Fix up manual pages in include/ including adding tick marks

Commit-type: documentation
/spend 4h

Merge branch 'barry/2022-08-09/fix-manualpage-rot' into 'main'

Stop make allmanpages if an error is detected. Otherwise errors are hidden and never fixed.

See merge request petsc/petsc!5510

Put blank lines around some manual page comments to see if that fixes sowing not processing them correctly

Merge branch 'marboeuf/plex-naturalpointsf' into 'main'

Plex: create the natural point SF

See merge request petsc/petsc!5502

Plex: add and implement DMPlexCreateNaturalVector

DMPlexCreateNaturalVector gives a Vec capable of holding the natural ordering
and distribution. The routine mimicks DMCreateGlobalVector.

Merge branch 'knepley/feature-plex-periodic-separation' into 'main'

Fix periodicity for higher order coordinates

See merge request petsc/petsc!5333

DM: Reorganized periodic coordinates into a separate representation
- Split coordinates into two representations
- No longer specify the boundary type for periodicity. We can tell if a
given boundary

DM: Reorganized periodic coordinates into a separate representation
- Split coordinates into two representations
- No longer specify the boundary type for periodicity. We can tell if a
given boundary is periodic by a positive L[d]
- Added DMPlexGetCellCoordinates_Internal() to get localized cell
coordinates automatically, and used in plexgeometry.c
- Moved coordinate functions into dmcoordinates.c
- Moved periodicity functions into dmperiodicity.c

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Merge branch 'knepley/feature-plex-label-overlap' into 'main'

Plex: Allow a user to create a custom parallel overlap using labels

See merge request petsc/petsc!5349

Plex: Allow a user to create a custom parallel overlap using labels - The test is in PyLith

Merge branch 'ksagiyam/dmplex_reorder_1d_options' into 'main'

plex: add DMPlexReorder{Set,Get}Default()

See merge request petsc/petsc!5245

plexreorder: add DMPlexReorder{Set,Get}Default()

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 'jwallwork23/metric-input' of https://gitlab.com/jwallwork23/petsc into 'main'

Pass metric `Vec`s rather than their addresses

See merge request petsc/petsc!5044

Merge branch 'haplav/extend-plex-checkpointsf' into 'main'

extend DMPlexCheckPointSF()

See merge request petsc/petsc!5217

add DMPlexCheck()

extend DMPlexCheckPointSF(), add PetscSF arg

plex metric: pass output metric, rather than its address

plex metric: add DMPlexMetricDeterminantCreate

Merge branch 'knepley/fix-plex-submesh-hybrid' into 'main'

Knepley/fix plex submesh hybrid

See merge request petsc/petsc!5213

Plex: Add label value argument to Hybrid mesh and COhesive completion

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 'knepley/feature-plex-parallel-submesh' into 'main'

Adding parallel handling of extracted submanifolds

See merge request petsc/petsc!5101

Plex: Factor out point queue structure
- Added DMPlexPointQueue and API
- Updated SBR refinement
- Fixed small bug with DMLabelPropagatPush() in serial