Plex ex1: Fix name of local coordinate vector

Fix docstring of PetscPartitionerShellSetPartition

Plex: Fix for TetGen wrapper

Note refcounting in DMPlexGetPartitioner

Add programmatic interface to set partitioner on DMPlex

Counterpart to DMPlexGetPartitioner.

Plex ex12: Add test output

Plex: Restore Fortran binding for DMPlexDistribute()

Merge branch 'mlange/feature-parallel-distribute'

* mlange/feature-parallel-distribute: (33 commits)
Plex+Label: Fix logic for label distribution - It is restrictive now, but doing it right would

Merge branch 'mlange/feature-parallel-distribute'

* mlange/feature-parallel-distribute: (33 commits)
Plex+Label: Fix logic for label distribution - It is restrictive now, but doing it right would mean a ton of infrastructure I think
Plex ex12: Fix output after label distribution fix
Plex: Only call SetFromOptions() after Distribute, since we cannot avoid it
TS ex11: Since DMPlexDistribute() calls SetFromOptions(), do not call it again, and cleaned up tests
Plex+FV: If using FVM adjacency, do not create ghost cells for faces in the overlap, or set BC on them
Plex: If using FVM adjacency, we must include the closure in the overlap
Plex+Label: All processes with a valid label should participate in label distribution - Formerly it was just proc 0
Plex: Add check that parallel renumbering fully covers the cone points
Plex: For one level adjacency, include the point itself since this makes sense when looking in parallel from the overlap
Plex: Cannot Malloc2() the arrays passed to PetscSFSetGraph()
Plex: Preallocation fixes for indegree > 1 - Again this should be rewritten
SNES ex62: Changes to output for fixes with quads
Plex ex1: Fixed LaTeX output
Plex ex12: Fixed overlap test
Plex: Fixed incorrect usage of PetscSFGatherBegin/End() in preallocation - This should be rewritten using new style
PetscSF: Incorrect check for computed degrees
Builder: Fix for Barry's change
PetscSF: Fixes for sparse leaves - When sf->mine exists, the leaves can be numbered non-sequentially. This causes allocation based upon sf->nleaves to underallocate. Replacing sf->nleaves with the maximum leaf number is sufficient in this case.
Plex: Fix leaks
Configure: How did this break?
...

Conflicts:
config/builder.py

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Merge branch 'knepley/feature-plex-partitioner-shell'

* knepley/feature-plex-partitioner-shell:
Plex: Cleanup of examples to use new interfaces
Plex: Added DMPlexCreateFromFile() - Dispatches to

Merge branch 'knepley/feature-plex-partitioner-shell'

* knepley/feature-plex-partitioner-shell:
Plex: Cleanup of examples to use new interfaces
Plex: Added DMPlexCreateFromFile() - Dispatches to the right constructor based on extension
Plex ex1: Added test partitioner
Plex: Added DMPlexGetPartitioner() and PetscPartitionerShellSetPartition()
PetscSection: Added PetscSectionCopy()
Plex ex1: Cleaned up mesh creation - Now use -dm_refine for uniform refinement
Plex: Remove superfluous argument from DMPlexDisitrbute()
Plex: Fixed Fortran stub
PetscFV: Lots of small naming fixes
Partitioner+Plex: Added PetscPartitioner class - Plex holds a PetscPartitioner - Changed args so that PetscSections are modified, not created (also of DMPlexEnlargePartition) - Now partition routine takes a number of partitions instead of assuming commSize - Added a shell partitioner intended to be used for regression testing

Conflicts:
src/dm/impls/plex/examples/tests/ex1.c

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Merge branch 'knepley/feature-plex-label-output'

* knepley/feature-plex-label-output:
Plex+Label: Set default output flag to PETSC_TRUE
Plex+Label: Added output flag for labels - Meant storing l

Merge branch 'knepley/feature-plex-label-output'

* knepley/feature-plex-label-output:
Plex+Label: Set default output flag to PETSC_TRUE
Plex+Label: Added output flag for labels - Meant storing labels in a struct inside Plex - Added DMPlexGetLabelByNum() - Added DMPlexGet/SetLabelOutput() - Got rid of most of the mucking with the internal label storage

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Merge branch 'knepley/feature-parallel-partition'

* knepley/feature-parallel-partition:
Plex: Silence compiler warning
Plex: Needs custom Fortran binding
Plex: Fix distribution for meshes with

Merge branch 'knepley/feature-parallel-partition'

* knepley/feature-parallel-partition:
Plex: Silence compiler warning
Plex: Needs custom Fortran binding
Plex: Fix distribution for meshes without coordinates
Plex ex12: Added test from Michael
Plex: Added methods to support distributed overlap calculation - Added DMPlexCreateTwoSidedProcessSF() - Added DMPlexDistributeOwnership() - Added DMPlexCreateOverlap()
PetscSF: Fix ComputeDegree and GetMultiSF for sparse SFs
Plex: Added DMPlexDistributeFieldIS() - Small doc fix
Plex: DMPlexCreateProcessSF() is now documented and the outputs are optional - The root space is also correct
PetscSF: The declaration of PetscSFNode should be in the types header
Plex ex12: Add overlap
Plex ex12: Added test for parallel partitioning
SNES ex12: Misspelling
Plex ex1: Typo
Plex: Fix LaTeX mesh output

Conflicts:
include/petscdmplex.h

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Plex+Label: Fix logic for label distribution
- It is restrictive now, but doing it right would mean a ton of infrastructure I think

Plex ex12: Fix output after label distribution fix

Plex: Only call SetFromOptions() after Distribute, since we cannot avoid it

Plex+FV: If using FVM adjacency, do not create ghost cells for faces in the overlap, or set BC on them

Plex: If using FVM adjacency, we must include the closure in the overlap

Plex+Label: All processes with a valid label should participate in label distribution
- Formerly it was just proc 0

Plex: Add check that parallel renumbering fully covers the cone points

Plex: For one level adjacency, include the point itself since this makes sense when looking in parallel from the overlap

Plex: Cannot Malloc2() the arrays passed to PetscSFSetGraph()

cleanup of use of PetscOptionsInt and friends including use of flag final argument

Plex: Preallocation fixes for indegree > 1
- Again this should be rewritten

Merge branch 'knepley/feature-plex-label-output' into mlange/feature-parallel-distribute

* knepley/feature-plex-label-output:
Plex+Label: Set default output flag to PETSC_TRUE

Plex+Label: Set default output flag to PETSC_TRUE

Plex ex1: Fixed LaTeX output