Fix PyChaste Build for Chaste 2024.1

[kwabenantim]

• Supports Release PyChaste 2024.1 #62

[kwabenantim]

The bindings seem to be having problems finding the constructors for MutableElement<1,2>, which is needed by ImmersedBoundaryElement<2,2>:

/usr/bin/ld:
CMakeFiles/_chaste_project_PyChaste_mesh.dir/dynamic/wrappers/mesh/MutableElement1_2.cppwg.cpp.o: 
in function `MutableElement<1u, 2u>* pybind11::detail::initimpl::construct_or_initialize<MutableElement<1u, 2u>, unsigned int, 0>(unsigned int&&)':
~/PyChaste/dynamic/pybind11/include/pybind11/detail/init.h:76: 
undefined reference to `MutableElement<1u, 2u>::MutableElement(unsigned int)'

/usr/bin/ld: 
CMakeFiles/_chaste_project_PyChaste_mesh.dir/dynamic/wrappers/mesh/MutableElement1_2.cppwg.cpp.o: 
in function `MutableElement1_2_Overloads::MutableElement(unsigned int)':
~/Chaste/projects/PyChaste/dynamic/wrappers/mesh/MutableElement1_2.cppwg.cpp:19: 
undefined reference to `MutableElement<1u, 2u>::MutableElement(unsigned int)'

collect2: error: ld returned 1 exit status

[kwabenantim]

import chaste.visualization

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "~/pychaste-env/lib/python3.10/site-packages/chaste/visualization/__init__.py", line 38, in <module>
    from chaste.visualization.fortests import *
  File "~/pychaste-env/lib/python3.10/site-packages/chaste/visualization/fortests.py", line 45, in <module>
    import chaste.cell_based
  File "~/pychaste-env/lib/python3.10/site-packages/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 
'pOdeSolver: boost::shared_ptr<AbstractCellCycleModelOdeSolver>' in 
method '<class 'chaste.cell_based._chaste_project_PyChaste_cell_based.TysonNovakCellCycleModel'>.__init__' 
into a Python object (type not registered yet?)

[kwabenantim]

import chaste.cell_based

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "~/pychaste-env/lib/python3.10/site-packages/chaste/cell_based/__init__.py", line 40, in <module>
    from chaste.cell_based._chaste_project_PyChaste_cell_based import *
ImportError: generic_type: type "AbstractCellCycleModel" is already registered!

[kwabenantim]

The registration issues were corrected by fixing the registration order in 3fe4c00

[kwabenantim]

Immersed Boundary Tutorial and visualization are working okay except for an error in the last example with a FluidSource:

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
/tmp/ipykernel_57426/1620215830.py in <module>
      6 simulator.SetEndTime(1000 * dt)
      7 # Perform the simulation
----> 8 simulator.Solve()
      9 # Visualize the end state
     10 nb_manager.vtk_show(scene, height=300)

RuntimeError: 
Chaste error: ./mesh/src/utilities/ObsoleteBoxCollection.cpp:123: Location in dimension 0 is -nan which is not in the domain [0, 1].

[kwabenantim]

Immersed Boundary Tutorial and visualization are working okay except for an error in the last example with a FluidSource:

Fixed in 1f56164 by reducing the simulation run length to the value in the original C++ tutorial.