[New WfMS] Implement Python Workflow Definition in pyiron_workflow (#111)

* Implement Python Workflow Definition in pyiron_workflow

* black formatting

* bug fix

* add function to load workflow from JSOn - not working

* black formatting

* Add json-to-Workfow function

Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com>

* Update python_workflow_definition/src/python_workflow_definition/pyiron_workflow.py

* merge Liam's changes

* black formatting

* update notebooks

* fix file name

* Add pyiron_workflow to all universal notebooks

* update notebooks for other workflow frameworks

* fix reuse of functions

* black formatting

* Add NFDI example

* dynamic get_dict() function

* dynamic get_list() function

* add s_ to input parameters

* uniquue child names

* silence validation

* handle special case of get_list()

* black formatting

* test quantum espresso export

* Add files via upload

* update write_workflow_json()

* black formatting

* update notebook

* Add files via upload

---------

Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com>
Co-authored-by: liamhuber <liamhuber@greyhavensolutions.com>
Co-authored-by: Liam Huber <liam.huber@gmail.com>

Author: jan-janssen

.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

@@ -9,6 +9,7 @@ dependencies:
 - httpcore =1.0.7
 - jobflow =0.2.0
 - pyiron_base =0.12.0
+- pyiron_workflow =0.13.0
 - pygraphviz =1.14
 - aiida-workgraph =0.5.2
 - conda_subprocess =0.0.7

example_workflows/arithmetic/aiida.ipynb

@@ -232,6 +232,39 @@
     }
    ],
    "execution_count": 15
+  },
+  {
+   "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_filename)"
+  },
+  {
+   "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()"
   }
  ]
 }

example_workflows/arithmetic/jobflow.ipynb

@@ -369,18 +369,42 @@
    }
   },
   {
-   "id": "c199b28f3c0399cc",
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## Load Workflow with pyiron_workflow",
+   "id": "7da4733bfeffee63"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "from python_workflow_definition.pyiron_workflow import load_workflow_json",
+   "id": "6c87661996ff840b"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf = load_workflow_json(file_name=workflow_json_filename)",
+   "id": "33b1e9408924f9c0"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf.draw(size=(10,10))",
+   "id": "df63b2963a0d90a5"
+  },
+  {
+   "metadata": {},
    "cell_type": "code",
-   "source": "",
-   "metadata": {
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    },
-    "trusted": true
-   },
    "outputs": [],
-   "execution_count": null
+   "execution_count": null,
+   "source": "wf.run()",
+   "id": "bf110395454bd694"
   }
  ]
 }

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"
   }
  ]
 }