Bump structuretoolkit from 0.0.26 to 0.0.27

.ci_support/environment-docs.yml

@@ -20,11 +20,11 @@ dependencies:
 - pyiron_base =0.9.6
 - pyiron_snippets =0.1.2
 - pylammpsmpi =0.2.20
-- pyscal =2.10.18
+- pyscal3 =3.2.5
 - scikit-learn =1.5.1
 - scipy =1.14.0
 - seekpath =2.1.0
 - spglib =2.4.0
-- structuretoolkit =0.0.26
+- structuretoolkit =0.0.27
 - pyxtal =0.6.2
 - jupyter-book =1.0.0

.ci_support/environment-old.yml

@@ -16,11 +16,11 @@ dependencies:
 - pyiron_base =0.9.4
 - pyiron_snippets =0.1.1
 - pylammpsmpi =0.2.18
-- pyscal =2.10.15
+- pyscal3 =3.2.5
 - monty =2024.3.31
 - pyxtal =0.6.1
 - scikit-learn =1.2.1
 - scipy =1.11.1
 - seekpath =1.9.5
 - spglib =2.0.2
-- structuretoolkit =0.0.19
+- structuretoolkit =0.0.27

.ci_support/environment.yml

@@ -18,10 +18,10 @@ dependencies:
 - pyiron_base =0.9.6
 - pyiron_snippets =0.1.2
 - pylammpsmpi =0.2.20
-- pyscal =2.10.18
+- pyscal3 =3.2.5
 - scikit-learn =1.5.1
 - scipy =1.14.0
 - seekpath =2.1.0
 - spglib =2.4.0
-- structuretoolkit =0.0.26
+- structuretoolkit =0.0.27
 - pyxtal =0.6.2

binder/environment.yml

@@ -16,12 +16,12 @@ dependencies:
 - pyiron_base =0.9.6
 - pyiron_snippets =0.1.2
 - pylammpsmpi =0.2.20
-- pyscal =2.10.18
+- pyscal3 =3.2.5
 - scikit-learn =1.5.1
 - scipy =1.14.0
 - seekpath =2.1.0
 - spglib =2.4.0
-- structuretoolkit =0.0.26
+- structuretoolkit =0.0.27
 - pyxtal =0.6.2
 - pyiron-data >=0.0.22
 - sqsgenerator
@@ -32,4 +32,3 @@ dependencies:
 - sphinxdft-data
 - nglview
 - seaborn
-- pyscal

pyproject.toml

@@ -38,11 +38,12 @@ dependencies = [
     "pyiron_base==0.9.6",
     "pyiron_snippets==0.1.2",
     "pylammpsmpi==0.2.20",
+    "pyscal3==3.2.5",
     "scipy==1.14.0",
     "scikit-learn==1.5.1",
     "seekpath==2.1.0",
     "spglib==2.4.0",
-    "structuretoolkit==0.0.26",
+    "structuretoolkit==0.0.27",
 ]
 dynamic = ["version"]
 

tests/atomic/structure/test_pyscal.py

@@ -4,7 +4,7 @@
 
 import unittest
 import numpy as np
-import pyscal.core as pc
+import pyscal3 as pc
 from pyiron_atomistics.atomistics.structure.atoms import Atoms, CrystalStructure
 from ase.build import bulk
 from pyiron_atomistics.atomistics.structure.atoms import ase_to_pyiron
@@ -25,8 +25,7 @@ def test_simple_system(self):
         """
         Test a simple ase to pyscal conversion
         """
-        sysp = pc.System()
-        sysp.read_inputfile(self.structure, format="ase")
+        sysp = pc.System(self.structure, format="ase")
         self.assertEqual(len(sysp.atoms), 256)
 
     def test_steinhardt_parameters_returns(self):
@@ -210,8 +209,7 @@ def test_analyse_pyscal_cna_adaptive(self):
 
     def test_analyse_pyscal_diamond_structure(self):
         pyscal_keys = [
-            'others', 'fcc', 'hcp', 'bcc', 'ico',
-            'cubic diamond', 'cubic diamond 1NN', 'cubic diamond 2NN',
+            'others', 'cubic diamond', 'cubic diamond 1NN', 'cubic diamond 2NN',
             'hex diamond', 'hex diamond 1NN', 'hex diamond 2NN'
         ]
         ovito_keys = [
@@ -234,7 +232,7 @@ def test_analyse_pyscal_diamond_structure(self):
         self.assertEqual(res_dict_total[pyscal_keys[0]], len(self.ti_hcp))
         res_dict_total = self.si_dia.analyse.pyscal_diamond_structure(mode="total", ovito_compatibility=False)
         self.assertEqual(sum([k in res_dict_total.keys() for k in pyscal_keys]), len(pyscal_keys))
-        self.assertEqual(res_dict_total[pyscal_keys[5]], len(self.si_dia))
+        self.assertEqual(res_dict_total[pyscal_keys[1]], len(self.si_dia))
 
         res_numeric = self.al_fcc.analyse.pyscal_diamond_structure(mode="numeric", ovito_compatibility=False)
         self.assertEqual(len(res_numeric), len(self.al_fcc))
@@ -247,7 +245,7 @@ def test_analyse_pyscal_diamond_structure(self):
         self.assertTrue(all([v == 0 for v in res_numeric]))
         res_numeric = self.si_dia.analyse.pyscal_diamond_structure(mode="numeric", ovito_compatibility=False)
         self.assertEqual(len(res_numeric), len(self.si_dia))
-        self.assertTrue(all([v == 5 for v in res_numeric]))
+        self.assertTrue(all([v == 1 for v in res_numeric]))
 
         res_str = self.al_fcc.analyse.pyscal_diamond_structure(mode="str", ovito_compatibility=False)
         self.assertEqual(len(res_str), len(self.al_fcc))