Merge branch 'barry/2025-10-24/fix-dmshellsetdestroyctx' into 'main'

Finish converting the function prototypes of destroy for contexts to use PetscCtxDestroyFn

See merge request petsc/petsc!8810

The goal of all the commits in this MR is to unify the destruction of "application" contexts.

This will help with supporting language bindings. For example, for Fortran the application context
would

The goal of all the commits in this MR is to unify the destruction of "application" contexts.

This will help with supporting language bindings. For example, for Fortran the application context
would be a user derived type

Fix prototype of DMShellSetDestroyCtx function argument to use PETSc standard way of doing it with PetscCtxDestroyF.

Also fix PetscViewerGLVisSetFields prototype of destroy function

These two locations were missed when PetscCtxDestroyFn was introduced as the universal function prototype for context destruction in 3.23

Reported-by: Victor Eijkhout

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Merge branch 'jrwrigh/fix_viewer_format_destroy' into 'main'

viewer: Add back "data_destroy function to PetscViewerAndFormat"

See merge request petsc/petsc!8232

viewer: Add data_destroy function to PetscViewerAndFormat

Co-authored-by: Jed Brown <jed@jedbrown.org>

Merge branch 'barry/2024-04-29/add-fortran-enums' into 'main'

Major updates to Fortran interface

See merge request petsc/petsc!7517

Fortran 90: fully embrace After 34 years!

- deprecate use of 'F90' in Fortran function names
- use Fortran pointers when appropriate
- the new Fortran API is not backward compatible with previous ve

Fortran 90: fully embrace After 34 years!

- deprecate use of 'F90' in Fortran function names
- use Fortran pointers when appropriate
- the new Fortran API is not backward compatible with previous versions!
- also clean up inconsistent PETSc code detected by new Fortran generation tools
- drop use of bfort
- automatically generate all the Fortran PETSc objects, enums etc from the include files
- generate most of the Fortran interface definitions and functions from the source code
- simplify the number and organization of Fortran modules

Co-authored-by: Jose E. Roman <jroman@dsic.upv.es>

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Merge branch 'jrwrigh/viewer_and_format_destroy_data' into 'main'

viewer: Add data_destroy function to PetscViewerAndFormat

See merge request petsc/petsc!8023

viewer: Add data_destroy function to PetscViewerAndFormat

Co-authored-by: Jed Brown <jed@jedbrown.org>

Merge branch 'jolivet/fix-overflow-seqdense' into 'main'

Mat: avoid overflow when loading a MatSeqDense

See merge request petsc/petsc!8008

Mat: avoid overflow when loading a MatSeqDense

Merge branch 'knepley/feature-plex-plot' into 'main'

Plex+Viewer: PETSCVIEWERPYTHON and PyVista support for DMPLEX

See merge request petsc/petsc!7884

Plex+Viewer: Added Python and PyVista viewers
- Enable viewer filename interface for Python viewer
- Add -viewer_python_filename to set the output filename
- Add -dm_plex_transform_active_values to e

Plex+Viewer: Added Python and PyVista viewers
- Enable viewer filename interface for Python viewer
- Add -viewer_python_filename to set the output filename
- Add -dm_plex_transform_active_values to explicitly set values in the label
- Add -dm_plex_option_phases to control sequencing of setup from the command line

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Merge branch 'barry/2024-09-02/rebased-fix-conversion-warnings' into 'main'

Compiler finds (and forbid) casts from higher precision integers to lower

See merge request petsc/petsc!7806

Add to CI compilers flags '-Wconversion', '-Wno-sign-conversion', '-Wno-float-conversion', '-Wno-implicit-float-conversion']

Also fix the code to repository to compile cleanly with these flags in th

Add to CI compilers flags '-Wconversion', '-Wno-sign-conversion', '-Wno-float-conversion', '-Wno-implicit-float-conversion']

Also fix the code to repository to compile cleanly with these flags in the CI

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Merge branch 'jczhang/2024-07-02/revise-vecduplicatevecs' into 'main'

Simplify VecDuplicateVecs

See merge request petsc/petsc!7668

viewer: add comments on PETSC_VIEWER_ASCII_INFO_DETAIL

Merge branch 'barry/2024-07-01/fix-petscoptionsgetviewer' into 'main'

The use case of PetscOptionsGetViewer() has evolved to no longer be the get/restore model

See merge request petsc/petsc!7667

The use case of PetscOptionsGetViewer() has evolved to no longer be the get/restore model

Hence the code needs to be refactored

Introduce PetscCallNull() and PetscCallMPINull() to simplify PETSC_VI

The use case of PetscOptionsGetViewer() has evolved to no longer be the get/restore model

Hence the code needs to be refactored

Introduce PetscCallNull() and PetscCallMPINull() to simplify PETSC_VIEWER_XXXX_() routines

Reported-by: James Wright
Thanks-to: Jeremy L Thompson

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Merge branch 'barry/2024-05-29/minor-fortran-stub-cleanup' into 'main'

More improvements to Fortran stubs and interfaces

See merge request petsc/petsc!7598

All constructors should do PetscAssertPointer on output object

Reported-by: Blaise Bourdin

Constructors should not initialize the output to NULL upon entry, serves no purpose

Fix some formatting i

All constructors should do PetscAssertPointer on output object

Reported-by: Blaise Bourdin

Constructors should not initialize the output to NULL upon entry, serves no purpose

Fix some formatting in constructors

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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 'barry/2023-11-21/fix-thread-safety-petscoptionsgetviewer' into 'main'

Fix PetscOptionsGetViewer() so it works in a thread-safe way

See merge request petsc/petsc!7047

Fix PetscOptionsGetViewer() so it works in a thread-safe way

When PetscOptionsGetViewer() returns, for example, PETSC_VIEWER_STDOUT_SELF the same object is shared
by all threads that call PetscOptio

Fix PetscOptionsGetViewer() so it works in a thread-safe way

When PetscOptionsGetViewer() returns, for example, PETSC_VIEWER_STDOUT_SELF the same object is shared
by all threads that call PetscOptionsGetViewer(). In the previous code PetscObjectReference() and
dereference (via PetscViewerDestroy() where called on the viewer by multiple threads after the viewer
was accessed thus corrupting the object.

This branch introduces a PetscOptionsRestoreViewer() that allows not doing the referencing and dereferencing
on persistant viewers, thus removing the specific race condition above.

Other possible solutions include

Use a lock on each PetscObjectReference/Dereference() just in case they are shared. Could be time consuming so one
could mark each object as either threadshared or independent and only do the locks on threadshared objects. This lowers
the cost but would require more extensive changes to PETSc infrastructure. And I do not know if this shared/not shared model
is what we need in the long run, though it might be.

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