Merge remote-tracking branch 'origin/release'

Merge branch 'barry/2023-05-27/improve-tutorials/release' into 'release'

Minor cleanup of website tutorials

See merge request petsc/petsc!6520

change to consistent use of ch_xxx for chapter names in the docs, instead of a mix of ch_xx and chapter_xx

Merge branch 'jacobf/2022-12-10/petscerrorcode-nodiscard' into 'main'

Feature: Non-discardable PetscErrorCode

See merge request petsc/petsc!5923

Make PetscErrorCode a non-discardable enum

Merge remote-tracking branch 'origin/release'

Merge branch 'barry/2022-10-16/fix-ts-man-pages/release' into 'release'

Clean up ts manual pages

See merge request petsc/petsc!5748

Clean up ts manual pages

To be safe I am triggering a full test even though this was intended to be docs-only

Commit-type: documentation
/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

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 '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/2022-03-26/variadic-chkerrq-stragglers' into 'main'

Clean Up Variadic-CHKERRQ Stragglers

See merge request petsc/petsc!5033

fixup some remaining stragglers from !4889

Merge remote-tracking branch 'origin/release'

Merge branch 'jolivet/fix-documentation' into 'release'

Documentation fixes

See merge request petsc/petsc!3851

Documentation fixes

Merge commit 'd47bf9aaf1e5266cc3f0ff499f934c85788965a9' into jed/fix-matcreatempibaij/maint

Obtain changed (v3.5) handling of MatMPIBAIJSetPreallocationCSR to match
documentation.

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
ini

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
initialize ap as complained by the nightly tests
Plex ex3: Update to new point function API
initialize some variables as complained by nightly tests
SNES ex12: Mix misnaming Nf --> Nc
update tests
add tests
add MatView_SeqXAIJ_ASCII_structonly(); enable A->structure_only in MatSetValuesBlocked_SeqBAIJ
typo
fill-in some references
Bib: Fixed ref
Plex: Added PLY to file support
Plex: Adding PLY support
PetscDS: Turn off Fortran bindings for Constants
Plex tests: Updated to new point function API
SNES ex56: Moved tests to new format
DM: Allow field projection functions to take an array of scalars - This will allow us to pass in user data to kernels without void *, more efficiency than aux fields
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tutorials/ex63.c

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

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes

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

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
rename struct Mat_SubMat -> Mat_SubSppt
add a little information to the manual about using tchem
rename MatCreateSubMatrixComposite -> MatCreateSubMatrixVirtual; Mat_SubMatrix -> Mat_SubVirtual
need to protect the \ passed on the makefile on my Mac
Bib: Updated ref
update src/mat/examples/tests/output/ex23_#.out
rename MatGetSubMat -> MatCreateSubMat
Mark MatCreateMPIAIJWithSplitArrays() and MatMPIAIJSetPreallocationCSR() with MAT_NO_OFF_PROC_ENTRIES
superlu: libray is installed in PREFIX/lib64 - fix this to use PREFIX/lib
backport fixes cc105cc3 2b35c90a - required for 3bf428d - that was backported from master - 80c96bb
'echo -n' fails on opensolaris/osx - so avoid using it.
fix diffs in nightlybuilds due to options in ~/.petscrc
add Kelley03 to src/docs/tex/petsc.bib
build: determine moudles, mpi.h used during buildtime and print in 'info'
fix analyzer warnings
fix build failure on opensolaris - where -lm from flibs is removed due to -lm in cxxlibs. But then - only flib gets used for some configure tests [blaslapack, parms]
config: prefer __restrict over C99 restrict keyword
...

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Merge branch 'barry/remove-funct'

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-t

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-to: Andreas Mang <andreas@ices.utexas.edu>

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Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_A

Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_ATTRIBUTEALIGNED flag to makefile
PCSetUp_SVD() used incorrect matrix for matrix size in parallel, also need to skip LAPACK call if matrix size is zero
strumpack: update to latest version 1.0.4
Remove valgrind warning about MPI_Allreduce() with uninitialized data
sed for test output that has atol convergence with quad precision
updated ex1_nest tests
fixed incorrect key value
fix: bad merge a69d34a
test: move runex78 to TESTEXAMPLES_C_NOTSINGLE
build: fix warnings
sys: update test to produce same result - irrespective of debug/opt build - and presence of ~/.petscrc
sys: src/sys/examples/tests/ex30.c -> src/sys/examples/tests/ex32.c to avoid conflict in master
Sed output, since quad precision reduces below atol on these tests
remove automatically generated matrix names from test output files since can be different
Fixes for MatMPIXXXSetPreallocation(), they were not reentrant, since they kept the information used for matrix-vector products
GAMG: fix PCView_GAMG() format - and update output/ex56_0.out
superlu_dist: 64-bit-indices fix https://github.com/xiaoyeli/superlu_dist/issues/4
Add SNESSetDivergenceTolerance / -snes_divergence_tolerance.
fixed unit read in Plex
...

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