small clean-ups, and fixed requirements

future.annotations requires Cython>=3

Signed-off-by: Nick Papior <[email protected]>

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"}]
 

src/sisl/geom/neighs/CMakeLists.txt

@@ -1,11 +1,5 @@
 # In this directory we have a set of libraries
 # We will need to link to the Numpy includes
-set_property(DIRECTORY
-  APPEND
-  PROPERTY INCLUDE_DIRECTORIES
-  ${CMAKE_CURRENT_SOURCE_DIR}/..
-  )
-
 foreach(source _neigh_operations)
   add_cython_library(
     SOURCE ${source}.py
@@ -14,4 +8,4 @@ foreach(source _neigh_operations)
     )
   install(TARGETS ${source} LIBRARY
     DESTINATION ${SKBUILD_PROJECT_NAME}/geom/neighs)
-endforeach()
+endforeach()

src/sisl/geom/neighs/_neigh_operations.py

@@ -38,9 +38,12 @@ def build_table(nbins: cnp.int64_t, bin_indices: cnp.int64_t[:]):
     """
     n_atoms = bin_indices.shape[0]
 
-    list_array: cnp.int64_t[:] = np.zeros(n_atoms, dtype=np.int64)
-    counts: cnp.int64_t[:] = np.zeros(nbins, dtype=np.int64)
-    heads: cnp.int64_t[:] = np.full(nbins, -1, dtype=np.int64)
+    list_array_obj = np.zeros(n_atoms, dtype=np.int64)
+    list_array: cnp.int64_t[:] = list_array_obj
+    counts_obj = np.zeros(nbins, dtype=np.int64)
+    counts: cnp.int64_t[:] = counts_obj
+    heads_obj = np.full(nbins, -1, dtype=np.int64)
+    heads: cnp.int64_t[:] = heads_obj
 
     # Loop through all atoms
     for at in range(n_atoms):
@@ -54,10 +57,10 @@ def build_table(nbins: cnp.int64_t, bin_indices: cnp.int64_t[:]):
         heads[bin_index] = at
 
         # Update the count of this bin (increment it by 1).
-        counts[bin_index] = counts[bin_index] + 1
+        counts[bin_index] += 1
 
     # Return the memory views as numpy arrays
-    return np.asarray(list_array), np.asarray(heads), np.asarray(counts)
+    return list_array_obj, heads_obj, counts_obj
 
 
 @cython.boundscheck(False)
@@ -135,20 +138,22 @@ def get_pairs(
     """
     N_ind = at_indices.shape[0]
 
-    i_pair: cython.int = 0
+    i_pair: cython.size_t = 0
 
     ref_xyz: cnp.float64_t[:] = np.zeros(3, dtype=np.float64)
     neigh_isc: cnp.int64_t[:] = np.zeros(3, dtype=np.int64)
 
-    neighs: cnp.int64_t[:, :] = np.zeros((max_npairs, 5), dtype=np.int64)
-    split_indices: cnp.int64_t[:] = np.zeros(N_ind, dtype=np.int64)
+    neighs_obj: cnp.ndarray = np.zeros([max_npairs, 5], dtype=np.int64)
+    neighs: cnp.int64_t[:, :] = neighs_obj
+    split_indices_obj: cnp.ndarray = np.zeros(N_ind, dtype=np.int64)
+    split_indices: cnp.int64_t[:] = split_indices_obj
 
     for search_index in range(N_ind):
         at = at_indices[search_index]
 
         for j in range(8):
             # Find the bin index.
-            bin_index = indices[search_index, j]
+            bin_index: cnp.int64_t = indices[search_index, j]
 
             # Get the first atom index in this bin
             neigh_at: cnp.int64_t = heads[bin_index]
@@ -181,11 +186,10 @@ def get_pairs(
                 # instead of moving potential neighbors to the unit cell
                 # because in this way we reduce the number of operations.
                 for i in range(3):
-                    ref_xyz[i] = (
-                        ref_xyz[i]
-                        - cell[0, i] * neigh_isc[0]
-                        - cell[1, i] * neigh_isc[1]
-                        - cell[2, i] * neigh_isc[2]
+                    ref_xyz[i] -= (
+                        cell[0, i] * neigh_isc[0]
+                        + cell[1, i] * neigh_isc[1]
+                        + cell[2, i] * neigh_isc[2]
                     )
 
             # Loop through all atoms that are in this bin.
@@ -228,7 +232,7 @@ def get_pairs(
         # We have finished this search, store the breakpoint.
         split_indices[search_index] = i_pair
 
-    return np.asarray(neighs), np.asarray(split_indices)
+    return neighs_obj, split_indices_obj
 
 
 @cython.boundscheck(False)
@@ -306,12 +310,12 @@ def get_all_unique_pairs(
 
     N_ats = list_array.shape[0]
 
-    i_pair: cython.int = 0
+    i_pair: cython.size_t = 0
 
     ref_xyz: cnp.float64_t[:] = np.zeros(3, dtype=np.float64)
     neigh_isc: cnp.int64_t[:] = np.zeros(3, dtype=np.int64)
 
-    neighs: cnp.int64_t[:, :] = np.zeros((max_npairs, 5), dtype=np.int64)
+    neighs: cnp.int64_t[:, :] = np.zeros([max_npairs, 5], dtype=np.int64)
 
     for at in range(N_ats):
         if self_interaction:
@@ -325,7 +329,7 @@ def get_all_unique_pairs(
 
         for j in range(8):
             # Find the bin index.
-            bin_index = indices[at, j]
+            bin_index: cnp.int64_t = indices[at, j]
 
             # Get the first atom index in this bin
             neigh_at: cnp.int64_t = heads[bin_index]
@@ -358,11 +362,10 @@ def get_all_unique_pairs(
                 # instead of moving potential neighbors to the unit cell
                 # because in this way we reduce the number of operations.
                 for i in range(3):
-                    ref_xyz[i] = (
-                        ref_xyz[i]
-                        - cell[0, i] * neigh_isc[0]
-                        - cell[1, i] * neigh_isc[1]
-                        - cell[2, i] * neigh_isc[2]
+                    ref_xyz[i] -= (
+                        cell[0, i] * neigh_isc[0]
+                        + cell[1, i] * neigh_isc[1]
+                        + cell[2, i] * neigh_isc[2]
                     )
 
             # Loop through all atoms that are in this bin.
@@ -483,7 +486,7 @@ def get_close(
 
     N_ind = search_xyz.shape[0]
 
-    i_pair: cython.int = 0
+    i_pair: cython.size_t = 0
 
     ref_xyz: cnp.float64_t[:] = np.zeros(3, dtype=np.float64)
     neigh_isc: cnp.int64_t[:] = np.zeros(3, dtype=np.int64)
@@ -494,7 +497,7 @@ def get_close(
     for search_index in range(N_ind):
         for j in range(8):
             # Find the bin index.
-            bin_index = indices[search_index, j]
+            bin_index: cnp.int64_t = indices[search_index, j]
 
             # Get the first atom index in this bin
             neigh_at: cnp.int64_t = heads[bin_index]
@@ -527,11 +530,10 @@ def get_close(
                 # instead of moving potential neighbors to the unit cell
                 # because in this way we reduce the number of operations.
                 for i in range(3):
-                    ref_xyz[i] = (
-                        ref_xyz[i]
-                        - cell[0, i] * neigh_isc[0]
-                        - cell[1, i] * neigh_isc[1]
-                        - cell[2, i] * neigh_isc[2]
+                    ref_xyz[i] -= (
+                        cell[0, i] * neigh_isc[0]
+                        + cell[1, i] * neigh_isc[1]
+                        + cell[2, i] * neigh_isc[2]
                     )
 
             # Loop through all atoms that are in this bin.

src/sisl/geom/neighs/tests/test_neighfinder.py

@@ -1,38 +1,31 @@
+from functools import partial
+
 import numpy as np
 import pytest
 
 from sisl import Geometry
 from sisl.geom import NeighFinder
 
+pytestmark = [pytest.mark.neighbour]
 
-@pytest.fixture(scope="module", params=[True, False])
-def sphere_overlap(request):
-    return request.param
 
+tr_fixture = partial(pytest.fixture, scope="module", params=[True, False])
 
-@pytest.fixture(scope="module", params=[True, False])
-def multiR(request):
-    return request.param
 
-
-@pytest.fixture(scope="module", params=[True, False])
-def self_interaction(request):
+def request_param(request):
     return request.param
 
 
-@pytest.fixture(scope="module", params=[False, True])
-def post_setup(request):
-    return request.param
-
-
-@pytest.fixture(scope="module", params=[False, True])
-def pbc(request):
-    return request.param
+sphere_overlap = tr_fixture()(request_param)
+multiR = tr_fixture()(request_param)
+self_interaction = tr_fixture()(request_param)
+post_setup = tr_fixture()(request_param)
+pbc = tr_fixture()(request_param)
 
 
 @pytest.fixture(scope="module")
 def neighfinder(sphere_overlap, multiR):
-    geom = Geometry([[0, 0, 0], [1.2, 0, 0], [9, 0, 0]], lattice=np.diag([10, 10, 7]))
+    geom = Geometry([[0, 0, 0], [1.2, 0, 0], [9, 0, 0]], lattice=[10, 10, 7])
 
     R = np.array([1.1, 1.5, 1.2]) if multiR else 1.5
 
@@ -75,7 +68,7 @@ def expected_neighs(sphere_overlap, multiR, self_interaction, pbc):
 
 
 def test_neighfinder_setup(sphere_overlap, multiR, post_setup):
-    geom = Geometry([[0, 0, 0], [1, 0, 0]], lattice=np.diag([10, 10, 7]))
+    geom = Geometry([[0, 0, 0], [1, 0, 0]], lattice=[10, 10, 7])
 
     R = np.array([0.9, 1.5]) if multiR else 1.5
 
@@ -243,7 +236,7 @@ def test_R_too_big(pbc):
     """Test the case when R is so big that it needs a bigger bin
     than the unit cell."""
 
-    geom = Geometry([[0, 0, 0], [1, 0, 0]], lattice=np.diag([2, 10, 10]))
+    geom = Geometry([[0, 0, 0], [1, 0, 0]], lattice=[2, 10, 10])
 
     neighfinder = NeighFinder(geom, R=1.5)
 
@@ -265,7 +258,5 @@ def test_R_too_big(pbc):
     if pbc:
         expected_neighs.insert(0, [0, 1, -1, 0, 0])
 
-    print(neighs, expected_neighs)
-
     assert neighs.shape == (len(expected_neighs), 5)
     assert np.all(neighs == expected_neighs)