Merge branch 'jacobf/2022-09-17/slimmer-petscobject' into 'main'

Feature: Slimmer PetscObject

See merge request petsc/petsc!5649

Remove parent, parentid, flops, time, mem, and memchildren. Deprecate PetscLogObjectParent(), PetscLogObjectMemory(), and PetscNewLog()

Merge branch 'barry/2022-08-23/fix-sys-man' into 'main'

Fix up all manual pages in src/sys directory

See merge request petsc/petsc!5559

Fix up all manual pages in src/sys directory

Commit-type: documentation
/spend 10h

Merge branch 'jolivet/fix-style-one-liners' into 'main'

Remove braces from one-liners

See merge request petsc/petsc!5557

Remove braces from one-liners

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 'wence/petsc-check-do-while' into 'main'

Wrap PetscCheck and PetscAssert in do { } while (0)

Closes #1199

See merge request petsc/petsc!5291

Wrap PetscCheck and PetscAssert in do { } while (0)

These macros look like functions, so they should behave like
functions. Fix up the resulting invalid syntax due to the previous
behaviour of these

Wrap PetscCheck and PetscAssert in do { } while (0)

These macros look like functions, so they should behave like
functions. Fix up the resulting invalid syntax due to the previous
behaviour of these macros being "if (...)
statement_without_semicolon". Fixes #1199.

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Merge branch 'stefanozampini/fix-function-composition' into 'main'

fix function composition

See merge request petsc/petsc!5274

PetscObjectFunctionCompose: clean up composed functions at Destroy time

Merge branch 'jolivet/fix-excl-rank' into 'main'

Replace !rank with rank == 0

See merge request petsc/petsc!5223

Merge branch 'psanan/docs-seealso-formatting' into 'main'

Docs: Fix man page .seealso entries missing spaces after commas

Closes #1176

See merge request petsc/petsc!5202

Replace !rank with rank == 0

See also https://gitlab.com/petsc/petsc/-/merge_requests/4146

Docs: Fix man page .seealso entries missing spaces after commas

```python

import os
import re
import fileinput

START_PATTERN = re.compile(r"^( *\.seealso:? )(.*$)")
FIX_PATTERN = re.compile(r",([^

Docs: Fix man page .seealso entries missing spaces after commas

```python

import os
import re
import fileinput

START_PATTERN = re.compile(r"^( *\.seealso:? )(.*$)")
FIX_PATTERN = re.compile(r",([^ $\n])")

def _fix_comma(matchobj):
return "`, `%s" % matchobj.group(1)

def process_file(filename_full):
""" Find/fix commas w/o trailing spaces or newlines in .seealso blocks """
with fileinput.FileInput(filename_full, inplace=True) as the_file:
in_block = False
for line in the_file:
line_stripped = line.strip()
# end ".seealso blocks" on a blank line or C-style comment close
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:
in_block = True
if in_block:
if re.search(FIX_PATTERN, line):
line_fixed = re.sub(FIX_PATTERN, _fix_comma, line)
print(line_fixed, end="") # prints to file
else:
print(line, end="") # prints to file
else:
print(line, end="") # prints to 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 files in local tree(s) """
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)
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 'psanan/docs-sphinx-man-pages' into 'main'

Integrate Man Pages into Sphinx Docs

Closes #1132 and #1015

See merge request petsc/petsc!4989

Merge branch 'barry/2022-04-29/rm-petsccheckfalse-sys' into 'main'

Remove PetscCheckFalse() from sys directory

See merge request petsc/petsc!5187

Remove PetscCheckFalse() from sys directory

Commit-type: housekeeping
/spend 30m

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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Docs: Add MyST formatting to PetscViewerBinaryGetMPIIOffset and PetscViewerSetMPIIOOffset to suppress Sphinx warning

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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