Bump base/atomistics/pymatgen together

.binder/environment.yml

@@ -7,22 +7,20 @@ dependencies:
 - codacy-coverage
 - matplotlib =3.8.3
 - numpy =1.26.4
-- pyiron_base =0.9.10
-- pyiron_atomistics =0.6.1
-- pyiron_snippets =0.1.1
+- pyiron_base =0.9.11
+- pyiron_atomistics =0.6.10
+- pyiron_snippets =0.1.3
 - pyparsing =3.1.2
-- scipy =1.12.0
+- scipy =1.13.0
 - seaborn =0.13.2
 - scikit-image =0.24.0
 - randspg =0.0.1
 - boto3 =1.34.122
 - moto =5.0.9
-- pycp2k =0.2.2
 - aws-sam-translator =1.77.0
 - distributed =2024.5.2
 - h5io_browser =0.0.17
-- pymatgen =2024.5.1
-- pympipool =0.8.4
+- pymatgen =2024.7.18
 - python >= 3.10
 - lammps
 - nglview >=3.0.8

.ci_support/environment.yml

@@ -7,19 +7,17 @@ dependencies:
 - codacy-coverage
 - matplotlib =3.8.3
 - numpy =1.26.4
-- pyiron_base =0.9.10
-- pyiron_atomistics =0.6.9
-- pyiron_snippets =0.1.1
+- pyiron_base =0.9.11
+- pyiron_atomistics =0.6.10
+- pyiron_snippets =0.1.3
 - pyparsing =3.1.2
-- scipy =1.12.0
+- scipy =1.13.0
 - seaborn =0.13.2
 - scikit-image =0.24.0
 - randspg =0.0.1
 - boto3 =1.34.122
 - moto =5.0.9
-- pycp2k =0.2.2
 - aws-sam-translator =1.77.0
 - distributed =2024.5.2
 - h5io_browser =0.0.17
-- pymatgen =2024.5.1
-- pympipool =0.8.4
+- pymatgen =2024.7.18

.github/workflows/daily.yml

@@ -8,5 +8,5 @@ on:
 
 jobs:
   codeql:
-    uses: pyiron/actions/.github/workflows/tests-and-coverage.yml@actions-1.1.0b
-    secrets: inherit
+    uses: pyiron/actions/.github/workflows/tests-and-coverage.yml@actions-3.2.1
+    secrets: inherit

.github/workflows/dependabot-pr.yml

@@ -6,5 +6,5 @@ on:
 
 jobs:
   pyiron:
-    uses: pyiron/actions/.github/workflows/dependabot-pr.yml@actions-1.1.0b
-    secrets: inherit
+    uses: pyiron/actions/.github/workflows/dependabot-pr.yml@actions-3.2.1
+    secrets: inherit

.github/workflows/pr-labeled.yml

@@ -8,5 +8,5 @@ on:
 
 jobs:
   pyiron:
-    uses: pyiron/actions/.github/workflows/pr-labeled.yml@actions-1.1.0b
-    secrets: inherit
+    uses: pyiron/actions/.github/workflows/pr-labeled.yml@actions-3.2.1
+    secrets: inherit

.github/workflows/pr-target-opened.yml

@@ -8,5 +8,5 @@ on:
 
 jobs:
   pyiron:
-    uses: pyiron/actions/.github/workflows/pr-target-opened.yml@actions-1.1.0b
-    secrets: inherit
+    uses: pyiron/actions/.github/workflows/pr-target-opened.yml@actions-3.2.1
+    secrets: inherit

.github/workflows/push-pull.yml

@@ -9,7 +9,7 @@ on:
 
 jobs:
   pyiron:
-    uses: pyiron/actions/.github/workflows/push-pull-main.yml@actions-1.1.0b
+    uses: pyiron/actions/.github/workflows/push-pull.yml@actions-3.2.1
     secrets: inherit
     with:
-      notebooks-env-files: .ci_support/environment.yml .ci_support/environment-notebooks.yml
+      notebooks-env-files: .ci_support/environment.yml .ci_support/environment-notebooks.yml

.github/workflows/release.yml

@@ -7,5 +7,5 @@ on:
 
 jobs:
   pyiron:
-    uses: pyiron/actions/.github/workflows/release.yml@actions-1.1.0b
-    secrets: inherit
+    uses: pyiron/actions/.github/workflows/release.yml@actions-3.2.1
+    secrets: inherit

.github/workflows/weekly.yml

@@ -8,5 +8,5 @@ on:
 
 jobs:
   codeql:
-    uses: pyiron/actions/.github/workflows/codeql.yml@actions-1.1.0b
-    secrets: inherit
+    uses: pyiron/actions/.github/workflows/codeql.yml@actions-3.2.1
+    secrets: inherit

docs/environment.yml

@@ -6,25 +6,24 @@ dependencies:
 - nbsphinx
 - sphinx-gallery
 - sphinx-rtd-theme
+- versioneer
 - ase =3.23.0
 - coveralls
 - coverage
 - codacy-coverage
 - matplotlib =3.8.3
 - numpy =1.26.4
-- pyiron_base =0.9.10
-- pyiron_atomistics =0.6.1
-- pyiron_snippets =0.1.1
+- pyiron_base =0.9.11
+- pyiron_atomistics =0.6.10
+- pyiron_snippets =0.1.3
 - pyparsing =3.1.2
-- scipy =1.12.0
+- scipy =1.13.0
 - seaborn =0.13.2
 - scikit-image =0.24.0
 - randspg =0.0.1
 - boto3 =1.34.122
 - moto =5.0.9
-- pycp2k =0.2.2
 - aws-sam-translator =1.77.0
 - distributed =2024.5.2
 - h5io_browser =0.0.17
-- pymatgen =2024.5.1
-- pympipool =0.8.4
+- pymatgen =2024.7.18

pyiron_contrib/jobfactories/__init__.py

@@ -355,7 +355,7 @@ def _prepare_job(self, job, structure):
             try:
                 job.potential[k] = v
             except AttributeError:
-                pass # element k does not exist in the current structure
+                pass  # element k does not exist in the current structure
         if self.storage.nband_nelec_map is not None:
             # ensure we apply the hack only for structures where we know an NBAND estimate for all elements
             elems = set(self.storage.nband_nelec_map.keys())

pyiron_contrib/tinybase/creator.py

@@ -34,7 +34,7 @@
 
 import ase.build
 
-from pympipool import Executor as PyMPIPoolExecutor
+from executorlib import Executor as PyMPIPoolExecutor
 from dask.distributed import Client, LocalCluster
 
 

setup.py

@@ -33,15 +33,15 @@
         'matplotlib==3.8.3',
         'numpy==1.26.4',
         'pyiron_snippets==0.1.3',
-        'pyiron_base==0.9.10',
-        'scipy==1.12.0',
+        'pyiron_base==0.9.11',
+        'scipy==1.13.0',
         'seaborn==0.13.2',
         'pyparsing==3.1.2',
     ],
     extras_require={
         'atomistic': [
             'ase==3.23.0',
-            'pyiron_atomistics==0.6.9',
+            'pyiron_atomistics==0.6.10',
             'pycp2k==0.2.2',
         ],
         'fenics': [
@@ -55,7 +55,7 @@
         ],
         'tinybase': [
             'distributed==2024.5.2',
-            'pymatgen==2024.5.1',
+            'pymatgen==2024.7.18',
             'pympipool==0.8.4',
             'h5io_browser==0.0.17',
         ]