Merge pull request #898 from hackingmaterials/fix-spglib

Fix spglib compatability

.github/workflows/docs.yml

@@ -14,14 +14,14 @@ jobs:
 
     - uses: actions/setup-python@v5
       with:
-        python-version: '3.9'
+        python-version: '3.10'
         cache: pip
         cache-dependency-path: requirements.txt
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install numpy wheel packaging
+        pip install numpy==1.25.0 wheel packaging
         pip install -r requirements.txt
         pip install -e .[docs]
 

.github/workflows/release.yml

@@ -21,7 +21,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install numpy wheel packaging setuptools setuptools_scm
+          pip install numpy==2.0.1 cython wheel packaging setuptools setuptools_scm
           pip install -r requirements.txt
           pip install -e .[tests]
 

.github/workflows/tests.yml

@@ -26,14 +26,14 @@ jobs:
 
     - uses: actions/setup-python@v5
       with:
-        python-version: '3.9'
+        python-version: '3.10'
         cache: pip
         cache-dependency-path: requirements.txt
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install numpy wheel packaging
+        pip install numpy==2.0.1 cython wheel packaging
         pip install -r requirements.txt
         pip install -e .[docs]
 
@@ -44,7 +44,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.10"]
 
     steps:
     - uses: actions/checkout@v4
@@ -58,7 +58,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install numpy==1.25.0 wheel packaging
+        pip install numpy==2.0.1 cython wheel packaging
         pip install -r requirements.txt
         pip install -e .[tests]
 

.pre-commit-config.yaml

@@ -1,28 +1,28 @@
 repos:
   - repo: https://github.com/myint/autoflake
-    rev: v2.2.1
+    rev: v2.3.1
     hooks:
     - id: autoflake
       args: [--in-place, --remove-all-unused-imports, --remove-unused-variable, --ignore-init-module-imports]
   - repo: https://github.com/psf/black
-    rev: 23.11.0
+    rev: 24.4.2
     hooks:
     - id: black
   - repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
+    rev: 7.1.0
     hooks:
       - id: flake8
         files: ^amset/
         args: [--max-line-length=125, "--extend-ignore=E203,W503"]
         language_version: python3
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
   - repo: https://github.com/pycqa/isort
-    rev: 5.13.0
+    rev: 5.13.2
     hooks:
       - id: isort
         name: isort (python)

CITATION.cff

@@ -1,17 +1,4 @@
 cff-version: 1.2.0
-message: |
-  If you use AMSET in your research, please cite the following:
-title: 'Efficient calculation of carrier scattering rates from first principles'
-version: 0.4.17 # replace with whatever version you use
-doi: 10.1038/s41467-021-22440-5
-date-released: 2021-04-13
-url: https://github.com/hackingmaterials/amset
-issn: 2041-1723
-journal: Nature Communications
-pages: 2222
-volume: 12
-year: 2021
-type: software
 authors:
 - family-names: Ganose
   given-names: Alex M.
@@ -27,3 +14,34 @@ authors:
 - family-names: Jain
   given-names: Anubhav
   orcid: https://orcid.org/0000-0001-5893-9967
+doi: 10.1038/s41467-021-22440-5
+title: 'Efficient calculation of carrier scattering rates from first principles'
+message: |
+  If you use AMSET in your research, please cite the following:
+preferred-citation:
+  authors:
+  - family-names: Ganose
+    given-names: Alex M.
+    orcid: https://orcid.org/0000-0002-4486-3321
+  - family-names: Park
+    given-names: Junsoo
+  - family-names: Faghaninia
+    given-names: Alireza
+  - family-names: Woods-Robinson
+    given-names: Rachel
+  - family-names: Persson
+    given-names: Kristin A.
+  - family-names: Jain
+    given-names: Anubhav
+    orcid: https://orcid.org/0000-0001-5893-9967
+  title: 'Efficient calculation of carrier scattering rates from first principles'
+  version: 0.4.17 # replace with whatever version you use
+  date-published: 2021-04-13
+  doi: 10.1038/s41467-021-22440-5
+  url: https://www.nature.com/articles/s41467-021-22440-5
+  issn: 2041-1723
+  journal: Nature Communications
+  pages: 2222
+  volume: 12
+  year: 2021
+  type: article

amset/__init__.py

@@ -1 +1 @@
-__version__ = "0.4.20"
+__version__ = "0.4.21"

amset/constants.py

@@ -1,4 +1,5 @@
 """Module defining constants and default parameters."""
+
 import numpy as np
 from monty.serialization import loadfn
 from pkg_resources import resource_filename

amset/electronic_structure/dos.py

@@ -1,6 +1,7 @@
 """
 Customised implementation of FermiDos. Will Move back to pymatgen at some point.
 """
+
 import logging
 from typing import Dict, Optional, Tuple, Union
 

amset/electronic_structure/kpoints.py

@@ -115,12 +115,17 @@ def get_kpoints_tetrahedral(
         kpoint_mesh = get_kpoint_mesh(structure, kpoint_mesh)
 
     atoms = AseAtomsAdaptor().get_atoms(structure)
+    cell = (
+        np.array(atoms.get_cell().T, dtype="double", order="C"),  # lattice
+        np.array(atoms.get_scaled_positions(), dtype="double", order="C"),  # positions
+        np.array(atoms.get_atomic_numbers(), dtype="intc"),  # numbers
+    )
 
     if not symprec:
         symprec = 1e-8
 
     grid_mapping, grid_address = spglib.get_ir_reciprocal_mesh(
-        kpoint_mesh, atoms, symprec=symprec, is_time_reversal=time_reversal_symmetry
+        kpoint_mesh, cell, symprec=symprec, is_time_reversal=time_reversal_symmetry
     )
     full_kpoints = grid_address / kpoint_mesh
 

amset/scattering/calculate.py

@@ -172,10 +172,10 @@ def __init__(
 
                 # calculate the coefficients for all bands and k-point simultaneously
                 try:
-                    self._coeffs[
-                        spin
-                    ] = self.amset_data.overlap_calculator.get_coefficients(
-                        spin, spin_b_idxs, self.amset_data.kpoints[spin_k_idxs]
+                    self._coeffs[spin] = (
+                        self.amset_data.overlap_calculator.get_coefficients(
+                            spin, spin_b_idxs, self.amset_data.kpoints[spin_k_idxs]
+                        )
                     )
                     # because we are only storing the coefficients for the
                     # band/k-points we want, we need a way of mapping from the original
@@ -232,9 +232,11 @@ def initialize_workers(self):
 
         # deformation potential is a large tensor that should be put into shared memory
         elastic_scatterers = [
-            s.to_reference()
-            if isinstance(s, AcousticDeformationPotentialScattering)
-            else s
+            (
+                s.to_reference()
+                if isinstance(s, AcousticDeformationPotentialScattering)
+                else s
+            )
             for s in self.elastic_scatterers
         ]
 
@@ -562,9 +564,11 @@ def scattering_worker(
             raise ValueError(f"Unrecognised overlap type: {overlap_type}")
 
         elastic_scatterers = [
-            AcousticDeformationPotentialScattering.from_reference(*s)
-            if isinstance(s, tuple)
-            else s
+            (
+                AcousticDeformationPotentialScattering.from_reference(*s)
+                if isinstance(s, tuple)
+                else s
+            )
             for s in elastic_scatterers
         ]
 

amset/tools/cli.py

@@ -1,6 +1,7 @@
 """
 This module contains a script for using amset from the command line.
 """
+
 import warnings
 
 import click

amset/util.py

@@ -1,6 +1,7 @@
 """
 Module defining utility functions.
 """
+
 import collections
 import copy
 import logging

docs/src/changelog.md

@@ -1,10 +1,13 @@
 # Change log
 
+## v0.4.21
+
+Fix compatbility with spglib.
+
 ## v0.4.20
 
 Fix intermittent casting bug.
 
-
 ## v0.4.19
 
 Fix numpy deprecations.

requirements.txt

@@ -1,15 +1,15 @@
-pymatgen==2024.4.13
-scipy==1.13.1
-monty==2024.5.24
-matplotlib==3.9.0
-BoltzTraP2==24.1.1
+pymatgen==2024.7.18
+scipy==1.14.0
+monty==2024.7.12
+matplotlib==3.9.1
+BoltzTraP2==24.7.2
 tqdm==4.66.4
 tabulate==0.9.0
 memory_profiler==0.61.0
-spglib==2.2.0
+spglib==2.5.0
 click==8.1.7
 sumo==2.3.8
 h5py==3.11.0
-pyFFTW==0.13.1
-interpolation==2.2.4
-numba==0.58.0
+pyFFTW==0.14.0
+interpolation==2.2.7
+numba==0.60.0

setup.py

@@ -51,14 +51,14 @@
         ],
         extras_require={
             "docs": [
-                "mkdocs==1.5.3",
-                "mkdocs-material==9.5.16",
+                "mkdocs==1.6.0",
+                "mkdocs-material==9.5.30",
                 "mkdocs-minify-plugin==0.8.0",
-                "mkdocs-macros-plugin==1.0.4",
+                "mkdocs-macros-plugin==1.0.5",
                 "markdown-include==0.8.1",
-                "markdown-katex==202112.1034",
+                "markdown-katex==202406.1035",
             ],
-            "tests": ["pytest==8.2.1", "pytest-cov==5.0.0"],
+            "tests": ["pytest==8.3.1", "pytest-cov==5.0.0"],
             "all-electron": ["pawpyseed==0.7.1"],
             "dev": ["pre-commit==3.7.1"],
         },

tests/core/test_run.py

@@ -19,6 +19,7 @@
 - don't write mesh, using projections + deformation potential tuple + single elastic
   constant/piezoelectric for K2ReF6 (tricky spin polarized system)
 """
+
 from copy import deepcopy
 from pathlib import Path
 from typing import Any, Dict
@@ -190,7 +191,7 @@ def test_run_tricky_spin_polarized(band_structure_data):
     files = ["transport", "!mesh"]
     scats = ["ADP"]
     transport = {
-        ("mobility", ("overall", (0, 0))): 1.261213643946453,
+        ("mobility", ("overall", (0, 0))): 1.3902421061518926,
         ("seebeck", (0, 0)): 1356.1341462605026,
     }
 

tests/electronic_structure/test_symmetry.py

@@ -277,7 +277,12 @@ def _sort_kpoints(kp):
 
     # generate true k-points and IR k-points using spglib
     atoms = AseAtomsAdaptor.get_atoms(symmetry_structure)
-    mapping, addresses = get_ir_reciprocal_mesh(mesh, atoms, is_shift=shift)
+    cell = (
+        np.array(atoms.get_cell().T, dtype="double", order="C"),  # lattice
+        np.array(atoms.get_scaled_positions(), dtype="double", order="C"),  # positions
+        np.array(atoms.get_atomic_numbers(), dtype="intc"),  # numbers
+    )
+    mapping, addresses = get_ir_reciprocal_mesh(mesh, cell, is_shift=shift)
     true_kpoints = addresses / mesh + shift / (mesh * 2)
     true_kpoints = _kpoints_to_first_bz(true_kpoints)
     true_kpoints_sort = _sort_kpoints(true_kpoints)