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[train] main train 2026-11-06: C47 Cython 3 binding fix, C7.1 Phase D per-rank restart views, ADR docs - #216
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…ticmethods; MiscibleDisplacement runs
Cython 3 compiles def functions with binding=True: a compiled function stored
on a class (class-body `from .ctransportCoefficients import f`) and called as
self.f(...) receives self as an extra first argument, like a Python function.
test/MiscibleDisplacement stopped at the first transport evaluate with
TypeError: groundwaterTransportCoefficientsEvaluate_hetMat() takes exactly
12 positional arguments (13 given)
Each of the 17 class-stored compiled functions in this file (24 call lines
through self, including the two-phase Darcy classes TwophaseDarcyCoefficients
subclasses) is now wrapped with staticmethod right after its import. The call
sites are unchanged; staticmethod returns the wrapped callable whether or not
it binds, so the same code is correct on Cython 0.29 and 3.x.
test/MiscibleDisplacement had no test. The deck gets context options
(unstructured_mesh, refinement_level, ndays, nDTout; defaults unchanged) so a
test can run it on a regular triangular mesh, which needs material type 0;
test_miscible_displacement.py runs flow (p1-nc) + transport on an 8x8 mesh to
500 d and pins the tracer mass.
Measured (Cython 3.0.11, macOS arm64, env proteus-bc-261025):
test_miscible_displacement.py before: TypeError after: pass, 0.9 s
parun md_so.py (default deck: triangle, 5000 d, 50 outputs)
before: exit 1, 3.5 s after: exit 0, 9.4 s
tracer mass at 500 d, 8x8: 26191.0447689 (identical in 2 runs)
min c (SUPG + shock capturing undershoot): -0.155 (8x8), -0.29 (16x16),
-3e-5 (32x32); the test's lower bound is -0.5
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…and TimeIntegration; invariant test The same wrap as the previous commit, in every other file outside the mprans models (C0, after C0 round 5 lands) and TimeIntegration (C17/C14): file stored live self.f( calls TwophaseDarcyCoefficients 3 3 TransportCoefficients 1 0 (call commented out) richards/Richards 2 1 m_comp_co2/m_comp_co2 2 1 ADR, AuxiliaryVariables 1+1 0 PostProcessingTools VPP_P1nc_RT0 9 0 (calls use cpostprocessing.f) test/dg/la_gauss_2d_p.py 1 1 PostProcessingTools.VPP_POINT_EVAL_GWVD is left alone: #203 deletes the class. test/test_cython_class_attributes.py checks the premise (a compiled function stored on a class binds self; staticmethod returns it unwrapped) and, for each of the 23 modules that store compiled functions on classes, that the set of binding class attributes equals a DEFERRED list (TimeIntegration 16, mprans 39, PostProcessingTools 1). The set is exact in both directions, so fixing a deferred site fails the test until its entry goes. Inventory: a runtime scan of every importable proteus module found 89 class attributes holding a binding compiled function in 23 modules; an AST scan of test/, scripts/, experimental/ found one more (test/dg). This commit and the previous one fix 34; 56 remain, listed in DEFERRED. Measured (Cython 3.0.11, macOS arm64, env proteus-bc-261025): test_cython_class_attributes.py without the wraps: 8 of 24 module checks fail; with them: 25/25 parun la_gauss_2d_p.py la_gauss_2d_dgp2_n.py (test/dg) main: TypeError in TimeIntegration, computeElementNeighborShapeGradients() 5 for 6 TimeIntegration's 16 wrapped at run time (file untouched), deck unfixed: TypeError: unitSquareRotationEvaluate() takes exactly 6 positional arguments (7 given) both: exit 0, 66 s Existing tests on this branch (richards, griffiths_lane_6, single_phase_gw, post_processing, poisson_2d, levelset, LS_with_edgeBased_EV/MCorr, test_adr_problem, test_analyticalSolutions, multilevel): 821 passed, 32 failed with -n 8. None comes from this change: the 8 multilevel failures fail identically on unchanged main (ce43b73); 23 were xdist workers sharing reference_triangle.* in one cwd and pass serially (93 passed); 1 (test_ymfrun_knows_which_domains_fix_the_mesh) fails on main too, because the env's ymf has no discretizations.mesh_from_domain. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…icmethods TimeIntegration is C17/C14 territory. cekees decided on 2026-11-05 that C47 applies this change on #204, because the change is mechanical and no C17/C14 session is running this week. C17/C14: the only change is one `f = staticmethod(f)` line after each class-body `from .ctimeIntegration import f`, as in the two previous commits. 16 class attributes in 14 classes (DGlimiterP1Lagrange1d/2d, P2, PkMonomial, Durlofsky, the _Sw variants, UnstructuredLimiter_base, CockburnNotesLimiter2d_base, PsiTCtte, PsiTCtte_new) and 16 live self.f(...) call lines. Each raised TypeError (N+1 arguments) under Cython 3 when reached. DEFERRED in test_cython_class_attributes.py loses its TimeIntegration entry. Measured (Cython 3.0.11, macOS arm64, env proteus-bc-261025): parun la_gauss_2d_p.py la_gauss_2d_dgp2_n.py (test/dg, DGlimiterP2Lagrange2d) before: TypeError: computeElementNeighborShapeGradients() takes exactly 5 positional arguments (6 given) after: exit 0, 38.6 s test_cython_class_attributes.py: 24/24 test/shallow_water/dambreak_1d (DGlimiterP1Lagrange1d) still does not run, for an unrelated reason: its flux subclass calls RusanovNumericalFlux_Diagonal without getPeriodicConditions. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…hing deferred After C0 round 5 (#199) and #203 reached cekees/main (c09280c, merged into this branch), the last sites: mprans Dissipation 2, Kappa 2, MCorr 2, MCorr3P 2, NCLS 1, NCLS3P 1, RANS2P 4, RANS3PF 4, RANS3PSed 4, RDLS 1, TADR 3, VOF 3, VOF3P 3, VOS3P 3 (35) Their 12 live self.f(...) call lines are all in Coefficients.evaluate, which the mprans models do not call (the kernels evaluate the coefficients), so no mprans result changes. VPP_POINT_EVAL_GWVD went with #203. DEFERRED in test_cython_class_attributes.py is empty: a runtime scan of every importable proteus module finds no class attribute holding a binding compiled function (89 at the start of C47: 88 in proteus/ plus the test/dg deck). Measured (Cython 3.0.11, macOS arm64, env proteus-bc-261025, serial): test_cython_class_attributes.py, MiscibleDisplacement, LS_with_edgeBased_EV, levelset, TwoPhaseFlow, test_scatter_dof_array, test_two_stage_newton, test_{vof,tadr,twophaseflow}_partition_independence, test_numerical_flux_arguments: 103 passed (7 min 20 s). test_damBreak_hotstart needed this tree's scripts/parun on PATH (the env's installed parun predates --hotStartMode); with the env's parun it fails on that option, not on C47. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…ain with its own numbering
A per-rank view must give the solver back the subdomain partitionMesh built: the partition's maps
number its element boundaries and edges, so those numbers must come back too. generateFromArrays
numbers boundaries and edges its own way; generateFromNumberedArrays takes each element's boundary
numbers and the edge list and calls what partitioning.cpp calls on a subdomain:
constructElementBoundaryElementsArrayWithGivenElementBoundaryAndEdgeNumbers_{triangle,tetrahedron},
then allocate/computeGeometricInfo, then the element boundary flags. mesh.cpp and partitioning.cpp
are not edited. The arrays are allocated with new[] (the Mesh frees them with delete[]); the node and
element fill is shared with generateFromArrays (_fillNodesAndElements).
Measured (macOS arm64, MPICH, env proteus-bc-261025): every rank's subdomain of square4x4_tagged,
square4x4 and cube_3x3x3, owners scattered and reversed, on 2 and 3 ranks (30 rank subdomains):
- generateFromArrays from the same nodes and elements: 7 arrays differ in every case
(elementBoundariesArray, elementBoundaryNodesArray, elementBoundaryElementsArray,
elementBoundaryLocalElementBoundariesArray, interior/exteriorElementBoundariesArray, edgeNodesArray);
- generateFromNumberedArrays: all 33 arrays equal (nodeDiametersArray aside, which partitionMesh
finishes across the ranks afterwards).
test_numbered_arrays (subdomains from partitionNodesLocal in process): 7 passed, serial and 2 ranks.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…tart that reads them Decided by cekees 2026-11-05 (decision 3, after C32 round 2): per-rank views written into per-rank archives (archive-modes layouts B and C) as the same-rank restart source. - Write: on a per-rank archive's first mesh write (Mesh.writeMeshXdmf, driver per-rank), each rank writes subdomain_view/<name> into its own <archive>_p<rank>.h5: the step-H ymf grid (its arrays as datasets beside it, the grid in the `ymf` attribute), and what rebuilding the solver's subdomain needs: each element's boundary numbers, the edges, every element boundary's flag (-1 included), the partition's eight maps, the global mesh's counts and scalars, its fingerprint and whether the partition renumbered. - Read: subdomainViewMesh(archive) -- an open archive or its path -- builds on every rank the mesh that stands for the global one (counts, scalars, maps, no arrays; as cartesianSubdomain's) with the subdomain rebuilt by cmeshTools.generateFromNumberedArrays, then _finishPartitioning. Collective: every rank reads its view or every rank raises SubdomainViewUnavailable with the first reason (no per-rank file, no view, another number of ranks, another view format). - generateMesh(..., restartArchive=None): with an archive whose views fit, a one-level hierarchy from them (multilevelMeshFromSubdomainViews), no global mesh and no partitioner; otherwise, or with more than one level, the old path, logged with the reason. NumericalSolution does not pass it yet (C17/C14's file: the hand-off line is agreed separately); the tests' driver passes the run's open archive. - The input maps and fingerprint carry over a views-built mesh (_localInputNumbering, _inputFingerprint), so the restart's archive records them as the global path's does. Measured (macOS arm64, MPICH, env proteus-bc-261025, ymf c2e646f, PETSC_OPTIONS -mat_partitioning_type current): - write then read, square4x4_tagged and cube_3x3x3, 2 and 3 ranks, layouts B and C: on every rank all 33 subdomain arrays, the 8 maps, the 17 global scalars and the -1 marking equal partitionMesh's (cut faces per rank 6/0, 8/0/8, ...). - same-rank restart, vortex2D (ls + rdls + vof + mcorr, 4 models), stopped at step 3, hot started to step 7 from the same archive with the mesh from the views and with the mesh generated and partitioned: on 2 ranks, partitioned (regularGrid global) and per-rank generated meshes, layouts B and C, every dataset of both ranks' files equal: 138/138 (fields, lagged solver state, mesh, maps). On 3 ranks the run is not reproducible against itself on either path: two global restarts differ by up to 1.7e-12 (18 datasets per rank), two view restarts by up to 2.1e-12 once in four, and views vs global by at most 1.0e-12, inside that spread. Not this change's (both paths); for C3/C17. - unpinned (the graph partitioner), the global restart's partition differed from the run it restarted (rank 0: 420 elements against 416), so its per-rank lagged state was another partition's; the views restart keeps the run's partition by construction. - test_subdomain_view_restart 8 passed (35 s); test_archive_*, test_archiver_write_field, test_hotstart_*, test_gauges*, mesh_tests, ci, poisson_2d, test_adr_problem, test_domain_ymf, multilevel, rank-interface, periodic: 1629 passed, 3 xfailed. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…eed with C17/C14) The hand-off point agreed with the C17/C14 session (2026-11-05): NumericalSolution's mesh setup passes restartArchive=self.ar[0] -- the run's open archive, not its path: a hot start opens each rank's file for append, and HDF5 refuses a second, read-only open in the same process -- unless opts.hotStartMesh is 'global' (an options attribute for now; a parun flag waits for C15). Nothing else in NumericalSolution changes. The vortex2D driver now sets opts.hotStartMesh instead of wrapping generateMesh, and the bit-identity test fails if either hot start logs "no solver state to restore" (a mesh numbered otherwise than the archive's makes a hot start a silent restart; C17/C14's request). Measured: test_subdomain_view_restart + test_hotstart_parallel_state + test_hotstart_state: 16 passed. That log line, counted in the earlier runs: unpinned global restart 4 (one per model: the graph partitioner gave another partition, so every model restarted without its lagged state); views restart 0; pinned global restart 0. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…cients - docs/source/models/adr.rst (new, in the Models toctree): what the ADR model solves, the embedded boundary (CutFEM: Nitsche or Robin, ghost penalty) and the immersed interface (IFEM: two-branch P1/P2 basis, SCIFEM edge terms, interior penalty, prescribed jumps), triply-cut cells, the drivers that reproduce the paper (paper=True, test/option map, an example command), the two-layer overlap needed in parallel, the test/IFEM tests, and the reference. - proteus/ADR.py: NumPy-style docstring for ADR.Coefficients (rendered by napoleon) describing all 42 arguments: defaults, sign conventions, the values the paper uses, that aOfX must agree with mua/mub when the immersed interface is on, and which arguments are accepted but unused (immersedBoundary_penalty, immersedBoundary_u, test). Docstring only; no code change. - docs/source/index.rst: Running path test/ci (was tests/ci); the ADR capability bullet mentions unfitted interfaces and links the new page; the paper added to the references. - docs/source/models/navier_stokes.rst: RANS2P_IB described consistently as two-phase flow with immersed solid boundaries (was "three-phase" in one place), and distinguished from the immersed finite elements of ADR. Built locally with Sphinx 8.2.3 and graphviz 14.1.2 (no doxygen): no warnings from these files; the new page, the Coefficients parameter list, the cross-references and the inheritance diagrams render. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01HEhZZbGLmd57vYntPKW6am (cherry picked from commit e8664b4)
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Fork CI on the combination before the proteustoolkit pull request merges. Each change below was reviewed, and passed CI, as its own pull request on cekees/proteus. This branch merges them
onto
mainat c09280c with one merge commit per pull request, in the order listed.Merge with "Create a merge commit", not squash or rebase, so the commits keep their hashes and the fork's pull requests close themselves.
Diff against
main: 39 files changed, 1208 insertions(+), 52 deletions(-).Note: #215 alone failed only the coverage floor of
proteus/mprans/NCLS3P.py(main 76f3e12 from #199 moved 15 covered statements to Transport); #213 carries the one-line floor change (76.2 -> 75.6), so the train coverage job is expected green.🤖 Generated with Claude Code