ENH,BIND: Return more PointClouds

[RuhiRG]

In dSEAMS raw pointers have been used, but in pybind11 when I bind a function with raw pointers. It gives segmentation error. Here is the git commit I made. The error it shows when I try to use ipython is as follows:

In [1]: cyoda.clearPointCloud(mpt)
Out[1]: <bbdir.cyoda.PointCloudDouble at 0x7f72d1e91130>

In [2]: mpt = cyoda.clearPointCloud(mpt)

In [3]: mpt
Out[3]: <bbdir.cyoda.PointCloudDouble at 0x7f72d1c333f0>

In [4]: cyoda.readXYZ("conftest.xyz", mpt)
Stack trace (most recent call last):
#31   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e8aa08d, in _PyRun_SimpleFileObject
#30   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e8aa70f, in 
#29   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e895772, in 
#28   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e899369, in 
#27   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e87a9de, in PyEval_EvalCode
#26   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e87b325, in 
#25   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e7c73ce, in _PyEval_EvalFrameDefault
#24   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e7efc70, in PyObject_Call
#23   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e806802, in 
#22   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e806a73, in 
#21   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e7c385c, in _PyEval_EvalFrameDefault
#20   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e7d04cb, in PyObject_Vectorcall
#19   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e7ee728, in 
#18   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e88f996, in 
#17   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e88edb8, in 
#16   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e7c6478, in _PyEval_EvalFrameDefault
#15   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e88edb8, in 
#14   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e7c6478, in _PyEval_EvalFrameDefault
#13   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e88edb8, in 
#12   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e7c385c, in _PyEval_EvalFrameDefault
#11   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e7d04cb, in PyObject_Vectorcall
#10   Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e7d05de, in 
#9    Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e89208d, in 
#8    Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e87a9de, in PyEval_EvalCode
#7    Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e87b325, in 
#6    Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e7c385c, in _PyEval_EvalFrameDefault
#5    Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e7b6e12, in _PyObject_MakeTpCall
#4    Object "/users/home/ruhila/micromamba/envs/dseams/bin/python3.11", at 0x56400e7d6d45, in 
#3    Object "/users/home/ruhila/Git/Github/dSEAMS/pyseams/bbdir/cyoda.cpython-311-x86_64-linux-gnu.so", at 0x7f72d1be08a7, in 
#2    Object "/users/home/ruhila/Git/Github/dSEAMS/pyseams/bbdir/cyoda.cpython-311-x86_64-linux-gnu.so", at 0x7f72d1be94a3, in 
#1    Object "/users/home/ruhila/micromamba/envs/dseams/lib/libyodaLib.so", at 0x7f72d1aef46c, in sinp::readXYZ(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, molSys::PointCloud<molSys::Point<double>, double>*)
#0    Object "/lib64/libc.so.6", at 0x7f72e1700e0b, in 
Segmentation fault (Address not mapped to object [0x30])
Segmentation fault (core dumped)

The C++ function code takes the input and process the object in place, returning an integer status code. The pybind11 documentation notes that there are issues with changes to native containers. The simplest solution would be to change the seams-core function to take a single input string (filename) and return a populated PointCloud object instead of an int.

[HaoZeke]

I agree, @amritagos the function signature is here [rendered doc]:

seams-core/src/seams_input.cpp

Lines 73 to 96 in 13e0104

	int sinp::readXYZ(std::string filename,
	molSys::PointCloud<molSys::Point<double>, double> *yCloud) {
	std::unique_ptr<std::ifstream> xyzFile;
	xyzFile = std::make_unique<std::ifstream>(filename);
	std::string line; // Current line being read in
	std::vector<std::string> tokens; // Vector containing word tokens
	std::vector<double> numbers; // Vector containing type double numbers
	int nop = -1; // Number of atoms in targetFrame
	int iatom = 1; // Current atom being filled into the PointCloud
	molSys::Point<double> iPoint; // Current point being read in from the file
	double xLo, xHi, yLo, yHi, zLo,
	zHi; // Box lengths extrapolated from the least and greatest coordinates
	if (!(gen::file_exists(filename))) {
	std::cout
	<< "Fatal Error: The file does not exist or you gave the wrong path.\n";
	// Throw exception?
	return 1;
	}
	// --------
	// Before filling up the PointCloud, if the vectors are filled
	// empty them
	*yCloud = molSys::clearPointCloud(yCloud);

It seems like the best way would indeed be to return pointCloud instances. @RuhiRG it would be fantastic to have a PR closing this :)