Description
Add text in wrappers explaining that the code is auto-generated.

Summary

Wrappers are created for methods in template specializations that may not have been implemented. In the example below, the Foo(unsigned u) constructor is not implemented in the specialization.

Foo.hpp

template<unsigned DIM_A, unsigned DIM_B>
class Foo : public AbstractFoo<DIM_A, DIM_B>
{
public:
  Foo(unsigned u);
  Foo(unsigned u, double d);
};

// Specialization
template<unsigned DIM_B>
class Foo<1, DIM_B> : public AbstractFoo<1,DIM_B>
{
public:
  Foo(unsigned u, double d);
  Foo(unsigned u);
};

Foo.cpp

template<unsigned DIM_A, unsigned DIM_B>
Foo<DIM_A, DIM_B>::Foo(unsigned u) : AbstractFoo<DIM_A, DIM_B>(u)
{
  // implementation
}

template<unsigned DIM_A, unsigned DIM_B>
Foo<DIM_A, DIM_B>::Foo(unsigned u, double d) : AbstractFoo<DIM_A, DIM_B>(u, d)
{
  // implementation
}

// Specialization
template<unsigned DIM_B>
Foo<1, DIM_B>::Foo(unsigned u, double d) : AbstractFoo<1, DIM_B>(u, d)
{
  // implementation
}

The wrapper below is generated for Foo<1,2>:

py::class_<Foo1_2, Foo1_2_Overloads>, AbstractFoo<1,2> >(m, "Foo1_2")
  .def(py::init<unsigned int>(), py::arg("u"))
  .def(py::init<unsigned int, double>(), py::arg("u"), py::arg("d"))

This results in a linker error:

undefined reference to `Foo<1u, 2u>::Foo(unsigned int)'

Summary

Add a clearer way to call explicitly instantiated C++ template classes from Python.

For example:

# This:
simulation = OffLatticeSimulation2_2(cell_population)

# would become:
simulation = OffLatticeSimulation[2][2](cell_population)

# and this:
cell_population = VertexBasedCellPopulation2(mesh, cells)

# would become:
cell_population = VertexBasedCellPopulation[2](mesh, cells)

Summary

Empty initializer lists {} like

.def(py::init<::std::vector<Foo *> >(), py::arg("laminas") = {})

generate a warning

error: converting to ‘pybind11::arg’ from initializer list would use explicit 
constructor ‘constexpr pybind11::arg::arg(const char*)’ [-Werror]                                                                                                ^
note: in C++11 and above a default constructor can be explicit
cc1plus: all warnings being treated as errors

Possible fix:

.def(py::init<::std::vector<Foo *> >(), py::arg("laminas") = std::vector<Foo *>{})

Description

Use templating to reduce number of generated wrapper files. Many wrappers only vary in template arguments and the rest of the code is exactly the same.

For example, the aim would be to refactor this

register_AbstractCellPopulation2_2_class(m);
register_AbstractCellPopulation3_3_class(m);

into this:

register_AbstractCellPopulation_class<2, 2>(m);
register_AbstractCellPopulation_class<3, 3>(m);

The first requires separate wrappers to be created for AbstractCellPopulation2_2 and AbstractCellPopulation3_3. Counting hpp and cpp, this generates 4 files.

The second requires a single templated wrapper to be created for AbstractCellPopulation. This would only generate 2 files regardless of the number of different sets of template arguments required. This approach would only need each set of arguments to be explicitly instantiated.

Summary

Add a pyproject.toml to enable pip install . :

• Eliminates the need to modify PYTHONPATH manually.
• Dependencies can be specified for auto installation e.g. pygccxml and castxml.
• Prepares for packaging to PyPI or conda.

Description

This works fine in the example:

from pyshapes.geometry import Point2

This does not seem to work, however:

import pyshapes.geometry.Point2

It throws this error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'pyshapes.geometry.Point2'

Description

• Add tests to check wrappers generated for various scenarios.
• Add CI scripts to run the tests on PRs etc.

Dear saviours,

Firstly, I want to thank you for this wonderful library. Seems robust and should make the lives of plethora of python developers in our world a good one. I tried generating the library using the examples but with one tiny change in the Cmakelists.txt i.e., setting the version of python from 2.7 to 3.5

#set(PYBIND11_PYTHON_VERSION 2.7)
set(PYBIND11_PYTHON_VERSION 3.5)

The library was sucessfully built inside the build directory with the test_classes.py and test_functions.py contained in the same directory. When I run the examples as shown in the README.md

python3 test_classes.py

I get this error (not able to import the module)

Traceback (most recent call last):
  File "test_classes.py", line 2, in <module>
    import pyshapes.geometry
  File "/home/ashok/libraries/cppwg/build/pyshapes/geometry/__init__.py", line 2, in <module>
    from _pyshapes_geometry import *
ImportError: No module named '_pyshapes_geometry'

I checked if those modules are available and indeed the pyshapes directory can be seen with the subdirectories containing the relevant so files. I am using Ubuntu 16.04 with the GNOME flavor on an AMD machine.

Any ideas where this is going wrong?

Regards,

#0K

Description
Wrappers generated for member functions with double pointer args do not compile.

Example:

class TysonNovak2001OdeSystem : public AbstractOdeSystemWithAnalyticJacobian
{
public:
    virtual void AnalyticJacobian(const std::vector<double>& rSolutionGuess, double** jacobian, double time, double timeStep);
};

produces:

.def(
    "AnalyticJacobian", 
    (void(TysonNovak2001OdeSystem::*)(::std::vector<double> const &, double * *, double, double)) &TysonNovak2001OdeSystem::AnalyticJacobian, 
    " " , py::arg("rSolutionGuess"), py::arg("jacobian"), py::arg("time"), py::arg("timeStep") )

Error

pybind11/include/pybind11/cast.h:1217
error: no matching function for call to ‘pybind11::detail::type_caster<double, void>::cast(double**&, pybind11::return_value_policy, std::nullptr_t)’

Description
Parent class is missing from some generated wrappers.

Original Class

template<unsigned DIM>
class VertexBasedCellPopulation : public AbstractOffLatticeCellPopulation<DIM>
{
...
    VertexBasedCellPopulation(MutableVertexMesh<DIM, DIM>& rMesh,
                              std::vector<CellPtr>& rCells,
                              bool deleteMesh=false,
                              bool validate=true,
                              const std::vector<unsigned> locationIndices=std::vector<unsigned>());
...
}

Generated wrapper

 py::class_<VertexBasedCellPopulation2 , VertexBasedCellPopulation2_Overloads , boost::shared_ptr<VertexBasedCellPopulation2 >   >(m, "VertexBasedCellPopulation2")

Correct wrapper

py::class_<VertexBasedCellPopulation2 , VertexBasedCellPopulation2_Overloads , boost::shared_ptr<VertexBasedCellPopulation2 > , AbstractOffLatticeCellPopulation<2, 2> >(m, "VertexBasedCellPopulation2")

Hello! The following is a set of steps to reproduce the error of a bug in the writing of the wrapped code that can be reproduced in the "shapes" directory within the repository. The "wrapper_header_collection" template instantiations are not created when the total number of template replacements per substitution is 1.

Steps to reproduce:
rm -rf shapes/src/primatives
Alter shapes/wrapper/package_info.yaml to match the following diff:

diff --git a/shapes/wrapper/package_info.yaml b/shapes/wrapper/package_info.yaml
index f1cace8..d66268d 100644
--- a/shapes/wrapper/package_info.yaml
+++ b/shapes/wrapper/package_info.yaml
@@ -2,7 +2,7 @@ name: pyshapes # Unique name prepended to all modules
smart_ptr_type: std::shared_ptr
template_substitutions:

• signature:
• replacement: [[2], [3]]

• replacement: [[2]]

modules:

• name: math_funcs # Name of the module
  @@ -13,9 +13,3 @@ modules:
  source_locations:
  classes:
  • name: Point
    -- name: primitives
• source_locations:
• classes:
• • name: Shape
• • name: Cuboid
• • name: Rectangle

The run of cppwg

python3 wrapper/generate.py --source_root ~/Work/TRI/cppwg/shapes --wrapper_root ~/Work/TRI/cppwg/shapes/wrapper/ --castxml_binary ~/Work/TRI/CastXML/build/bin/castxml --package_info ~/Work/TRI/cppwg/shapes/wrapper/package_info.yaml --includes ~/Work/TRI/cppwg/shapes/src/

reports the following error:

Thank you for making this code available!

Summary
Auto-format generated wrapper code to make debugging and testing wrappers easier. One option is clang-format.

Description

Template parameters are not correctly handled in some cases e.g.

.def(
"SetUpBoxCollection", 
(void(PeriodicNodesOnlyMesh3::*)(double, ::boost::numeric::ublas::c_vector<double, 6>, int, ::boost::numeric::ublas::c_vector<bool, 3>)) &PeriodicNodesOnlyMesh3::SetUpBoxCollection, " " , 
py::arg("cutOffLength"), 
py::arg("domainSize"), 
py::arg("numLocalRows") = -1, 
py::arg("isDimPeriodic") = zero_vector<bool(PeriodicNodesOnlyMesh::SPACE_DIM) )

should be instead (SPACE_DIM should be replaced):

.def(
"SetUpBoxCollection", 
(void(PeriodicNodesOnlyMesh3::*)(double, ::boost::numeric::ublas::c_vector<double, 6>, int, ::boost::numeric::ublas::c_vector<bool, 3>)) &PeriodicNodesOnlyMesh3::SetUpBoxCollection, " " , 
py::arg("cutOffLength"), 
py::arg("domainSize"), 
py::arg("numLocalRows") = -1, 
py::arg("isDimPeriodic") = zero_vector<bool>(3) )

Compile Error

~/Chaste/projects/PyChaste/dynamic/wrappers/mesh/PeriodicNodesOnlyMesh2.cppwg.cpp: In function ‘void register_PeriodicNodesOnlyMesh2_class(pybind11::module&)’:
~/Chaste/projects/PyChaste/dynamic/wrappers/mesh/PeriodicNodesOnlyMesh2.cppwg.cpp:78:141: error: expected primary-expression before ‘(’ token
   78 | g("domainSize"), py::arg("numLocalRows") = -1, py::arg("isDimPeriodic") = zero_vector<bool>(PeriodicNodesOnlyMesh::SPACE_DIM) )
      |                                                                                            ^

~/Chaste/projects/PyChaste/dynamic/wrappers/mesh/PeriodicNodesOnlyMesh2.cppwg.cpp:78:142: error: ‘template<unsigned int SPACE_DIM> class PeriodicNodesOnlyMesh’ used without template arguments
   78 | ("domainSize"), py::arg("numLocalRows") = -1, py::arg("isDimPeriodic") = zero_vector<bool>(PeriodicNodesOnlyMesh::SPACE_DIM) )
      |                                                                                            ^~~~~~~~~~~~~~~~~~~~~

Summary

Retrieve Python help text from C++ docstrings.

Description
The pybind11 template code and other TODO bits need updating.

TODO

• Replace PYBIND11_OVERLOAD -> PYBIND11_OVERRIDE and PYBIND11_OVERLOAD_PURE -> PYBIND11_OVERRIDE_PURE : https://pybind11.readthedocs.io/en/stable/upgrade.html#v2-6
• Replace pyplusplus in wrapper templates with cppwg.
• Add #include <pybind11/pybind11.h> in wrapper hpp files and remove namespace py = pybind11;.
• Remove unused code.
• Return strings from generators rather than appending to input strings.
• Fix TODOs in code.

Summary

Add an entry point script for calling cppwg from command line.

Summary

The order in which classes are added in package_info.yml is important. This order is propragated forward to the include order in the wrapper header collection. Base classes come before derived classes, a class should come before other classes that refer to it etc. When there are many classes in package_info.yml, figuring out an order that works can be hit or miss by trial and error, when adding a new class to an existing configuration.

It would be a useful feature if cppwg could automatically work out the order to include classes in. Users could add classes to package_info.yml in any order without having to manually work out an order that won't break things. Classes could be added in alphabetical order, for instance, which would make it easier to find things when manually inspecting the configuration.

Description

Wrapper generation throws errors when it encounters C++ 17 features. For example:

INFO: Parsing Code
In file included from /tmp/tmpabzfnu6m.h:1:
In file included from Chaste/projects/PyChaste/dynamic/wrappers//wrapper_header_collection.hpp:9:
Chaste/global/src/FileFinder.hpp:42:21: error: expected namespace name
namespace fs = std::filesystem;

Description
Generating wrappers throws errors for some classes: Unable to find declaration Clazz or 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

Summary

Jinja.

Pros

• Easier to maintain templates.
• Easier to write tests to check if the correct bindings are being generated.
• May make it easier to create custom generators.
• May make it easier to generate code for other targets apart from Pybind11.

Cons

• Adding an extra dependency

Summary

Tests are currently run for the shapes example, but don't cover all uses cases.

TODO

• Test on multiple Python versions (3.8 - 3.12).
• Update example shapes project CMake configuration.
• Update pybind11 version in example shapes project.
• Add testing with flake8
• Measure current test coverage.
• Increase test coverage to 25%.
• Increase test coverage to 50%.
• Increase test coverage to 75%.
• Increase test coverage to 100%.