doc: bugfix - edit only .html files [and not manual.pdf]

[ this was the original intent before the change in 3a818db72d7 ]

This is triggered by 'petsc4py' keyword in src/ksp/ksp/examples/tutorials/

doc: bugfix - edit only .html files [and not manual.pdf]

[ this was the original intent before the change in 3a818db72d7 ]

This is triggered by 'petsc4py' keyword in src/ksp/ksp/examples/tutorials/ex100.c

$ cat ex100.c | /home/balay/tmp/petsc/arch-build/bin/mapnames -map /home/balay/tmp/petsc/docs/manualpages/manualpages.cit -printmatch-link -o /dev/null |grep manual.pdf
petsc4py ../../manual.pdf#section.1.1

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Docs: manimplementations: bug fix to process functions in .h files

The previous behavior did not properly process functions found in .h
files (e.g. in src/mat/impls/sbaij/seq/relax.h). This commit u

Docs: manimplementations: bug fix to process functions in .h files

The previous behavior did not properly process functions found in .h
files (e.g. in src/mat/impls/sbaij/seq/relax.h). This commit updates
a grep command to only look in the appropriate file types, and updates
a sed command to include .h files.

Reported-by: Dave A. May <dave.mayhem23@gmail.com>

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Docs: manexamples: more-specific matching for counting example links

The manexamples target was counting the number of example links alredy
added to a man page by counting the occurences of "tutoria

Docs: manexamples: more-specific matching for counting example links

The manexamples target was counting the number of example links alredy
added to a man page by counting the occurences of "tutorials", which
lead to an incorrect count on pages (e.g. KSPSolve) which happened to
mention this word. This restricts to counting lines which start with a
link opening tag and contain /tutorials/.

Reported-by: Dave A. May <dave.mayhem23@gmail.com>

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cusp: remove misc references to cusp

Merge remote-tracking branch 'origin/pr1206/arcowie-rem/feature-error-logging/master'

Merge branch 'knepley/fix-dmplex-fortran' [PR #1277]

* knepley/fix-dmplex-fortran:
Doc: Fix spelling of DMLabelGetNumValues
Plex: Add PetscPartitioner to Fortran list

Commit f20c2d659b168217cb455989f28afe052d71a64c broke lex.py
so the users manual was no longer being built. There reverted
the changes to lex.py

Commit-type: bug-fix

Plex: Add PetscPartitioner to fort list
Suggested-by: Jiaoyan Li <Jiaoyan.Li@inl.gov>

Merge branch 'jed/ascii-filter' [PR #1271]

* jed/ascii-filter:
conf/rules: replace Unicode quotes with ASCII (Python-3 support)

conf/rules: replace Unicode quotes with ASCII

If the compiler is really using Unicode quotes, we'll need to modify
config/install.py (which reads this file) to specify the encoding in
order to suppo

conf/rules: replace Unicode quotes with ASCII

If the compiler is really using Unicode quotes, we'll need to modify
config/install.py (which reads this file) to specify the encoding in
order to support legacy locales with Python-3 (where the file is
opened as text, not binary).

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Add try and except to the new command line argument problem

Updated petsc_tas_analysis to take a command line argument for the name of the problem, and search the configTAS.py module for the names of the fields. If no argument is specified then it will defau

Updated petsc_tas_analysis to take a command line argument for the name of the problem, and search the configTAS.py module for the names of the fields. If no argument is specified then it will default to naming fields using numbers.

Also improved the data output formating.

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Fixed inheritence problem with File and Field objects.

Add utility script to open a new browser window and render XML log files

dashboard: add p4est column

Replace more occurences of string functions. Keep using the string library for string constants (e.g., string.ascii_letters or string.digits), as this functionality has not been removed in python 3

Stop using string module for string manipulations, for compatibility with python3

Merge branch 'maint'

nightlytests: invoke git prune before fetch

Merge branch 'master' into arcowie-rem/feature-error-logging

* master:
sys_tutorials-ex19_1: ignore check_pointer_intensity used in bitbucket pipelines
python2.6: provide subprocess.check_output

Merge branch 'master' into arcowie-rem/feature-error-logging

* master:
sys_tutorials-ex19_1: ignore check_pointer_intensity used in bitbucket pipelines
python2.6: provide subprocess.check_output (introduced in python2.7)
ctags: switch to supbrocess in d35930a37ac51e1f78ebfaaf074c663076f75215 results in verbose output on screen
slepc: use slepc-3.10.1 with petsc-3.10
slepc: fix download with prefix
plexexodusii.c: Vec array type changed from PetscReal* to PetscScalar*.
PCPatch: correct logic for setFromOptions calls on subksps
PCPatch: fix setFromOptions for !save_operators
PCPatch: fix getGlobalDofs for !combined
PCPatch: fix patchSection setup for case !combined
*change* added const to input parameters in BLAS method declarations
sowing: add check for cygwin/g++

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python2.6: provide subprocess.check_output (introduced in python2.7)

Reported-by: Mark Adams <mfadams@lbl.gov>
Thanks-to: Satish Balay <balay@mcs.anl.gov>

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (393 commits)
Bib: Update reference
Mat: Doc fix
Bib: Updated ref
PetscDS: Doc fixes
PC+LU: Do not try to refactor an

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (393 commits)
Bib: Update reference
Mat: Doc fix
Bib: Updated ref
PetscDS: Doc fixes
PC+LU: Do not try to refactor an already factored matrix
Mat: Small fix for checking and docs
Mat: Added MatSetFactorType() - Needed it when making a shell matrix look factored
PetscDS: Added PetscDSUpdateBoundary() - Lets the user change the boundary condition
single precision produces different convergence history
p4est: has a dependency on zlib - so handle it correctly
Add -mat_mffd_complex to use the Lyness complex number trick to compute J_u * v instead of differencing.
Replace VecWAXPY by VecAXPY if needed
Revert "Replace VecWAXPY by VecAXPY if needed"
Replace VecWAXPY by VecAXPY if needed
MatHermitianTransposeGetMat and MatCreateVecs
ex19: Updated test filter to avoid false positives.
DM: Improved Global-To-Natural docs Suggested-by: Josh L <ysjosh.lo@gmail.com>
Do not build shared openblas when doing static build
Upgrade OpenBLAS to 0.3.3
test: add alt output file for changes in OSX-10.14 and Xcode-10.0 [perhaps related to ML]
...

Conflicts:
src/vec/is/utils/vsectionis.c

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ctags: switch to supbrocess in d35930a37ac51e1f78ebfaaf074c663076f75215 results in verbose output on screen

restore old behavior by suppressing this.

Reported-by: Jose E. Roman <jroman@dsic.upv.es>

Merge branch 'jed/python3-futurize' [PR #1122]

Merge announces support for Python 3.4+ in changes/dev.html.

* jed/python3-futurize: (44 commits)
gmakegentest: avoid prefix matching in regex
dm

Merge branch 'jed/python3-futurize' [PR #1122]

Merge announces support for Python 3.4+ in changes/dev.html.

* jed/python3-futurize: (44 commits)
gmakegentest: avoid prefix matching in regex
dm tests ex23.c: fix test args: -one -two -three
gmakegentest: more fixes
gmakegentest: fix processing of arguments containing number followed by "-"
gmakegentest: always loop over nsize; Python-3 fixes
python3: add in a python-3.4 test
python: fix build on osx/opensolaris - where 'RANLIB=ranlib -c' i.e with a space..
python3: fix --download-ptscotch error
configure: glob() gets executed early - whereas we need to get file list later [after 'make all' or equivalent] so revert back to using shell to get file-list
python3: map() requires a list modifier for this usage.
python: replace ModuleNotFoundError a python3.6+ feature with ImportError
config: call setup to ensure that debugLevel is set
nightlies: switch linux-pkg-dbg-ftn-interfaces to python3
config: enable Python-3
config: urllib/urlparse updates for Python-3 compatibility
config fblaslapack: use isIBM instead of manual test
python: replace commands with subprocess
Fix LOCDIR paths
generateetags.py: switch from commands to subprocess; unicode fix
python: don't import commands when it isn't used
...

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Added feature that if no -file/-f is specified the scrypt will automatically look for and use all files found in the directory specified in configTas.py absoluteData.

Also added error handling if no

Added feature that if no -file/-f is specified the scrypt will automatically look for and use all files found in the directory specified in configTas.py absoluteData.

Also added error handling if no files are specified or found.

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