Merge branch 'main' into 'main'

configure: switch hashlib usage from md5 to sha256

See merge request petsc/petsc!8943

configure: switch hashlib usage from md5 to sha256

and avoid "usedforsecurity = False" as its incompatible with Python <3.9.

Merge remote-tracking branch 'origin/release'

Merge branch 'jose/codespell-typos' into 'release'

A few more codespell fixes

See merge request petsc/petsc!5786

A few more codespell fixes

Merge branch 'balay/disable-python2' into 'main'

Balay/disable python2

See merge request petsc/petsc!5131

disable python2 support - now python3.4+ is required
- update CI tests to use python3
- continue to use python2 on MacOS CI [due to python3 issues on 10.15.7]

remove '#!' from non-stand-alone python sources

ci: fixes for vermin python syntax checker

vermin -vv --backport argparse -t=2.6- -t=3.4- config

Merge branch 'balay/ci-vermin/maint' into 'master'

Balay/ci vermin/maint

See merge request petsc/petsc!2686

ci: fixes for vermin python syntax checker

vermin -vv --backport argparse -t=2.6- -t=3.4- config

Merged petsc/petsc into master

Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merge branch 'master' into jpustay/feature-swarm-example

Merged petsc/petsc into master

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (393 commits)
Bib: Update reference
Mat: Doc fix
Bib: Updated ref
PetscDS: Doc fixes
PC+LU: Do not try to refactor an

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (393 commits)
Bib: Update reference
Mat: Doc fix
Bib: Updated ref
PetscDS: Doc fixes
PC+LU: Do not try to refactor an already factored matrix
Mat: Small fix for checking and docs
Mat: Added MatSetFactorType() - Needed it when making a shell matrix look factored
PetscDS: Added PetscDSUpdateBoundary() - Lets the user change the boundary condition
single precision produces different convergence history
p4est: has a dependency on zlib - so handle it correctly
Add -mat_mffd_complex to use the Lyness complex number trick to compute J_u * v instead of differencing.
Replace VecWAXPY by VecAXPY if needed
Revert "Replace VecWAXPY by VecAXPY if needed"
Replace VecWAXPY by VecAXPY if needed
MatHermitianTransposeGetMat and MatCreateVecs
ex19: Updated test filter to avoid false positives.
DM: Improved Global-To-Natural docs Suggested-by: Josh L <ysjosh.lo@gmail.com>
Do not build shared openblas when doing static build
Upgrade OpenBLAS to 0.3.3
test: add alt output file for changes in OSX-10.14 and Xcode-10.0 [perhaps related to ML]
...

Conflicts:
src/vec/is/utils/vsectionis.c

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Merge branch 'jed/python3-futurize' [PR #1122]

Merge announces support for Python 3.4+ in changes/dev.html.

* jed/python3-futurize: (44 commits)
gmakegentest: avoid prefix matching in regex
dm

Merge branch 'jed/python3-futurize' [PR #1122]

Merge announces support for Python 3.4+ in changes/dev.html.

* jed/python3-futurize: (44 commits)
gmakegentest: avoid prefix matching in regex
dm tests ex23.c: fix test args: -one -two -three
gmakegentest: more fixes
gmakegentest: fix processing of arguments containing number followed by "-"
gmakegentest: always loop over nsize; Python-3 fixes
python3: add in a python-3.4 test
python: fix build on osx/opensolaris - where 'RANLIB=ranlib -c' i.e with a space..
python3: fix --download-ptscotch error
configure: glob() gets executed early - whereas we need to get file list later [after 'make all' or equivalent] so revert back to using shell to get file-list
python3: map() requires a list modifier for this usage.
python: replace ModuleNotFoundError a python3.6+ feature with ImportError
config: call setup to ensure that debugLevel is set
nightlies: switch linux-pkg-dbg-ftn-interfaces to python3
config: enable Python-3
config: urllib/urlparse updates for Python-3 compatibility
config fblaslapack: use isIBM instead of manual test
python: replace commands with subprocess
Fix LOCDIR paths
generateetags.py: switch from commands to subprocess; unicode fix
python: don't import commands when it isn't used
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config: futurize filter()

Returns a list in Python-2, but a filter object in Python-3. There
are many places that test isinstance(f, list) to distinguish strings
from lists, but a filter object beh

config: futurize filter()

Returns a list in Python-2, but a filter object in Python-3. There
are many places that test isinstance(f, list) to distinguish strings
from lists, but a filter object behaves like a list for most purposes.

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python: check for attr close to identify files

Python-3 files are not nicely identified by inheriting from a public
file object. Probably better in the long run to make the interface
clear about wh

python: check for attr close to identify files

Python-3 files are not nicely identified by inheriting from a public
file object. Probably better in the long run to make the interface
clear about what is being passed, e.g., by a keyword argument. But
for now, just change the test to work with both Python-2 and Python-3.

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config: use open() instead of file() to open files

This is the recommended usage and file is not defined in Python-3.

config: use pickle instead of cPickle for Python-3 compatibility

The performance benefits of cPickle are not significant for our usage,
so not worth selecting dynamically. (Note that pickle in Pyth

config: use pickle instead of cPickle for Python-3 compatibility

The performance benefits of cPickle are not significant for our usage,
so not worth selecting dynamically. (Note that pickle in Python-3 is
fast.)

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Merge branch 'master' into knepley/feature-plex-elasticity-test

* master: (1553 commits)
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
config

Merge branch 'master' into knepley/feature-plex-elasticity-test

* master: (1553 commits)
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Plex test ex5: Removed "future" test, as it resulted in issues in the nightly tests.
Some minor typos in TS
Add ADIOS2.py which I forgot to git add in the past
Plex ex5: Disable test
Doc: Added note for interface change
KSPLSQRMonitorDefault fixed for quad precision
Tao: Added alternative output for chwirut2 test.
TS ex45,ex46: Removed overly refined tests for faster nightly tests.
KSP ex72: Fixed needlessly long-running PCTFS tests.
SNES ex56: Reduced test size to speed up nightly test suite.
KSPSolve_LSQR: don't compute unused norm of rhs
SNES ex13: Reduced problem sizes for nightly tests.
PetscOptionsDeprecated(): fix for NULL prefix
PetscOptionsDeprecated(): add option to print additional info
SNES ex12: Reduced sizes for BDDC tests.
PetscFileRetrieve(): Suppress output to STDERR when downloading a file.
MatMatMult: Fixed unused variable pN.
DMDestroy: Guard call to dm->ops->destroy * Similar guards are in place in many other methods (IS,Vec,Mat) and permit the DM to be destroyed even if DMSetType() was never called.
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Merge branch 'master' into knepley/feature-plex-parallel-submesh

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComp

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

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComplex type is missing from fortran
initialize variables so that static analyzer doesn't mistakenly think they are used uninitialized.
Move access of prefix until it is actually used
Remove DMDASplitComm2d(), used in one example that was not tested
Functions that do not return PetscErrorCode should not use PetscFunctionBegin/End paradgm
remove unneeded reassignment of same value
Missing CHKERRQ(); Mostly in Tao code
Remove clang static analyser warning about passing NULL variable to strncat()
missing newline in -ts_monitor_extreme
minor fixes for integer counters
Configure: Deal with '__func__' in C89 builds with newer Clang and GCC.
Jenkinsfile: Increased timeout for tests to 5 minutes.
3.9 changes: further clarify removal of -pc_factor_mat_solver_package
Options deprecations: add "PETSc" to inline warning
removing unused variable
MatShift support added to MATSUBMAT. Mimics MATSHELL functionality. Needed for matrix-free Hessians in TAO Newton-Line-Search methods.
Add -ts_monitor_extreme
Dev manual: add note on deprecating options database keys
...

Conflicts:
src/dm/impls/plex/examples/tests/ex4.c

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Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead

Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead code.
Add JuMP citation
Copyedits and updates to developers manual
Add more protection to intrinsics
MPI: protect arguments in MPI macros
Add the missing conditionals for 64-bit build
Plex+VTK: Fix field type determination
Fix bug in name cleanup
Bib: Added ref
Plex+VTK: Fix field type determination
Plex: Updated test output - I am now hating this shit
forgot to save file after moving prototypes to petscsys.h
update Apple example project settings per Xcode
Two functions should actually be public, used, for example from Apple MacOS and iOS programs
includes should always be included relative to include directory
Apple removed old locations of docsets
SNES ex12: Updated test output
...

Conflicts:
src/snes/examples/tutorials/ex13.c

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Merge branch 'master' into knepley/fix-plex-residual-loop
Warning: This merge includes real changes

* master: (188 commits)
Add JuMP citation
Copyedits and updates to developers manual
Add mor

Merge branch 'master' into knepley/fix-plex-residual-loop
Warning: This merge includes real changes

* master: (188 commits)
Add JuMP citation
Copyedits and updates to developers manual
Add more protection to intrinsics
MPI: protect arguments in MPI macros
Add the missing conditionals for 64-bit build
Plex+VTK: Fix field type determination
Fix bug in name cleanup
Bib: Added ref
Plex+VTK: Fix field type determination
Plex: Updated test output - I am now hating this shit
forgot to save file after moving prototypes to petscsys.h
update Apple example project settings per Xcode
Two functions should actually be public, used, for example from Apple MacOS and iOS programs
includes should always be included relative to include directory
Apple removed old locations of docsets
SNES ex12: Updated test output
SNES ex62: Set name of solution vector - Update test output
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
move output file to the correct location. i.e fix 305862f9cd0dc399542ae11dd744508e4b6ad2e3
...

Conflicts:
src/snes/utils/dmplexsnes.c
src/ts/utils/dmplexts.c

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