Linear and efficient neighbour finder

CITATION.cff

@@ -9,6 +9,9 @@ authors:
     given-names: Nick
     orcid: "https://orcid.org/0000-0003-3038-1855"
     alias: zerothi
+  - family-names: Febrer
+    given-names: Pol
+    alias: pfebrer
 title: sisl
 identifiers:
   - description: "Collection DOI for any sisl version."

ci/doc.yml

@@ -12,7 +12,7 @@ dependencies:
   - pyproject-metadata
   - pyparsing>=1.5.7
   - numpy>=1.13
-  - cython>=0.29.28
+  - cython>=3.0.0
   - scipy>=1.5.0
   - netcdf4
   - xarray>=0.10.0

pyproject.toml

@@ -12,7 +12,7 @@
 requires = [
     "setuptools_scm[toml]>=6.2",
     "scikit-build-core[pyproject]",
-    "Cython>=0.29.28",
+    "Cython>=3",
     # see https://github.com/scipy/oldest-supported-numpy/
     # should fix #310
     "oldest-supported-numpy; sys_platform != 'win32'",
@@ -49,7 +49,8 @@ dependencies = [
 ]
 
 authors = [
-    {name = "Nick Papior", email = "[email protected]"}
+    {name = "Nick Papior", email = "[email protected]"},
+    {name = "Pol Febrer"}
 ]
 maintainers = [{name="sisl developers"}]
 
@@ -136,9 +137,9 @@ analysis = [
 ]
 
 viz = [
+    "netCDF4",
     "dill >= 0.3.2",
     "pathos",
-    "netCDF4",
     "scikit-image",
 
     "plotly",
@@ -147,34 +148,34 @@ viz = [
 ]
 
 viz-plotly = [
+    "netCDF4",
     "dill >= 0.3.2",
     "pathos",
-    "netCDF4",
     "scikit-image",
 
     "plotly",
 ]
 
 viz-matplotlib = [
+    "netCDF4",
     "dill >= 0.3.2",
     "pathos",
-    "netCDF4",
     "scikit-image",
 
     "matplotlib",
 ]
 
 viz-blender = [
+    "netCDF4",
     "dill >= 0.3.2",
     "pathos",
-    "netCDF4",
     "scikit-image",
 ]
 
 viz-ase = [
+    "netCDF4",
     "dill >= 0.3.2",
     "pathos",
-    "netCDF4",
     "scikit-image",
 
     "ase",
@@ -186,10 +187,10 @@ test = [
     "pytest-env",
     "pytest-faulthandler",
     "coveralls",
+    "netCDF4",
     "tqdm",
     "dill >= 0.3.2",
     "pathos",
-    "netCDF4",
     "scikit-image",
     "matplotlib",
     "plotly",

src/sisl/CMakeLists.txt

@@ -12,3 +12,4 @@ endforeach()
 add_subdirectory("_core")
 add_subdirectory("io")
 add_subdirectory("physics")
+add_subdirectory("geom")

src/sisl/conftest.py

@@ -227,6 +227,7 @@ def pytest_configure(config):
         "hamiltonian",
         "geometry",
         "geom",
+        "neighbor",
         "shape",
         "state",
         "electron",

src/sisl/geom/CMakeLists.txt

@@ -0,0 +1 @@
+add_subdirectory("neighs")

src/sisl/geom/__init__.py

@@ -43,6 +43,7 @@
 
 """
 from ._composite import *
+from ._neighbors import *
 from .basic import *
 from .bilayer import *
 from .category import *

src/sisl/geom/_neighbors/CMakeLists.txt

@@ -0,0 +1,11 @@
+# In this directory we have a set of libraries
+# We will need to link to the Numpy includes
+foreach(source _operations)
+  add_cython_library(
+    SOURCE ${source}.py
+    LIBRARY ${source}
+    OUTPUT ${source}_C
+    )
+  install(TARGETS ${source} LIBRARY
+    DESTINATION ${SKBUILD_PROJECT_NAME}/geom/neighs)
+endforeach()

src/sisl/geom/_neighbors/__init__.py

@@ -0,0 +1 @@
+from ._finder import NeighborFinder