Merge branch 'barry/2024-03-13/fix-snes-mf-operator-with-tssetijacobian-and-no-snessetup' into 'main'

Fix use of SNESSetUpMatrices() with -snes_mf_operator but no user call to...

See merge request

Merge branch 'barry/2024-03-13/fix-snes-mf-operator-with-tssetijacobian-and-no-snessetup' into 'main'

Fix use of SNESSetUpMatrices() with -snes_mf_operator but no user call to...

See merge request petsc/petsc!7367

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Merge branch 'jolivet/add-matmatsolvetranspose_seqaij' into 'main'

MatMatSolveTranspose_SeqAIJ and minor housekeeping

See merge request petsc/petsc!7386

Fix use of SNESSetUpMatrices() with -snes_mf_operator but no user call to SNESSetUp() with TSSetIJaccobian(ts,NULL,NULL);

reported by James Wright

Docs: fix missing or extra dash in right-hand side

Merge branch 'jolivet/clang-format-18' into 'main'

clang-format version 18

See merge request petsc/petsc!6902

Remove multiple parentheses and extra semicolon

git grep -l -E "\(\([a-zA-Z0-9_]+\)\(\*[a-zA-Z0-9_]+\)[, )]" | xargs sed -r -i'' 's#\(\(([a-zA-Z0-9_]+)\)\(\*([a-zA-Z0-9_]+)\)([, )])#\(\(\1\)\*\2\3#g

Remove multiple parentheses and extra semicolon

git grep -l -E "\(\([a-zA-Z0-9_]+\)\(\*[a-zA-Z0-9_]+\)[, )]" | xargs sed -r -i'' 's#\(\(([a-zA-Z0-9_]+)\)\(\*([a-zA-Z0-9_]+)\)([, )])#\(\(\1\)\*\2\3#g'
git grep -l -E "Petsc(.)*\(\(\*[a-zA-Z0-9_]*\)," | xargs sed -r -i'' 's#Petsc([a-zA-Z0-9_]*)\(\(\*([a-zA-Z0-9_]*)\), #Petsc\1(*\2, #g'
git grep -l -E "([\!\&\~\*\(]|\)\)|\([^,\*\(]+\**\))\(([a-zA-Z0-9_]+((\.|->)[a-zA-Z0-9_]+|\[[a-zA-Z0-9_ \%\+\*\-]+\])+)\)" | xargs sed -r -i'' 's#([\!\&\~\*\(]|\)\)|\([^,\*\(]+\**\))\(([a-zA-Z0-9_]+((\.|->)[a-zA-Z0-9_]+|\[[a-zA-Z0-9_ \%\+\*\-]+\])+)\)#\1\2#g'

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checkbadSource: rules for PetscFunctionBegin and derivatives

Merge branch 'jolivet/fix-double' into 'main'

Fix words appearing twice in a row for no good reason

See merge request petsc/petsc!7307

Fix words appearing twice in a row for no good reason

Merge branch 'barry/2024-01-19/typedef-snes-functions' into 'main'

add typedef for functions passed to SNESSetFunction() etc to match approach in TS

See merge request petsc/petsc!7206

Change the use of the _Fn suffix to indicate a typedef of a function to just Fn

As determined on a vote on GitLab

Merge branch 'barry/2024-01-30/use-petscusetypemethod' into 'main'

Fix places where PetscUseTypeMethod() and related macros should be used.

See merge request petsc/petsc!7254

Fix places where PetscUseTypeMethod() and related macros should be used.

add typedef for functions passed to SNESSetFunction() etc to match approach in TS

I never liked Jed's use of typedef for function prototypes for a couple of reasons

1) you don't see immediately tha

add typedef for functions passed to SNESSetFunction() etc to match approach in TS

I never liked Jed's use of typedef for function prototypes for a couple of reasons

1) you don't see immediately that the argument to the function is a function pointer instead of standard variable when looking at source
2) you don't see at the exact location in the code the prototype of the function being passed in

but there is something to say for using these typedefs so

I've prototyped the change for SNES but slightly differently than what Jed did for TS

1) I append the typedef with _Ftn to mark that it is a function (helping to relieve the problem 1 above)
2) I made the typedef to be for a function, not a function pointer so it can also be used directly for things like

PETSC_EXTERN SNESJacobian_Ftn SNESComputeJacobianDefault;

I think the TS usage could be switched to this style without user code breakage, and deprecate the current TS typedef

Thoughts?

Just do SNES the same way as TS and live with less clarity?

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Merge branch 'stefanozampini/fix-snestestjacobian-multilevel' into 'main'

SNESTestJacobian: fix for multilevel solvers

See merge request petsc/petsc!7186

SNESTestJacobian: fix for multilevel solvers

Merge remote-tracking branch 'origin/release'

Merge branch 'stefanozampini/minsurf-local' into 'main'

Improve support for nonlinear domain decomposition solvers

See merge request petsc/petsc!7084

Merge branch 'barry/2023-12-04/fix-manpage-references/release' into 'release'

Update references in the manual pages to use Sphinx citation processing

See merge request petsc/petsc!7101

Update references in the manual pages to use Sphinx citation processing

SNES: Add support to test finite differencing the objective function

SNESGetNPC: pass usercompute instead of application context if present

Merge remote-tracking branch 'origin/release'

Merge branch 'stefanozampini/fix-snes-objective' into 'release'

fix snes objective for nonzero rhs

See merge request petsc/petsc!7093

SNESComputeObjective: add missing <rhs,x_k> term