Merge branch 'main' into io_info_as_classmethod

.binder/environment.yml

@@ -7,18 +7,18 @@ dependencies:
 - cloudpickle =3.0.0
 - graphviz =9.0.0
 - h5io =0.2.2
-- h5io_browser =0.0.9
+- h5io_browser =0.0.10
 - matplotlib =3.8.3
-- pyiron_base =0.7.9
-- pyiron_contrib =0.1.15
-- pympipool =0.7.13
+- pyiron_base =0.8.0
+- pyiron_contrib =0.1.16
+- pympipool =0.7.17
 - python-graphviz =0.20.3
 - toposort =1.10
-- typeguard =4.1.5
+- typeguard =4.2.1
 - ase =3.22.1
-- atomistics =0.1.23
+- atomistics =0.1.24
 - lammps
-- phonopy =2.21.2
-- pyiron_atomistics =0.4.17
+- phonopy =2.22.1
+- pyiron_atomistics =0.5.0
 - 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 =0.1.23
+  - atomistics =0.1.24
   - lammps
-  - phonopy =2.21.2
-  - pyiron_atomistics =0.4.17
+  - phonopy =2.22.1
+  - pyiron_atomistics =0.5.0
   - pyiron-data =0.0.29
   - numpy =1.26.4

.ci_support/environment.yml

@@ -7,11 +7,11 @@ dependencies:
 - cloudpickle =3.0.0
 - graphviz =9.0.0
 - h5io =0.2.2
-- h5io_browser =0.0.9
+- h5io_browser =0.0.10
 - matplotlib =3.8.3
-- pyiron_base =0.7.9
-- pyiron_contrib =0.1.15
-- pympipool =0.7.13
+- pyiron_base =0.8.0
+- pyiron_contrib =0.1.16
+- pympipool =0.7.17
 - python-graphviz =0.20.3
 - toposort =1.10
-- typeguard =4.1.5
+- typeguard =4.2.1

docs/environment.yml

@@ -12,11 +12,11 @@ dependencies:
 - cloudpickle =3.0.0
 - graphviz =9.0.0
 - h5io =0.2.2
-- h5io_browser =0.0.9
+- h5io_browser =0.0.10
 - matplotlib =3.8.3
-- pyiron_base =0.7.9
-- pyiron_contrib =0.1.15
-- pympipool =0.7.13
+- pyiron_base =0.8.0
+- pyiron_contrib =0.1.16
+- pympipool =0.7.17
 - python-graphviz =0.20.3
 - toposort =1.10
-- typeguard =4.1.5
+- typeguard =4.2.1

pyiron_workflow/job.py

@@ -24,7 +24,7 @@
 import os
 import sys
 
-from pyiron_base import GenericJob, TemplateJob, JOB_CLASS_DICT
+from pyiron_base import TemplateJob, JOB_CLASS_DICT
 from pyiron_base.jobs.flex.pythonfunctioncontainer import (
     PythonFunctionContainerJob,
     get_function_parameter_dict,
@@ -122,17 +122,6 @@ def run_static(self):
         self.to_hdf()
         self.status.finished = True
 
-    def save(self):
-        # PythonFunctionContainerJob.save assumes that the job is being created
-        # exclusively from pyiron_base.Project.wrap_python_function, and therefore
-        # always dynamically renames the job based on the wrapped function and the
-        # input.
-        # Here, the jobs are created in the usual way, with the usual use of job name,
-        # so it is just confusing if this renaming happens; thus, we save as usual.
-        # If at any point PythonFunctionContainerJob.save behaves in the usual way,
-        # this override can be removed
-        GenericJob.save(self)
-
 
 JOB_CLASS_DICT[NodeOutputJob.__name__] = NodeOutputJob.__module__
 

pyiron_workflow/node.py

@@ -10,7 +10,6 @@
 import sys
 from abc import ABC
 from concurrent.futures import Future
-import platform
 from typing import Any, Literal, Optional, TYPE_CHECKING
 import warnings
 
@@ -647,16 +646,8 @@ def draw(
         Returns:
             (graphviz.graphs.Digraph): The resulting graph object.
 
-        Warnings:
-            Rendering a PDF format appears to not be working on Windows right now.
         """
-        if format == "pdf" and platform.system() == "Windows":
-            warnings.warn(
-                "Graphviz does not appear to be playing well with Windows right now,"
-                "this will probably fail and you will need to try a different format."
-                "If it _doesn't_ fail, please contact the developers by raising an "
-                "issue at github.com/pyiron/pyiron_workflow"
-            )
+
         if size is not None:
             size = f"{size[0]},{size[1]}"
         graph = GraphvizNode(self, depth=depth, rankdir=rankdir, size=size).graph

setup.py

@@ -32,21 +32,21 @@
         'cloudpickle==3.0.0',
         'graphviz==0.20.3',
         'h5io==0.2.2',
-        'h5io_browser==0.0.9',
+        'h5io_browser==0.0.10',
         'matplotlib==3.8.3',
-        'pyiron_base==0.7.9',
-        'pyiron_contrib==0.1.15',
-        'pympipool==0.7.13',
+        'pyiron_base==0.8.0',
+        'pyiron_contrib==0.1.16',
+        'pympipool==0.7.17',
         'toposort==1.10',
-        'typeguard==4.1.5',
+        'typeguard==4.2.1',
     ],
     extras_require={
         "node_library": [
             'ase==3.22.1',
-            'atomistics==0.1.23',
+            'atomistics==0.1.24',
             'numpy==1.26.4',
-            'phonopy==2.21.2',
-            'pyiron_atomistics==0.4.17',
+            'phonopy==2.22.1',
+            'pyiron_atomistics==0.5.0',
         ],
     },
     cmdclass=versioneer.get_cmdclass(),

tests/unit/test_job.py

@@ -29,39 +29,11 @@ def tearDown(self) -> None:
 
 
 class TestNodeOutputJob(_WithAJob):
-    def make_a_job_from_node(self, node, job_name=None):
-        job = self.pr.create.job.NodeOutputJob(
-            node.label if job_name is None else job_name
-        )
+    def make_a_job_from_node(self, node):
+        job = self.pr.create.job.NodeOutputJob(node.label)
         job.input["node"] = node
         return job
 
-    @unittest.skipIf(sys.version_info < (3, 11), "Storage will only work in 3.11+")
-    def test_job_name_override(self):
-        job_name = "my_name"
-        job = self.make_a_job_from_node(
-            Workflow.create.standard.UserInput(42),
-            job_name=job_name
-        )
-        self.assertEqual(
-            job_name,
-            job.job_name,
-            msg="Sanity check"
-        )
-        try:
-            job.save()
-            self.assertEqual(
-                job_name,
-                job.job_name,
-                msg="Standard behaviour for the parent class is to dynamically rename "
-                    "the job at save time; since we create these jobs as usual from "
-                    "the job creator, this is just confusing and we want to avoid it. "
-                    "If this behaviour is every changed in pyiron_base, the override "
-                    "and this test can both be removed."
-            )
-        finally:
-            job.remove()
-
     @unittest.skipIf(sys.version_info >= (3, 11), "Storage should only work in 3.11+")
     def test_clean_failure(self):
         with self.assertRaises(

tests/unit/test_node.py

@@ -1,7 +1,5 @@
 from concurrent.futures import Future
 import os
-import platform
-from subprocess import CalledProcessError
 import sys
 from typing import Literal, Optional
 import unittest
@@ -322,29 +320,17 @@ def test_draw(self):
 
             for fmt in ["pdf", "png"]:
                 with self.subTest(f"Testing with format {fmt}"):
-                    if fmt == "pdf" and platform.system() == "Windows":
-                        with self.assertRaises(
-                            CalledProcessError,
-                            msg="Graphviz doesn't seem to be happy about the "
-                                "combindation PDF format and Windows right now. We "
-                                "throw a warning for it in `Node.draw`, so if this "
-                                "test ever fails and this combination _doesn't_ fail, "
-                                "remove this extra bit of testing and remove the "
-                                "warning."
-                        ):
-                            self.n1.draw(save=True, format=fmt)
-                    else:
-                        self.n1.draw(save=True, format=fmt)
-                        expected_name = self.n1.label + "_graph." + fmt
-                        # That name is just an implementation detail, update it as
-                        # needed
-                        self.assertTrue(
-                            self.n1.working_directory.path.joinpath(
-                                expected_name
-                            ).is_file(),
-                            msg="If `save` is called, expect the rendered image to "
-                                "exist in the working directory"
-                        )
+                    self.n1.draw(save=True, format=fmt)
+                    expected_name = self.n1.label + "_graph." + fmt
+                    # That name is just an implementation detail, update it as
+                    # needed
+                    self.assertTrue(
+                        self.n1.working_directory.path.joinpath(
+                            expected_name
+                        ).is_file(),
+                        msg="If `save` is called, expect the rendered image to "
+                            "exist in the working directory"
+                    )
 
             user_specified_name = "foo"
             self.n1.draw(filename=user_specified_name, format=fmt)