Finished converting DMDALocalToLocalBegin()/End() to internal functions (DMLocalToLocalBegin()/End() should now be used) and deprecated this interface.

Merged petsc/petsc into rmills/petsc master.

Merge branch 'barry/fix-docs-regarding-xxxtype'

Removed the ability of XXXType to be the string name of a library and function in that library but forgot to remove this form from all the XXXAType manual pages

DMInterpolation: Fixed declarations

DMInterpolation: Fixed declarations

DMMesh: Removed all trace and salted the earth, Carthago delenda est!

Merge branch 'barry/fix-xxxviewsetfromoptions'

* barry/fix-xxxviewsetfromoptions:
*ViewFromOptions: update documentation, providing disabled man pages
fixed bug where XXXViewFromOptions() used p

Merge branch 'barry/fix-xxxviewsetfromoptions'

* barry/fix-xxxviewsetfromoptions:
*ViewFromOptions: update documentation, providing disabled man pages
fixed bug where XXXViewFromOptions() used prefix of object rather than appropriate prefix of KSP or SNES

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fixed bug where XXXViewFromOptions() used prefix of object rather than appropriate prefix of KSP or SNES

Merge branch 'knepley/plex'

Improved support for discretizing PDEs. Cell geometry and FVM. Little to
no topology.

* knepley/plex:
SNES ex12: Fix leak
TS ex11: error if dim != DIM because memory

Merge branch 'knepley/plex'

Improved support for discretizing PDEs. Cell geometry and FVM. Little to
no topology.

* knepley/plex:
SNES ex12: Fix leak
TS ex11: error if dim != DIM because memory corruption occurs otherwise
DMPlex: All quadrilateral geometry tests working
DMPlex: remove unused variable
DMPlex: Hexahedron geometry tests now pass
DMPlex: More geometry work
DMPlex: use PETSC_HAVE_TGAMMA to get the build working on windows
configure: add test for tgamma() [this is missing on windows]
DMPlex: Added random transform tests for tets - Fixed memory leak
DMPlex: Fixed 3D geometry
DMPlex: FVM geometry tests now work for triangles
DMPlex: one more win32/complex fix
DMPlex: Enhanced geometry tests - Added random transforms of the reference triangle in 2D
DMPlex: Fixed complex problems in geometry calculation
DMPlex: Fixed Fortran test output
DMDT: M_PI --> PETSC_PI
DMPlex: Reorganized geometry testing
TS ex11: Put in 3D inflow and outflow ids from the command line
DMPlex: Added DMPlexRestoreCone/Support() to F90 interface definition header - Also added to test ex1f90
TS ex11: Need to make these ids input from the command line
DMPlex: Add Fortran bindings
DMPlex: Reorder tet output since I order tets differently
Builder: Link Fortran examples with Fortran linker
DMPlex: Fixed leak in example
DMPlex: Tutorial now shows how to output VTK
PetscViewer: Added VTK type for Fortran
DMPlex: Remove parameter names from prototype
DMPlex: Geometry fixes for C++ complex
DMAKKT: Remove from build
DMPlex: Now DMPlexCreateSection() only has an F90 interface
SNES: add Fortran bindings to DMSNESSet{Function,Jacobian}
SNES: remove superfluous casting in DM local Fortran bindings
SNES: compile zdmlocalsnesf.c
DMDT: Fix Fortran wrapper
DMPlex: Added Fortran interface for DMPlexMatSetClosure()
PetscSection: Added docs, enabled Fortran wrappers
DM: Added Fortran bindings for DMSNESSetFunction/JacobianLocal()
SNES ex12: Looks like 3D Neumann conditions are working
DMPlex: Fix volume determination for 2D in 3D
DMPlex: Better error reporting
SNES ex12: Boundary integration seems to work in 2D
DMPlex+FEM: Fix for boundary integration
TS ex11: Better error reporting
DMPlex ex8: Added FVM geometry tests
DMPlex: Fixed FVM geometry for 2D in 3D
SNES ex62: Now using PetscDT quadrature
DMDT: Translated FIAT's Gauss-Jacobi quadrature
DMPlex: Fix geometry tests - Fix tests for 2D projection
DMPlex: Geometry fixes
DMPlex: Small fixes for geometry
DMPlex: Fixed damn prototype
PetscSection: Added VecSetValuesSectionF90() - Fixed bug in Vec Fortran header
DMPlex: Added Fortran defines for additional insert modes
DMPlex: Silence warning in DMPlexInvertCells_Internal()
DMPlex: Functions passed to evaluation routines now return void and pass results in arguments
DMPlex: Now we give an explicit embedding dimension to the FVM geometry methods
DMPlex: Fixed complication with complex - Started to add 3D geometry stuff
TS ex11: Replace edge geometry with call to DMPlexComputeCellGeometryFVM()
DMPlex: Added normal argument to DMPlexComputeCellGeometryFVM() - This is only calculated for faces - Added calculation for faces in 2D
DMPlex: Damn makefiles
DMPlex: Added declaration for DMPlexCreateCGNS()
TS ex11: Reorganized computation of geometry in preparation for 3D
Builder: Now individual tests can have requirements - The key is 'requires', and it takes a list of package names - Also fixed up showSingleRun()
TS ex11: Use new DMPlexComputeCellGeometryFVM()
DMPlex: Added DMPlexComputeCellGeometryFVM() - Added internal volume methods
DMPlex: fix const and int vs. PetscInt
DMPlex: Better error reporting
DMPlex+ExodusII: Fixed reading of quads - Was broken by 2e1b13c25062c3c40593ce7412c5cd227259ade7
DMPlex: Hex cell geometry was broken - I don't see how this test passed before
DMPlex: Regression cleanup
DMPlex: Regression cleanup
SNES ex12: Fixed sign for Neumann BC
DMPlex+FEM: The dimension does not change for boundary elements
DMPlex: Geometry now works for boundary elements
DMPlex+FEM: Fixed quadrature coordinate handling for boundary integrals
SNES ex12: Reorganized tests, still working on Neumann conditions - Fixed boundary face label
DMPlex: Turn off CGNS by default
DMPlex: Added 1D cell geometry
DMPlex: DMPlexCreateCGNS()
DMPlex: Updated test ex1 output
DMPlex: Fixed compiler problems with complex
SNES ex12: Now does boundary integration - Still not verifying exact solution for Neumann conditions
DMPlex: Fix DMPlexComputeCellGeometry() to handle lower dimensional cells
DMPlex: Fixed error in projection from 3D to 2D - Need to check for case where normal is already z
DMPlex: Adding boundary integration
DMPlex: Fixed cell inversion for TetGen to commute with mesh interpolation
SNES ex12: Cleaning up ex12 testing
DMPlex: Added integration over boundary to DMPlexComputeResidualFEM() - Added quadBd, f0/1BdFuncs to PetscFEM struct - Needs to be tested
FEM Generation: We now allow a *_bd.h header that holds boundary discreization
Builder: Fixed regression requirements
Builder: Fixed specification of multiple tests to run
DMPlex ex7: Orientations now working properly
DMPlex: Changed orientation convention and fixed many bugs
SNEX ex12: Ignore generated headers
SNEX ex12 and ex52: Remove CTetGen warnings from test output - Fixed this in CTetGen repository
DMPlex: Fix default |J| for DMPlexComputeCellGeometry()
DMPlex: Fix for cell geometry (unbelievable screwup)
DMPlex ex7: Check that |J| is nonzero for each cell in interpolated mesh
DMPlex: Allow DMPlexComputeCellGeometry() to work with interpolated meshes
DMPlex: Added prototype for DMPlexCopyCoordinates(), and docs for that and DMPlexInterpolate()
DMPlex: Added F90 interface for DMPlexComputeCellGeometry()

Conflicts:
include/petscdmplex.h

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Merge bug fix/patch releases up to 3.2-p7 into maint-3.2

* commit 'a9157d915ed96804280c3dc077186a2a633fd603': (157 commits)
Fix PyPI download URL to help pip figure out the release version
#1109

Merge bug fix/patch releases up to 3.2-p7 into maint-3.2

* commit 'a9157d915ed96804280c3dc077186a2a633fd603': (157 commits)
Fix PyPI download URL to help pip figure out the release version
#110990 fix timestamp order for .so vs .a during 'make install'
Update FFTW download
Increase patchlevel to 3.2-p7
...

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Merge branch 'karpeev/dm-rmakkt'

Idea abandoned in favor of implementing at PCGAMG level rather than in DM.

* karpeev/dm-rmakkt:
DMAKKT: remove name macro
Removed DMAKKT source.

DMAKKT: remove name macro

DMPlex: Fixed damn prototype

Merged petsc/petsc into rmills/petsc master

Merge branch 'barry/rm-xxxregisterdynamic'

* barry/rm-xxxregisterdynamic:
Registration: remove stale 'XXRegisterDynamic)' entries in man pages
TS examples: fix use of PetscFunctionList and add t

Merge branch 'barry/rm-xxxregisterdynamic'

* barry/rm-xxxregisterdynamic:
Registration: remove stale 'XXRegisterDynamic)' entries in man pages
TS examples: fix use of PetscFunctionList and add to nightlies
Changes: Note updates to XRegisterDynamic/PetscObjectComposeFunctionDynamic
PetscObjectComposeFunctionDynamic: remove stale docs and usage
developers.tex: remove complications from function composition with dlls
removed string version of function name for XXXRegister(), PetscFunctionListAdd() and PetscObjectComposeFunction()
changes: document PetscFunctionListAdd() API change
developers.tex: update documentation of PetscObjectComposeFunction
removed path and MPI_Comm arguments from PetscFunctionListFind/Add()
removed path argument to XXXInitializePackage() and XXXRegister()
removed XXXRegisterDynamic() but kept the APIs for everything else underneath the same phase I of the update to handling registering function pointers

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Merge branch 'tautges/dmmoab'

* 'tautges/dmmoab'
DMMoab: Remove OBJSC from makefile
TS ex30.cxx: write output file matching example number (ex30-final.h5m)
DMMoab: alltest run TS ex30
DMMoab

Merge branch 'tautges/dmmoab'

* 'tautges/dmmoab'
DMMoab: Remove OBJSC from makefile
TS ex30.cxx: write output file matching example number (ex30-final.h5m)
DMMoab: alltest run TS ex30
DMMoab: ops pointers initialized in DMCreate_Moab
DMMoab: fix test example makefile
DMMoab: close memory leaks by explicitly calling C++ destructors
DMMoab: interface does not require that all of PETSc be built using C++
DMMoab: include <sstream> to use ostringstream
DMMoab: do not mix CHKERRXX() with CHKERRQ()
Fixing uninitialized memory, and adding output.
Fixing compile error in dmmoab.
Changes suggested by Jed and Barry.
Changes suggested by Matt in pull request.
Adding DMMoab and VecMoab, along with various examples and tests.

Conflicts:
src/ts/examples/tutorials/makefile

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Merge branch 'barry/rm-xxxregisterdynamic' into jed/ts-eimex

PetscObjectComposeFunctionDynamic() and TSRegisterDynamic() were
replaced by PetscObjectComposeFunction() and TSRegister(), both of which

Merge branch 'barry/rm-xxxregisterdynamic' into jed/ts-eimex

PetscObjectComposeFunctionDynamic() and TSRegisterDynamic() were
replaced by PetscObjectComposeFunction() and TSRegister(), both of which
drop the string name argument.

* barry/rm-xxxregisterdynamic: (82 commits)
...

Conflicts:
src/ts/interface/tsregall.c

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removed string version of function name for XXXRegister(), PetscFunctionListAdd() and PetscObjectComposeFunction()

removed path argument to XXXInitializePackage() and XXXRegister()

removed XXXRegisterDynamic() but kept the APIs for everything else underneath the same
phase I of the update to handling registering function pointers

Merge branch 'knepley/plex-surface-integration' into knepley/plex

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic b

Merge branch 'knepley/plex-surface-integration' into knepley/plex

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

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DMPlex: Added integration over boundary to DMPlexComputeResidualFEM()
- Added quadBd, f0/1BdFuncs to PetscFEM struct
- Needs to be tested

Merge branch 'master' into jed/ts-eimex

Sync to include Git conversion, PETSC_EXTERN, and minor API changes.

Conflicts:
src/ts/interface/tsregall.c

Adding DMMoab and VecMoab, along with various examples and tests.