DMPlexCopy_Internal: copy overlap

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 'balay/add-memcheck.h' into 'main'

valgrind: add in memcheck.h [and update valgrind.h]

See merge request petsc/petsc!5188

Merge branch 'knepley/plex-gmsh-group-name' into 'main'

Knepley/plex gmsh group name

See merge request petsc/petsc!5183

Plex+Doc: Fixed documentation for affine transformation
Reported-by: Aidan Hamilton <aidan@udel.edu>

Plex: Added mem init to projection
- Pointwise functions no longer initialize their array, so it has to be
done here

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 remote-tracking branch 'origin/release'

Plex ex1f90: Fix parallel runs

plex metric: reduce duplication; avoid PetscCheckFalse

Merge branch 'barry/2022-04-24/rm-petsccheckfalse-dm' into 'main'

Remove PetscCheckFalse from use in the src/dm directory

Closes #1141

See merge request petsc/petsc!5160

Merge remote-tracking branch 'origin/release'

Plex: Fix general interpolant for multiple fields

Plex ex46: Update for multiple fields

fix valgrind warning

not ok dm_impls_plex_tutorials-ex13_gyroid_1 # Error code: 10
==1339793== Conditional jump or move depends on uninitialised value(s)
==1339793== at 0x544AEE9: P

fix valgrind warning

not ok dm_impls_plex_tutorials-ex13_gyroid_1 # Error code: 10
==1339793== Conditional jump or move depends on uninitialised value(s)
==1339793== at 0x544AEE9: PetscKernel_A_gets_inverse_A_3 (dgefa3.c:86)
==1339793== by 0x5993329: TPSNearestPoint (plexcreate.c:2329)
==1339793== by 0x5998FCB: DMPlexCreateTPSMesh_Internal (plexcreate.c:2780)
==1339793== by 0x599A283: DMPlexCreateTPSMesh (plexcreate.c:2871)
==1339793== by 0x109B2A: main (ex13.c:24)
==1339793== Uninitialised value was created by a stack allocation
==1339793== at 0x5992981: TPSNearestPointResJac (plexcreate.c:2265)

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Remove PetscCheckFalse from use in the src/dm directory

Commit-type: housekeeping
/45m

Merge remote-tracking branch 'origin/release'

Plex+Gmsh: Now handle all entity tags

DMPlexInterpolate manpage: update Notes

Merge remote-tracking branch 'origin/release'

DMPlex: typo in Mmg parameter name

Plex+Gmsh: Allow group name aliasing by putting a colon at the end of the basename

configure: SCOTCH 7.0.1

Enable PETSC_ATTRIBUTE_FORMAT()

Plex ex5: Added parallel fault tests - SF creation still broken