Merge branch 'main' into pw

Author: jan-janssen

.gitignore

@@ -199,4 +199,4 @@ jobflow_to_aiida_qe.json
 aiida_to_jobflow_qe.json
 pyiron_base_to_aiida_simple.json
 pyiron_base_to_jobflow_qe.json
-
+**/*.h5

binder/environment.yml

@@ -3,15 +3,15 @@ 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_base =0.15.5
 - pyiron_workflow =0.15.4
 - pygraphviz =1.14
-- aiida-workgraph =0.5.2
+- aiida-workgraph =0.7.4
+- plumpy =0.25.0
 - conda_subprocess =0.0.7
 - networkx =3.4.2
 - cwltool =3.1.20250110105449

example_workflows/quantum_espresso/aiida.ipynb

@@ -5,5 +5,5 @@ dependencies:
 - matplotlib=3.10.1
 - xmlschema=3.4.3
 - optimade=1.2.3
-- qe=7.4
+- qe=7.5
 - qe-tools=2.0.0

example_workflows/quantum_espresso/environment.yml

@@ -1036,7 +1036,7 @@ datecode 220603
   <complexType name="symmetriesType">
     <sequence>
       <element type="unsignedByte" name="nsym"/>
-      <element type="unsignedByte" name="colin_mag"/>
+      <element type="integer" name="colin_mag"/>
       <element type="unsignedByte" name="nrot"/>
       <element type="unsignedByte" name="space_group"/>
       <element type="qes:symmetryType" name="symmetry" maxOccurs="48" minOccurs="1"/>

example_workflows/quantum_espresso/jobflow.ipynb

@@ -17,21 +17,21 @@ authors = [
 license = { file = "LICENSE" }
 dependencies = [
     "numpy>=1.21,<2",
-    "pydantic>=2.7.0,<=2.11.4",
+    "pydantic>=2.7.0,<=2.12.3",
 ]
 
 [project.optional-dependencies]
 aiida = [
-    "aiida-workgraph>=0.5.1,<=0.5.2",
+    "aiida-workgraph>=0.5.1,<=0.7.4",
 ]
 jobflow = [
     "jobflow>=0.1.18,<=0.2.0",
 ]
 pyiron = [
-    "pyiron_base>=0.11.10,<=0.12.0",
+    "pyiron_base>=0.11.10,<=0.15.5",
 ]
 plot = [
     "pygraphviz>=1.10,<=1.14",
-    "networkx>=2.8.8,<=3.4.2",
+    "networkx>=2.8.8,<=3.5",
     "ipython>=7.33.0,<=9.0.2",
 ]

example_workflows/quantum_espresso/pyiron_base.ipynb

@@ -3,14 +3,14 @@
 
 from aiida import orm
 from aiida_pythonjob.data.serializer import general_serializer
-from aiida_workgraph import WorkGraph, task
+from aiida_workgraph import WorkGraph, task, Task, namespace
 from aiida_workgraph.socket import TaskSocketNamespace
-
+from dataclasses import replace
+from node_graph.node_spec import SchemaSource
 from python_workflow_definition.models import PythonWorkflowDefinitionWorkflow
 from python_workflow_definition.shared import (
     convert_nodes_list_to_dict,
     update_node_names,
-    remove_result,
     set_result_node,
     NODES_LABEL,
     EDGES_LABEL,
@@ -24,11 +24,8 @@
 
 
 def load_workflow_json(file_name: str) -> WorkGraph:
-    data = remove_result(
-        workflow_dict=PythonWorkflowDefinitionWorkflow.load_json_file(
-            file_name=file_name
-        )
-    )
+
+    data = PythonWorkflowDefinitionWorkflow.load_json_file(file_name=file_name)
 
     wg = WorkGraph()
     task_name_mapping = {}
@@ -40,24 +37,28 @@ def load_workflow_json(file_name: str) -> WorkGraph:
             p, m = identifier.rsplit(".", 1)
             mod = import_module(p)
             func = getattr(mod, m)
-            wg.add_task(func)
-            # Remove the default result output, because we will add the outputs later from the data in the link
-            del wg.tasks[-1].outputs["result"]
-            task_name_mapping[id] = wg.tasks[-1]
+            decorated_func = task(outputs=namespace())(func)
+            new_task = wg.add_task(decorated_func)
+            new_task.spec = replace(new_task.spec, schema_source=SchemaSource.EMBEDDED)
+            task_name_mapping[id] = new_task
         else:
             # data task
             data_node = general_serializer(identifier)
             task_name_mapping[id] = data_node
 
     # add links
     for link in data[EDGES_LABEL]:
+        # TODO: continue here
         to_task = task_name_mapping[str(link[TARGET_LABEL])]
         # if the input is not exit, it means we pass the data into to the kwargs
         # in this case, we add the input socket
-        if link[TARGET_PORT_LABEL] not in to_task.inputs:
-            to_socket = to_task.add_input("workgraph.any", name=link[TARGET_PORT_LABEL])
-        else:
-            to_socket = to_task.inputs[link[TARGET_PORT_LABEL]]
+        if isinstance(to_task, Task):
+            if link[TARGET_PORT_LABEL] not in to_task.inputs:
+                to_socket = to_task.add_input_spec(
+                    "workgraph.any", name=link[TARGET_PORT_LABEL]
+                )
+            else:
+                to_socket = to_task.inputs[link[TARGET_PORT_LABEL]]
         from_task = task_name_mapping[str(link[SOURCE_LABEL])]
         if isinstance(from_task, orm.Data):
             to_socket.value = from_task
@@ -69,16 +70,14 @@ def load_workflow_json(file_name: str) -> WorkGraph:
                 # we add it here, and assume the output exit
                 if link[SOURCE_PORT_LABEL] not in from_task.outputs:
                     # if str(link["sourcePort"]) not in from_task.outputs:
-                    from_socket = from_task.add_output(
+                    from_socket = from_task.add_output_spec(
                         "workgraph.any",
                         name=link[SOURCE_PORT_LABEL],
-                        # name=str(link["sourcePort"]),
-                        metadata={"is_function_output": True},
                     )
                 else:
                     from_socket = from_task.outputs[link[SOURCE_PORT_LABEL]]
-
-                wg.add_link(from_socket, to_socket)
+                if isinstance(to_task, Task):
+                    wg.add_link(from_socket, to_socket)
             except Exception as e:
                 traceback.print_exc()
                 print("Failed to link", link, "with error:", e)
@@ -90,12 +89,18 @@ def write_workflow_json(wg: WorkGraph, file_name: str) -> dict:
     node_name_mapping = {}
     data_node_name_mapping = {}
     i = 0
+    GRAPH_LEVEL_NAMES = ["graph_inputs", "graph_outputs", "graph_ctx"]
+
     for node in wg.tasks:
-        executor = node.get_executor()
+
+        if node.name in GRAPH_LEVEL_NAMES:
+            continue
+
         node_name_mapping[node.name] = i
 
-        callable_name = executor["callable_name"]
-        callable_name = f"{executor['module_path']}.{callable_name}"
+        executor = node.get_executor()
+        callable_name = f"{executor.module_path}.{executor.callable_name}"
+
         data[NODES_LABEL].append({"id": i, "type": "function", "value": callable_name})
         i += 1
 
@@ -141,6 +146,7 @@ def write_workflow_json(wg: WorkGraph, file_name: str) -> dict:
                         SOURCE_PORT_LABEL: None,
                     }
                 )
+
     data[VERSION_LABEL] = VERSION_NUMBER
     PythonWorkflowDefinitionWorkflow(
         **set_result_node(workflow_dict=update_node_names(workflow_dict=data))