python cphd module has broken SWIG bindings

[echeipesh]

Building a wheel from the latest release branch: release/SIX-3.2.5 results in the following failure to import the pysix.cphd module.

I'm not hip with C++ data structures so I'm not sure if there is an obvious way to fix these.
Any pointers would be much appreciated 🙏

To reproduce:

python3 -c "from pysix import cphd"

Traceback (most recent call last):
  File "/usr/local/lib/python3.10/dist-packages/pysix/cphd.py", line 14, in swig_import_helper
    return importlib.import_module(mname)
  File "/usr/lib/python3.10/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1050, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1027, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 674, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 571, in module_from_spec
  File "<frozen importlib._bootstrap_external>", line 1176, in create_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
ImportError: /usr/local/lib/python3.10/dist-packages/pysix/_cphd.cpython-310-x86_64-linux-gnu.so: undefined symbol: _ZNK4cphd12SupportBlock4readERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEmRSt10unique_ptrIA_hSt14default_deleteISA_EE

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/local/lib/python3.10/dist-packages/pysix/cphd.py", line 17, in <module>
    _cphd = swig_import_helper()
  File "/usr/local/lib/python3.10/dist-packages/pysix/cphd.py", line 16, in swig_import_helper
    return importlib.import_module('_cphd')
  File "/usr/lib/python3.10/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ImportError: /usr/local/lib/python3.10/dist-packages/pysix/_cphd.cpython-310-x86_64-linux-gnu.so: undefined symbol: _ZNK4cphd12SupportBlock4readERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEmRSt10unique_ptrIA_hSt14default_deleteISA_EE

The unmangled name of missing symbol is:

# c++filt _ZNK4cphd12SupportBlock4readERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEmRSt10unique_ptrIA_hSt14default_deleteISA_EE

cphd::SupportBlock::read(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long, std::unique_ptr<unsigned char [], std::default_delete<unsigned char []> >&) const

Looking further

Inspecting _cphd.cpython-310-x86_64-linux-gnu.so we can see there are three unlinked symbols for cphd module:

nm /usr/local/lib/python3.10/dist-packages/pysix/_cphd.cpython-310-x86_64-linux-gnu.so

...
                 U _ZNK4cphd12SupportBlock4readERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEmRSt10unique_ptrIA_hSt14default_deleteISA_EE
                 U _ZNK4cphd12SupportBlock7readAllEmRSt10unique_ptrIA_hSt14default_deleteIS2_EE
                 U _ZNK4cphd8PVPBlock10getPVPdataEmRSt6vectorIhSaIhEE
...

_ZNK4cphd12SupportBlock4readERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEmRSt10unique_ptrIA_hSt14default_deleteISA_EE

cphd::SupportBlock::read(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long, std::unique_ptr<unsigned char [], std::default_delete<unsigned char []> >&) const

Declared here:

six-library/six/modules/c++/cphd/include/cphd/SupportBlock.h

Line 137 in d864815

void read(const std::string& id, size_t numThreads, mem::ScopedArray<sys::ubyte>&) const; // for existing SWIG bindings

Does not match the implementation here:

six-library/six/modules/c++/cphd/source/SupportBlock.cpp

Lines 80 to 87 in d864815

	void SupportBlock::read(const std::string& id,
	size_t numThreads,
	const mem::BufferView<sys::ubyte>& data_) const
	{
	void* pData = data_.data;
	auto data = sys::make_span<std::byte>(pData, data_.size);
	read(id, numThreads, data);
	}

_ZNK4cphd12SupportBlock7readAllEmRSt10unique_ptrIA_hSt14default_deleteIS2_EE

cphd::SupportBlock::readAll(unsigned long, std::unique_ptr<unsigned char [], std::default_delete<unsigned char []> >&) const

Declared here:

six-library/six/modules/c++/cphd/include/cphd/SupportBlock.h

Line 152 in d864815

void readAll(size_t numThreads, mem::ScopedArray<sys::ubyte>&) const; // for existing SWIG bindings

Does not appear to be implemented, with closest method here:

six-library/six/modules/c++/cphd/source/SupportBlock.cpp

Lines 116 to 126 in d864815

	std::vector<std::byte> SupportBlock::readAll(size_t numThreads) const
	{
	std::vector<std::byte> retval(mSupportSize);
	for (auto& supportArrayMapPair : mData.supportArrayMap)
	{
	const size_t bufSize = supportArrayMapPair.second.getSize();
	auto pData = &retval[supportArrayMapPair.second.arrayByteOffset];
	read(supportArrayMapPair.first, numThreads, sys::make_span(pData, bufSize));
	}
	return retval;
	}

_ZNK4cphd8PVPBlock10getPVPdataEmRSt6vectorIhSaIhEE

cphd::PVPBlock::getPVPdata(unsigned long, std::vector<unsigned char, std::allocator<unsigned char> >&) const

six-library/six/modules/c++/cphd/include/cphd/PVPBlock.h

Lines 253 to 254 in d864815

	void getPVPdata(size_t channel,
	std::vector<sys::ubyte>& data) const; // for existing SWIG bindings

doesn't match implementation, only byte version available:

six-library/six/modules/c++/cphd/source/PVPBlock.cpp

Lines 568 to 576 in d864815

	void PVPBlock::getPVPdata(size_t channel,
	std::vector<std::byte>& data) const
	{
	verifyChannelVector(channel, 0);
	data.resize(getPVPsize(channel));
	std::fill(data.begin(), data.end(), static_cast<std::byte>(0));
	getPVPdata(channel, data.data());
	}