Merge remote-tracking branch 'upstream/main' into aw

Author: GeigerJ2

.github/workflows/pipeline.yml

@@ -71,6 +71,7 @@ jobs:
         papermill cwl.ipynb cwl_out.ipynb -k "python3"
         papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
         papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
+        papermill pyiron_workflow.ipynb pyiron_workflow_out.ipynb -k "python3"
         papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"
 
   quantumespresso:
@@ -105,6 +106,7 @@ jobs:
         papermill cwl.ipynb cwl_out.ipynb -k "python3"
         papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
         papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
+        papermill pyiron_workflow.ipynb pyiron_workflow_out.ipynb -k "python3"
         papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"
 
   arithmetic:
@@ -133,6 +135,7 @@ jobs:
         papermill cwl.ipynb cwl_out.ipynb -k "python3"
         papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
         papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
+        papermill pyiron_workflow.ipynb pyiron_workflow_out.ipynb -k "python3"
         papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"
 
   documentation:

binder/environment.yml

@@ -3,14 +3,14 @@ channels:
 dependencies:
 - python =3.12
 - click =8.1.8
-- pydantic =2.11.4
-- hatch =1.14.1
+- pydantic =2.12.3
 - hatchling =1.27.0
 - httpcore =1.0.7
 - jobflow =0.2.0
 - pyiron_base =0.12.0
+- pyiron_workflow =0.13.0
 - pygraphviz =1.14
 - aiida-workgraph =0.7.4
 - conda_subprocess =0.0.7
-- networkx =3.4.2
+- networkx =3.5
 - cwltool =3.1.20250110105449

example_workflows/arithmetic/pyiron_base.ipynb

@@ -274,15 +274,49 @@
    ],
    "execution_count": 18
   },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## Load Workflow with pyiron_workflow",
+   "id": "406fd07dd4bd8006"
+  },
   {
    "id": "cf76f305-24de-45a7-be8e-cfe45cd6458e",
    "cell_type": "code",
-   "source": "",
+   "source": "from python_workflow_definition.pyiron_workflow import load_workflow_json",
    "metadata": {
-    "trusted": true
+    "trusted": true,
+    "ExecuteTime": {
+     "end_time": "2025-05-24T08:25:33.797570Z",
+     "start_time": "2025-05-24T08:25:33.771214Z"
+    }
    },
    "outputs": [],
    "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf = load_workflow_json(file_name=workflow_json_filename)",
+   "id": "5b442611457aa5a8"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf.draw(size=(10,10))",
+   "id": "2ca33c8590a54866"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf.run()",
+   "id": "d36522a1c315b7f5"
   }
  ]
 }

example_workflows/arithmetic/pyiron_workflow.ipynb

@@ -288,6 +288,39 @@
    ],
    "execution_count": 17
   },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## Load Workflow with pyiron_workflow"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "from python_workflow_definition.pyiron_workflow import load_workflow_json"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf = load_workflow_json(file_name=\"workflow.json\")"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf.draw(size=(10,10))"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf.run()"
+  },
   {
    "cell_type": "markdown",
    "source": "## Python",

example_workflows/arithmetic/universal_workflow.ipynb

@@ -355,6 +355,44 @@
     }
    ],
    "execution_count": 24
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## Load Workflow with pyiron_workflow",
+   "id": "afaf2bc0b3a491ca"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "from python_workflow_definition.pyiron_workflow import load_workflow_json",
+   "id": "6172b410eb776fc4"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf = load_workflow_json(file_name=workflow_json_filename)",
+   "id": "668fe64b18b4d604"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf.draw(size=(10,10))",
+   "id": "8c4fd72394841ffa"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf.run()",
+   "id": "c1427e3ce0716f64"
   }
  ]
 }

example_workflows/nfdi/aiida.ipynb

@@ -327,6 +327,44 @@
     }
    ],
    "execution_count": 22
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## Load Workflow with pyiron_workflow",
+   "id": "8e73fa07cebd7b72"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "from python_workflow_definition.pyiron_workflow import load_workflow_json",
+   "id": "aa99fbd94b03a869"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf = load_workflow_json(file_name=workflow_json_filename)",
+   "id": "728b8684fee475b5"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf.draw(size=(10,10))",
+   "id": "7b814f0f74f0b15a"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf.run()",
+   "id": "447506cdca5080e6"
   }
  ]
 }

example_workflows/nfdi/jobflow.ipynb

@@ -312,6 +312,44 @@
     }
    ],
    "execution_count": 22
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## Load Workflow with pyiron_workflow",
+   "id": "385acbf585763632"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "from python_workflow_definition.pyiron_workflow import load_workflow_json",
+   "id": "927d0118cc4edfba"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf = load_workflow_json(file_name=workflow_json_filename)",
+   "id": "50055483ca2c9909"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf.draw(size=(10,10))",
+   "id": "7d25a578c431e0f5"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf.run()",
+   "id": "fff9513c4a127a96"
   }
  ]
 }

example_workflows/nfdi/pyiron_base.ipynb

@@ -289,9 +289,42 @@
    "execution_count": 17
   },
   {
+   "metadata": {},
    "cell_type": "markdown",
-   "source": "## Python",
-   "metadata": {}
+   "source": "## Load Workflow with pyiron_workflow"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "from python_workflow_definition.pyiron_workflow import load_workflow_json"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf = load_workflow_json(file_name=\"workflow.json\")"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf.draw(size=(10,10))"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf.run()"
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## Python"
   },
   {
    "cell_type": "code",