Overview

This week I started by making a github repository named pyseams. Me and my mentor worked together on writing a meson build file. After this, I realised that dSEAMS had some enums which had to be converted to enum class to prevent the implicit conversion to other types i.e., to another enum or int and made a pull request for the same thing. Then I proceeded with writing bindings using pybind11, tested it locally, and committed to the git repo pyseams.

// The following bindings are still in progress:

#include <pybind11/pybind11.h>
#include "../subprojects/seams-core/src/include/internal/mol_sys.hpp"

namespace py = pybind11;

PYBIND11_MODULE(cyoda, m) {
  py::class_<molSys::Point<double>>(m, "PointDouble")
          .def(py::init<>())
          .def_readwrite("c_type", &molSys::Point<double>::type)
          .def_readwrite("molID", &molSys::Point<double>::molID)
          .def_readwrite("atomID", &molSys::Point<double>::atomID)
          .def_readwrite("x", &molSys::Point<double>::x)
          .def_readwrite("y", &molSys::Point<double>::y)
          .def_readwrite("z", &molSys::Point<double>::z);

  py::enum_<molSys::bond_type>(m, "BondType")
          .value("staggered", molSys::bond_type::staggered)
          .value("eclipsed", molSys::bond_type::eclipsed)
          .value("out_of_range", molSys::bond_type::out_of_range);

  py::enum_<molSys::atom_state_type >(m, "AtomStateType")
          .value("cubic", molSys::atom_state_type ::cubic)
          .value("hexagonal", molSys::atom_state_type ::hexagonal)
          .value("water", molSys::atom_state_type ::water)
          .value("interfacial", molSys::atom_state_type ::interfacial)
          .value("clathrate", molSys::atom_state_type ::clathrate)
          .value("interClathrate", molSys::atom_state_type ::interClathrate)
          .value("unclassified", molSys::atom_state_type ::unclassified)
          .value("reCubic", molSys::atom_state_type ::reCubic)
          .value("reHex", molSys::atom_state_type ::reHex);

  py::class_<molSys::Result>(m, "Result")
          .def(py::init<>())
          .def_readwrite("classifier", &molSys::Result::classifier)
          .def_readwrite("c_value", &molSys::Result::c_value);
}

Check-in Questions

What did you do this week?

1. Made a Github repository named pyseams.

2. Pull request for enum to enum class change.

3. Made a meson build file.

4. Started compiling the extensions and running the python bindings.

What is coming up next?

1. Finishing the python bindings for the first workflow in the lua design as discussed earlier.

2. Writing documentation and tests

3. Moving the pyseams repository to the dseams-core.

Did you get stuck anywhere?

I was a bit stuck at the meson build file process, but my mentor helped me with it. I think I am on track.