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/2022-02-23/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()

show more ...

chkerr and friends wrapped

Merge branch 'stefanozampini/dlpack' into 'main'

improve dlpack support

See merge request petsc/petsc!4858

Mat: remove unused MatMultConstrained

Merge branch 'stefanozampini/tao-python' into 'main'

TAOPYTHON

See merge request petsc/petsc!4768

MATH2OPUS: expose low rank update operation

add Python bindings

Merge branch 'jolivet/fix-matstructure-enum' into 'main'

MatStructures: no space in enumeration

See merge request petsc/petsc!4804

MatStructures: no space in enumeration

Merge branch 'stefanozampini/hara-to-h2opus-rebased-v7' into 'main'

Update distributed hierarchical matrix package H2Opus

See merge request petsc/petsc!4347

Update H2 package

Merge remote-tracking branch 'origin/release'

Merge branch 'jolivet/fix-missing-petsclogeventregister' into 'release'

MatQRFactor: missing PetscLogEventRegister()

See merge request petsc/petsc!4151

MatQRFactor: missing PetscLogEventRegister()

Merge branch 'jed/fix-essl' into 'main'

ESSL fixes, support for LLNL liblapackforessl, and Lassen example

Closes #813

See merge request petsc/petsc!4090

ESSL: upgrade to 5.2 and above

As of ESSL 5.2, interfaces to functions like ?geev now match that of
standard LAPACK, where they previously had a different calling
convention.

Co-authored-by: Jed Br

ESSL: upgrade to 5.2 and above

As of ESSL 5.2, interfaces to functions like ?geev now match that of
standard LAPACK, where they previously had a different calling
convention.

Co-authored-by: Jed Brown <jed@jedbrown.org>

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Merge branch 'barry/2021-05-16/fix-double-lines' into 'main'

Fix typos in source

See merge request petsc/petsc!3984

Remove all double blank lines from source

Commit-type: petsc-style
/2h

Merge branch 'tisaac/feature-qr-factorization-cuda' into 'main'

QR factorization: cusolver dense

See merge request petsc/petsc!3690

Use cusolverDn QR factorization

Squashme: make sure seqdense matrices can still be solved with cuda

Fix memory leak in densecuda.cu

Use workvec to avoid cudaMalloc in MatSolve_SeqDenseCUDA_Interna

Use cusolverDn QR factorization

Squashme: make sure seqdense matrices can still be solved with cuda

Fix memory leak in densecuda.cu

Use workvec to avoid cudaMalloc in MatSolve_SeqDenseCUDA_Internal

squashme: remove timings

squashme: simplify copy-back logic in MatMatSolve_SeqDenseCUDA_Internal

Remove WaitForCUDA()

show more ...

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

Add DMDAVecGetKokkosOffsetView and friends

See merge request petsc/petsc!3383

Rename -mat_cusparse_transgen to -mat_form_explicit_transpose

Merge branch 'tisaac/feature-qr-factorization' into 'main'

QR Factorization

See merge request petsc/petsc!3680