Swarm ex12: Tests for DMDA periodic point location

Swarm: Uniform coordinates should use the bounding box

Remove extra "" after format specifier ending a string

git grep -l -E "_FMT \"\"," | xargs sed -r -i'' 's#_FMT \"\",#_FMT,#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

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

Swarm: View should only set timestep if it is active

Swarm ex11: Tests for multicomponent projection

Swarm: Generalize projection to multiple components
- Generalize mass matrix to multiple components
- Add DMSwarmGetFieldInfo()
- Add DMSwarmVectorGetField()

Swarm: Add continuous DM argument to DMSwarmProjectFields()

Merge branch 'knepley/fix-plex-io-section-perm' into 'main'

Plex: Flexible creation of section permutations

See merge request petsc/petsc!7258

Plex: Flexible creation of section permutations
- Add createsectionpermutation to DM ops
- Change DMPlexReorderDefaultFlag to DMReorderDefaultFlag
- Move DMReorderDefaultFlag to the correct header

A

Plex: Flexible creation of section permutations
- Add createsectionpermutation to DM ops
- Change DMPlexReorderDefaultFlag to DMReorderDefaultFlag
- Move DMReorderDefaultFlag to the correct header

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Swarm: Make the particle mass matrix compatible with FV

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

As determined on a vote on GitLab

Update `PetscSimplePointFunc` to new naming convention `PetscSimplePoint_Fn`

Commit-type: housekeeping

Merge branch 'barry/2024-01-03/docs-c2html' into 'main'

Remove recursive build of c2html files; no longer uses classic makefiles

See merge request petsc/petsc!7167

Use < instead of " for includes of PETSc include files

And Remove unneeded duplicate includes

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

Fix "Extra spaces in test harness rules" in checkbadSource

First batch of fixes

Merge branch 'barry/2023-12-22/rm-libbase' into 'main'

LIBBASE is no longer used in make so remove it

See merge request petsc/petsc!7139