Update pyiron-verse dependencies (#302)

* Update pyiron-verse dependencies

Synchronized to avoid headaches with patch number upper limits, so we can get it all done in a single pull

* [dependabot skip] Update env file

* Format black

* Bypass failure point

Everything still looks totally fine locally. Let's skip the failing doctest line and see if 3.10 has any problems at the unit test stage.

* Add it back with some debug

* Reduce debug

`instance.result` exists and is the expected `DynamicFoo` object

---------

Co-authored-by: pyiron-runner <[email protected]>

.binder/environment.yml

@@ -7,18 +7,18 @@ dependencies:
 - cloudpickle =3.0.0
 - graphviz =9.0.0
 - h5io =0.2.2
-- h5io_browser =0.0.10
-- matplotlib =3.8.3
-- pyiron_base =0.8.0
+- h5io_browser =0.0.12
+- matplotlib =3.8.4
+- pyiron_base =0.8.2
 - pyiron_contrib =0.1.16
 - pympipool =0.7.17
 - python-graphviz =0.20.3
 - toposort =1.10
 - typeguard =4.2.1
 - ase =3.22.1
-- atomistics =0.1.24
+- atomistics =0.1.27
 - lammps
 - phonopy =2.22.1
-- pyiron_atomistics =0.5.0
+- pyiron_atomistics =0.5.3
 - pyiron-data =0.0.29
 - numpy =1.26.4

.ci_support/environment-notebooks.yml

@@ -2,9 +2,9 @@ channels:
   - conda-forge
 dependencies:
   - ase =3.22.1
-  - atomistics =0.1.24
+  - atomistics =0.1.27
   - lammps
   - phonopy =2.22.1
-  - pyiron_atomistics =0.5.0
+  - pyiron_atomistics =0.5.3
   - pyiron-data =0.0.29
   - numpy =1.26.4

.ci_support/environment.yml

@@ -7,9 +7,9 @@ dependencies:
 - cloudpickle =3.0.0
 - graphviz =9.0.0
 - h5io =0.2.2
-- h5io_browser =0.0.10
-- matplotlib =3.8.3
-- pyiron_base =0.8.0
+- h5io_browser =0.0.12
+- matplotlib =3.8.4
+- pyiron_base =0.8.2
 - pyiron_contrib =0.1.16
 - pympipool =0.7.17
 - python-graphviz =0.20.3

docs/environment.yml

@@ -12,9 +12,9 @@ dependencies:
 - cloudpickle =3.0.0
 - graphviz =9.0.0
 - h5io =0.2.2
-- h5io_browser =0.0.10
-- matplotlib =3.8.3
-- pyiron_base =0.8.0
+- h5io_browser =0.0.12
+- matplotlib =3.8.4
+- pyiron_base =0.8.2
 - pyiron_contrib =0.1.16
 - pympipool =0.7.17
 - python-graphviz =0.20.3

pyiron_workflow/channels.py

@@ -616,13 +616,15 @@ def _all_args_arg_optional(self, callback):
     def _has_required_args(func):
         return any(
             (
-                param.kind in (
+                param.kind
+                in (
                     inspect.Parameter.POSITIONAL_ONLY,
                     inspect.Parameter.POSITIONAL_OR_KEYWORD,
                     inspect.Parameter.KEYWORD_ONLY,
                 )
                 and param.default == inspect.Parameter.empty
-            ) for param in inspect.signature(func).parameters.values()
+            )
+            for param in inspect.signature(func).parameters.values()
         )
 
     @property

pyiron_workflow/executors/cloudpickleprocesspool.py

@@ -109,8 +109,11 @@ class CloudpickleProcessPoolExecutor(ProcessPoolExecutor):
         >>> print(fs.done())
         True
 
+        >>> import time
+        >>> time.sleep(1)  # Debugging doctest on github CI for python3.10
         >>> print(instance.result.result)
         This was an arg
+
     """
 
     def submit(self, fn, /, *args, **kwargs):

setup.py

@@ -32,9 +32,9 @@
         'cloudpickle==3.0.0',
         'graphviz==0.20.3',
         'h5io==0.2.2',
-        'h5io_browser==0.0.10',
-        'matplotlib==3.8.3',
-        'pyiron_base==0.8.0',
+        'h5io_browser==0.0.12',
+        'matplotlib==3.8.4',
+        'pyiron_base==0.8.2',
         'pyiron_contrib==0.1.16',
         'pympipool==0.7.17',
         'toposort==1.10',
@@ -43,10 +43,10 @@
     extras_require={
         "node_library": [
             'ase==3.22.1',
-            'atomistics==0.1.24',
+            'atomistics==0.1.27',
             'numpy==1.26.4',
             'phonopy==2.22.1',
-            'pyiron_atomistics==0.5.0',
+            'pyiron_atomistics==0.5.3',
         ],
     },
     cmdclass=versioneer.get_cmdclass(),