Merge branch 'hzhang/external-matfactor-options' into 'main'

Get options in symbolic factorization instead of MatGetFactor() using KSP/PC prefix when inside KSP

See merge request petsc/petsc!5230

Change matrix factor database options that occur in KSP/PC to always use KSP/PC options prefix

Add MatSetOptionsPrefixFactor() and MatAppendOptionsPrefixFactor() to allow controlling the options pre

Change matrix factor database options that occur in KSP/PC to always use KSP/PC options prefix

Add MatSetOptionsPrefixFactor() and MatAppendOptionsPrefixFactor() to allow controlling the options prefix
used by factors created from this matrix

Change MatSetOptionsPrefix() to no longer affect the options prefix used by factors created from this matrix

As part of the above work the handling of the factor matrix options is now done in code in the factor matrix
not in the code that originates the factor matrix

Update examples output to the new approach where the factored matrix prefix is set from the KSP/PC

Much of this work was performed by Hong Zhang

Commit-type: usability
/spend 5h

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Merge branch 'jolivet/feature-tile-matdensegetsubmatrix' into 'main'

MatDenseGetSubMatrix(): allow selection of rows

See merge request petsc/petsc!5337

MatDenseGetSubMatrix(): allow selection of rows

Merge branch 'stefanozampini/gdsw-mg' into 'main'

Implement AGDSW coarse spaces for PCMG

See merge request petsc/petsc!5256

Housekeeping: fix MatOperation enum values

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 'jolivet/fix-variableblockenvelope' into 'main'

MatComputeVariableBlockSizes() -> BlockEnvelope()

See merge request petsc/petsc!5209

MatComputeVariableBlockSizes() -> BlockEnvelope()

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 'barry/2020-10-08/invert-block-diagonal-aij' into 'main'

add MatInvertVariableBlockEnvelope

See merge request petsc/petsc!3544

Implement MatInvertVariableBlockEnvelope() with test example

Commit-type: feature, example
/spend 12h
Reported-by: Olivier Jamond <olivier.jamond@cea.fr>

Merge branch 'barry/2022-04-01/fix-petsc-options-begin-end/release' into 'main'

Remove bogus error returns from Begin/End() macros

See merge request petsc/petsc!5069

Cleanup of introduction of PetscCall()

* remove bogus error flags from XXXBegin()/End() macros such as PetscOptionsBegin()/End()

* rename for consistency certain XXXBegin()/End() macros such as Mat

Cleanup of introduction of PetscCall()

* remove bogus error flags from XXXBegin()/End() macros such as PetscOptionsBegin()/End()

* rename for consistency certain XXXBegin()/End() macros such as MatPreallocateInitialize()/Finalize()

* fix many lingering ierr = XXX that arose from multiline function calls

* sync slepc/hpddm - to use snapshots with the same changes

Commit-type: error-checking, style-fix
/spend 8h

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Merge branch 'jczhang/feature-hypre-coo' into 'main'

Support COO for MatHypre

See merge request petsc/petsc!5023

Mat: add MatSeqAIJGetCSRAndMemType()

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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rewrote the PetscLL macros as functions to let the linter understand them. Also helps
reduce the staggering amount of code duplication in Mat

chkerr and friends wrapped

Merge branch 'barry/2022-03-13/fix-some-manualpages/release' into 'main'

Improve generation of manual pages/fix a variety of manul pages basic formatting

See merge request petsc/petsc!4969

Merge branch 'stefanozampini/dlpack' into 'main'

improve dlpack support

See merge request petsc/petsc!4858

doc: Fix a variety of manual page formatting issues

/spend 1h