Merge branch 'barry/2022-08-21/clang-format-source' into 'main'

format repository with clang-format

See merge request petsc/petsc!5541

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

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/2022-02-23/variadic-chkerr' into 'main'

Variadic CHKERRQ()

See merge request petsc/petsc!4889

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 'jacobf/2021-11-02/attribute-format-sys' into 'main'

Feature: PETSC_ATTRIBUTE_FORMAT - sys

See merge request petsc/petsc!4520

apply PETSC_ATTRIBUTE_FORMAT and related fixes to sys sources

Merge branch 'jacobf/2021-09-16/petscstack-on-the-stack' into 'main'

Move PetscStack onto the stack

See merge request petsc/petsc!4321

PetscStack is on the stack now, removing the need to 'initialize' it so it can always be
used. The entire API has also been intern'ed since it is only internally used in select
instances.

Merge remote-tracking branch 'origin/jose/fix-manpages'

Fix manpages to avoid errors reported by doctext

See merge request petsc/petsc!4309

Fix manpages: Argument --> Parameter (required to enable sowing checks)

Merge remote-tracking branch 'origin/balay/add-valgrind.h'

valgrind.h: add to petsc repo

See merge request petsc/petsc!4094

valgrind.h: add to petsc at include/private/valgrind

Merge branch 'stefanozampini/update-checkbadsource' into 'main'

Update badsource rules

See merge request petsc/petsc!4064

Update badsource rules

- Zero or more spaces are not allowed for more returning types
- zero spaces not allowed for for|if|while

Merge branch 'barry/2020-09-23/gpu-resource-error' into 'master'

Add specific PETSc error flag for GPU not having resources available

See merge request petsc/petsc!3241

Add specific PETSc error flag for GPU not having resources available

Try three times to initialize CUDA/cuBLAS and cuSPARSE before erroring. This is for GPU tests that sometimes fail since the GPU
i

Add specific PETSc error flag for GPU not having resources available

Try three times to initialize CUDA/cuBLAS and cuSPARSE before erroring. This is for GPU tests that sometimes fail since the GPU
is busy with other tests when a new test is started.

Commit-type: error-checking, testing
/spend 1h

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Merge branch 'jczhang/add-kokkos-init' into 'master'

Add Kokkos initialization

See merge request petsc/petsc!3048

Add support of CUDA/HIP initialization at the same time

Merge branch 'jczhang/feature-delay-cuda-init' into 'master'

Do not init cuda if a code does not create any petsc cuda objects

See merge request petsc/petsc!2987

Do lazy petsc cuda initialization and validation

So that we can avoid overburdening the GPU in CI.
See more at https://gitlab.com/petsc/petsc/-/issues/360#note_373723821

Merge remote-tracking branch 'origin/jczhang/feature-sf-pack-direct'

Directly pass root/leafdata to MPI in SF when possible

See merge request petsc/petsc!2506