[All] Move fetched guis folders into dedicated folder (sofa-framework#5356)

* Put guis in a dedicated folder to enable dependencies of plugins to guis

* Fix fetching

* Restore deleted files

* Restore doc for external plugins

* Squashed commit of the following:

commit d1d4ee8
Author: Hugo <[email protected]>
Date:   Wed Apr 2 15:31:53 2025 +0200

    [examples] Minor update default scene (sofa-framework#5373)

    Co-authored-by: Paul Baksic <[email protected]>

commit 7ae2862
Author: Hugo <[email protected]>
Date:   Wed Apr 2 15:30:58 2025 +0200

    [Mapping] Remove warning in DistanceToPlaneMapping_test.cpp (sofa-framework#5374)

    Co-authored-by: Paul Baksic <[email protected]>

commit 82b05c6
Author: Paul Baksic <[email protected]>
Date:   Wed Apr 2 15:29:27 2025 +0200

    [CMake] Fetch in build dir instead of source to avoid lots of cmake errors (sofa-framework#5332)

    * Fetch in build dir instead of source to avoid lots of cmake errors

    * Use sofa_add_generic in macros instead of sofa_add_subdirectory, because it makes no sense + remove deprecated macros

    * Fix reference handling

    * Fix topology regression

    * Remove plugisn directory ans set everything in the cmakelist

    * Fix config

commit c038c1d
Author: Frederick Roy <[email protected]>
Date:   Mon Mar 31 16:53:03 2025 +0900

    [Examples] Add an option to (not) build SimpleAPI examples (sofa-framework#5362)

    * add an option to build simplapi examples

    * add option in presets

    ---------

    Co-authored-by: Hugo <[email protected]>

commit b5afc3f
Author: Frederick Roy <[email protected]>
Date:   Mon Mar 31 16:31:36 2025 +0900

    [All] Fix warnings (sofa-framework#5369)

    * remove nagging deprecation warnings

    * remove trivial warnings

commit 5179ed3
Author: Hugo <[email protected]>
Date:   Fri Mar 28 09:20:18 2025 +0100

    [all] Lifecycle : Disable SOFA_ATTRIBUTE_DEPRECATED  (sofa-framework#5360)

    * [all] Lifecycle : Disable SOFA_ATTRIBUTE_DEPRECATED

    * forgotten PartialFixedConstraint.h

commit 8f8989f
Author: Alex Bilger <[email protected]>
Date:   Fri Mar 28 06:58:56 2025 +0100

    [GUI.Common] Clean and fix MouseOperation (sofa-framework#5336)

    * fix typo

    * propagate fix typo

    * minimal cleaning + variable initialization

    * fix function return

    * fix compilation for clang

    ---------

    Co-authored-by: Frederick Roy <[email protected]>

commit 3f98c18
Author: Hugo <[email protected]>
Date:   Fri Mar 28 02:24:30 2025 +0100

    [examples] Fix wrong topology Data arrays on the surface mesh in HexahedralFEMForceField.scn  (sofa-framework#5367)

    * Update HexahedralFEMForceField.scn

    * Update HexahedralFEMForceField.scn

    ---------

    Co-authored-by: erik pernod <[email protected]>

commit 80fa9d7
Author: Frederick Roy <[email protected]>
Date:   Thu Mar 27 17:29:13 2025 +0900

    [CMake] Remove references to deleted projects/option (sofa-framework#5361)

    remove references to deleted stuff

    Co-authored-by: Paul Baksic <[email protected]>

commit 688cd89
Author: Frederick Roy <[email protected]>
Date:   Thu Mar 27 16:46:31 2025 +0900

    [CMake] Fix install process with default option SOFA_INSTALL_RESOURCES_FILES (sofa-framework#5363)

    * remove install of now-externalized sofa-launcher

    * Update CMakeLists.txt

commit c7807fc
Author: Hugo <[email protected]>
Date:   Thu Mar 27 04:37:18 2025 +0100

    [all] Lifecycle : Remove SOFA_ATTRIBUTE_DISABLED, forgotten files (sofa-framework#5359)

commit 183fee1
Author: Paul Baksic <[email protected]>
Date:   Wed Mar 26 21:02:30 2025 +0100

    [CMake] Remove compatibility layer in macro (sofa-framework#5349)

    Remove compatibility layer meant for SOFA modules

    Co-authored-by: Hugo <[email protected]>

commit a86f468
Author: Paul Baksic <[email protected]>
Date:   Wed Mar 26 19:17:28 2025 +0100

    [All] Spring cleaning 5: reduce size of ressources (sofa-framework#5341)

    * Remove unused heavy mesh files + some config files + unused behavior models

    * Restore needed raw file

    * restore missing file

    ---------

    Co-authored-by: Hugo <[email protected]>

commit 878d3e9
Author: Paul Baksic <[email protected]>
Date:   Wed Mar 26 17:37:08 2025 +0100

    [Tutorials] Spring cleaning 3: remove old c++ tutorials (sofa-framework#5339)

    * delete old tutorials and exctract the two missing examples and implement them in xml

    * Fix cmake config

    * Add version of fallingBeam in SimpleAPI

    * Add GUI but not working...

    * Gui fixed

    * Fix config file in current dir

    * fix constraint attach button

commit 2ed5cf2
Author: Paul Baksic <[email protected]>
Date:   Wed Mar 26 16:04:14 2025 +0100

    [All] Spring cleaning 1: clean main & tools directories (sofa-framework#5325)

    * Clean main directory + tools directory by removing unused stuff

    * Take comment into account

commit 1c8cf17
Author: Paul Baksic <[email protected]>
Date:   Wed Mar 26 16:03:13 2025 +0100

    [examples] Propose a new default scene (sofa-framework#5324)

    * Propose a new simple default scene

    * some perf improvements

    * Set it as the default scene

    * Reduce timestep to get better dynamic

    * Add regression test

    * Add required plugins to try to fix regression

    * Add comments as requested

    * Apply suggestions from code review

    Co-authored-by: Hugo <[email protected]>

    * Apply suggestions from code review

    Co-authored-by: Hugo <[email protected]>

    ---------

    Co-authored-by: Hugo <[email protected]>

commit 95cb283
Author: Alex Bilger <[email protected]>
Date:   Wed Mar 26 14:03:28 2025 +0100

    [ODESolver] Introduction of generic Newton-Raphson algorithm (sofa-framework#5173)

    * introduce files for NewtonRaphsonSolver

    * start implementation

    * move into Core

    * create module for integration methods

    * files for backward euler

    * register objects

    * function to get matrices factors

    * start computation of right-hand side

    * matrix factors

    * start manipulation of vectors

    * some comments

    * rhs input

    * apply projective

    * compute error

    * introduce first convergence criterion

    * introduce example

    * start the loop

    * fix convergence criterion

    * solve system

    * update state

    * some comments

    * another simpler example

    * fix intermediateVelocity

    * check for convergence

    * fix force computation

    * fix some vector operations

    * fix mass factor

    * adjust parameters

    * clear debug stuff

    * cleaning

    * show iteration count in the failing case

    * implement line search

    * support no line search with nb iter = 0

    * Rayleigh damping

    * extract force from the input because it's not an input

    * update the scenes

    * compute true residual

    * implementation of relative stopping criteria

    * rename

    * implement relative successive stopping criteria

    * compare to initial guess (not the first iteration)

    * implement absolute estimate difference criterion

    * implement relative estimate difference criterion

    * update scenes

    * test and feedback on convergence

    * fix

    * fix modules

    * test another form

    * missing test

    * remove duplicated test

    * refactor state list

    * move convergence criteria in files

    * try to fix algorithm

    * add residual graph

    * don't add residual if line search failed

    * fix

    * Introduce static solver

    * Move integration method into Sofa.Component.ODESolver.Backward

    * introduce ode solvers

    * New design working with scalar in tests and in the static solver

    * work on linear multi step

    * add comments

    * Remove Static (which is replaced by StaticOdeSolver)

    * introduction of BDF2

    * Introduce unique component for BDF

    * cleaning and fix

    * revert unnecessary

    * clean and comments

    * show squared

    * more details

    * implement line search with prediction

    * data to warn or not

    * fix static

    * stopping criteria group

    * test on coefficients

    * callback on the order

    * cleaning

    * make sure order is >0

    * remove backup

    * restore alpha=1 after failed line search

    * restore absolute estimate difference

    * restore relative estimate difference measure

    * remove static solver

    * speed up the solver

    * remove static solver scene

    * Apply suggestions from code review

    Co-authored-by: Hugo <[email protected]>

    ---------

    Co-authored-by: Hugo <[email protected]>

commit 5ceafe0
Author: Hugo <[email protected]>
Date:   Wed Mar 26 09:11:00 2025 +0100

    [all] Lifecycle : Remove SOFA_ATTRIBUTE_DEPRECATED (part 2) (sofa-framework#5347)

    * Remove SOFA_ATTRIBUTE_DEPRECATED__RENAME_DATA_IN_IO_MESH

    * Remove SOFA_ATTRIBUTE_DEPRECATED__RENAME_DATA_IN_VISUAL

    * Remove SOFA_ATTRIBUTE_DEPRECATED__RENAME_DATA_IN_SETTING

    * Cleaning : remove unnecessary includes

    * forgotten VEC3STATE_AS_VISUALSTATE

    * Remove SOFA_ATTRIBUTE_DEPRECATED__RENAME_DATA_IN_PLAYBACK

    * fix compilation

    * Remove SOFA_ATTRIBUTE_DEPRECATED__RENAME_DATA_IN_TOPOLOGY_CONTAINER_DYNAMIC

    * Remove SOFA_ATTRIBUTE_DEPRECATED__RENAME_DATA_IN_ENGINE_GENERATE

    * Remove ALL SOFA_ATTRIBUTE_DEPRECATED__RENAME_DATA*

    * Disabling all v24.12 SOFA_ATTRIBUTE_DEPRECATED

    * Disable all SOFA_HEADER_DEPRECATED and Fix older lifecycle forgotten

    * Disable all SOFA_ATTRIBUTE_DEPRECATED

    * forgotten setOriginalData

    * complete removal of SparseCommon.cpp

    * remove SOFAGENERALLOADER_HAVE_ZLIB compat

    * Remove RemovedData d_draw

    * fix compilation

    * Fix PluginManager_Test

    * Fix all uses of vec_id

    * Fix compilation: macro didn't exists

    * Fix scenes using plane definition in TrianglePressureForceField

    ---------

    Co-authored-by: Frederick Roy <[email protected]>
    Co-authored-by: Paul Baksic <[email protected]>
    Co-authored-by: Frederick Roy <[email protected]>

commit c3ef5ce
Author: Alex Bilger <[email protected]>
Date:   Wed Mar 26 06:16:07 2025 +0100

    [GUI.Common] Change inheritance of ConstraintAttachOperation (sofa-framework#5338)

commit 761ddfc
Author: Themis Skamagkis <[email protected]>
Date:   Wed Mar 26 05:50:52 2025 +0100

    [IO.Mesh.BlenderExporter] Inherit from BaseSimulationExporter (sofa-framework#5334)

    * [BlenderExporter] Example scene added in Component/IO/Mesh

    * [IO.Mesh] Changed inheritance of BlenderExporter to BaseSimulationExporter

    * [BlenderExporter] Refactoring under BaseSimulationExporter

    * Substituted member frameCounter with BaseSimulationExporter::m_stepCounter

    * The code block that does the writing in BlenderExporter::handleEvent was
      moved to BlenderExporter::write

    * fileName is now created through BaseSimulationExporter::getOrCreateTargetPath

    * Use of Base::isComponentValid instead of d_componentState

    [Scenes] Adjusted BlenderExporter.scn to new variables

    * [IO.Mesh] Removed redundant calls to BaseSimulationExporter::handleEvent

    A few of the exporter components in IO/Mesh (BlenderExporter, MeshExporter,
    VisualModelOBJExporter) override the handleEvent method yet do nothing except
    call the one in the parent class. This call was removed.

    * [BlenderExporter] Implemented intializations in doInit, called by doReInit

    * Update examples/Component/IO/Mesh/BlenderExporter.scn

    Co-authored-by: Hugo <[email protected]>

    ---------

    Co-authored-by: Hugo <[email protected]>

commit 55425f4
Author: Paul Baksic <[email protected]>
Date:   Tue Mar 25 23:54:46 2025 +0100

    [examples] Fix SofaScene not launched during scene tests (sofa-framework#5353)

    * Expand RequiredPlugins

    * Remove false diffs

    * Apply suggestions from code review

    ---------

    Co-authored-by: Hugo <[email protected]>

* Remove wrongly positionned option

* Change order to fit dependencies (activate gui bindings)

* Update applications/guis/CMakeLists.txt

Co-authored-by: Hugo <[email protected]>

---------

Co-authored-by: Frederick Roy <[email protected]>
Co-authored-by: Hugo <[email protected]>

Author: 3 people

CMakeLists.txt

@@ -193,11 +193,8 @@ sofa_add_subdirectory(plugin applications/plugins/SceneCreator SceneCreator OFF
     WHEN_TO_SHOW "NOT SOFA_BUILD_SCENECREATOR AND NOT SOFA_BUILD_TESTS AND NOT SOFA_BUILD_RELEASE_PACKAGE"
     VALUE_IF_HIDDEN "ON")
 
-## Plugins
-add_subdirectory(applications/plugins)
-
-## Applications
-add_subdirectory(applications/projects)
+## add SofaPython3, guis, plugins, projects
+add_subdirectory(applications)
 
 ## SimpleAPI examples
 option(SOFA_BUILD_SIMPLEAPI_EXAMPLES "Build SOFA scenes based on SimpleAPI." OFF)

applications/CMakeLists.txt

@@ -0,0 +1,11 @@
+cmake_minimum_required(VERSION 3.22)
+
+#Add SofaPython3 first to enable all bindings in plugins
+sofa_add_external(directory SofaPython3 GIT_REF master GIT_REPOSITORY https://www.github.com/sofa-framework/SofaPython3.git)
+
+#Add guis second to enable GUI dependent codes in plugins
+add_subdirectory(guis)
+
+#Add plugins before project so project can depend on plugins
+add_subdirectory(plugins)
+add_subdirectory(projects)

applications/guis/CMakeLists.txt

@@ -0,0 +1,4 @@
+cmake_minimum_required(VERSION 3.22)
+
+sofa_add_external(directory SofaGLFW GIT_REF master GIT_REPOSITORY https://www.github.com/sofa-framework/SofaGLFW.git)
+sofa_add_external(plugin Sofa.Qt GIT_REF master GIT_REPOSITORY https://www.github.com/sofa-framework/Sofa.Qt.git)

applications/plugins/CMakeLists.txt

@@ -21,7 +21,6 @@ sofa_add_subdirectory(plugin DiffusionSolver DiffusionSolver) # Depends on CImgP
 sofa_add_subdirectory(plugin image image) # Depends on CImgPlugin, DiffusionSolver, MultiThreading (soft)
 sofa_add_subdirectory(plugin SofaNewmat SofaNewmat)
 
-sofa_add_external(directory SofaPython3 GIT_REF master GIT_REPOSITORY https://www.github.com/sofa-framework/SofaPython3.git)
 sofa_add_external(plugin CGALPlugin GIT_REF master GIT_REPOSITORY https://www.github.com/sofa-framework/CGALPlugin.git)     # Depends on image
 sofa_add_external(plugin Registration GIT_REF master GIT_REPOSITORY https://www.github.com/sofa-framework/Registration.git) # Depends on image, SofaPython, SofaGui and SofaDistanceGrid
 sofa_add_subdirectory(plugin BulletCollisionDetection BulletCollisionDetection) # Depends on Compliant and LMConstraint

applications/projects/CMakeLists.txt

@@ -5,8 +5,6 @@ sofa_add_subdirectory(application Modeler Modeler OFF)
 
 sofa_add_subdirectory(application SofaPhysicsAPI SofaPhysicsAPI)
 
-sofa_add_external(directory SofaGLFW GIT_REF master GIT_REPOSITORY https://www.github.com/sofa-framework/SofaGLFW.git)
-sofa_add_external(plugin Sofa.Qt GIT_REF master OFF GIT_REPOSITORY https://www.github.com/sofa-framework/Sofa.Qt.git)
 sofa_add_subdirectory(application runSofa runSofa ON)
 
 sofa_add_external(directory Regression GIT_REF master GIT_REPOSITORY https://www.github.com/sofa-framework/Regression.git)