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 'jed/plex-cgns' into 'main'

DMPlex: add support for writing CGNS files in parallel

See merge request petsc/petsc!5449

DMPlex: add support for writing CGNS files in parallel

Also --download-cgns. This supports most kinds of quadratic and
cubic elements, plus some quartic (not supported in Paraview-5.10.1).
Parallel

DMPlex: add support for writing CGNS files in parallel

Also --download-cgns. This supports most kinds of quadratic and
cubic elements, plus some quartic (not supported in Paraview-5.10.1).
Parallel IO uses collective contiguous writes.

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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 'Fande-Kong/print_eigenvalues_svd' into 'main'

Added an option to output all singular values in SVD

See merge request petsc/petsc!5014

Added an option to output all singular values in SVD

It is mainly used for debugging

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

Feature: C99 and C++11

See merge request petsc/petsc!4700

deprecate PETSC_STATIC_INLINE

Merge branch 'jacobf/2021-11-02/attribute-format-sys' into 'main'

Feature: PETSC_ATTRIBUTE_FORMAT - sys

See merge request petsc/petsc!4520

apply PETSC_ATTRIBUTE_FORMAT and related fixes to sys sources

Merge branch 'haplav/remove-adios2' into 'main'

remove nonworking PETSCVIEWERADIOS2 impl

Closes #867

See merge request petsc/petsc!3791

remove nonworking PETSCVIEWERADIOS2 impl

Merge branch 'haplav/fix-viewer-file-modes' into 'main'

PetscViewer: Improve handling of file modes.

See merge request petsc/petsc!3760

PetscViewer: Improve handling of file modes.

* add FILE_MODE_UNDEFINED for initial invalid value (internal use only)
* distinguish between not yet set and unsupported mode
* unify error messages in

PetscViewer: Improve handling of file modes.

* add FILE_MODE_UNDEFINED for initial invalid value (internal use only)
* distinguish between not yet set and unsupported mode
* unify error messages in PetscViewerFileSetName_XXX
* PetscViewerFileSetName_HDF5(): FILE_MODE_UPDATE = FILE_MODE_APPEND
* PetscViewerHDF5Open(): improve doc
* Deprecate PetscViewerVUSetMode, replace by PetscViewerFileSetMode_VU()

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Merge branch 'connorjward/add-flamegraph-tool' into 'main'

Add flamegraph generation tool

See merge request petsc/petsc!3607

Add flamegraph generation option to logging output

This commit also adds a Python script to convert the XML logging output
into the same format.