Fix up all manual pages in src/sys directory

Commit-type: documentation
/spend 10h

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 '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/2022-02-23/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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pluck ~1000 low hanging PetscCheckFalse() -> PetscCheck() fruit

chkerr and friends wrapped

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

Feature: C99 and C++11

See merge request petsc/petsc!4700

rename PetscAssert() -> PetscCheck() and PetscAssertDebug() -> PetscAssert()

add PetscAssert() and PetscAssertFalse()

SETERRQ[1-9]+ begone

Merge branch 'jacobf/2021-05-13/promote-petscrandom-headers' into 'main'

move petscrandom headers to include/petsc/private

See merge request petsc/petsc!3971

move petscrandom headers to include/petsc/private

Merge branch 'stefanozampini/feature-vecrandom-minmax-device' into 'master'

Support VecSetRandom and VecMin/Max for VECCUDA

See merge request petsc/petsc!3578

PetscRandom: add CURAND support

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 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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