Remove all double blank lines from source

Commit-type: petsc-style
/2h

Merge branch 'jolivet/fix-formatting-bracket' into 'master'

checkbadSource: new rule for wrongfully placed "{"

See merge request petsc/petsc!3655

checkbadSource: new rule for wrongfully placed "{"

Merge branch 'barry/2020-08-16/fix-source-formatting' into 'master'

Turn on checkbadSource test to generate an error when found; fix all source code that causes errors

See merge request petsc/petsc

Merge branch 'barry/2020-08-16/fix-source-formatting' into 'master'

Turn on checkbadSource test to generate an error when found; fix all source code that causes errors

See merge request petsc/petsc!3064

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Turn on checkbadSource test to generate an error when found; fix all source code that causes errors

Commit-type: portability-fix, testing-fix, style-fix, feature, maintainability
/spend 1.5h

Merge branch 'master' into 'stefanozampini/sfwin-reuse-win'

# Conflicts:
# config/BuildSystem/config/packages/MPI.py

Merge remote-tracking branch 'origin/maint'

Merge branch 'jolivet/fix-double-chkerrq' into 'maint'

Double CHKERRQ

See merge request petsc/petsc!2427

Double CHKERRQ

Merge branch 'barry/2019-10-16/use-error-codes' into 'master'

Replace use of 1 with appropriate error code; use PetscObjecComm() instead of...

See merge request petsc/petsc!2182

Replace use of 1 with appropriate error code; use PetscObjecComm() instead of PETSC_COMM_SELF for errors when appropriate

Commit-type: error-checking, testing-fix, style-fix, examples

Merged in barry/fix-naming-cg-methods (pull request #1650)

Fixed inconsistent naming with CG methods for TR

Approved-by: Matthew Knepley <knepley@gmail.com>

Fixed inconsistent naming with CG methods for TR

Some of the KSPXXX macros for xxx had an inconsisten KSPCGXXX that was not in the string xxx name
The KSPCGXXX was used for KSPCreate_CGXXX() but the

Fixed inconsistent naming with CG methods for TR

Some of the KSPXXX macros for xxx had an inconsisten KSPCGXXX that was not in the string xxx name
The KSPCGXXX was used for KSPCreate_CGXXX() but the other method functions were missing the CG, for example, KSPSolve_XXX()
(these meant using tags to find functions was cumbersome due to the special cases)
Missing Fortran macro

Removed the extraneous CG from the macros and the function usage; now all macros and functions have consistent PETSc style usage
that match the string names
Added deprecation messages for out-dated use
Added new configure check for PETSC_DEPRECATED_MACRO

I decided to remove the CG from the KSPCGXXX instead of adding a cg to the string name because 1) it was not possible to deprecate
the string names at compile time, we would have to have runtime warnings. 2) the string names are shorter, 3) the stcg already
had a cg (at the end and not the beginning) and that would have to be removed or we'd have the absurd cgstcg. If starting from
sratch today not worrying about legacy I would have all the string names begin with cg consistently (and naturally the KSPXXX would
have them as well), but for legacy reasons we have the current naming which is not ideal because it does not clearly
indicate which methods are CG methods. (We have this problem with other subclasses in PETSc also).

Commit-type: style-fix

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Merge branch 'master' of bitbucket.org:petsc/petsc

Merge branch 'stefano_zampini/fix-tao-update-ctx' [PR #1443]

* stefano_zampini/fix-tao-update-ctx:
Few small fixes to Tao before the release.

- TAOSetUpdate: change the Update callback
In SNES, t

Merge branch 'stefano_zampini/fix-tao-update-ctx' [PR #1443]

* stefano_zampini/fix-tao-update-ctx:
Few small fixes to Tao before the release.

- TAOSetUpdate: change the Update callback
In SNES, the update function does not uses contexts, and thus it does not appear in the callback prototype.
With TAO, since we are explcitily passing the ctx via TAOSetUpdate, we have to give it back to the user when performing the call

- Tao: PETSc does not print warnings

- MatAssembled: there's no point in checking the type
a matrix with type not set cannot be assembled

- TaoBNKEstimateActiveSet: Call MatHasOperation() only if the matrix has been assembled
the previous logic for MatGetDiagonal still holds. With this fix, the code will not error in case the hessian has not been assembled at this time

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TAOSetUpdate: change the Update callback

In SNES, the update function does not uses contexts, and thus it does not appear in the callback prototype
With TAO, since we are explcitily passing the ctx

TAOSetUpdate: change the Update callback

In SNES, the update function does not uses contexts, and thus it does not appear in the callback prototype
With TAO, since we are explcitily passing the ctx via TAOSetUpdate, we have to give it back to the user when performing the call

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Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merge branch 'master' into jpustay/feature-swarm-example

Merged petsc/petsc into master

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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Merged petsc/petsc into master

Merge branch 'denera/tao-gauss-newton-wrapper' [PR #1151]

* denera/tao-gauss-newton-wrapper:
Regularized Gauss-Newton algorithm/wrapper
New BRGN algorithm added for regularized Gauss-Newton formulat

Merge branch 'denera/tao-gauss-newton-wrapper' [PR #1151]

* denera/tao-gauss-newton-wrapper:
Regularized Gauss-Newton algorithm/wrapper
New BRGN algorithm added for regularized Gauss-Newton formulation.
This algorithm is a thin wrapper that relies on TaoSetResidualRoutine() and TaoSetResidualJacobianRoutine() interfaces to accept the residual and Jacobian associated with a least-squares problem,
and then construct the internal objective, gradient and Hessian evaluation functions for the regularized problem formulation.
Currently only Tikhonov regularization is available, but other smooth regularizers are planned in the future.
The resulting regularized problem is passed onto an existing bound-constrained algorithm (e.g.: BQNLS or BNTL), controlled by the -tao_brgn_subsolver flag.

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Regularization changed to x-x_old, user hook added into optimization loops, eliminated explicit MatTransposeMatMult option in Hessian computation

Merge branch 'master' into knepley/feature-plex-functionals

* master: (984 commits)
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out

Merge branch 'master' into knepley/feature-plex-functionals

* master: (984 commits)
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out
fix gcov obj path
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Dev manual: remove duplicate entry
Plex test ex5: Removed "future" test, as it resulted in issues in the nightly tests.
Some minor typos in TS
Add ADIOS2.py which I forgot to git add in the past
Plex ex5: Disable test
Doc: Added note for interface change
KSPLSQRMonitorDefault fixed for quad precision
Tao: Added alternative output for chwirut2 test.
TS ex45,ex46: Removed overly refined tests for faster nightly tests.
KSP ex72: Fixed needlessly long-running PCTFS tests.
SNES ex56: Reduced test size to speed up nightly test suite.
KSPSolve_LSQR: don't compute unused norm of rhs
SNES ex13: Reduced problem sizes for nightly tests.
PetscOptionsDeprecated(): fix for NULL prefix
PetscOptionsDeprecated(): add option to print additional info
SNES ex12: Reduced sizes for BDDC tests.
...

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Merge branch 'master' into knepley/feature-plex-elasticity-test

* master: (1553 commits)
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
config

Merge branch 'master' into knepley/feature-plex-elasticity-test

* master: (1553 commits)
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Plex test ex5: Removed "future" test, as it resulted in issues in the nightly tests.
Some minor typos in TS
Add ADIOS2.py which I forgot to git add in the past
Plex ex5: Disable test
Doc: Added note for interface change
KSPLSQRMonitorDefault fixed for quad precision
Tao: Added alternative output for chwirut2 test.
TS ex45,ex46: Removed overly refined tests for faster nightly tests.
KSP ex72: Fixed needlessly long-running PCTFS tests.
SNES ex56: Reduced test size to speed up nightly test suite.
KSPSolve_LSQR: don't compute unused norm of rhs
SNES ex13: Reduced problem sizes for nightly tests.
PetscOptionsDeprecated(): fix for NULL prefix
PetscOptionsDeprecated(): add option to print additional info
SNES ex12: Reduced sizes for BDDC tests.
PetscFileRetrieve(): Suppress output to STDERR when downloading a file.
MatMatMult: Fixed unused variable pN.
DMDestroy: Guard call to dm->ops->destroy * Similar guards are in place in many other methods (IS,Vec,Mat) and permit the DM to be destroyed even if DMSetType() was never called.
...

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