Merge branch 'libAtoms:master' into master

.github/workflows/documentation.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/paper.yml

@@ -6,15 +6,15 @@ jobs:
     name: Paper Draft
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Build draft PDF
         uses: openjournals/openjournals-draft-action@master
         with:
           journal: joss
           # This should be the path to the paper within your repo.
           paper-path: paper/paper.md
       - name: Upload
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v4
         with:
           name: paper
           # This is the output path where Pandoc will write the compiled

.github/workflows/tests.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -44,7 +44,7 @@ jobs:
           pytest -v --junitxml=report.xml --durations=20
 
       - name: report
-        uses: mikepenz/action-junit-report@v2
+        uses: mikepenz/action-junit-report@v4
         if: always()
         with:
           report_paths: "**/report.xml"

.github/workflows/wheels.yml

@@ -25,7 +25,9 @@ jobs:
       matrix:
         buildplat:
         - [ubuntu-20.04, manylinux, x86_64]
+        - [ubuntu-20.04, manylinux, aarch64]
         - [macos-12, macosx, x86_64]
+        - [macos-12, macosx, arm64]
         - [windows-2019, win, AMD64]
 
         python: ["cp38", "cp39", "cp310", "cp311", "cp312"]
@@ -35,29 +37,34 @@ jobs:
       IS_32_BIT: ${{ matrix.buildplat[2] == 'x86' }}
 
     steps:
-      - uses: actions/checkout@v3
+      - if: matrix.buildplat[2] == 'aarch64'
+        uses: docker/setup-qemu-action@v3
+        with:
+          platforms: all
+
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.8'
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.16.2
+        uses: pypa/cibuildwheel@v2.19.2
         env:
           CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}*
           CIBW_ARCHS: ${{ matrix.buildplat[2] }}
           CIBW_ENVIRONMENT_PASS_LINUX: RUNNER_OS
           CIBW_TEST_COMMAND: python {project}/tests/test_ffi.py
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
           path: ./wheelhouse/*.whl
           name: ${{ matrix.python }}-${{ matrix.buildplat[1] }}-${{ matrix.buildplat[2] }}
 
       - name: Release wheels
-        uses: softprops/action-gh-release@v1
+        uses: softprops/action-gh-release@v2
         if: startsWith(github.ref, 'refs/tags/')
         with:
           files: wheelhouse/*.whl

ChangeLog.md

@@ -1,9 +1,15 @@
 Change log
 ==========
 
-v1.0.0 (24Jan24)
+v1.1.0 (not yet released)
 -------------------------
 
+- Fixes for recent ASE and numpy 2.0
+- Fix correct number of cores for quad of dissociated dislocations
+
+v1.0.0 (24Jan24)
+----------------
+
 - JOSS paper!
 - Significant updates documentation packages
 - Displacement field and associated deformation tensors for dislocations in anisotropic elastic media

c/angle_distribution.cpp

@@ -22,16 +22,13 @@
 #include <Python.h>
 #define PY_ARRAY_UNIQUE_SYMBOL MATSCIPY_ARRAY_API
 #define NO_IMPORT_ARRAY
-#define NPY_NO_DEPRECATED_API NPY_1_5_API_VERSION
+#define NPY_NO_DEPRECATED_API NPY_2_0_API_VERSION
 #include <numpy/arrayobject.h>
 
-#ifdef _MSC_VER
-#define _USE_MATH_DEFINES
-#include <cmath>
-#endif
-
 #include "angle_distribution.h"
 
+#define	M_PI ((double)3.14159265358979323846) /* pi */
+
 /*
  * Compute bond angle distribution
  */
@@ -47,25 +44,25 @@ py_angle_distribution(PyObject *self, PyObject *args)
                         &j_arr, &PyArray_Type, &r_arr, &nbins, &cutoff))
     return NULL;
 
-  if (PyArray_NDIM(i_arr) != 1 || PyArray_TYPE(i_arr) != NPY_INT) {
+  if (PyArray_NDIM((PyArrayObject *) i_arr) != 1 || PyArray_TYPE((PyArrayObject *) i_arr) != NPY_INT) {
     PyErr_SetString(PyExc_TypeError, "First argument needs to be one-dimensional "
                     "integer array.");
     return NULL;
   }
-  if (PyArray_NDIM(j_arr) != 1 || PyArray_TYPE(j_arr) != NPY_INT) {
+  if (PyArray_NDIM((PyArrayObject *) j_arr) != 1 || PyArray_TYPE((PyArrayObject *) j_arr) != NPY_INT) {
     PyErr_SetString(PyExc_TypeError, "Second argument needs to be one-dimensional "
                     "integer array.");
     return NULL;
   }
-  if (PyArray_NDIM(r_arr) != 2 || PyArray_DIM(r_arr, 1) != 3 ||
-      PyArray_TYPE(r_arr) != NPY_DOUBLE) {
+  if (PyArray_NDIM((PyArrayObject *) r_arr) != 2 || PyArray_DIM((PyArrayObject *) r_arr, 1) != 3 ||
+      PyArray_TYPE((PyArrayObject *) r_arr) != NPY_DOUBLE) {
     PyErr_SetString(PyExc_TypeError, "Third argument needs to be two-dimensional "
                     "double array.");
     return NULL;
   }
 
-  npy_intp npairs = PyArray_DIM(i_arr, 0);
-  if (PyArray_DIM(j_arr, 0) != npairs || PyArray_DIM(r_arr, 0) != npairs) {
+  npy_intp npairs = PyArray_DIM((PyArrayObject *) i_arr, 0);
+  if (PyArray_DIM((PyArrayObject *) j_arr, 0) != npairs || PyArray_DIM((PyArrayObject *) r_arr, 0) != npairs) {
     PyErr_SetString(PyExc_RuntimeError, "First three arguments need to be arrays of "
                     "identical length.");
     return NULL;
@@ -75,11 +72,10 @@ py_angle_distribution(PyObject *self, PyObject *args)
   PyObject *h_arr = PyArray_ZEROS(1, &dim, NPY_INT, 1);
   PyObject *tmp_arr = PyArray_ZEROS(1, &dim, NPY_INT, 1);
 
-  npy_int *i = (npy_int*)PyArray_DATA(i_arr);
-  npy_int *j = (npy_int*)PyArray_DATA(j_arr);
-  double *r = (double*)PyArray_DATA(r_arr);
-  npy_int *h = (npy_int*)PyArray_DATA(h_arr);
-  npy_int *tmp = (npy_int*)PyArray_DATA(tmp_arr);
+  npy_int *i = (npy_int*)PyArray_DATA((PyArrayObject *) i_arr);
+  double *r = (double*)PyArray_DATA((PyArrayObject *) r_arr);
+  npy_int *h = (npy_int*)PyArray_DATA((PyArrayObject *) h_arr);
+  npy_int *tmp = (npy_int*)PyArray_DATA((PyArrayObject *) tmp_arr);
 
   npy_int last_i = i[0], i_start = 0;
   memset(tmp, 0, nbins*sizeof(npy_int));