getting closer I hope

CMakeLists.txt

@@ -10,40 +10,34 @@ set(PYBIND11_FINDPYTHON ON)
 find_package(pybind11 CONFIG REQUIRED)
 
 
-##############################################################################
-
 # Some screen output
 message(STATUS "OS detected: ${CMAKE_SYSTEM_NAME}")
 message(STATUS "CXX Compiler detected: ${CMAKE_CXX_COMPILER_ID}")
 message(STATUS "CMake additional search path for libraries: ${CMAKE_LIBRARY_PATH}")
 
+# CGAL and its components
+find_package(CGAL)
+message(STATUS "CGAL version: ${CGAL_VERSION}")
 
-# # CGAL and its components
-# find_package(CGAL)
-# message(STATUS "CGAL version: ${CGAL_VERSION}")
-
-# if (NOT CGAL_FOUND)
-#   message(STATUS "This project requires the CGAL library, and will not be compiled.")
-#   return()
-# endif()
-
+if (NOT CGAL_FOUND)
+  message(STATUS "This project requires the CGAL library, and will not be compiled.")
+  return()
+endif()
 
+# include helper file
+include( ${CGAL_USE_FILE})
+message(STATUS "CGAL_USE_FILE: ${CGAL_USE_FILE}")
 
-# # include helper file
-# include( ${CGAL_USE_FILE})
-# message(STATUS "CGAL_USE_FILE: ${CGAL_USE_FILE}")
+set (CPP_SRC "src/tyssue_cpp/")
 
-
-
-pybind11_add_module(tyssue_cpp MODULE src/main.cpp)
+# This is needed
+pybind11_add_module(tyssue_cpp MODULE "src/main.cpp" )
 install(TARGETS tyssue_cpp DESTINATION ${SKBUILD_PROJECT_NAME})
 
-# set (COLLISION_SRCE "src/tyssue/collisions/cpp")
-# pybind11_add_module(c_collisions SHARED "${COLLISION_SRCE}/c_collisions.cpp" )
-# install(TARGETS c_collisions DESTINATION ${COLLISION_SRCE})
-# message(STATUS "installed c_collisions")
-
+pybind11_add_module(_mesh_generation MODULE "${CPP_SRC}/mesh_generation.cpp" )
+install(TARGETS _mesh_generation DESTINATION ${SKBUILD_PROJECT_NAME})
 
-# set (GENERATION_SRCE "src/tyssue/generation/cpp")
-# pybind11_add_module(mesh_generation SHARED "${GENERATION_SRCE}/mesh_generation.cpp" )
-# install(TARGETS mesh_generation DESTINATION ${GENERATION_SRCE})
+set (COLLISION_SRCE "src/tyssue_cpp")
+pybind11_add_module(_collisions SHARED "${CPP_SRC}/c_collisions.cpp" )
+install(TARGETS _collisions DESTINATION ${SKBUILD_PROJECT_NAME})
+message(STATUS "installed c_collisions")

pyproject.toml

@@ -60,7 +60,6 @@ Changelog = "https://githib.com/damcb/tyssue/releases"
 
 [tool.scikit-build]
 minimum-version = "0.4"
-build-dir = "build/{wheel_tag}"
 metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
 
 sdist.exclude = [".github"]

src/main.cpp

@@ -1,11 +1,5 @@
 #include <pybind11/pybind11.h>
 
-namespace py = pybind11;
-// include "tyssue_cpp/c_collsions.cpp"
-// include "tyssue_cpp/mesh_generation.cpp"
-
-
-
 namespace py = pybind11;
 
 size_t free_function() {

src/tyssue/_version.py

@@ -12,5 +12,5 @@
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.9.1.dev122+gebbdeb7.d20240107'
-__version_tuple__ = version_tuple = (0, 9, 1, 'dev122', 'gebbdeb7.d20240107')
+__version__ = version = '0.9.1.dev123+ge62491c.d20240108'
+__version_tuple__ = version_tuple = (0, 9, 1, 'dev123', 'ge62491c.d20240108')

src/tyssue/generation/shapes.py

@@ -21,14 +21,14 @@
 from ..topology import type1_transition
 from .from_voronoi import from_3d_voronoi
 
-try:
-    from .cpp import mesh_generation
-except ImportError:
-    print(
-        "CGAL-based mesh generation utilities not found, you may need to install"
-        " CGAL and build from source"
-    )
-    mesh_generation = None
+from .._mesh_generation import make_spherical
+
+# except ImportError:
+#     print(
+#         "CGAL-based mesh generation utilities not found, you may need to install"
+#         " CGAL and build from source"
+#     )
+#     make_sphertical = None
 
 from ..utils import single_cell, swap_apico_basal
 from .modifiers import extrude
@@ -182,6 +182,8 @@ def generate_ring(Nf, R_in, R_out, R_vit=None, apical="in"):
 """
 Flat lateral 2D sheet
 """
+
+
 def generate_lateral_tissue(Nf, length, height):
     """
     Generate a 2D lateral tyssue object
@@ -208,26 +210,23 @@ def generate_lateral_tissue(Nf, length, height):
     vert_df = pd.DataFrame(
         index=pd.Index(range(Nv + 2), name="vert"),
         columns=specs["vert"].keys(),
-        dtype=float
+        dtype=float,
     )
 
     edge_df = pd.DataFrame(
         index=pd.Index(range(Ne), name="edge"),
         columns=specs["edge"].keys(),
-        dtype=float
+        dtype=float,
     )
 
     face_df = pd.DataFrame(
         index=pd.Index(range(Nf), name="face"),
         columns=specs["face"].keys(),
-        dtype=float
+        dtype=float,
     )
 
     inner_edges = np.array(
-        [
-            [f0, v0, v1 + 1]
-            for f0, v0, v1 in zip(range(Nf), range(Nf), range(Nf))
-        ]
+        [[f0, v0, v1 + 1] for f0, v0, v1 in zip(range(Nf), range(Nf), range(Nf))]
     )
 
     outer_edges = np.zeros_like(inner_edges)
@@ -253,7 +252,9 @@ def generate_lateral_tissue(Nf, length, height):
     # Setting vertices position
     vert_df.loc[range(Nf + 1), "x"] = [length / Nf * i for i in range(Nf + 1)]
     vert_df.loc[range(Nf + 1), "y"] = 0
-    vert_df.loc[range(Nf + 1, 2 * (Nf + 1)), "x"] = [length / Nf * i for i in range(Nf + 1)]
+    vert_df.loc[range(Nf + 1, 2 * (Nf + 1)), "x"] = [
+        length / Nf * i for i in range(Nf + 1)
+    ]
     vert_df.loc[range(Nf + 1, 2 * (Nf + 1)), "y"] = height
 
     vert_df["segment"] = "basal"
@@ -263,8 +264,8 @@ def generate_lateral_tissue(Nf, length, height):
 
     edge_df.loc[range(2 * Nf, 4 * Nf), "segment"] = "lateral"
 
-    vert_df['is_active'] = 1
-    face_df['is_alive'] = 1
+    vert_df["is_active"] = 1
+    face_df["is_alive"] = 1
 
     datasets = {"vert": vert_df, "edge": edge_df, "face": face_df}
 
@@ -384,7 +385,7 @@ def spherical_sheet(radius, Nf, Lloyd_relax=False, **kwargs):
     the given number of cells
     """
 
-    centers = np.array(mesh_generation.make_spherical(Nf))
+    centers = np.array(make_spherical(Nf))
     eptm = sheet_from_cell_centers(centers, **kwargs)
 
     rhos = (eptm.vert_df[eptm.coords] ** 2).sum(axis=1).mean()
@@ -542,7 +543,6 @@ def Lloyd_relaxation(sheet, geom, steps=10, coords=None, update_method=None):
 
 
 def update_on_sphere(sheet):
-
     update_spherical(sheet)
 
     thetas = sheet.face_df["theta"].to_numpy()