Merge branch 'barry/2023-10-25/rename-rules-doc' into 'main'

Rename rules.doc and rules.utils because GitLab treats the former as a MS Word document.

See merge request petsc/petsc!6965

Rename rules.doc and rules.utils because GitLab treats the former as a MS Word document.

Thanks-to: Jed Brown

Merge branch 'barry/2023-10-18/rm-dirs-from-makefiles' into 'main'

Remove use of and the DIRS variables from the makefiles

See merge request petsc/petsc!6945

Remove DIRS variable and unneeded tabs from all makefiles since no longer needed

Commit-type: housekeeping

Merge branch 'barry/2023-03-17/rm-unneeded-test-from-makefiles' into 'main'

simplify/cleanup makefile system

See merge request petsc/petsc!6201

non-test and tutorial makefiles only need rules.doc not the full rules

Commit-type: documentation

Only makefiles in the test and tutorial directories need lib/petsc/conf/test

Commit-type: housekeeping

Merge branch 'barry/2023-03-14/rm-sourceh-from-makefiles' into 'main'

Remove unneeded SOURCE* from makefiles

See merge request petsc/petsc!6186

Remove unneeded SOURCEH from makefiles

No longer used by docs or build

Merge branch 'barry/2023-02-22/rm-locdir' into 'main'

Remove need for hardwired LOCDIR in all makefiles

See merge request petsc/petsc!6113

Remove unneeded declarations of LOCDIR from all the makefiles

Commit-type:documentation

Merge branch 'barry/2022-05-03/cleanup-makefiles' into 'main'

remove unneeded stuff from makefiles

See merge request petsc/petsc!5211

remove garbage from makefiles

Including
* unused FLAGS variables
* All: lib that did not work
* stray blank lines etc

Commit-type: housekeeping
/spend 1h

Merge remote-tracking branch 'origin/maint'

Merge remote-tracking branch 'origin/jolivet/fix-symlink-free' into maint

Single petscdir.mk

Merge remote-tracking branch 'origin/more-updates-for-missing-petsc_dir'

More support for not needing to set PETSC_DIR yet build with PETSc, also...

See merge request petsc/petsc!2626

build: add more support for not needing to set PETSC_DIR yet build with PETSc, also support for GNU make to directly use "make test" instead of "make -f gmakefile.test"

Still needs -include ../petsc

build: add more support for not needing to set PETSC_DIR yet build with PETSc, also support for GNU make to directly use "make test" instead of "make -f gmakefile.test"

Still needs -include ../petscdir.mk in many of the makefiles
Still needs the link for ../petscdir.mk in many directories

GNUMakefile: call legacy makefile recursively instead of including it

GNUMakefile: promote default "all" target; "libs" builds libpetsc*

GNUMakefile: If gnumake < 4.2 prefer makefile wrapper interface over direct gmakefile interface to avoid the following warnings

gmakefile.test:92: arch-ci-linux-cxx-cmplx-pkgs-64idx/tests/testfiles: No such file or directory
gmakefile:67: arch-ci-linux-cxx-cmplx-pkgs-64idx/lib/petsc/conf/files: No such file or directory

Commit-type: testing-fix, feature, usability
Thanks-to: Jed Brown jed@jedbrown.org

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Merge branch 'jed/promote-examples-tests-tutorials' [petsc/petsc!2610]

* jed/promote-examples-tests-tutorials:
Promote examples/{tests,tutorials}/ to {tests,tutorials}/

Promote examples/{tests,tutorials}/ to {tests,tutorials}/

This shortens paths and improves consistency between test target names
and paths to the source and output files. Most of the work was
compl

Promote examples/{tests,tutorials}/ to {tests,tutorials}/

This shortens paths and improves consistency between test target names
and paths to the source and output files. Most of the work was
completed by this script, followed by mild cleanup of nonconforming
cases.

for makefile in `git ls-files 'src/*makefile'`; do
if rg -q 'DIRS.*\bexamples\b' $makefile; then
base=$(dirname $makefile)
dirs=$(cd $base/examples && ls -d tests tutorials 2>/dev/null | xargs echo)
perl -pi -e "s#^(DIRS.*)\bexamples\b#\1${dirs}#" $makefile
git rm $base/examples/makefile
for t in $dirs; do
git mv $base/examples/$t $base/
perl -pi -e "s#^(LOCDIR[[:space:]]*=).*#\1 $base/$t/#" $base/$t
done
fi
done

git grep -l -E -z 'examples/(tutorials|tests)' | xargs -0 perl -pi -e 's#examples/(tutorials|tests)#\1#g'
git checkout @ \
src/docs/website/documentation/changes/ \
src/benchmarks/results/

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

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

Merge branch 'master' into stefano_zampini/feature-gmsh-periodic

* master: (1016 commits)
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
fix compile warni

Merge branch 'master' into stefano_zampini/feature-gmsh-periodic

* master: (1016 commits)
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ may be used uninitialized in this function [-Wmaybe-uninitialized] ierr = DMInterpolationSetUp(interpolator, dm, pointsAllProcs);CHKERRQ(ierr);
migrate 'build requires: !mpiuni' to new format
migrate 'build requires: !complex' to new format
workarround 'division by zero' compiler warning on windows C:\cygwin64\home\petsc\PETSC~3.CLO\src\ts\examples\TUTORI~1\ex11.c(416): warning #39: division by zero if (uL->h < 0 || uR->h < 0) {for (i=0; i<1+dim; i++) flux[i] = 0./0.; return;} /* SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Reconstructed thickness is negative"); */
dos2unix to prevent warnings on opensolaris "/export/home/petsc/petsc.clone/src/ksp/ksp/examples/tests/ex53.c", line 6: warning: invalid white space character in directive
fix output file - corresponding to code changes in efd4aadf157bf1ba2d80c2be092fcf4247860003
disable test on windows
update log from opensolaris so that the diff is clean on linux aswell
update grep in sync with change in efd4aadf157bf1ba2d80c2be092fcf4247860003
Fixed code that did not correctly set current color for block insertion
Update output files that did not get fixed after previous merges
Change MPIUni to not immediately abort on operations it cannot perform, instead return error code
Add filter for example that can produce 1 different iteration count
Example add system calloc, bad formating of %d in print, commented out code
Always use (void) for functions that take no arguments, never ()
always need to caste PetscReal variables to (double) in print statements
updates to manual page for clarity
update help menu for MatRARt() -- MatRARt_mpiaij_mpiaij is supported now, but not efficient.
fix nightlybuild error with c1cbb1def3f8ddca04c3998b9c06618fd1ffef35 on arch-linux-IPL64 src/ksp/pc/examples/tests ex5_1
...

Conflicts:
include/petscdm.h
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/dm/impls/plex/plexhdf5.c

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Merge branch 'master' into knepley/feature-dm-bc-components

* master: (320 commits)
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ m

Merge branch 'master' into knepley/feature-dm-bc-components

* master: (320 commits)
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ may be used uninitialized in this function [-Wmaybe-uninitialized] ierr = DMInterpolationSetUp(interpolator, dm, pointsAllProcs);CHKERRQ(ierr);
migrate 'build requires: !mpiuni' to new format
migrate 'build requires: !complex' to new format
workarround 'division by zero' compiler warning on windows C:\cygwin64\home\petsc\PETSC~3.CLO\src\ts\examples\TUTORI~1\ex11.c(416): warning #39: division by zero if (uL->h < 0 || uR->h < 0) {for (i=0; i<1+dim; i++) flux[i] = 0./0.; return;} /* SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Reconstructed thickness is negative"); */
dos2unix to prevent warnings on opensolaris "/export/home/petsc/petsc.clone/src/ksp/ksp/examples/tests/ex53.c", line 6: warning: invalid white space character in directive
fix output file - corresponding to code changes in efd4aadf157bf1ba2d80c2be092fcf4247860003
disable test on windows
update log from opensolaris so that the diff is clean on linux aswell
update grep in sync with change in efd4aadf157bf1ba2d80c2be092fcf4247860003
Fixed code that did not correctly set current color for block insertion
Update output files that did not get fixed after previous merges
Change MPIUni to not immediately abort on operations it cannot perform, instead return error code
Add filter for example that can produce 1 different iteration count
Example add system calloc, bad formating of %d in print, commented out code
Always use (void) for functions that take no arguments, never ()
always need to caste PetscReal variables to (double) in print statements
updates to manual page for clarity
update help menu for MatRARt() -- MatRARt_mpiaij_mpiaij is supported now, but not efficient.
fix nightlybuild error with c1cbb1def3f8ddca04c3998b9c06618fd1ffef35 on arch-linux-IPL64 src/ksp/pc/examples/tests ex5_1
output has changed with e6d0a238963c2a97dd04845ea512b529992c7cdb so update the output file
...

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Merge branch 'stefano_zampini/feature-kspguess-class'

Added the KSPGuess class

- Old KPSFischerGuess is now KSPGUESSFISCHER
- Added KSPGUESSPOD

KSPGUESSPOD computes an initial guess by projecting the problem on a lower dimensional basis
generated usin

Added the KSPGuess class

- Old KPSFischerGuess is now KSPGUESSFISCHER
- Added KSPGUESSPOD

KSPGUESSPOD computes an initial guess by projecting the problem on a lower dimensional basis
generated using Proper Orthogonal Decomposition

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