Merge branch 'master' into shri/ts-is-for-differential-variables

Conflicts:
include/petsc-private/tsimpl.h
src/ts/impls/eimex/eimex.c
src/ts/interface/ts.c

Merge branch 'master' into jed/chem
Note merging a branch with good stuff in it for a year and a half is insane!

Conflicts:
src/ts/examples/tutorials/makefile
src/ts/interface/ts.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c
src/sys/threadcomm/interface/threadcomm.c

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Merge branch 'master' into pr252/dmay/PetscViewerBinarySkipHeaderVecViewLoad
Manual merge of makefile

Conflicts:
src/sys/classes/viewer/examples/tutorials/makefile

Merge branch 'barry/remove-unneeded-paren-petscmalloc'

Conflicts:
src/mat/impls/baij/seq/baij.c

Merge branch 'master' into mlange/refactor-plex-distribute

Conflicts:
src/dm/impls/plex/examples/tests/output/ex12_1.out
src/dm/impls/plex/examples/tests/output/ex12_2.out

convert some PetscMalloc() to PetscMalloc1()
remove unneeded () in first argument to PetscMalloc/Calloc1()
fixes for MATLAB examples

Merge branch 'shri/clone-dmnetwork'

DMNetwork: Added clone method for DMNetwork

Merge branch 'master' into knepley/fix-plex-examples-refinement

* master: (62 commits)
Plex+Label: Fix logic for label distribution - It is restrictive now, but doing it right would mean a ton of

Merge branch 'master' into knepley/fix-plex-examples-refinement

* master: (62 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+Label: Set default output flag to PETSC_TRUE
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 bad search and replace
Configure: Fix for Barry's change to organization - I do not know what happened here
Builder: Fix for Barry's change
...

Conflicts:
src/snes/examples/tutorials/ex12.c

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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-partitioner-shell' into mlange/feature-parallel-distribute

* knepley/feature-plex-partitioner-shell:
Plex: Cleanup of examples to use new interfaces
Plex: Adde

Merge branch 'knepley/feature-plex-partitioner-shell' into mlange/feature-parallel-distribute

* 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

Conflicts:
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/plexdistribute.c

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Plex: Remove superfluous argument from DMPlexDisitrbute()

Merge branch 'shri/rename-dmcircuit-to-dmnetwork'

DMCircuit: Use PetscMalloc1() instead of PetscMalloc()

DMCircuit: Finished renaming DMCircuit to DMNetwork