Plex ex1: Updated extrusion tests

Merge branch 'knepley/feature-ephemeral-mesh' into 'main'

Plex: First implementation of ephemeral meshes

See merge request petsc/petsc!5738

Plex: First implementation of ephemeral meshes
- Add DMPlexGet/RestoreOrientedCone()
- Add a transform to Plex, which makes it an ephemeral mesh
- Add depth information to PlexTransform
- Fix filter

Plex: First implementation of ephemeral meshes
- Add DMPlexGet/RestoreOrientedCone()
- Add a transform to Plex, which makes it an ephemeral mesh
- Add depth information to PlexTransform
- Fix filter transform
- Fix Plex view for ephemeral meshes
- Right now, check mesh->tr for an ephemeral mesh, but later we could
make a subclass
- Remove DMPlexAddConeSize()

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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

Merge branch 'barry/2022-08-21/clang-format-source' into 'main'

format repository with clang-format

See merge request petsc/petsc!5541

clang-format: convert PETSc sources to comply with clang-format

Merge branch 'knepley/fix-plex-periodic-latex' into 'main'

Plex ex1: Periodic latex

See merge request petsc/petsc!5450

Merge branch 'jolivet/feature-p4est-version' into 'main'

configure: add p4est version check

See merge request petsc/petsc!5492

configure: add p4est version check

Merge branch 'barry/2022-07-23/add-petscbeginuser' into 'main'

Add PetscFunctionBeginUser to all PETSc C/C++ examples

See merge request petsc/petsc!5470

Add PetscFunctionBeginUser to all PETSc C/C++ examples

Now the stack frames will contain the main program and the correct line numbers in them

git ls-files | egrep "(tutorials|tests)" | xargs sed -

Add PetscFunctionBeginUser to all PETSc C/C++ examples

Now the stack frames will contain the main program and the correct line numbers in them

git ls-files | egrep "(tutorials|tests)" | xargs sed -i "s?\(PetscCall(PetscInitialize(&argc\)?PetscFunctionBeginUser;\n \1?g"

Commit-type: error-checking, testing-fix
/spend 15m

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Plex ex1: Periodic latex - It is not perfect, but getting there

Merge branch 'knepley/feature-gmsh-pyramid' into 'main'

Plex: Activate pyramids in Gmsh

See merge request petsc/petsc!5422

Plex ex1: Added pyramid test

Merge branch 'knepley/fix-plex-gmsh-face-labels' into 'main'

Plex: Fix bug with reordering

See merge request petsc/petsc!5416

Fixed examples

Merge branch 'knepley/fix-dm-periodicity' into 'main'

Fixes for periodicity

See merge request petsc/petsc!5391

Plex: Instead of forcing periodic coordinates to [0, L], it should be [lower, lower + L]

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

Fix periodicity for higher order coordinates

See merge request petsc/petsc!5333

Fixed examples

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

extend DMPlexCheckPointSF()

See merge request petsc/petsc!5217

plex/tests/ex1.c: pack checks using DMPlexCheck()