Merge branch 'barry/2020-06-08/fix-matlabengine-details' into 'master'

MacOS needs -Wl,-rpath for Matlab Engine; reorganize simplify MatlabEngine.py

See merge request petsc/petsc!2846

MacOS needs -Wl,-rpath for Matlab Engine; reorganize simplify MatlabEngine.py
Change --with-matlabengine-lib to --with-matlab-engine-lib to match --with-matlab-engine
Move Matlab vec test to tutorial

MacOS needs -Wl,-rpath for Matlab Engine; reorganize simplify MatlabEngine.py
Change --with-matlabengine-lib to --with-matlab-engine-lib to match --with-matlab-engine
Move Matlab vec test to tutorial directory
Add make check for Matlab engine

Commit-type: error-checking, bug-fix, portability-fix, testing-fix, style-fix

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Merge remote-tracking branch 'origin/maint'

Merge branch 'jose/maint/faster-html' into 'maint'

Faster generation of HTML pages for source code

See merge request petsc/petsc!2740

Faster generation of HTML pages for source code

A python replacement of `fixinclude` speeds up `make alldoc2` by a
factor of 10

docs: Keep epydoc support by invoking python2 interpreter

Merge remote-tracking branch 'origin/more-updates-for-missing-petsc_dir'

More support for not needing to set PETSC_DIR yet build with PETSc, also...

See merge request petsc/petsc!2626

build: add more support for not needing to set PETSC_DIR yet build with PETSc, also support for GNU make to directly use "make test" instead of "make -f gmakefile.test"

Still needs -include ../petsc

build: add more support for not needing to set PETSC_DIR yet build with PETSc, also support for GNU make to directly use "make test" instead of "make -f gmakefile.test"

Still needs -include ../petscdir.mk in many of the makefiles
Still needs the link for ../petscdir.mk in many directories

GNUMakefile: call legacy makefile recursively instead of including it

GNUMakefile: promote default "all" target; "libs" builds libpetsc*

GNUMakefile: If gnumake < 4.2 prefer makefile wrapper interface over direct gmakefile interface to avoid the following warnings

gmakefile.test:92: arch-ci-linux-cxx-cmplx-pkgs-64idx/tests/testfiles: No such file or directory
gmakefile:67: arch-ci-linux-cxx-cmplx-pkgs-64idx/lib/petsc/conf/files: No such file or directory

Commit-type: testing-fix, feature, usability
Thanks-to: Jed Brown jed@jedbrown.org

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Merge branch 'psanan/docs-sphinx-dev-manual' into 'master'

Add Sphinx docs and port Developers Manual

See merge request petsc/petsc!2598

Docs: remove LaTeX dev manual

Replace links to it to with links to
https://docs.petsc.org/en/latest/developers/index.html

Merge branch 'jed/promote-examples-tests-tutorials' [petsc/petsc!2610]

* jed/promote-examples-tests-tutorials:
Promote examples/{tests,tutorials}/ to {tests,tutorials}/

Promote examples/{tests,tutorials}/ to {tests,tutorials}/

This shortens paths and improves consistency between test target names
and paths to the source and output files. Most of the work was
compl

Promote examples/{tests,tutorials}/ to {tests,tutorials}/

This shortens paths and improves consistency between test target names
and paths to the source and output files. Most of the work was
completed by this script, followed by mild cleanup of nonconforming
cases.

for makefile in `git ls-files 'src/*makefile'`; do
if rg -q 'DIRS.*\bexamples\b' $makefile; then
base=$(dirname $makefile)
dirs=$(cd $base/examples && ls -d tests tutorials 2>/dev/null | xargs echo)
perl -pi -e "s#^(DIRS.*)\bexamples\b#\1${dirs}#" $makefile
git rm $base/examples/makefile
for t in $dirs; do
git mv $base/examples/$t $base/
perl -pi -e "s#^(LOCDIR[[:space:]]*=).*#\1 $base/$t/#" $base/$t
done
fi
done

git grep -l -E -z 'examples/(tutorials|tests)' | xargs -0 perl -pi -e 's#examples/(tutorials|tests)#\1#g'
git checkout @ \
src/docs/website/documentation/changes/ \
src/benchmarks/results/

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Merge branch 'barry/2019-12-14/AMReX' into 'master'

Add --download-amrex add example that tests PETSc with AMReX

See merge request petsc/petsc!2395

Add --download-amrex add example that tests PETSc with AMReX

Commit-type: feature, example
Funded-by: ECP
Project: PETSc-AMReX

Update cmake to 3.15.6 for amrex

Merge branch 'stefanozampini/fix-snescomposite-update' into 'master'

Fix update vector in SNESCOMPOSITE

See merge request petsc/petsc!2582

make allgtags: $PETSC_DIR/bin not present

Merge branch 'jolivet/feature-hpddm-cleanup' into 'master'

HPDDM cleanup

See merge request petsc/petsc!2434

General PETSc fixes

* make generatefortranstubs.py handle .cxx
* bump HPDDM version + minor hypre cleaning

Merge remote-tracking branch 'origin/maint'

Merge branch 'barry/2019-12-19/fix-makefile-compile-output' into 'master'

when clanguage=c++ 1) don't error printing mpi.h path 2) print proper C...

See merge request petsc/petsc!2409

when clanguage=c++ 1) don't error printing mpi.h path 2) print proper C compiler 3) print message indicating clanguage=c++

Commit-type: bug-fix, feature
Reported-by: Lisandro Dalcin <dalcinl@gmail.c

when clanguage=c++ 1) don't error printing mpi.h path 2) print proper C compiler 3) print message indicating clanguage=c++

Commit-type: bug-fix, feature
Reported-by: Lisandro Dalcin <dalcinl@gmail.com>

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Merge branch 'scott/ci-coverage-dev' into 'maint'

Improve coverage output

See merge request petsc/petsc!2328

Enable .post stage

For coverage analysis now, but could do other analysis

Merge branch 'stefanozampini/update-suitesparse' into 'master'

Update SuiteSparse to use github releases + fixes to SBAIJ hermitian complex case

See merge request petsc/petsc!2305

Add suitesparse to make check