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

Merge branch 'barry/2022-08-15/fix-mat-manpages' into 'main'

Man pages in mat directory, manual material on matrices

See merge request petsc/petsc!5539

Fix manual pages in src/mat directory, very minor source code change

Commit-type: documentation
/spend 22h

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/2022-07-16/fix-mattranspose' into 'main'

Symbolic/numeric stages vs MatReuse flag discussion and additions to MatTranspose

See merge request petsc/petsc!5438

Update handling of MatTranspose() with MAT_REUSE_MATRIX

Add error checking for the use of the MAT_REUSE_MATRIX flag in MatTranspose()
Add tests to MatTranspose_XXX to error if the nonzero pattern ch

Update handling of MatTranspose() with MAT_REUSE_MATRIX

Add error checking for the use of the MAT_REUSE_MATRIX flag in MatTranspose()
Add tests to MatTranspose_XXX to error if the nonzero pattern changes
Add support for MAT_REUSE_MATRIX with changing nonzero pattern for MatTranspose_SeqAIJ()
Remove use of updateAt in MatProductNumeric_AtB_SeqAIJ_SeqAIJ() since MatTranspose() automatically
skips unneeded new transpose
Add MatTransposeSymbolic()
Update to SLEPc that supports these changes

Commit-type: feature, error-checking, documentation
/spend 5h

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Merge branch 'barry/2022-06-11/improve-mat-setable-values' into 'main'

Refactor handling of settable properties of matrix via MatSetOptions

See merge request petsc/petsc!5338

Refactor handling of setable properties of matrices via MatSetOptions()

Introduce PetscBool3 with enum values true, false, and unknown

Use PetscBool3 to store matrices properties in a matrix and cl

Refactor handling of setable properties of matrices via MatSetOptions()

Introduce PetscBool3 with enum values true, false, and unknown

Use PetscBool3 to store matrices properties in a matrix and cleanup interface to check these values

Add full support for symmetric, Hermitian, structurally symmetric, and SPD.

Commit-type: feature
/spend 6h

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Merge branch 'adams/mat-init-matops' into 'main'

Initialize MatOps_Values with two new NULLs

See merge request petsc/petsc!5382

Initialize MatOps_Values with two new NULLs

Merge branch 'barry/2022-06-23/docs-matgetownershiprangeis' into 'main'

docs for MPI rank ownership of matrix entries

See merge request petsc/petsc!5365

Provide more documentation on matrix layout meaning
and where matrix entries are stored across ranks (Elemental, SCALAPACK)

Commit-type: docs
/spend 1.5h

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/2022-04-28/rm-petsccheckfalse-mat' into 'main'

Remove the rest of the PetscCheckFalse() from the mat directory

See merge request petsc/petsc!5184

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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Remove the rest of the PetscCheckFalse() from the mat directory

Commit-type: housekeeping
/spend 45m

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 'jolivet/feature-less-checkfalse' into 'main'

Dividing by four the number of PetscCheckFalse()

See merge request petsc/petsc!5072

Remove some PetscCheckFalse()