PetscSFMerge: merge two SFs with possibly overlapping leaves

Merge branch 'haplav/petscsfconcatenate-add-global-renumbering' into 'main'

PetscSFConcatenate: add global rootmode

See merge request petsc/petsc!5726

PetscSFConcatenate: add global rootmode

Merge branch 'jacobf/2022-09-21/2-bike-2-shed' into 'main'

Feature: Bicycle Storage Facility 2

See merge request petsc/petsc!5661

source code format changes due to .clang-format changes

Transform all header-guards into ifndefs to make clang-format ignore them for preprocessor indentation

Merge branch 'haplav/add-petscsfgetgraphlayout' into 'main'

add PetscSFGetGraphLayout()

See merge request petsc/petsc!5629

add PetscSFGetGraphLayout(),

enable fortran interface for PetscSFSetGraphLayout(),
reformat zsfutilsf.c

Merge branch 'jacobf/2022-09-14/mpi-datatype-type-checking' into 'main'

Re-enable MPI_Datatype compiler type checking attributes

See merge request petsc/petsc!5636

Re-enable MPI_Datatype compiler type checking attributes, and add them to a few more places

Merge branch 'haplav/remove-petsclayoutscreatesf' into 'main'

remove deprecated PetscLayoutsCreateSF() -> PetscSFCreateFromLayouts()

See merge request petsc/petsc!5624

remove deprecated PetscLayoutsCreateSF() -> PetscSFCreateFromLayouts()

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/2022-08-13/fix-man-include' into 'main'

Fix up manual pages in include/ including adding tick marks

See merge request petsc/petsc!5528

Fix up manual pages in include/ including adding tick marks

Commit-type: documentation
/spend 4h

Merge branch 'barry/2022-05-03/cleanup-makefiles' into 'main'

remove unneeded stuff from makefiles

See merge request petsc/petsc!5211

Get values of makefile SOURCE etc from the file system instead of makefiles

Use SUBMANSEC from include files for manual sections instead of the makefile

Unfortunately this has to be one large commi

Get values of makefile SOURCE etc from the file system instead of makefiles

Use SUBMANSEC from include files for manual sections instead of the makefile

Unfortunately this has to be one large commit since the changes all have to be done at once

Commit-type: docs
/spend 10m

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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 'haplav/feature-petscsfconcatenate' into 'main'

add PetscSFConcatenate()

See merge request petsc/petsc!4876

add PetscSFConcatenate()

Merge branch 'haplav/sf-control-multileaves' into 'main'

SF: check for multileaves

See merge request petsc/petsc!4888

PetscSFSetGraph: sort ilocal, check for duplicates

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

Feature: C99 and C++11

See merge request petsc/petsc!4700