clang-format: convert PETSc sources to comply with clang-format

Merge branch 'barry/2022-06-28/add-petsccallmethod' into 'main'

Introduce PetscTryTypeMethod and PetscUseTypeMethod to replace ad hoc use of (*obj->ops->method) in source

See merge request petsc/

Merge branch 'barry/2022-06-28/add-petsccallmethod' into 'main'

Introduce PetscTryTypeMethod and PetscUseTypeMethod to replace ad hoc use of (*obj->ops->method) in source

See merge request petsc/petsc!5376

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Convert setfromoptions methods over to PetscTryTypeMethod() approach

Flipped the order of the arguments for the function pointers (*setfromoptions)(PetscOptionItem*,obj); and friends to make them co

Convert setfromoptions methods over to PetscTryTypeMethod() approach

Flipped the order of the arguments for the function pointers (*setfromoptions)(PetscOptionItem*,obj); and friends to make them consistent with PetscTryTypeMethod() and all the other methods

Commit-type: refactorization
/spend 4h

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Merge branch 'psanan/docs-sphinx-man-pages' into 'main'

Integrate Man Pages into Sphinx Docs

Closes #1132 and #1015

See merge request petsc/petsc!4989

Docs: bulk add backticks to .seealso man page fields

```python
import os
import re
import fileinput

def _process_word(word):
comma = "," if word.endswith(",") else ""
return "`%s`%s" % (wor

Docs: bulk add backticks to .seealso man page fields

```python
import os
import re
import fileinput

def _process_word(word):
comma = "," if word.endswith(",") else ""
return "`%s`%s" % (word.rstrip(","), comma)

def _process_stripped_line(line):
return " ".join(map(_process_word, line.split()))

start_pattern = re.compile(r"^( *\.seealso:? )(.*$)")

def process_file(filename_full):
with fileinput.FileInput(filename_full, inplace=True) as f:
in_block = False
for line in f:
line_stripped = line.strip()
# end ".seealso blocks" on a blank line or C-style comment close
line_modified = None
if not line_stripped:
in_block = False
elif line_stripped.endswith("*/"):
in_block = False
else:
match = re.match(start_pattern,
line) # not stripped line
if match:
indent = " " * len(match.group(1))
in_block = True
line_modified = match.group(
1) + _process_stripped_line(
match.group(2).strip())
elif in_block:
line_modified = indent + _process_stripped_line(
line_stripped)
if line_modified:
print(line_modified) # prints to the file
else:
print(line, end="") # prints to the file

BASE_DIRS = ["src", "include"]
EXT = [".c", ".cxx", ".cpp", ".cu", ".h", ".hpp", ".hxx"]
EXCLUDE_DIRS = ["tests", "tutorials", "ftn-auto", "ftn-custom", "benchmarks"]

def main():
""" Process everything """
for base in BASE_DIRS:
for root, dirs, files in os.walk(base):
for filename in files:
if os.path.splitext(filename)[1] in EXT:
filename_full = os.path.join(root, filename)
print("FILE ---", filename_full)
process_file(filename_full)
for exclude_dir in EXCLUDE_DIRS:
if exclude_dir in dirs:
dirs.remove(exclude_dir)

if __name__ == "__main__":
main()
```

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Merge branch 'jacobf/2022-04-05/petscattrformat-all-the-rest' into 'main'

Enable PETSC_ATTRIBUTE_FORMAT()

See merge request petsc/petsc!5085

Enable PETSC_ATTRIBUTE_FORMAT()

Merge branch 'barry/2022-04-01/fix-petsc-options-begin-end/release' into 'main'

Remove bogus error returns from Begin/End() macros

See merge request petsc/petsc!5069

Cleanup of introduction of PetscCall()

* remove bogus error flags from XXXBegin()/End() macros such as PetscOptionsBegin()/End()

* rename for consistency certain XXXBegin()/End() macros such as Mat

Cleanup of introduction of PetscCall()

* remove bogus error flags from XXXBegin()/End() macros such as PetscOptionsBegin()/End()

* rename for consistency certain XXXBegin()/End() macros such as MatPreallocateInitialize()/Finalize()

* fix many lingering ierr = XXX that arose from multiline function calls

* sync slepc/hpddm - to use snapshots with the same changes

Commit-type: error-checking, style-fix
/spend 8h

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Merge branch 'jacobf/2022-02-23/variadic-chkerr' into 'main'

Variadic CHKERRQ()

See merge request petsc/petsc!4889

The great renaming:

- CHKERRQ() -> PetscCall()
- CHKERRV() -> PetscCallVoid()
- CHKERRMPI() -> PetscCallMPI()
- CHKERRABORT() -> PetscCallAbort()
- CHKERRCONTINUE() -> PetscCallContinue()
- CHKERRXX

The great renaming:

- CHKERRQ() -> PetscCall()
- CHKERRV() -> PetscCallVoid()
- CHKERRMPI() -> PetscCallMPI()
- CHKERRABORT() -> PetscCallAbort()
- CHKERRCONTINUE() -> PetscCallContinue()
- CHKERRXX() -> PetscCallThrow()
- CHKERRCXX() -> PetscCallCXX()
- CHKERRCUDA() -> PetscCallCUDA()
- CHKERRCUBLAS() -> PetscCallCUBLAS()
- CHKERRCUSPARSE() -> PetscCallCUSPARSE()
- CHKERRCUSOLVER() -> PetscCallCUSOLVER()
- CHKERRCUFFT() -> PetscCallCUFFT()
- CHKERRCURAND() -> PetscCallCURAND()
- CHKERRHIP() -> PetscCallHIP()
- CHKERRHIPBLAS() -> PetscCallHIPBLAS()
- CHKERRHIPSOLVER() -> PetscCallHIPSOLVER()
- CHKERRQ_CEED() -> PetscCallCEED()
- CHKERR_FORTRAN_VOID_FUNCTION() -> PetscCallFortranVoidFunction()
- CHKERRMKL() -> PetscCallMKL()
- CHKERRMMG() -> PetscCallMMG()
- CHKERRMMG_NONSTANDARD() -> PetscCallMMG_NONSTANDARD()
- CHKERRCGNS() -> PetscCallCGNS()
- CHKERRPTSCOTCH() -> PetscCallPTSCOTCH()
- CHKERRSTR() -> PetscCallSTR()
- CHKERRTC() -> PetscCallTC()

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chkerr and friends wrapped

Merge branch 'jacobf/2022-01-05/c99' into 'main'

Feature: C99 and C++11

See merge request petsc/petsc!4700

SETERRQ[1-9]+ begone

Merge branch 'barry/2021-05-16/fix-double-lines' into 'main'

Fix typos in source

See merge request petsc/petsc!3984

Remove all double blank lines from source

Commit-type: petsc-style
/2h

Merge branch 'knepley/is-separate-section' into 'master'

Knepley/is separate section

See merge request petsc/petsc!2065

Knepley/is separate section

Merge branch 'jed/deprecate-dmgetdefaultsection' [PR #1969]

* jed/deprecate-dmgetdefaultsection:
DMGetDefaultSection et al: add PETSC_DEPRECATED_FUNCTION
These functions were deprecated in v3.9, but

Merge branch 'jed/deprecate-dmgetdefaultsection' [PR #1969]

* jed/deprecate-dmgetdefaultsection:
DMGetDefaultSection et al: add PETSC_DEPRECATED_FUNCTION
These functions were deprecated in v3.9, but no PETSC_DEPRECATED_FUNCTION was added at that time so many uses crept back into the source code. Here we mark it deprecated and fix all existing uses in PETSc.

DMGetLocalSection/DMSetLocalSection: add explicit names for DMGetSection/DMSetSection
These names are for symmetry with DMGetLocalVector() versus DMGetGlobalVector().

DMGetSection: replace all internal usage with DMGetLocalSection
Same for DMSetSection -> DMSetLocalSection. We retain the interface for DMGetSection/DMSetSection without deprecation warnings (for now).

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DMGetSection: replace all internal usage with DMGetLocalSection

Same for DMSetSection -> DMSetLocalSection. We retain the interface
for DMGetSection/DMSetSection without deprecation warnings (for n

DMGetSection: replace all internal usage with DMGetLocalSection

Same for DMSetSection -> DMSetLocalSection. We retain the interface
for DMGetSection/DMSetSection without deprecation warnings (for now).

Suggested-by: Barry Smith <bsmith@mcs.anl.gov>

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Merge from master

Merged petsc/petsc into master

Merge branch 'master' into knepley/fix-superdm-is

* master: (455 commits)
bib: spell out some names for format consistency with related refs
bib: two 2018 pubs now appeared
cleaning up analyze

Merge branch 'master' into knepley/fix-superdm-is

* master: (455 commits)
bib: spell out some names for format consistency with related refs
bib: two 2018 pubs now appeared
cleaning up analyzer warnings
compile fixes (workarround PGI bug?):
undoing the branch's changes to leastsquares outputs
more fixes for complex builds
compile error fix for complex builds
1) Look for 64 bit integer MKL BLAS if 64 bit indices are used with PETSc 2) Fix Pardiso code to only compile pardiso_init64 when needed, otherwise can generate warnings/errors
jenkins: run 'cleantest' before 'allgtest-tap' - an attempt to fix errors of type:
cuda: protect cuda includes
fix cuda warnings.
fix complex compile error
Revert "Improved polymorphism of interfaces for MatSetValuesBlocked()"
Bib: Updated ref
Doc: More function documentation
petscvec: move PetscSFCreateFromZero from vscat to vec sources
Fixed an uninitialized variable and got rid of an unused one.
memleak fixed and output files updated
fixing build errors on some archs
Mat: obey options prefix of Mat in MatNullSpaceTest
...

Conflicts:
include/petsc/private/dmpleximpl.h
src/dm/interface/dmi.c

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

* master: (281 commits)
compile fixes (workarround PGI bug?):
1) Look for 64 bit integer MKL BLAS if 64 bit indices are used with PETSc 2) Fix

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

* master: (281 commits)
compile fixes (workarround PGI bug?):
1) Look for 64 bit integer MKL BLAS if 64 bit indices are used with PETSc 2) Fix Pardiso code to only compile pardiso_init64 when needed, otherwise can generate warnings/errors
jenkins: run 'cleantest' before 'allgtest-tap' - an attempt to fix errors of type:
cuda: protect cuda includes
fix cuda warnings.
fix complex compile error
Revert "Improved polymorphism of interfaces for MatSetValuesBlocked()"
Bib: Updated ref
Doc: More function documentation
petscvec: move PetscSFCreateFromZero from vscat to vec sources
Mat: obey options prefix of Mat in MatNullSpaceTest
Plex+SNES: Must pass user context through
vscat: move ftn-custom to correct location remove custom vecscatterdestroy_()
vscat: move interface routines to correct location
vscat: delete dead code
fix compile error
FE: Correct coordinates in IntegrateBd
Bib: Added refs
SNES ex17: 3D tests must require a 3D grid generator
Plex+TS: We cannot run the check with the same vector that is the TS solution
...

Conflicts:
include/petsc/private/dmpleximpl.h
src/docs/website/documentation/changes/dev.html
src/snes/examples/tutorials/ex13.c
src/snes/utils/dmplexsnes.c

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

* master: (249 commits)
Bib: Added refs
Netcdf should always build netcdf-4 (needed for example by exodusii.
trivial fixes of incor

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

* master: (249 commits)
Bib: Added refs
Netcdf should always build netcdf-4 (needed for example by exodusii.
trivial fixes of incorrect formatting in SNES linesearch routines
ISSetBlockSize_General: removed blockwise contiguity check.
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out
config prefix: avoid ad-hoc path substitutions
config/install: no need to rename paths for installBinDir
rules: fix path in (evidently unimportant) uncrustify target
config pkgconfig: use ${prefix} in PETSc.pc and do not modify in install
fix gcov obj path
Improved polymorphism of interfaces for MatSetValuesBlocked()
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Dev manual: remove duplicate entry
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
...

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