Merge branch 'maint'

includes should always be included relative to include directory

Apple changed the location for DocSets

Commit-type: bug-fix, documentation

Merge branch 'master' into knepley/feature-pc-patch

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep us

Merge branch 'master' into knepley/feature-pc-patch

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep usage on solaris [use egrep]
opensolaris: fix errors
Update timer reporting and minor reporting fix
Remove redundant if statement. Found by @jedbrown
Fixed problem with order of developer photos on website.
superlu_dist: use correct flag in example [PETSC_HAVE_SUPERLU -> PETSC_HAVE_SUPERLU_DIST]
Bib: PERMON ref
fix for osx
doc: more author fixes
doc: more author fixes
Italicized "orderings" in MPI process placement discussion.
Added Richard to the user manual author list.
Added Richard to the list of active developers on the website.
add string check for MS-MPI and IMPI timeout errors
opensolaris does not have multiple grep utils - but default one does not support -F. So use fgrep instead
Standardizing timeout checks
Report wall clock time of total tests
Use time instead of date %s
...

Conflicts:
include/petscpc.h
src/ksp/ksp/interface/itfunc.c

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Merge branch 'psanan/dmswarm-namespacing' [PR #904]

* psanan/dmswarm-namespacing:
This attempts to namespace many of the internally-used components of DMSwarm.

DMSwarm: namespacing and symbol hiding

DataBucket --> DMSwarmDataBucket
DataEx --> DMSwarmDataEx
DataField --> DMSwarmDataField
DEObjectState --> DMSwarmDEObjectState
DATA_BUCKET_XXX --> DMSWARM_DAT

DMSwarm: namespacing and symbol hiding

DataBucket --> DMSwarmDataBucket
DataEx --> DMSwarmDataEx
DataField --> DMSwarmDataField
DEObjectState --> DMSwarmDEObjectState
DATA_BUCKET_XXX --> DMSWARM_DATA_BUCKET_XXX
DATAFIELD_XXX --> DMSWARM_DATAFIELD_XXX
StringInList/StringFindInList --> DMSwarmDataFieldStringInList/DMSwarmDataFieldStringFindInList
__DATATFIELD_XXX --> DMSWARM_DATAFIELD_XXX

Mark DMSwarmDataBucket and DMSwarmDataEx functions PETSC_INTERN

Update test output with new names DMSwarmDataEx and DMSwarmDataBucket

Fix alignment as needed, and perform other minor formatting fixes.

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Merge branch 'barry/add-ftn-linfinity-conv-test' of bitbucket.org:petsc/petsc into barry/add-ftn-linfinity-conv-test

Merge branch 'master' into scott/ksp-ksp-tutorials

Merge branch 'barry/all-new-test-harness-branches'

filter atomic size from swarm output because it depends on size of PetscInt

Commit-type: portability-fix, testing-fix
Reported-by: nightly builds

Converted a directory over to the new test harness

Includes adding missing tests and fixing the incorrect formating of several examples source code

Commit-type: testing-fix,style-fix,example

Merge remote-tracking branch 'origin/stefano_zampini/fix-dmwswarm-includes-andothers'

DMSwarm: remove unneded inclusion of petsc.h that was triggering recompilation when any of petscts.h etc was modified

Merge branch 'dmay/swarm-pic-tools-v3.8'

Fixed potential C89 compilation issues in code which might come into use upon user testing

Fixed C89 compilation errors (C++ comments, comma at end of enumerator)

http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2017/07/25/make_next_arch-linux-c89_el6.log

Fix conflict in makefile when merging dmay/swam-pic-tools into master

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
ini

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
initialize ap as complained by the nightly tests
Plex ex3: Update to new point function API
initialize some variables as complained by nightly tests
SNES ex12: Mix misnaming Nf --> Nc
update tests
add tests
add MatView_SeqXAIJ_ASCII_structonly(); enable A->structure_only in MatSetValuesBlocked_SeqBAIJ
typo
fill-in some references
Bib: Fixed ref
Plex: Added PLY to file support
Plex: Adding PLY support
PetscDS: Turn off Fortran bindings for Constants
Plex tests: Updated to new point function API
SNES ex56: Moved tests to new format
DM: Allow field projection functions to take an array of scalars - This will allow us to pass in user data to kernels without void *, more efficiency than aux fields
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tutorials/ex63.c

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SwarmPIC bug fixes:
* Must use a consistent comm on the pos vectors and the star forest object. Require PETSC_COMM_SELF for local point location

DMSwarm migrate:
* Initialise a cellSF with cell owners prior to calling the PointLocation method

DMSwarm migrate:
* Copy the values from the star-forest node list into the swarm field cellId.

DMSwarm migrate:
* Bug fix - require special removal stage in serial to delete points which left the domain

DMSwarm migrate: Updates for DMSwarmMigrate_CellDMScatter
* Removed the broken code
* Depreciated the variant which performs two full point locations on all npoints (before migration) and npoints+npo

DMSwarm migrate: Updates for DMSwarmMigrate_CellDMScatter
* Removed the broken code
* Depreciated the variant which performs two full point locations on all npoints (before migration) and npoints+npoints_recv (post migration)
* Added variant which performs point locations on all npoints (before migration) and then only on npoints_recv (post migration)

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DMSwarm/DataBucket:
* Add variable for using default buffer rather than putting in -1

Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes

Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
rename struct Mat_SubMat -> Mat_SubSppt
add a little information to the manual about using tchem
rename MatCreateSubMatrixComposite -> MatCreateSubMatrixVirtual; Mat_SubMatrix -> Mat_SubVirtual
need to protect the \ passed on the makefile on my Mac
Bib: Updated ref
update src/mat/examples/tests/output/ex23_#.out
rename MatGetSubMat -> MatCreateSubMat
Mark MatCreateMPIAIJWithSplitArrays() and MatMPIAIJSetPreallocationCSR() with MAT_NO_OFF_PROC_ENTRIES
superlu: libray is installed in PREFIX/lib64 - fix this to use PREFIX/lib
backport fixes cc105cc3 2b35c90a - required for 3bf428d - that was backported from master - 80c96bb
'echo -n' fails on opensolaris/osx - so avoid using it.
fix diffs in nightlybuilds due to options in ~/.petscrc
add Kelley03 to src/docs/tex/petsc.bib
build: determine moudles, mpi.h used during buildtime and print in 'info'
fix analyzer warnings
fix build failure on opensolaris - where -lm from flibs is removed due to -lm in cxxlibs. But then - only flib gets used for some configure tests [blaslapack, parms]
config: prefer __restrict over C99 restrict keyword
...

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Merge branch 'barry/remove-funct'