Merge branch 'release'

Merge branch 'barry/2025-11-24/fix-pc-factor-nonzeros-along-diagonal/release' into 'release'

Crash when using MUMPs sequentially with -pc_factor_nonzeros_along_diagonal...

See merge request petsc/p

Merge branch 'barry/2025-11-24/fix-pc-factor-nonzeros-along-diagonal/release' into 'release'

Crash when using MUMPs sequentially with -pc_factor_nonzeros_along_diagonal...

See merge request petsc/petsc!8866

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Crash when using MUMPs sequentially with -pc_factor_nonzeros_along_diagonal but using MUMPS ordering.

$ PETSC_OPTIONS="-pc_factor_mat_ordering_type external" python pythonprogram.py
[0]PETSC ERROR:

Crash when using MUMPs sequentially with -pc_factor_nonzeros_along_diagonal but using MUMPS ordering.

$ PETSC_OPTIONS="-pc_factor_mat_ordering_type external" python pythonprogram.py
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
[0]PETSC ERROR: --------------------- Stack Frames ------------------------------------
The line numbers in the error traceback are not always exact.
[0] #1 MatReorderForNonzeroDiagonal_SeqAIJ() at /Users/barrysmith/Src/petsc/src/mat/utils/zerodiag.c:77
[0] #2 MatReorderForNonzeroDiagonal() at /Users/barrysmith/Src/petsc/src/mat/utils/zerodiag.c:61
[0] #3 PCSetUp_LU() at /Users/barrysmith/Src/petsc/src/ksp/pc/impls/factor/lu/lu.c:84
[0] #4 PCSetUp() at /Users/barrysmith/Src/petsc/src/ksp/pc/interface/precon.c:1120
[0] #5 KSPSetUp() at /Users/barrysmith/Src/petsc/src/ksp/ksp/interface/itfunc.c:429

Bug was it still tried the nonzero diagonal reordering even when the ordering type was external so PETSc did not generate an ordering

Also fixed bug in PCSetUp_Cholesky() where it used GetBool on -pc_factor_nonzeros_along_diagonal when the argument may be followed by a numerical value

Reported-by: Jørgen Dokken

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Merge branch 'jolivet/clang-format-21' into 'main'

clang-format-21

See merge request petsc/petsc!8202

One-liners from petsc/petsc!5344 and petsc/petsc!5557

Slightly reworked regular expression

git ls-files -z -- '*.c' '*.cxx' '*.cu' '*.h' '*.hpp' '*.cpp' | while IFS= read -r -d '' file; do
cat

One-liners from petsc/petsc!5344 and petsc/petsc!5557

Slightly reworked regular expression

git ls-files -z -- '*.c' '*.cxx' '*.cu' '*.h' '*.hpp' '*.cpp' | while IFS= read -r -d '' file; do
cat $file | tr '\n' '\r' | sed -E 's/\r([ ]*)(for|if|while|else) ([^\r]*)\{\r[ ]*Petsc([a-zA-Z]*)\(([^\r]*)\);\r[ ]*\}\r/\r\1\2 \3Petsc\4(\5);\r/g' | tr '\r' '\n' > ${file}.joe; mv ${file}.joe ${file}
done

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Merge branch 'jolivet/housekeeping' into 'main'

Housekeeping

See merge request petsc/petsc!8326

Remove unneeded variable and functions

Merge branch 'jolivet/feature-pcmatapplytranspose' into 'main'

PC: add PCMatApplyTranspose()

See merge request petsc/petsc!8322

PC: add PCMatApplyTranspose()

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 remote-tracking branch 'origin/release'

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

Merge remote-tracking branch 'origin/release'

Merge branch 'barry/2023-11-24/fix-ksp-manpages/release' into 'release'

Fix manual pages in KSP

See merge request petsc/petsc!7055

Fix manual pages in KSP

Merge branch 'jolivet/rm-first-empty-line' into 'main'

Remove first and last empty lines

See merge request petsc/petsc!6892

Remove first and last empty lines

Merge branch 'stefanozampini/fix-issue-1365' into 'main'

MatGetFactor: support returning NULL

Closes #1365

See merge request petsc/petsc!6377

MatGetFactor: support returning NULL

This is only for those combinations that cannot be checked if not at runtime

Merge branch 'jacobf/2022-12-10/petscerrorcode-nodiscard' into 'main'

Feature: Non-discardable PetscErrorCode

See merge request petsc/petsc!5923

Make PetscErrorCode a non-discardable enum

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

Feature: Bicycle Storage Facility 2

See merge request petsc/petsc!5661

source code format changes due to .clang-format changes