Merge branch 'barry/2025-10-18/optimize-aij-ops' into 'main'

Refactor handling of diagonal marking in *AIJ and SELL matrices

See merge request petsc/petsc!8797

- Replace MatMissingDiagonal() and MatMarkDiagonals_SeqXXX() with MatGetDiagonalMarkers_SeqXXX()

- Mat_SeqXXX->diag is not automatically created during MatAssemblyEnd() saving memory and time

- Replace MatMissingDiagonal() and MatMarkDiagonals_SeqXXX() with MatGetDiagonalMarkers_SeqXXX()

- Mat_SeqXXX->diag is not automatically created during MatAssemblyEnd() saving memory and time

- Accessing Mat_SeqXXX->diag now requires the use of MatGetDiagonalMarkers_SeqXXX() except when the current values are known to be correct; for example during numerical factorizations and solves

- Mat_SeqXXX->diag is now never shared among matrices; hence the free_diag flag is gone. That was always a risky proposition since any of the owning matrices could chang the values thus making them incorrect for other owners.

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This MR optimize some MAT[SB]AIJ operations related to the diagonal

The longer term goal is to refactor some Mat_SeqXXX non-numeric code to make it easier to also implement it on GPUs. For example,

This MR optimize some MAT[SB]AIJ operations related to the diagonal

The longer term goal is to refactor some Mat_SeqXXX non-numeric code to make it easier to also implement it on GPUs. For example, MatGetDiagonal() and friends

This commit
- MatMarkDiagonal_SeqAIJ/ELL()
- now use change in mat->nonzerostate to determine if it needs to recheck the diagonal locations
- sets diagDense flag for a complete diagonal
- MatInvertDiagonal_SeqAIJ/ELL()
- now uses change in mat->state to determine if diagonal entries and inverses need to be recomputed
- name changed to MatInvertDiagonalForSOR_SeqAIJ/ELL() for code clarity
- Added MatInvertDiagonal_SeqAIJ_Inode() for use by MatSOR_SeqAIJ_Inode()
- now uses change in mat->state to determine if block diagonal entries and inverses need to be recomputed

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Merge branch 'jolivet/fix-pchpddm-scatter' into 'main'

Minor fixes and cleanup

See merge request petsc/petsc!8702

Remove more unneeded braces

Merge branch 'jolivet/clang-format-20' into 'main'

clang-format-20

See merge request petsc/petsc!7849

Update to clang-format-20

Merge remote-tracking branch 'origin/release'

Merge branch 'barry/2024-11-26/improve-man-pages/release' into 'release'

Improve some manual pages in KSP/SNES

See merge request petsc/petsc!8071

Improve some manual pages in KSP/SNES

Merge branch 'stefanozampini/useless-cast' into 'main'

Remove useless cast

See merge request petsc/petsc!7894

Brain dead fixes for useless casts

PetscCeilInt: inline method

Merge remote-tracking branch 'origin/release'

Merge branch 'barry/2024-05-27/fix-bug-baij-setvaluesblocked/release' into 'release'

Fix serious bug in MatSetValuesBlocked for SeqBAIJ when a reallocation is needed.

See merge request petsc/petsc!

Merge branch 'barry/2024-05-27/fix-bug-baij-setvaluesblocked/release' into 'release'

Fix serious bug in MatSetValuesBlocked for SeqBAIJ when a reallocation is needed.

See merge request petsc/petsc!7578

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Fix serious bugs in MatSetValuesBlocked for SeqBAIJ and MPIBAIJ when a reallocation is needed.

Reported-by: Adrian Croucher <a.croucher@auckland.ac.nz>

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

clang-format version 18

See merge request petsc/petsc!6902

Remove carriage return in Petsc(Assert|Check)()

git grep -l -E "Petsc(Assert|Check)\(.*\\\n\"[,)]" | xargs sed -r -i'' 's#Petsc(Assert|Check)\((.*)\\n"([,)])#Petsc\1\(\2\"\3#g'

Suggested-by: Stefan

Remove carriage return in Petsc(Assert|Check)()

git grep -l -E "Petsc(Assert|Check)\(.*\\\n\"[,)]" | xargs sed -r -i'' 's#Petsc(Assert|Check)\((.*)\\n"([,)])#Petsc\1\(\2\"\3#g'

Suggested-by: Stefano Zampini

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

Pacify UBSan

See merge request petsc/petsc!7158

Sys: add PetscSafePointerPlusOffset() to pacify UBSan

Merge remote-tracking branch 'origin/release'

Merge branch 'jolivet/fix-typos' into 'release'

Fix typos

See merge request petsc/petsc!6908

Fix typos

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