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Replace scifem.compat and scifem.ufl_compat with fenicsx-compat - #267

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Replace scifem.compat and scifem.ufl_compat with fenicsx-compat#267
jorgensd merged 10 commits into
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finsberg/fenicsx-compat

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@finsberg

@finsberg finsberg commented Oct 12, 2026

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All cross-version DOLFINx workarounds now come from fenicsx-compat (>=0.2.0), which centralises them for scifem, io4dolfinx and dolfinx-adjoint. scifem keeps no compat layer of its own:

  • scifem.compat and scifem.ufl_compat are removed, along with compat in scifem.all and their API reference section. Their callers use the fenicsx_compat equivalents.
  • Inline duplicates of fenicsx-compat functions are replaced too: facet quadrature permutations, Expression.eval entity shapes, interpolate_f, Expression entity_maps, index map creation and unwrapping, MeshTags.topology, create_sub_index_map, local_range, the gmsh model_to_mesh ghost mode, the ADIOS2 scope and the PETSc lifting helpers.
  • Branches that cannot run on DOLFINx >= 0.10, the floor fenicsx-compat sets, become plain DOLFINx calls: compute_integration_domains, the cpp Topology constructor, pack_constants/pack_coefficients, determine_point_ownership, the *_block PETSc API, and the 0.8/0.9 paths in point_source.py and solvers.py.
  • NewtonSolver arranges its boundary conditions with fenicsx_compat.bcs_by_block, as dolfinx.fem.bcs_by_block cannot be called directly across 0.11 and 0.12 (dolfinx#4342).
  • scifem.petsc.apply_lifting_and_set_bc keeps its single-form calling convention, [form] with [bcs], and passes the form and its boundary conditions on to fenicsx-compat.

The minimum Python version goes from 3.10 to 3.12, as fenicsx-compat requires it, and packaging moves from the runtime dependencies to the test extra, as only the tests still use it.

finsberg and others added 2 commits October 12, 2026 12:17
@finsberg @claude
Replace scifem.compat and scifem.ufl_compat with fenicsx-compat
a938659 
All cross-version DOLFINx workarounds now come from fenicsx-compat
(>=0.2.0), which centralises them for scifem, io4dolfinx and
dolfinx-adjoint. scifem keeps no compat layer of its own:

- scifem.compat and scifem.ufl_compat are removed, along with
  `compat` in scifem.__all__ and their API reference section. Their
  callers use the fenicsx_compat equivalents.
- Inline duplicates of fenicsx-compat functions are replaced too:
  facet quadrature permutations, Expression.eval entity shapes,
  interpolate_f, Expression entity_maps, index map creation and
  unwrapping, MeshTags.topology, create_sub_index_map, local_range,
  the gmsh model_to_mesh ghost mode, the ADIOS2 scope and the PETSc
  lifting helpers.
- Branches that cannot run on DOLFINx >= 0.10, the floor fenicsx-compat
  sets, become plain DOLFINx calls: compute_integration_domains, the
  cpp Topology constructor, pack_constants/pack_coefficients,
  determine_point_ownership, the *_block PETSc API, and the 0.8/0.9
  paths in point_source.py and solvers.py.
- NewtonSolver arranges its boundary conditions with
  fenicsx_compat.bcs_by_block, as dolfinx.fem.bcs_by_block cannot be
  called directly across 0.11 and 0.12 (dolfinx#4342).
- scifem.petsc.apply_lifting_and_set_bc keeps its single-form calling
  convention, `[form]` with `[bcs]`, and passes the form and its
  boundary conditions on to fenicsx-compat.

The minimum Python version goes from 3.10 to 3.12, as fenicsx-compat
requires it, and `packaging` moves from the runtime dependencies to the
test extra, as only the tests still use it.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@finsberg
Merge branch 'main' into finsberg/fenicsx-compat
86ff705
@finsberg
finsberg marked this pull request as ready for review October 12, 2026 19:11
@finsberg
finsberg requested a review from jorgensd October 12, 2026 19:11
@jorgensd

jorgensd commented Oct 13, 2026

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Do we really want the compat package to depend on PETSc? If we do I think we should aim to make scifem PETSc free over time :)

@finsberg

finsberg commented Oct 13, 2026

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Do we really want the compat package to depend on PETSc? If we do I think we should aim to make scifem PETSc free over time :)

No, it should not depend strictly on PETSc. Right now it is guarded by an if dolfinx.has_petsc4py , but perhaps we should add a test suite that tests this on dolfinx built without PETSc?

jorgensd
jorgensd reviewed Oct 21, 2026
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Comment thread src/scifem/periodic/gmsh.py Resolved
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Comment thread src/scifem/periodic/gmsh.py Outdated
else:
pairs = PeriodicNodes(0)
mesh_data = model_to_mesh(
mesh = model_to_mesh(

@jorgensd jorgensd Oct 21, 2026

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How is this correct?

@finsberg finsberg Oct 21, 2026

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This was because the helper function (model_to_mesh) inside periodic/gmsh.py returned only the mesh, but this is very confusing with two functions with the same name. Fixed in d6e76e9

jorgensd
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Comment thread src/scifem/periodic/mesh.py Resolved
jorgensd
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Comment thread src/scifem/periodic/mesh.py Outdated
Comment on lines +382 to +383
ghosting_ranks = np.asarray(ghosting_ranks, dtype=np.int32)
ghosting_offsets = np.asarray(ghosting_offsets, dtype=np.int64)

@jorgensd jorgensd Oct 21, 2026

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Shouldn't this wrapping be done inside fenicsx_compat?

@finsberg finsberg Oct 21, 2026

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Agree! Fixed in 3156f3f

jorgensd
jorgensd reviewed Oct 21, 2026
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Comment thread src/scifem/periodic/mesh.py Resolved
jorgensd
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Comment thread src/scifem/geometry.py Resolved
jorgensd
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Comment thread src/scifem/mesh.py Resolved
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Comment thread src/scifem/point_source.py Outdated
src_ranks = collision_data.src_owner
else:
raise NotImplementedError(f"Unsupported version of dolfinx: {dolfinx.__version__}")
collision_data = dolfinx.geometry.determine_point_ownership(

@jorgensd jorgensd Oct 21, 2026

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This is simplified as we support only 0.10 and ownards?

@finsberg finsberg Oct 21, 2026

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Yes, that is the reason. Are you OK with dropping support for < 0.10?

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Comment thread src/scifem/solvers.py Resolved
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Comment thread tests/test_interpolation.py Resolved
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Some minor things to clarify

finsberg and others added 8 commits October 21, 2026 17:25
@finsberg @jorgensd
Update src/scifem/periodic/gmsh.py
377c144 
Co-authored-by: Jørgen Schartum Dokken <dokken92@gmail.com>
@finsberg @claude
Remove scifem.periodic.gmsh.model_to_mesh in favour of fenicsx-compat's
d6e76e9 
The wrapper shared its name with dolfinx.io.gmsh.model_to_mesh and
fenicsx_compat.model_to_mesh but, unlike them, returned the mesh rather
than the MeshData. Since this branch it only forwarded to
fenicsx_compat.model_to_mesh, whose defaults (shared_facet ghosting,
max_facet_to_cell_links=2) are the same, so read_periodic_mesh_from_msh
and the tests call that directly and take `.mesh` themselves.

This removes a public function that shipped in v0.26.0.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@finsberg @jorgensd
Update src/scifem/periodic/mesh.py
826b070 
Co-authored-by: Jørgen Schartum Dokken <dokken92@gmail.com>
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
e2e2dcb 
for more information, see https://pre-commit.ci
@finsberg
Remove array casting of ghosing ranks and offsets
3156f3f
@finsberg @jorgensd
Update src/scifem/geometry.py
cfc2098 
Co-authored-by: Jørgen Schartum Dokken <dokken92@gmail.com>
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
25a45d1 
for more information, see https://pre-commit.ci
@finsberg @claude
Fix the mypy errors reported against DOLFINx's type hints
def7ba6 
With a typed DOLFINx installed (0.12.0.dev0), mypy reported 96 errors
in src and tests; the pre-commit hook runs without DOLFINx, so they
never showed there. None changes behaviour:

- Wrong annotations are corrected: NewtonSolver's _F and _J hold a list
  and a list of lists of forms, entity_maps is a sequence of EntityMap
  from DOLFINx 0.10 on, the _EntityMap protocol's members are read-only
  properties, and create_space_of_simple_functions' value_shape is a
  tuple of ints.
- typing.cast where the type is known but not to the stubs, chiefly
  ufl.domain.extract_domains, typed AbstractDomain but a ufl.Mesh here.
- A narrow `# type: ignore[<code>]` with its reason where a stub is
  wrong and the code right: the float32/float64 cpp class picked at
  runtime, a blocked x0 in apply_lifting, numpy index arrays passed to
  petsc4py, and compiled forms passed through dolfinx.fem.form.
- PeriodicNodes(0) becomes PeriodicNodes(): the 0 went into the
  `replaced` array, not num_nodes_global. Harmless, as that branch runs
  only on ranks that never read either.
- KSP.create takes the vector's PETSc communicator directly rather than
  its mpi4py conversion.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@finsberg
finsberg added this pull request to stack #270 October 21, 2026 19:38
@finsberg
finsberg removed this pull request from stack #270 October 21, 2026 19:40
@jorgensd
jorgensd merged commit 57b2185 into main Oct 23, 2026
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