spglib 2.5 compatibility (#943)

* update spglib symmetry dataset access and pin min version

* move spglib version pin

* ensure correct spglib installed in requirements

* ensure correct spglib installed in requirements

* add a few attempts to connect to dataset downloads in case internet has bad day

* remove mac hidden ds_stores and add to gitignore

* precommit

* ensure backwards compat with older spglib, loosen lower pin on spglib version, upper pin on numpy

* precommit

* repin spglib == 2.5, add read permissions for workflow actions (somehow GH token not being read

* Update .github/workflows/test.yml

---------

Co-authored-by: Matthew Evans <7916000+ml-evs@users.noreply.github.com>

.github/workflows/test.yml

@@ -3,6 +3,9 @@
 # The ext package is also only tested in this workflow. Coverage is also computed based on this platform.
 name: Testing
 
+permissions:
+  contents: read
+
 env:
   PYTEST_ADDOPTS: "--color=yes"
 

.gitignore

@@ -9,6 +9,8 @@ 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 = getattr(sym_data, "equivalent_atoms", sym_data["equivalent_atoms"])
+        wyckoffs = getattr(sym_data, "wyckoffs", sym_data["wyckoffs"])
         sym_struct = SymmetrizedStructure(s, sg, equiv_atoms, wyckoffs)
         equivs = sym_struct.find_equivalent_sites(site)
         return equivs

pyproject.toml

@@ -1,8 +1,8 @@
 [build-system]
 requires = [
      # pin NumPy version used in the build
-     "numpy>=1.20.1",
-     "setuptools>=43.0.0"
+     "numpy>=1.20.1, <2",
+     "setuptools>=43.0.0",
 ]
 build-backend = "setuptools.build_meta"