Fix manual pages in a variety of parts of src/dm

Still many other parts of DM need to have their manual pages updated

Commit-type: housekeeping
/spend 4h

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

Fix periodicity for higher order coordinates

See merge request petsc/petsc!5333

DM+FE: Create DG coordinate DS and add PetscFECreateFromSpaces()
- Refactor FE creation
- Create DS for DG coordinates
- Error on DG face coordinates

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 'jed/plex-coordinates-project' into 'main'

DMPlex: skip coordinate projection when FE space matches modulo quadrature

See merge request petsc/petsc!4891

DMPlex: skip coordinate projection when FE space matches modulo quadrature

This requires checking that dual spaces are equal so that an legit
projection is not required. For example, high order Gmsh

DMPlex: skip coordinate projection when FE space matches modulo quadrature

This requires checking that dual spaces are equal so that an legit
projection is not required. For example, high order Gmsh meshes have
equally spaced vertices while we prefer Gauss-Lobatto spacing, so that's
a case where a projection is required. (It could be made faster, but
that's for another day.)

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Merge branch 'knepley/feature-fe-wxy-again' into 'main'

FE on triangular prisms

See merge request petsc/petsc!4826

DM+FE+DT: Added correct geometry and quadrature for triangular prism
- Added affine geometry for triangular prism
- Added PetscDTTensorQuadratureCreate()
- Added PetscFECreateByCell()
- Added PetscFE

DM+FE+DT: Added correct geometry and quadrature for triangular prism
- Added affine geometry for triangular prism
- Added PetscDTTensorQuadratureCreate()
- Added PetscFECreateByCell()
- Added PetscFECreateLagrangeByCell()
- Added DMCreateFEDefault()
- Now DMField uses PetscFECreateLagrange()
- Refactored FE creation
- If the degree is prescribed on a prism, do not create a tensor space
- Use new interface in DMField_DS
- Fix default creation when number of components is changed by command line

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FE: Add WXY enrichment

PetscDualSpace: Specify ref cell with DMPolytopeType

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

Feature: C99 and C++11

See merge request petsc/petsc!4700

rename PetscAssert() -> PetscCheck() and PetscAssertDebug() -> PetscAssert()

deprecate PETSC_STATIC_INLINE

apply PetscAssertFalse() -> PetscAssert() transformation to headers

add PetscAssert() and PetscAssertFalse()