source code format changes due to .clang-format changes

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

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/2021-03-26/clang-static-linter' into 'main'

Feature: libClang PETSc Macro Static Analyzer

See merge request petsc/petsc!3773

Linter using libClang that checks PetscValidHeaderSpecifcType, PetscValidHeaderSpecific, PetscValidHeader, PetscValid[XXX]Pointer, PetscValidType, PetscCheckSameComm, PetscValidLogicalCollectiveXXX f

Linter using libClang that checks PetscValidHeaderSpecifcType, PetscValidHeaderSpecific, PetscValidHeader, PetscValid[XXX]Pointer, PetscValidType, PetscCheckSameComm, PetscValidLogicalCollectiveXXX for validity. Automatically generates diff files for problems with a known solution.

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Merge branch 'barry/2020-09-07/matstructure-unknown' into 'master'

Barry/2020 09 07/matstructure unknown

See merge request petsc/petsc!3182

Introduce UNKNOW_NONZERO_PATTERN for MatAXPY() make it the default for TS when using both IJacobian and RHSJacobian

Provide TSSetMatStructure() to allows users to indicate the nonzero structure rela

Introduce UNKNOW_NONZERO_PATTERN for MatAXPY() make it the default for TS when using both IJacobian and RHSJacobian

Provide TSSetMatStructure() to allows users to indicate the nonzero structure relationship between the RHS and I Jacobian

When the RHS Jacobian matrix is not set and is obtained with a MatDuplicate() from the I Jacobian set the flag to SAME_NONZERO_PATTERN

Add MatStructures and update SLEPc to compile with no warning message after the new MatStructure MAT_UNKNOWN_PATTERN was introduced

Commit-type: optimization
/spend 25m
Thanks-to: Ed Buler

/spend 35m

Update SLEPc branch to support new enum type

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Merge remote-tracking branch 'origin/dalcinl/fix-null'

TS/SNES/Tao: Fix 0 ->NULL for pointers

See merge request petsc/petsc!2783

TS: Replace 0 -> NULL for pointers

Merge branch 'master' of gitlab.com:petsc/petsc

Merge branch 'hongzh/fix-ex20opt-p' into 'master'

Fix a bug in ex20opt_p

See merge request petsc/petsc!2077

Fix wrong error message

Also add convergence check for TSForwardStep

Funded-by:
Project: FASTMath adjoint
Time: 1.0 hours
Reported-by:
Thanks-to:

Merge branch 'master' into 'barry/2019-08-22/fix-fblaslapack-for-nag'

# Conflicts:
# lib/petsc/conf/test

Merge branch 'barry/2019-09-08/fix-tsconvergedreason' into 'master'

Barry/2019 09 08/fix tsconvergedreason

See merge request petsc/petsc!2025

TSConvergedReasons[] was not correctly updated when TSConvergedReason add new values added

Commit-type: bug-fix
Reported-by: gitlab-ci

Merged in barry/update-collective-on (pull request #1744)

Update the use of Collective on in the manual pages to reflect the new style

Update the use of Collective on in the manual pages to reflect the new style

Commit-type: style-fix, documentation
Thanks-to: Patrick Sanan <patrick.sanan@gmail.com>

Merged in psanan/man-pages-remove-keywords (pull request #1717)

Man pages: Remove .keywords fields

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be unif

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be uniformly used or maintained.

Thus, remove all .keywords: fields, and a following blank line, if present.

This is accomplished with GNU sed (gsed on OS X), with the following commands.
*Warning* that this type of command can corrupt a .git directory,
so be cautious in reusing or modifying these commands. They first look
for and delete matching lines with a following line consisting of only whitespace,
and then delete any remaining matching lines.

find src/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find src/ -type f -exec gsed -i '/keywords:/d' {} +
find include/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find include/ -type f -exec gsed -i '/keywords:/d' {} +

Hints on the sed command obtained from: https://unix.stackexchange.com/questions/100754/how-to-delete-a-specific-line-and-the-following-blank-line-using-gnu-sed

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Merge from master