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 'maint'

Remove use of _ and __ in front of PETSc include guards. Reason: C99 Reserved Identifiers

Commit-type: portability-fix

Merge branch 'master' into knepley/feature-plex-parallel-submesh

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComp

Merge branch 'master' into knepley/feature-plex-parallel-submesh

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComplex type is missing from fortran
initialize variables so that static analyzer doesn't mistakenly think they are used uninitialized.
Move access of prefix until it is actually used
Remove DMDASplitComm2d(), used in one example that was not tested
Functions that do not return PetscErrorCode should not use PetscFunctionBegin/End paradgm
remove unneeded reassignment of same value
Missing CHKERRQ(); Mostly in Tao code
Remove clang static analyser warning about passing NULL variable to strncat()
missing newline in -ts_monitor_extreme
minor fixes for integer counters
Configure: Deal with '__func__' in C89 builds with newer Clang and GCC.
Jenkinsfile: Increased timeout for tests to 5 minutes.
3.9 changes: further clarify removal of -pc_factor_mat_solver_package
Options deprecations: add "PETSc" to inline warning
removing unused variable
MatShift support added to MATSUBMAT. Mimics MATSHELL functionality. Needed for matrix-free Hessians in TAO Newton-Line-Search methods.
Add -ts_monitor_extreme
Dev manual: add note on deprecating options database keys
...

Conflicts:
src/dm/impls/plex/examples/tests/ex4.c

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Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead

Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead code.
Add JuMP citation
Copyedits and updates to developers manual
Add more protection to intrinsics
MPI: protect arguments in MPI macros
Add the missing conditionals for 64-bit build
Plex+VTK: Fix field type determination
Fix bug in name cleanup
Bib: Added ref
Plex+VTK: Fix field type determination
Plex: Updated test output - I am now hating this shit
forgot to save file after moving prototypes to petscsys.h
update Apple example project settings per Xcode
Two functions should actually be public, used, for example from Apple MacOS and iOS programs
includes should always be included relative to include directory
Apple removed old locations of docsets
SNES ex12: Updated test output
...

Conflicts:
src/snes/examples/tutorials/ex13.c

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Merge branch 'barry/tao-to-new-test-harness' into barry/all-new-test-harness-branches

Merge remote-tracking branch 'origin/knepley/feature-adaptor-plex' into next-tmp

Merge branch 'knepley/feature-adaptor-plex' into knepley/feature-plex-adjoint-prelim

* knepley/feature-adaptor-plex: (38 commits)
SNES ex12: Fixed AMR tests - Cleaned up use of r Vec - Updated out

Merge branch 'knepley/feature-adaptor-plex' into knepley/feature-plex-adjoint-prelim

* knepley/feature-adaptor-plex: (38 commits)
SNES ex12: Fixed AMR tests - Cleaned up use of r Vec - Updated output
DMAdaptor: Fixes handling of original Vec and DM - Fix handling of input vector x - Only LABEL needs a Plex conversion
fixed uninitialized var
SNES ex12: Added adaptation test for p4est
DMAdaptor: Error indicator working for p4est on SNES ex12 - Changed DMAdaptor to a DM class - Added DMAdaptorComputeErrorIndicator_Private() - Added DMAdaptorSimpleErrorIndicator_Private() - Name projected solution vector
PetscFE: Added PetscFEInterpolateFieldAndGradient_Internal()
DMPlexComputeGradientClementInterpolant: fix debug statement for complex
SMAdaptor: Fix for complex ev decamp
compile fixes
DMAdaptor: Correct warnings and complex problems
Plex: Added versions of the Det functions that take Scalar data
DMAdaptor: Declare DMAdaptorSet/GetSequenceLength()
SNES+ex12: Added support for ascii_info_detail in -snes_converged_reason - It prints the L_2 error using the DS information - SNES ex12 output updated
DMAdaptor: Added options - Added options for N_adapt, refinement factor, h_min and h_max
SNES ex12: I finally think test output is correct
DMAdaptor: Refine viewing
SNES ex12: Updated adaptation tests - Added sequential adaptation
SNES: Added -snes_adapt_sequence - Eventually remove snes_grid_sequence
DMAdaptor: - Added sequential adaptation - Added DMAdaptorGet/SetSequenceLength() - Use AdaptationCriterion now - Added untested unstructured interpolation
DMAdaptor: Now I have AdaptationStrategy and AdaptationCriterion - Fixed some docs
...

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DMAdaptor: Declare DMAdaptorSet/GetSequenceLength()

DMAdaptor: Now I have AdaptationStrategy and AdaptationCriterion
- Fixed some docs

DMAdaptor: Now adaptation can change the DM and solution Vec
- Use the DS exact solution if available to reinitialize on the new grid (need to get real interpolation working)
- Starting to flesh out

DMAdaptor: Now adaptation can change the DM and solution Vec
- Use the DS exact solution if available to reinitialize on the new grid (need to get real interpolation working)
- Starting to flesh out adaptation types

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DMAdaptor: Allow user to set function for solution transfer

DM: Added DMAdaptor
- The idea here is to package up the control flow for adaptation, so that a user can do it with no code changes
- The mesh manipulation is still done by DMAdaptMetric() and DMAdap

DM: Added DMAdaptor
- The idea here is to package up the control flow for adaptation, so that a user can do it with no code changes
- The mesh manipulation is still done by DMAdaptMetric() and DMAdaptLabel()

show more ...