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 'jczhang/fix-kokkos-complex-alignment' into 'main'

Turn off Kokkos_ENABLE_COMPLEX_ALIGN

See merge request petsc/petsc!5038

Config: turn off Kokkos_ENABLE_COMPLEX_ALIGN

Merge branch 'knepley/fix-doc-errors' into 'main'

Doc: Trying to remove all reported errors

See merge request petsc/petsc!4930

Doc: Trying to remove all reported errors - Since it reports as an error, and only occurs a very few times, I have removed the Imput/Output Parameters sections and replaced them by Output Parameters

Doc: Trying to remove all reported errors - Since it reports as an error, and only occurs a very few times, I have removed the Imput/Output Parameters sections and replaced them by Output Parameters with documentation

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Merge branch 'jczhang/feature-add-kokkos-doc' into 'main'

Add manuals for PETSc/Kokkos APIs and fully implement DMDAVecGetKokkosOffsetView()

See merge request petsc/petsc!4864

Vec: add manual for VecKokkos

Merge branch 'adams/aijkokkos-gpu-logging' into 'main'

Cleanup diagnostics and remove unneeded calls to WaitForKokkos

See merge request petsc/petsc!4748

VecKokkos+AIJKokkos: cleanup timers and remove WaitForKokkos

Merge branch 'jacobf/2021-09-04/petscdevice-cupminitialization' into 'main'

Replace current CUPM initialization with unified PetscDevice version

See merge request petsc/petsc!4310

- Replace the current CUPM initialization infrastructure with PetscDevice.
- Remove -petsc_use_default_null_stream and -[cuda|hip]_synchronize options
- Remove PetscCUDASynchronize and PetscHIPSynchr

- Replace the current CUPM initialization infrastructure with PetscDevice.
- Remove -petsc_use_default_null_stream and -[cuda|hip]_synchronize options
- Remove PetscCUDASynchronize and PetscHIPSynchronize
- Remove PetscCUDAInitialize(), PetscCUDAInitializeCheck(), PetscHIPInitialize(), and
PetscHIPInitializeCheck()
- Remove PetscCUBLASInitializeHandle(), PetscCUSOLVERDnInitializeHandle(),
PetscHIPBLASInitializeHandle(), and PetscHIPSOLVERInitializeHandle().
- Remove petsc_gputimer_begin and petsc_gputimer_begin
- Add -device_enable, -device_select and -device_view options
- Replace -[cuda|hip]_device with split options -device_enable_[cuda|hip] and -device_select_[cuda|hip]
- Replace -[cuda|hip]_view with -device_view_[cuda|hip]
- Add PetscDeviceInitType
- Add PetscDeviceInitialize() and PetscDeviceInitialized()
- Add PetscDeviceView()

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Merge branch 'jczhang/fix-kokkos-complex' into 'main'

Use Kokkos::complex when available

See merge request petsc/petsc!3904

Sys: use Kokkos::complex for .kokkos.cxx files

Merge remote-tracking branch 'origin/jczhang/add-DMDAVecGetKokkosOffsetView'

Add DMDAVecGetKokkosOffsetView and friends

See merge request petsc/petsc!3383

Add template VecGetKokkosView