Small but important doc for DMNetwork

Commit-type: docs-only

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 '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/2022-03-30/fix-mpiu_allreduce' into 'main'

Fix mpiu_allreduce to always return PetscErrorCodes, never MPI error codes

See merge request petsc/petsc!5052

Fix mpiu_allreduce to always return PetscErrorCodes, never MPI error codes

Both for debug and optimized builds

Also removes shadow declaration errors from use of mpiu_allreduce

Commit-type: error-

Fix mpiu_allreduce to always return PetscErrorCodes, never MPI error codes

Both for debug and optimized builds

Also removes shadow declaration errors from use of mpiu_allreduce

Commit-type: error-checking
Reported-by: Lisandro Dalcin <dalcinl@gmail.com>

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Merge branch 'jacobf/2022-02-23/variadic-chkerr' into 'main'

Variadic CHKERRQ()

See merge request petsc/petsc!4889

The great renaming:

- CHKERRQ() -> PetscCall()
- CHKERRV() -> PetscCallVoid()
- CHKERRMPI() -> PetscCallMPI()
- CHKERRABORT() -> PetscCallAbort()
- CHKERRCONTINUE() -> PetscCallContinue()
- CHKERRXX

The great renaming:

- CHKERRQ() -> PetscCall()
- CHKERRV() -> PetscCallVoid()
- CHKERRMPI() -> PetscCallMPI()
- CHKERRABORT() -> PetscCallAbort()
- CHKERRCONTINUE() -> PetscCallContinue()
- CHKERRXX() -> PetscCallThrow()
- CHKERRCXX() -> PetscCallCXX()
- CHKERRCUDA() -> PetscCallCUDA()
- CHKERRCUBLAS() -> PetscCallCUBLAS()
- CHKERRCUSPARSE() -> PetscCallCUSPARSE()
- CHKERRCUSOLVER() -> PetscCallCUSOLVER()
- CHKERRCUFFT() -> PetscCallCUFFT()
- CHKERRCURAND() -> PetscCallCURAND()
- CHKERRHIP() -> PetscCallHIP()
- CHKERRHIPBLAS() -> PetscCallHIPBLAS()
- CHKERRHIPSOLVER() -> PetscCallHIPSOLVER()
- CHKERRQ_CEED() -> PetscCallCEED()
- CHKERR_FORTRAN_VOID_FUNCTION() -> PetscCallFortranVoidFunction()
- CHKERRMKL() -> PetscCallMKL()
- CHKERRMMG() -> PetscCallMMG()
- CHKERRMMG_NONSTANDARD() -> PetscCallMMG_NONSTANDARD()
- CHKERRCGNS() -> PetscCallCGNS()
- CHKERRPTSCOTCH() -> PetscCallPTSCOTCH()
- CHKERRSTR() -> PetscCallSTR()
- CHKERRTC() -> PetscCallTC()

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chkerr and friends wrapped

Merge remote-tracking branch 'origin/release'

Merge branch 'barry/2022-03-17/minor-docs-dmnetwork/release' into 'release'

Add some clarity to manual pages on how DMNetworkGetLocalVecOffset() and...

See merge request petsc/petsc!4981

Add some clarity to manual pages on how DMNetworkGetLocalVecOffset() and DMNetworkGetGlobalVecOffset() can be used

Commit-type: documentation
/spend 10m

Merge branch 'hzhang/dmnetworksharedvertex-update' into 'main'

optimize TableAddSVtx()

See merge request petsc/petsc!4763

optimize TableAddSVtx()
cleanup GetEdgelist_Coupling()
update network->subnet[net].nvtx for ghoted subnetworks in DMNetworkLayoutSetUp()

add changes made by Barry in MR4883: DMNetworkGetGlobalEdge/V

optimize TableAddSVtx()
cleanup GetEdgelist_Coupling()
update network->subnet[net].nvtx for ghoted subnetworks in DMNetworkLayoutSetUp()

add changes made by Barry in MR4883: DMNetworkGetGlobalEdge/VertexIndex() work before calling DMSetUp()
use local Nvtx = nvtx_max - nvtx_min + 1 as the size for table as suggested by Barry

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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

add PetscAssert() and PetscAssertFalse()

SETERRQ[1-9]+ begone

Merge branch 'gbetrie/fix-dmnetworkaddcomponent' into 'main'

Gbetrie/fix dmnetworkaddcomponent

See merge request petsc/petsc!4658

Adding/modify tests on zero size components to several examples;
DMNetworkAddComponent(): the owning rank and all ghost ranks must call it to add a component and nvar in the same order
Update doc for

Adding/modify tests on zero size components to several examples;
DMNetworkAddComponent(): the owning rank and all ghost ranks must call it to add a component and nvar in the same order
Update doc for DMNetworkAddComponent
merge DMNetworkLayoutSetUp_Coupling() into DMNetworkLayoutSetUp() to remove duplication

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Merge remote-tracking branch 'origin/release'

Merge branch 'barry/2021-11-24/dmnetwork-errorcheck-selfconnect/release' into 'release'

Check that DMNetwork does not have any self-connections, an edge between a single vertex

See merge request pe

Merge branch 'barry/2021-11-24/dmnetwork-errorcheck-selfconnect/release' into 'release'

Check that DMNetwork does not have any self-connections, an edge between a single vertex

See merge request petsc/petsc!4594

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Check that DMNetwork does not have any self-connections, an edge between a single vertex

This input causes a corrupted DMPLEX and difficult to debug errors

Commit-type: error-checking
\spend 15m
Re

Check that DMNetwork does not have any self-connections, an edge between a single vertex

This input causes a corrupted DMPLEX and difficult to debug errors

Commit-type: error-checking
\spend 15m
Reported-by: Getnet Betrie <gbetrie@anl.gov>

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