Merge branch 'knepley/feature-plex-periodic-separation' into 'main'

Fix periodicity for higher order coordinates

See merge request petsc/petsc!5333

DM: Reorganized periodic coordinates into a separate representation
- Split coordinates into two representations
- No longer specify the boundary type for periodicity. We can tell if a
given boundary

DM: Reorganized periodic coordinates into a separate representation
- Split coordinates into two representations
- No longer specify the boundary type for periodicity. We can tell if a
given boundary is periodic by a positive L[d]
- Added DMPlexGetCellCoordinates_Internal() to get localized cell
coordinates automatically, and used in plexgeometry.c
- Moved coordinate functions into dmcoordinates.c
- Moved periodicity functions into dmperiodicity.c

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Merge branch 'barry/2022-06-13/make-one-line-if-call' into 'main'

Change if () { PetscCall() } three liner to one liner

See merge request petsc/petsc!5344

Change if () { PetscCall() } three liner and friends to one liners

for i in `git ls-files | grep "\.[ch]$"` ; do sed 's?\$?ZZZ?g' $i | tr '\n' '$' | sed 's?\([ ]*\)if (\([-;,.\*+=a-z0-9A-Z_>]*\)) {\

Change if () { PetscCall() } three liner and friends to one liners

for i in `git ls-files | grep "\.[ch]$"` ; do sed 's?\$?ZZZ?g' $i | tr '\n' '$' | sed 's?\([ ]*\)if (\([-;,.\*+=a-z0-9A-Z_>]*\)) {\$[ ]*PetscCall(\([- ._+=a-z0-9A-Z>*,()]*);\)\$[ ]*}\$?\1if (\2) PetscCall(\3$?g' | tr '$' '\n' | sed 's?ZZZ?$?g' > $i.joe ; mv $i.joe $i ; done

for i in `git ls-files | grep "\.[hc]$"` ; do sed 's?\$?ZZZ?g' $i | tr '\n' '$' | sed 's?\([ }else]*\)if (\([-;,.\*+=a-z0-9A-Z_>]*\)) {\$[ ]*PetscCall(\([- ._+=a-z0-9A-Z>*,()]*);\)\$\([ ]*\)} \([- ._+=a-z0-9A-Z>*,()]*);\)\$?\1if (\2) PetscCall(\3$\4\5$?g' | tr '$' '\n' | sed 's?ZZZ?$?g' > $i.joe ; mv $i.joe $i ; done

Yes, really ugly but Barry still cannot master awk

Commit-type: housekeeping

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Merge branch 'knepley/feature-plex-label-overlap' into 'main'

Plex: Allow a user to create a custom parallel overlap using labels

See merge request petsc/petsc!5349

Plex: Allow a user to create a custom parallel overlap using labels - The test is in PyLith

Merge branch 'ksagiyam/dmplex_reorder_1d_options' into 'main'

plex: add DMPlexReorder{Set,Get}Default()

See merge request petsc/petsc!5245

plexreorder: add DMPlexReorder{Set,Get}Default()

Merge remote-tracking branch 'origin/release'

Merge branch 'jolivet/fix-excl-rank' into 'main'

Replace !rank with rank == 0

See merge request petsc/petsc!5223

Merge branch 'jacobf/2022-05-10/fix-plex-create-from-file-underflow' into 'release'

Fix `DMPlexCreateFromFile()` Underflow

See merge request petsc/petsc!5244

fixup! fix size_t underflow when extension is shorter than file name

fixup! fix size_t underflow when extension is shorter than file name

fixup! fix size_t underflow when extension is shorter than file name

fix size_t underflow when extension is shorter than file name

Merge branch 'haplav/extend-plex-checkpointsf' into 'main'

extend DMPlexCheckPointSF()

See merge request petsc/petsc!5217

add DMPlexCheck()

extend DMPlexCheckPointSF(), add PetscSF arg

add/use DMPlexSetOverlap_Plex()

Merge branch 'haplav/plex-minor' into 'main'

Plex: minor maintenance changes

See merge request petsc/petsc!5218

DMCreate_Plex: NULL doesn't need to be set -

PetscNew zeroes structure fields

Replace !rank with rank == 0

See also https://gitlab.com/petsc/petsc/-/merge_requests/4146

Merge branch 'haplav/plex-copy-overlap' into 'main'

DMPlexCopy_Internal: copy overlap

See merge request petsc/petsc!5200

DMPlexCopy_Internal: copy overlap

Merge branch 'psanan/docs-sphinx-man-pages' into 'main'

Integrate Man Pages into Sphinx Docs

Closes #1132 and #1015

See merge request petsc/petsc!4989