Merge pull request #1466 from pyiron/scipy-1

Update scipy to 1.14.0

.ci_support/environment-docs.yml

@@ -7,7 +7,7 @@ dependencies:
 - myst-parser
 - aimsgb =1.1.0
 - ase =3.23.0
-- atomistics =0.1.29
+- atomistics =0.1.30
 - defusedxml =0.7.1
 - h5py =3.11.0
 - matplotlib-base =3.8.4
@@ -19,12 +19,12 @@ dependencies:
 - pint =0.24
 - pyiron_base =0.9.4
 - pyiron_snippets =0.1.2
-- pylammpsmpi =0.2.19
+- pylammpsmpi =0.2.20
 - pyscal =2.10.18
 - scikit-learn =1.5.0
-- scipy =1.13.1
+- scipy =1.14.0
 - seekpath =2.1.0
 - spglib =2.4.0
-- structuretoolkit =0.0.25
+- structuretoolkit =0.0.26
 - pyxtal =0.6.2
 - jupyter-book =1.0.0

.ci_support/environment.yml

@@ -3,7 +3,7 @@ channels:
 dependencies:
 - aimsgb =1.1.0
 - ase =3.23.0
-- atomistics =0.1.29
+- atomistics =0.1.30
 - coverage
 - codacy-coverage
 - defusedxml =0.7.1
@@ -17,11 +17,11 @@ dependencies:
 - pint =0.24
 - pyiron_base =0.9.4
 - pyiron_snippets =0.1.2
-- pylammpsmpi =0.2.19
+- pylammpsmpi =0.2.20
 - pyscal =2.10.18
 - scikit-learn =1.5.0
-- scipy =1.13.1
+- scipy =1.14.0
 - seekpath =2.1.0
 - spglib =2.4.0
-- structuretoolkit =0.0.25
+- structuretoolkit =0.0.26
 - pyxtal =0.6.2

binder/environment.yml

@@ -3,7 +3,7 @@ channels:
 dependencies:
 - aimsgb =1.1.0
 - ase =3.23.0
-- atomistics =0.1.29
+- atomistics =0.1.30
 - defusedxml =0.7.1
 - h5py =3.11.0
 - matplotlib-base =3.8.4
@@ -15,13 +15,13 @@ dependencies:
 - pint =0.24
 - pyiron_base =0.9.4
 - pyiron_snippets =0.1.2
-- pylammpsmpi =0.2.19
+- pylammpsmpi =0.2.20
 - pyscal =2.10.18
 - scikit-learn =1.5.0
-- scipy =1.13.1
+- scipy =1.14.0
 - seekpath =2.1.0
 - spglib =2.4.0
-- structuretoolkit =0.0.25
+- structuretoolkit =0.0.26
 - pyxtal =0.6.2
 - pyiron-data >=0.0.22
 - sqsgenerator

pyiron_atomistics/vasp/parser/report.py

@@ -3,7 +3,7 @@
 # Distributed under the terms of "New BSD License", see the LICENSE file.
 
 import numpy as np
-from scipy.integrate import cumtrapz
+from scipy.integrate import cumulative_trapezoid
 
 __author__ = "Sudarsan Surendralal"
 __copyright__ = (
@@ -43,7 +43,7 @@ def from_file(self, filename="REPORT"):
             ]
             rel_lines = [lines[i] for i, line in enumerate(lines) if "cc>" in line]
             cv = np.genfromtxt(rel_lines, usecols=[2])
-            fe = cumtrapz(lam, cv)
+            fe = cumulative_trapezoid(lam, cv)
             self.parse_dict["cv_full"] = cv
             self.parse_dict["derivative"] = lam
             self.parse_dict["cv"] = cv[:-1]

pyproject.toml

@@ -25,7 +25,7 @@ classifiers = [
 ]
 dependencies = [
     "ase==3.23.0",
-    "atomistics==0.1.29",
+    "atomistics==0.1.30",
     "defusedxml==0.7.1",
     "h5py==3.11.0",
     "matplotlib==3.8.4",
@@ -37,12 +37,12 @@ dependencies = [
     "pint==0.24",
     "pyiron_base==0.9.4",
     "pyiron_snippets==0.1.2",
-    "pylammpsmpi==0.2.19",
-    "scipy==1.13.1",
+    "pylammpsmpi==0.2.20",
+    "scipy==1.14.0",
     "scikit-learn==1.5.0",
     "seekpath==2.1.0",
     "spglib==2.4.0",
-    "structuretoolkit==0.0.25",
+    "structuretoolkit==0.0.26",
 ]
 dynamic = ["version"]