledForm"]
+        other: Union[ufl.Form, Term, "LabelledForm"]
     ) -> "LabelledForm":
         """Add a form, term or labelled form to this labelled form.
 
@@ -292,12 +289,12 @@ def __add__(
             A labelled form containing the terms.
 
         """
-        if type(other) is Term:
+        if isinstance(other, ufl.Form):
+            return LabelledForm(*self, Term(other))
+        elif type(other) is Term:
             return LabelledForm(*self, other)
         elif type(other) is LabelledForm:
             return LabelledForm(*self, *other)
-        elif isinstance(other, ufl.BaseForm):
-            return LabelledForm(*self, Term(other))
         elif other is None:
             return self
         else:
@@ -307,7 +304,7 @@ def __add__(
 
     def __sub__(
         self,
-        other: Union[ufl.BaseForm, Term, "LabelledForm"]
+        other: Union[ufl.Form, Term, "LabelledForm"]
     ) -> "LabelledForm":
         """Subtract a form, term or labelled form from this labelled form.
 
@@ -323,18 +320,15 @@ def __sub__(
 
         """
         if type(other) is Term:
-            return LabelledForm(*self, -other)
+            return LabelledForm(*self, Constant(-1.)*other)
         elif type(other) is LabelledForm:
-            return LabelledForm(*self, *[-t for t in other])
+            return LabelledForm(*self, *[Constant(-1.)*t for t in other])
         elif other is None:
             return self
         else:
             # Make new Term for other and subtract it
             return LabelledForm(*self, Term(Constant(-1.)*other))
 
-    def __rsub__(self, other):
-        return other + (-self)
-
     def __mul__(
         self,
         other: Union[float, Constant, ufl.algebra.Product]
@@ -377,9 +371,6 @@ def __truediv__(
 
     __rmul__ = __mul__
 
-    def __neg__(self):
-        return -1 * self
-
     def __iter__(self) -> Sequence:
         """Iterable of the terms in the labelled form."""
         return iter(self.terms)
@@ -436,7 +427,7 @@ def label_map(
         return new_labelled_form
 
     @property
-    def form(self) -> ufl.BaseForm:
+    def form(self) -> ufl.Form:
         """Provide the whole form from the labelled form.
 
         Raises
@@ -446,7 +437,7 @@ def form(self) -> ufl.BaseForm:
 
         Returns
         -------
-        ufl.BaseForm
+        ufl.Form
             The whole form corresponding to all the terms.
 
         """
@@ -488,7 +479,7 @@ def __init__(
 
     def __call__(
         self,
-        target: Union[ufl.BaseForm, Term, LabelledForm],
+        target: Union[ufl.Form, Term, LabelledForm],
         value: Any = None
     ) -> Union[Term, LabelledForm]:
         """Apply the label to a form or term.
@@ -503,7 +494,7 @@ def __call__(
         Raises
         ------
         ValueError
-            If the `target` is not a ufl.BaseForm, Term or
+            If the `target` is not a ufl.Form, Term or
             LabelledForm.
 
         Returns
@@ -523,7 +514,7 @@ def __call__(
             self.value = self.default_value
         if isinstance(target, LabelledForm):
             return LabelledForm(*(self(t, value) for t in target.terms))
-        elif isinstance(target, ufl.BaseForm):
+        elif isinstance(target, ufl.Form):
             return LabelledForm(Term(target, {self.label: self.value}))
         elif isinstance(target, Term):
             new_labels = target.labels.copy()

firedrake/fml/form_manipulation_language.py

@@ -403,6 +403,19 @@ def make_function_space(cls, mesh, element, name=None):
             new = cls.create(new, mesh)
         return new
 
+    def broken_space(self):
+        """Return a :class:`.WithGeometryBase` with a :class:`finat.ufl.BrokenElement`
+        constructed from this function space's FiniteElement.
+
+        Returns
+        -------
+        WithGeometryBase :
+            The new function space with a :class:`~finat.ufl.BrokenElement`.
+        """
+        return type(self).make_function_space(
+            self.mesh(), finat.ufl.BrokenElement(self.ufl_element()),
+            name=f"{self.name}_broken" if self.name else None)
+
     def reconstruct(
         self,
         mesh: MeshGeometry | None = None,

firedrake/functionspaceimpl.py

@@ -4756,6 +4756,7 @@ def Submesh(mesh, subdim, subdomain_id, label_name=None, name=None, ignore_halo=
         Whether to reorder the mesh entities.
     comm : PETSc.Comm | None
         An optional sub-communicator to define the submesh.
+        By default, the submesh is defined on `mesh.comm`.
 
     Returns
     -------
@@ -4817,26 +4818,24 @@ def Submesh(mesh, subdim, subdomain_id, label_name=None, name=None, ignore_halo=
         raise NotImplementedError("Can not create a submesh of a ``VertexOnlyMesh``")
     plex = mesh.topology_dm
     dim = plex.getDimension()
+    if subdim not in [dim, dim - 1]:
+        raise NotImplementedError(f"Found submesh dim ({subdim}) and parent dim ({dim})")
+    if label_name is None:
+        if subdim == dim:
+            label_name = dmcommon.CELL_SETS_LABEL
+        elif subdim == dim - 1:
+            label_name = dmcommon.FACE_SETS_LABEL
     if subdomain_id is None:
         # Filter the plex with PETSc's default label (cells owned by comm)
-        if label_name is not None:
-            raise ValueError("subdomain_id == None requires label_name == None.")
-        if subdim != dim:
-            raise NotImplementedError(f"Found submesh dim ({subdim}) and parent dim ({dim})")
-        subplex, _ = plex.filter(sanitizeSubMesh=True, ignoreHalo=ignore_halo, comm=comm)
+        if label_name != dmcommon.CELL_SETS_LABEL:
+            raise ValueError("subdomain_id == None requires label_name == CELL_SETS_LABEL.")
+        subplex, sf = plex.filter(sanitizeSubMesh=True, ignoreHalo=ignore_halo, comm=comm)
+        dmcommon.submesh_update_facet_labels(plex, subplex)
+        dmcommon.submesh_correct_entity_classes(plex, subplex, sf)
     else:
-        if comm is not None and comm != mesh.comm:
-            raise NotImplementedError("Submesh on subcommunicator not implemented on cell subsets.")
-        if subdim not in [dim, dim - 1]:
-            raise NotImplementedError(f"Found submesh dim ({subdim}) and parent dim ({dim})")
-        if label_name is None:
-            if subdim == dim:
-                label_name = dmcommon.CELL_SETS_LABEL
-            elif subdim == dim - 1:
-                label_name = dmcommon.FACE_SETS_LABEL
         subplex = dmcommon.submesh_create(plex, subdim, label_name, subdomain_id, ignore_halo, comm=comm)
-        comm = mesh.comm
 
+    comm = comm or mesh.comm
     name = name or _generate_default_submesh_name(mesh.name)
     subplex.setName(_generate_default_mesh_topology_name(name))
     if subplex.getDimension() != subdim:

firedrake/mesh.py

@@ -1,7 +1,6 @@
 import functools
 
 import ufl
-import finat.ufl
 
 import firedrake.dmhooks as dmhooks
 from firedrake.slate.static_condensation.sc_base import SCBase
@@ -90,8 +89,7 @@ def initialize(self, pc):
         TraceSpace = FunctionSpace(mesh[self.vidx], "HDiv Trace", tdegree)
 
         # Break the function spaces and define fully discontinuous spaces
-        broken_elements = finat.ufl.MixedElement([finat.ufl.BrokenElement(Vi.ufl_element()) for Vi in V])
-        V_d = FunctionSpace(mesh, broken_elements)
+        V_d = V.broken_space()
 
         # Set up the functions for the original, hybridized
         # and schur complement systems

firedrake/slate/static_condensation/hybridization.py

@@ -155,13 +155,13 @@ requires = [
   "mpi4py>3; python_version >= '3.13'",
   "mpi4py; python_version < '3.13'",
   "numpy",
+  # TODO RELEASE
+  # "petsc4py==3.24.0",
   "petsctools",
   "pkgconfig",
   "pybind11",
-  "setuptools>=77.0.3",
-  # TODO RELEASE
-  # "petsc4py==3.24.0",
   "rtree>=1.2",
+  "setuptools>=77.0.3",
 ]
 build-backend = "setuptools.build_meta"
 
@@ -178,6 +178,8 @@ script-files = [
 # Unless specified these files will not be installed along with the
 # rest of the package
 firedrake = [
+  "cython/*.pxi",
+  "cython/*.pyx",
   "evaluate.h",
   "locate.c",
   "icons/*.png",