Merge branch 'barry/2024-04-29/add-fortran-enums' into 'main'

Major updates to Fortran interface

See merge request petsc/petsc!7517

Fortran 90: fully embrace After 34 years!

- deprecate use of 'F90' in Fortran function names
- use Fortran pointers when appropriate
- the new Fortran API is not backward compatible with previous ve

Fortran 90: fully embrace After 34 years!

- deprecate use of 'F90' in Fortran function names
- use Fortran pointers when appropriate
- the new Fortran API is not backward compatible with previous versions!
- also clean up inconsistent PETSc code detected by new Fortran generation tools
- drop use of bfort
- automatically generate all the Fortran PETSc objects, enums etc from the include files
- generate most of the Fortran interface definitions and functions from the source code
- simplify the number and organization of Fortran modules

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

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Merge branch 'jacobf/2023-08-17/header-guard-check' into 'main'

Check header guards

See merge request petsc/petsc!6822

Convert all header guards to pragma once

Merge branch 'dcampbell/dmnetworkview-options' into 'main'

Add more useful viewing options for DMNetwork

See merge request petsc/petsc!6345

Add new command-line options for DMNetwork visualization
Placing the options in PetscOptionsBegin ... PetscOptionsEnd
Fix(DMNetwork): fix -draw_pause handling
Feat(DMNetwork): add setters for viewer

Add new command-line options for DMNetwork visualization
Placing the options in PetscOptionsBegin ... PetscOptionsEnd
Fix(DMNetwork): fix -draw_pause handling
Feat(DMNetwork): add setters for viewer options
Co-authored-by: Duncan Campbell <dccampbell1@shockers.wichita.edu>
Co-authored-by: Aidan Hamilton <aidan@udel.edu>
Co-authored-by: Hong Zhang <hzhang@mcs.anl.gov>

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Merge branch 'ahamilton/Feature-DMNetwork-CreateCoordinateDM_Network' into 'main'

Feature: Add DMGetCoordinateDM Support for DMNetwork

See merge request petsc/petsc!5745

-Add DMNetworkGetNumEdges and DMNetworkGetNumVertices, missing access functions for properties of DMNetwork.
-Add DMCreateCoordinates_Network, a missing DM function that now allows for DMNetwork to h

-Add DMNetworkGetNumEdges and DMNetworkGetNumVertices, missing access functions for properties of DMNetwork.
-Add DMCreateCoordinates_Network, a missing DM function that now allows for DMNetwork to handle coordinates in the same way as other DM objects.
-Add support for automatic migration of coordinate DM and coordinates on call to DMNetworkDistribute.
-Add simple test code for DMCreateCoordinates_Network and automatic migration to src/dm/impls/network/tests/ex2.c

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Merge branch 'jacobf/2022-09-21/2-bike-2-shed' into 'main'

Feature: Bicycle Storage Facility 2

See merge request petsc/petsc!5661

Transform all header-guards into ifndefs to make clang-format ignore them for preprocessor indentation

Merge branch 'barry/2022-08-21/clang-format-source' into 'main'

format repository with clang-format

See merge request petsc/petsc!5541

clang-format: convert PETSc sources to comply with clang-format

Merge branch 'ahamilton/fix-DMClone_Network' into 'main'

Fix DMClone_Network

See merge request petsc/petsc!5362

Changed DMClone_Network to only clone the topological part of the network. Adjusted DMDestroy_Network to compensate. Before this DMClone was broken, and essentially just giving you a shared pointer.

Changed DMClone_Network to only clone the topological part of the network. Adjusted DMDestroy_Network to compensate. Before this DMClone was broken, and essentially just giving you a shared pointer. You could use the clone to mess with the values of the components of the original for example. This is a step in getting DMClone to behave similarly for DMNetwork as other DMs.

Added DMNetworkFinalizeComponents() to setup the internal data structures for the components and dofs on a network. Necessary to work with cloned networks

Added basic example to test cloning of a network

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Merge branch 'hzhang/dmnetworksharedvertex-update' into 'main'

optimize TableAddSVtx()

See merge request petsc/petsc!4763

optimize TableAddSVtx()
cleanup GetEdgelist_Coupling()
update network->subnet[net].nvtx for ghoted subnetworks in DMNetworkLayoutSetUp()

add changes made by Barry in MR4883: DMNetworkGetGlobalEdge/V

optimize TableAddSVtx()
cleanup GetEdgelist_Coupling()
update network->subnet[net].nvtx for ghoted subnetworks in DMNetworkLayoutSetUp()

add changes made by Barry in MR4883: DMNetworkGetGlobalEdge/VertexIndex() work before calling DMSetUp()
use local Nvtx = nvtx_max - nvtx_min + 1 as the size for table as suggested by Barry

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Merge branch 'barry/2021-07-03/demonstrate-network-parallel-build' into 'main'

dmnetwork: bug fix for parallel input single subnetwork; API change, optimize and cleanup

See merge request petsc/pets

Merge branch 'barry/2021-07-03/demonstrate-network-parallel-build' into 'main'

dmnetwork: bug fix for parallel input single subnetwork; API change, optimize and cleanup

See merge request petsc/petsc!4176

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This example seems to demonstrate that one cannot construct a DMNetwork with one subnetwork in parallel correctly.

Commit-type: bug-report
\spend 40m

DMNetworkAddSubnetwork() does not need input nv

This example seems to demonstrate that one cannot construct a DMNetwork with one subnetwork in parallel correctly.

Commit-type: bug-report
\spend 40m

DMNetworkAddSubnetwork() does not need input nv; optimize DMNetworkLayoutSetUp_Coupling() and DMNetworkLayoutSetUp()
bugfix for DMNetworkDistribute(): subnet[].nvtx was over counted
cleanup network.c; add '-malloc_dump 0' to ex10.c: otherwise opensolaris-misc pipeline test fails
use the fix suggested by Satish. This fixes the opensolaris-misc pipeline test error of ex10.c, and harmless to other cases
rm #if 0. Previously kept for future work

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Merge branch 'hzhang/add-dmnetworkcreateis' into 'main'

Add DMNetworkCreateIS()

See merge request petsc/petsc!3999

add DMNetworkCreateIS() and DMNetworkCreateLocalIS()
rm subdir 'wash'
rename pipes1.c -> pipes.c

Merge branch 'hzhang/dmnetwork-netcoupling' into 'master'

Hzhang/dmnetwork netcoupling

See merge request petsc/petsc!3051

New design for the coupling of sub-dmnetowrks.
See email discussions on Nov 23, 2019, Subject: Re: petsc | DMNetwork: Update manual. (!2297)
See dev.html for changes made
using sf, DMNetworkVariables

New design for the coupling of sub-dmnetowrks.
See email discussions on Nov 23, 2019, Subject: Re: petsc | DMNetwork: Update manual. (!2297)
See dev.html for changes made
using sf, DMNetworkVariablesSetUp() handles shared vertex easily

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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 'shri/feature-dmnetwork-component-variables' into 'master'

setting/accessing component variables

See merge request petsc/petsc!2396