Flatten q-point indices for compatibility with Numpy 2.0 (#303)

* Flatten q-point indices for compatibility with Numpy 2.0

With Numpy 2.0, np.unique returns a 2-D array when applied to
q-points. This in turn gets broadcast and adds an extra dimension to
the frequency/mode arrays, causing all kinds of chaos.

Flattening the array here should be a no-op for Numpy <2 and fixes the
issue.

*  Update deprecated scipy.integrate simps -> simpson

*  Pin Mac tests to macos-12 environment for Brille compatibility

Hopefully we can return to macos-latest soon once Brille build issues are resolved

.github/workflows/build_upload_pypi_wheels.yml

@@ -14,7 +14,7 @@ jobs:
         include:
           - os: windows-latest
             wheelname: win
-          - os: macos-latest
+          - os: macos-12
             wheelname: macos
           - os: ubuntu-latest
             wheelname: manylinux

.github/workflows/run_tests.yml

@@ -17,7 +17,7 @@ jobs:
        (github.event_name == 'pull_request' && !contains(github.event.pull_request.labels.*.name, 'no_ci'))
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        os: [ubuntu-latest, windows-latest, macos-12]
       fail-fast: false
     runs-on: ${{ matrix.os }}
     steps:
@@ -29,7 +29,8 @@ jobs:
           channel-priority: true
       - name: Install llvm on Macos
         if: startsWith(matrix.os, 'macos')
-        run: brew install llvm
+        run: |
+          brew install llvm
       - name: Update pip and install dependencies
         shell: bash -l {0}
         run: |
@@ -96,7 +97,7 @@ jobs:
     if: success() || failure()
     steps:
       - name: Download Artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           path: artifacts
       - name: Publish test results

.github/workflows/test_release.yml

@@ -10,7 +10,7 @@ jobs:
   test:
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        os: [ubuntu-latest, windows-latest, macos-12]
       fail-fast: false
     runs-on: ${{ matrix.os }}
     steps:
@@ -22,7 +22,8 @@ jobs:
           channel-priority: true
       - name: Install llvm on Macos
         if: startsWith(matrix.os, 'macos')
-        run: brew install llvm
+        run: |
+          brew install llvm
       - name: Update pip and install dependencies
         shell: bash -l {0}
         run: |

CHANGELOG.rst

@@ -22,6 +22,17 @@
     spglib raises TypeError when using empty unit cell and this needs
     handling when looking for high-symmetry labels
 
+  - Compatibility fix for Numpy 2.0 update: avoid some
+    broadcasting issues with array shape returned by ``np.unique``
+
+  - Update reference to scipy.integrate.simpson (scipy.integrate.simps
+    is deprecated)
+
+  - Mac tests and builds are running against "macos-12" github runner
+    instead of "macos-latest", in order to test properly against
+    Brille. This should be restored to "macos-latest" when Brille
+    build system is updated and gives consistent results with
+    win/linux.
 
 -------------------------------------------------------------------------------
 

euphonic/force_constants.py

@@ -508,6 +508,8 @@ def _calculate_phonons_at_qpts(
             norm_qpts[gamma_i] = 0.
             reduced_qpts, qpts_i = np.unique(norm_qpts, return_inverse=True,
                                              axis=0)
+            qpts_i = qpts_i.flatten()
+
             n_rqpts = len(reduced_qpts)
             # Special handling of gamma points - don't reduce gamma
             # points if LO-TO splitting

setup.py

@@ -62,7 +62,7 @@ def get_c_extension():
         else:
             link_args = ['-fopenmp']
 
-        compile_args = ['-fopenmp']            
+        compile_args = ['-fopenmp']
 
     else:
         # Linux - assume gcc if CC not set

tests_and_analysis/test/euphonic_test/test_broadening.py

@@ -3,7 +3,7 @@
 from numpy.polynomial import Polynomial
 from numpy.random import RandomState
 import numpy.testing as npt
-from scipy.integrate import simps
+from scipy.integrate import simpson
 from scipy.ndimage import gaussian_filter
 
 from euphonic.broadening import (find_coeffs,
@@ -74,10 +74,10 @@ def test_area_unchanged_for_broadened_dos(material, qpt_freqs_json,
                                 fit='cheby-log')
     ebins_centres = ebins.magnitude[:-1] + 0.5*np.diff(ebins.magnitude)
     assert dos.y_data.units == 1/ebins.units
-    dos_area = simps(dos.y_data.magnitude, ebins_centres)
+    dos_area = simpson(dos.y_data.magnitude, x=ebins_centres)
     assert variable_width_broaden.units == 1/ebins.units
-    adaptively_broadened_dos_area = simps(variable_width_broaden.magnitude,
-                                          ebins_centres)
+    adaptively_broadened_dos_area = simpson(
+        variable_width_broaden.magnitude, x=ebins_centres)
     assert adaptively_broadened_dos_area == pytest.approx(dos_area, rel=0.01)