spglib 2.5 compatibility

.gitignore

@@ -8,6 +8,8 @@ docs/_build/*/*/*
 # C extensions
 *.so
 
+.DS_Store
+
 # Packages
 *.egg
 *.egg-info

matminer/datasets/tests/test_datasets.py

@@ -1,5 +1,6 @@
 import os
 import unittest
+from time import sleep
 
 import numpy as np
 import requests
@@ -20,6 +21,7 @@ def universal_dataset_check(
         numeric_headers=None,
         bool_headers=None,
         test_func=None,
+        max_connect_attempts: int = 5,
     ):
         # "Hard" integrity checks that take a long time.
         # These tests only run if the MATMINER_DATASET_FULL_TEST
@@ -75,7 +77,14 @@ def universal_dataset_check(
         # This runs when on a system with the CI environment var present
         # (e.g. when running a continuous integration VCS system)
         else:
-            download_page = requests.head(self.dataset_dict[dataset_name]["url"])
+            # try to be lenient in connecting to DB, in case a request fails once
+            for iconnect in range(max_connect_attempts):
+                download_page = requests.head(self.dataset_dict[dataset_name]["url"])
+                if download_page.ok:
+                    break
+                if iconnect < max_connect_attempts - 1:
+                    sleep(5)
+
             self.assertTrue(download_page.ok)
 
 

matminer/featurizers/structure/bonding.py

@@ -805,8 +805,8 @@ def get_equiv_sites(self, s, site):
         sga = SpacegroupAnalyzer(s, symprec=0.01)
         sg = sga.get_space_group_operations
         sym_data = sga.get_symmetry_dataset()
-        equiv_atoms = sym_data["equivalent_atoms"]
-        wyckoffs = sym_data["wyckoffs"]
+        equiv_atoms = sym_data.equivalent_atoms
+        wyckoffs = sym_data.wyckoffs
         sym_struct = SymmetrizedStructure(s, sg, equiv_atoms, wyckoffs)
         equivs = sym_struct.find_equivalent_sites(site)
         return equivs

pyproject.toml

@@ -2,7 +2,7 @@
 requires = [
      # pin NumPy version used in the build
      "numpy>=1.20.1",
-     "setuptools>=43.0.0"
+     "setuptools>=43.0.0",
 ]
 build-backend = "setuptools.build_meta"
 

requirements/ubuntu-latest_py3.10.txt

@@ -266,7 +266,7 @@ soupsieve==2.5
     # via beautifulsoup4
 sparse==0.15.4
     # via dscribe
-spglib==2.4.0
+spglib==2.5.0
     # via pymatgen
 sphinx==7.3.7
     # via matminer (setup.py)

requirements/ubuntu-latest_py3.11.txt

@@ -264,7 +264,7 @@ soupsieve==2.5
     # via beautifulsoup4
 sparse==0.15.4
     # via dscribe
-spglib==2.4.0
+spglib==2.5.0
     # via pymatgen
 sphinx==7.3.7
     # via matminer (setup.py)

requirements/ubuntu-latest_py3.9.txt

@@ -272,7 +272,7 @@ soupsieve==2.5
     # via beautifulsoup4
 sparse==0.15.4
     # via dscribe
-spglib==2.4.0
+spglib==2.5.0
     # via pymatgen
 sphinx==7.3.7
     # via matminer (setup.py)

setup.py

@@ -63,6 +63,7 @@ def local_version(version):
             "sympy ~= 1.11",
             "monty >= 2023",
             "pymatgen >= 2023",
+            "spglib>=2.5.0",
         ],
         extras_require=extras_require,
         classifiers=[