Bump pyiron ecosystem (#313)

* Bump pyiron ecosystem

* [dependabot skip] Update env file

* Bumpy pympipool in conda env

* Be more gracious in parallel for-loop speed test

* [dependabot skip] Update env file

* Bump base in the conda env

* [dependabot skip] Update env file

* Downgrade pympipool

pylammpsmpi, and thus pyiron_atomistics is still a patch behind, and to my chagrin patches remain hard-pinned in pyiron_atomistics

* Update deepdive notebook to use changed pympipool signature

* [dependabot skip] Update env file

---------

Co-authored-by: pyiron-runner <pyiron@mpie.de>

.binder/environment.yml

@@ -9,16 +9,16 @@ dependencies:
 - h5io =0.2.2
 - h5io_browser =0.0.12
 - matplotlib =3.8.4
-- pyiron_base =0.8.2
+- pyiron_base =0.8.3
 - pyiron_contrib =0.1.16
-- pympipool =0.7.17
+- pympipool =0.8.0
 - python-graphviz =0.20.3
 - toposort =1.10
 - typeguard =4.2.1
 - ase =3.22.1
 - atomistics =0.1.27
 - lammps
 - phonopy =2.22.1
-- pyiron_atomistics =0.5.3
+- pyiron_atomistics =0.5.4
 - pyiron-data =0.0.29
 - numpy =1.26.4

.ci_support/environment-notebooks.yml

@@ -5,6 +5,6 @@ dependencies:
   - atomistics =0.1.27
   - lammps
   - phonopy =2.22.1
-  - pyiron_atomistics =0.5.3
+  - pyiron_atomistics =0.5.4
   - pyiron-data =0.0.29
   - numpy =1.26.4

.ci_support/environment.yml

@@ -9,9 +9,9 @@ dependencies:
 - h5io =0.2.2
 - h5io_browser =0.0.12
 - matplotlib =3.8.4
-- pyiron_base =0.8.2
+- pyiron_base =0.8.3
 - pyiron_contrib =0.1.16
-- pympipool =0.7.17
+- pympipool =0.8.0
 - python-graphviz =0.20.3
 - toposort =1.10
 - typeguard =4.2.1

docs/environment.yml

@@ -14,9 +14,9 @@ dependencies:
 - h5io =0.2.2
 - h5io_browser =0.0.12
 - matplotlib =3.8.4
-- pyiron_base =0.8.2
+- pyiron_base =0.8.3
 - pyiron_contrib =0.1.16
-- pympipool =0.7.17
+- pympipool =0.8.0
 - python-graphviz =0.20.3
 - toposort =1.10
 - typeguard =4.2.1

setup.py

@@ -34,9 +34,9 @@
         'h5io==0.2.2',
         'h5io_browser==0.0.12',
         'matplotlib==3.8.4',
-        'pyiron_base==0.8.2',
+        'pyiron_base==0.8.3',
         'pyiron_contrib==0.1.16',
-        'pympipool==0.7.17',
+        'pympipool==0.8.0',
         'toposort==1.10',
         'typeguard==4.2.1',
     ],
@@ -46,7 +46,7 @@
             'atomistics==0.1.27',
             'numpy==1.26.4',
             'phonopy==2.22.1',
-            'pyiron_atomistics==0.5.3',
+            'pyiron_atomistics==0.5.4',
         ],
     },
     cmdclass=versioneer.get_cmdclass(),

tests/unit/test_for_loop.py

@@ -307,7 +307,7 @@ def test_body_node_executor(self):
             for_parallel.body_node_executor = exe
             for_parallel(t=n_procs*[t_sleep])
         dt = perf_counter() - t_start
-        grace = 1.1
+        grace = 1.25
         self.assertLess(
             dt,
             grace * t_sleep,