Update wrappers to current Chaste develop branch

[kwabenantim]

• Add wrappers for new functionality introduced into Chaste trunk by Jack & Alex
• List what needs wrapping
• Update wrapper generation yml
• Generate new wrappers with CPPWG
• Manually add wrappers that cannot be autogenerated
• Fix issues with automatically generated wrappers if necessary
• Rebuild conda package

[kwabenantim]

New classes to wrap

See Chaste/Chaste#104:

• BiasedBernoulliTrialCellCycleModel
• SlidingBoundaryCondition
• VonMisesVertexBasedDivisionRule
• ConstantTargetAreaModifier
• DivisionBiasTrackingModifier
• LabelDependentBernoulliTrialCellCycleModel
• PlanarPolarisedFarhadifarForce
• ExtrinsicPullModifier

See Chaste/Chaste#56:

• AlwaysDivideCellCycleModel
• CellEdgeData
• CellSrnModel
• DeltaNotchEdgeSrnModel
• DeltaNotchInteriorSrnModel
• DeltaNotchEdgeOdeSystem
• DeltaNotchInteriorOdeSystem
• VertexBasedPopulationSrn
• DeltaNotchEdgeInteriorTrackingModifier
• Edge
• EdgeHelper
• EdgeOperation

[kwabenantim]

CPPWG Error Description

Unable to find declaration Clazz< 2, 2 >

Error Message

Traceback (most recent call last):
  File "~/Chaste/projects/PyChaste/dynamic/wrapper_generators/generate.py", line 55, in <module>
    generator.generate_wrapper()
  File "~/cppwg/cppwg/generators.py", line 200, in generate_wrapper
    module_writer.write()
  File "~/cppwg/cppwg/writers/module_writer.py", line 112, in write
    class_decl = self.source_ns.class_(fullName.replace(" ",""))
  File "~/.local/lib/python3.10/site-packages/pygccxml/declarations/scopedef.py", line 546, in class_
    self._find_single(
  File "~/.local/lib/python3.10/site-packages/pygccxml/declarations/scopedef.py", line 464, in _find_single
    found = matcher.get_single(decl_matcher, decls, False)
  File "~/.local/lib/python3.10/site-packages/pygccxml/declarations/scopedef.py", line 90, in get_single
    raise runtime_errors.declaration_not_found_t(decl_matcher)
pygccxml.declarations.runtime_errors.declaration_not_found_t: Unable to find declaration. Matcher: [(decl type==class_t) and (name==AbstractCellBasedSimulationModifier< 2, 2 >)]
make[3]: *** [projects/PyChaste/CMakeFiles/project_PyChaste_Python_Bindings.dir/build.make:70: project_PyChaste_Python_Bindings] Error 1
make[2]: *** [CMakeFiles/Makefile2:21607: projects/PyChaste/CMakeFiles/project_PyChaste_Python_Bindings.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:21614: projects/PyChaste/CMakeFiles/project_PyChaste_Python_Bindings.dir/rule] Error 2
make: *** [Makefile:8103: project_PyChaste_Python_Bindings] Error 2

Affected Classes

AbstractLinearPde
AbstractLinearParabolicPde
RandomDirectionCentreBasedDivisionRule
FixedCentreBasedDivisionRule
AbstractCentreBasedDivisionRule
GeneralisedLinearSpringForce
DifferentialAdhesionGeneralisedLinearSpringForce
AbstractCellPopulationBoundaryCondition
PlaneBoundaryCondition
AttractingPlaneBoundaryCondition
AbstractCellPopulation
AbstractOffLatticeCellPopulation
AbstractCentreBasedCellPopulation
MeshBasedCellPopulation
OffLatticeSimulation
AbstractForce
AbstractTwoBodyInteractionForce
AbstractCellBasedSimulationModifier

Fix
The investigation continues on cppwg/issues/1

[kwabenantim]

CPPWG Error Description

Unable to find declaration Clazz

Error Message

Traceback (most recent call last):
  File "~/Chaste/projects/PyChaste/dynamic/wrapper_generators/generate.py", line 55, in <module>
    generator.generate_wrapper()
  File "~/cppwg/cppwg/generators.py", line 200, in generate_wrapper
    module_writer.write()
  File "~/cppwg/cppwg/writers/module_writer.py", line 112, in write
    class_decl = self.source_ns.class_(fullName.replace(" ",""))
  File "~/.local/lib/python3.10/site-packages/pygccxml/declarations/scopedef.py", line 546, in class_
    self._find_single(
  File "~/.local/lib/python3.10/site-packages/pygccxml/declarations/scopedef.py", line 464, in _find_single
    found = matcher.get_single(decl_matcher, decls, False)
  File "~/.local/lib/python3.10/site-packages/pygccxml/declarations/scopedef.py", line 90, in get_single
    raise runtime_errors.declaration_not_found_t(decl_matcher)
pygccxml.declarations.runtime_errors.declaration_not_found_t: Unable to find declaration. Matcher: [(decl type==class_t) and (name==EdgeHelper)]
make[3]: *** [projects/PyChaste/CMakeFiles/project_PyChaste_Python_Bindings.dir/build.make:70: project_PyChaste_Python_Bindings] Error 1
make[2]: *** [CMakeFiles/Makefile2:21607: projects/PyChaste/CMakeFiles/project_PyChaste_Python_Bindings.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:21614: projects/PyChaste/CMakeFiles/project_PyChaste_Python_Bindings.dir/rule] Error 2
make: *** [Makefile:8103: project_PyChaste_Python_Bindings] Error 2

Affected Classes

CellwiseOdeSystemInformation
CellCycleModelOdeSolver
EdgeHelper

Fix
The investigation continues on cppwg/issues/1

[kwabenantim]

Continuing Wrapper Creation Strategy

• Generate wrappers that can be generated with CPPWG
• Manually add remaining wrappers
• Fix Unable to find declaration errors (cppwg/issues/1) later.

[kwabenantim]

Error: "Already Registered"

import chaste.mesh

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
/tmp/ipykernel_49991/3595748004.py in <module>
----> 1 import chaste.mesh

~/Chaste/build/projects/PyChaste/python/chaste/mesh/__init__.py in <module>
     41 warnings.filterwarnings("ignore")
     42 
---> 43 from chaste.mesh._chaste_project_PyChaste_mesh import *

ImportError: generic_type: type "ChastePoint2" is already registered!

Fix

• It's not clear why we have this error. ChastePoint2 is registered only once in the codebase. However, this fixes it:

py::class_<ChastePoint2  ...  >(m, "ChastePoint2", py::module_local())

• Root cause was order of registrations. Resolved by correcting order and removing duplicate registrations by other modules. py::module_local() not necessary.

[kwabenantim]

Error: "could not convert default argument"

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "~/Chaste/build/projects/PyChaste/python/chaste/cell_based/__init__.py", line 40, in <module>
    from chaste.cell_based._chaste_project_PyChaste_cell_based import *
ImportError: arg(): could not convert default argument 'pMeshCuboid: boost::shared_ptr<ChasteCuboid<2u> >' in method '<class 'chaste.cell_based._chaste_project_PyChaste_cell_based.EllipticBoxDomainPdeModifier2'>.__init__' into a Python object (type not registered yet?)

Fix

• Wrap ChasteCuboid

[kwabenantim]

Excluded Classes (All Now Included)

• Alarcon2004OxygenBasedCellCycleModel
• EllipticBoxDomainPdeModifier
• ParabolicBoxDomainPdeModifier
• RandomCaSwitchingUpdateRule
• TysonNovakCellCycleModel

Excluded Methods

• Cylindrical2dNodesOnlyMesh::SetUpBoxCollection (unit_vector argument)
• PeriodicNodesOnlyMesh::SetUpBoxCollection (zero_vector argument)
• TysonNovak2001OdeSystem::AnalyticJacobian (double ** argument)
• VertexMesh::GetEdgeHelper (EdgeHelper is not constructible)

To Add Manually

• CylindricalHoneycombMeshGenerator
• ToroidalHoneycombMeshGenerator
• ToroidalHoneycombVertexMeshGenerator
• VoronoiVertexMeshGenerator
• ChasteCuboid

[kwabenantim]

Missing Parent Classes is some wrappers
See cppwg/5

Fix
Add parent classes in all wrappers where they are missing.

[kwabenantim]

Conda Build Issues
gcc 11.4.0 from conda has trouble with:

mEdges.push_back(std::make_unique<Edge<SPACE_DIM>> (mEdges.size(), nodeA, nodeB));

Error

Edge<SPACE_DIM>* EdgeHelper<SPACE_DIM>::GetEdgeFromNodes(Node<SPACE_DIM>*, Node<SPACE_DIM>*)':
/home/conda/feedstock_root/build_artifacts/chaste_1686921952219/work/mesh/src/common/EdgeHelper.cpp:49:31: error: 'make_unique' is not a member of 'std'
   49 |         mEdges.push_back(std::make_unique<Edge<SPACE_DIM>> (mEdges.size(), nodeA, nodeB));
      |                               ^~~~~~~~~~~
/home/conda/feedstock_root/build_artifacts/chaste_1686921952219/work/mesh/src/common/EdgeHelper.cpp:49:31: note: 'std::make_unique' is only available from C++14 onwards
/home/conda/feedstock_root/build_artifacts/chaste_1686921952219/work/mesh/src/common/EdgeHelper.cpp:49:57: error: expected primary-expression before '>' token
   49 |         mEdges.push_back(std::make_unique<Edge<SPACE_DIM>> (mEdges.size(), nodeA, nodeB));

However, this compiles fine with gcc 11.3.0 on Ubuntu 22.04

Temporary Workaround

mEdges.push_back(std::unique_ptr<Edge<SPACE_DIM>> (new Edge<SPACE_DIM>{mEdges.size(), nodeA, nodeB}));