Interface with libtopotoolbox through scikit-build-core and pybind11 (#…

…12)

The current approach using `ctypes` requires separately building and
installing libtopotoolbox in an appropriate directory, which is tricky
to get right in a cross-platform way without substantial intervention
from users. This set of changes introduces a new build system using
scikit-build-core and pybind11 to build an extension module that
includes an interface to our library.

pyproject.toml is modified to switch the build backend to
scikit-build-core to install pybind11 as a build-time dependency.

src/lib.cpp contains the bindings for libtopotoolbox, defined using
pybind11. The PYBIND11_MODULE declaration exposes a Python module _lib
within the topotoolbox package that contains the bindings. Right now,
it only binds `has_topotoolbox`, which has a trivial binding because
it requires no marshalling of Python data into C/C++ types. Other
functions such as `fillsinks` will require more complex binding
declarations, but pybind11 provides an interface to working with NumPy
arrays that should be helpful.

CMakeLists.txt is used by scikit-build-core to build the package. It
follows the guidance at
https://scikit-build-core.readthedocs.io/en/latest/getting_started.html
with the exception of adding libtopotoolbox using
FetchContent. This will download the source from GitHub and then build
a /static/ library for libtopotoolbox and link it into the /shared/
library that is built by pybind11.

src/topotoolbox/__init__.py shows how to access the binding from the
_lib module. In practice, we probably don't want to expose the raw
bindings from the topotoolbox module but instead use them to implement
methods within the proposed `GridObject` class.

CMakeLists.txt

@@ -0,0 +1,23 @@
+cmake_minimum_required(VERSION 3.15)
+
+project(${SKBUILD_PROJECT_NAME}
+  VERSION ${SKBUILD_PROJECT_VERSION}
+  LANGUAGES CXX)
+
+# Find TopoToolbox somewhere
+include(FetchContent)
+FetchContent_Declare(
+  topotoolbox
+  GIT_REPOSITORY https://github.com/TopoToolbox/libtopotoolbox.git
+  GIT_TAG main # In the future, we should track a specific tag/commit
+	       # and bump it as we release versions
+)
+FetchContent_MakeAvailable(topotoolbox)
+
+set(PYBIND11_NEWPYTHON ON)
+find_package(pybind11 CONFIG REQUIRED)
+
+pybind11_add_module(_lib src/lib.cpp)
+target_link_libraries(_lib PRIVATE topotoolbox)
+
+install(TARGETS _lib LIBRARY DESTINATION topotoolbox)

pyproject.toml

@@ -1,6 +1,6 @@
 [build-system]
-requires = ["hatchling"]
-build-backend = "hatchling.build"
+requires = ["scikit-build-core","pybind11"]
+build-backend = "scikit_build_core.build"
 
 [project]
 name = "topotoolbox"

src/lib.cpp

@@ -0,0 +1,11 @@
+extern "C" {
+  #include <topotoolbox.h>
+}
+
+#include <pybind11/pybind11.h>
+
+namespace py = pybind11;
+
+PYBIND11_MODULE(_lib, m) {
+  m.def("has_topotoolbox",&has_topotoolbox);
+}

src/topotoolbox/__init__.py

@@ -1 +1,2 @@
-from .grid_object import GridObject
+from .grid_object import GridObject
+from ._lib import has_topotoolbox