Merge branch 'barry/2026-01-13/ftn-generation-for-context-functions' into 'main'

Fortran generation of interface definitions for functions that take and return context variables (void *ctx and PetC

Merge branch 'barry/2026-01-13/ftn-generation-for-context-functions' into 'main'

Fortran generation of interface definitions for functions that take and return context variables (void *ctx and PetCtx ctx)

See merge request petsc/petsc!8956

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Add automatic generated fortran support for setting and returning contexts

Major cleanup of the code for setting and returning application (previously called user) contexts
- PetscCtx ctx is now t

Add automatic generated fortran support for setting and returning contexts

Major cleanup of the code for setting and returning application (previously called user) contexts
- PetscCtx ctx is now the standard for passing in contexts
- PetscCtxRt ctx is the standard for passing out contexts, including context destroy routines based on PetscCtxDestroyFn

Both of these are typedef to void*

Also removed most use of user and userctx for context arguments now consistently named ctx

Improved documentation on PetscCtx and PetscCtxRt and on how to use contexts (including getting them) from Fortran

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Merge branch 'knepley/feature-plex-transform-cohesive' into 'main'

Plex: Fix cohesive cell integration

See merge request petsc/petsc!8175

Plex: Fix hybrid integration
- Add DMFieldCreateDefaultFaceQuadrature() and PetscFEExpandFaceQuadrature()
- Add neighbor geometry to PetscFEIntegrateHybridResidual_Basic(), PetscFEIntegrateHybridJaco

Plex: Fix hybrid integration
- Add DMFieldCreateDefaultFaceQuadrature() and PetscFEExpandFaceQuadrature()
- Add neighbor geometry to PetscFEIntegrateHybridResidual_Basic(), PetscFEIntegrateHybridJacobian_Basic() and PetscFEEvaluateFieldJets_Hybrid_Internal()
- Add cell geometry to PetscFEIntegrateHybridResidual() and PetscFEIntegrateHybridJacobian()

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Merge branch 'knepley/feature-embedded-manifold' into 'main'

Plex+PetscFE: Fixes to allow embedded manifolds

See merge request petsc/petsc!8141

Plex+PetscFE: Fixes to allow embedded manifolds
- Add PetscFEGeomMode to describe geometry
- Reorganized PetscFEGeom
- PetscFEGeomCreate(), DMFieldCreateFEGeom() and DMSNESGetFEGeom() now take the Pe

Plex+PetscFE: Fixes to allow embedded manifolds
- Add PetscFEGeomMode to describe geometry
- Reorganized PetscFEGeom
- PetscFEGeomCreate(), DMFieldCreateFEGeom() and DMSNESGetFEGeom() now take the PetscFEGeomMode
- J and invJ have dE dimensions
- f1, g1, g2, g3 have dE dimensions
- FIX the dim argument of all point function is really dE because it is used to index the gradients
- Clarified behavior of PetscFEGeomGetCellPoint()
- Now -dm_plex_coordinate_dim can change the coordinate dimension of a mesh created by Plex
- Implicit cell geometry must be used when dim != cdim

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Merge remote-tracking branch 'origin/release'

Merge branch 'barry/2024-01-04/fix-includes-man-pages/release' into 'release'

Barry/2024 01 04/fix includes man pages/release

See merge request petsc/petsc!7165

Fix manual page formating in include directory

Merge branch 'jacobf/2023-08-17/header-guard-check' into 'main'

Check header guards

See merge request petsc/petsc!6822

Convert all header guards to pragma once

Merge branch 'stefanozampini/remove-unused-api' into 'main'

remove API definition of functions without any implementation code

See merge request petsc/petsc!6728

Remove unused some dead API. These had header declerations but no corresponding
definitions in the source tree.

Merge remote-tracking branch 'origin/release'

Merge branch 'barry/2023-03-30/fix-include-man-pages/release' into 'release'

Fix manual pages in include files

See merge request petsc/petsc!6272

Fix manual pages in include files

Merge branch 'jacobf/2022-09-21/2-bike-2-shed' into 'main'

Feature: Bicycle Storage Facility 2

See merge request petsc/petsc!5661

Transform all header-guards into ifndefs to make clang-format ignore them for preprocessor indentation

Merge branch 'barry/2022-08-21/clang-format-source' into 'main'

format repository with clang-format

See merge request petsc/petsc!5541

clang-format: convert PETSc sources to comply with clang-format

Merge branch 'barry/2022-08-13/fix-man-include' into 'main'

Fix up manual pages in include/ including adding tick marks

See merge request petsc/petsc!5528

Fix up manual pages in include/ including adding tick marks

Commit-type: documentation
/spend 4h

Merge branch 'knepley/feature-plex-periodic-separation' into 'main'

Fix periodicity for higher order coordinates

See merge request petsc/petsc!5333

DM: Reorganized periodic coordinates into a separate representation
- Split coordinates into two representations
- No longer specify the boundary type for periodicity. We can tell if a
given boundary

DM: Reorganized periodic coordinates into a separate representation
- Split coordinates into two representations
- No longer specify the boundary type for periodicity. We can tell if a
given boundary is periodic by a positive L[d]
- Added DMPlexGetCellCoordinates_Internal() to get localized cell
coordinates automatically, and used in plexgeometry.c
- Moved coordinate functions into dmcoordinates.c
- Moved periodicity functions into dmperiodicity.c

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Merge branch 'barry/2022-05-03/cleanup-makefiles' into 'main'

remove unneeded stuff from makefiles

See merge request petsc/petsc!5211