Test with aiida-workgraph 0.7.4#136

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Merged
GeigerJ2 merged 19 commits into from
Oct 23, 2025
Merged

Test with aiida-workgraph 0.7.4 #136

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9b38c17
Update pyproject.toml
jan-janssen Oct 22, 2025
79c8edf
Update environment.yml
jan-janssen Oct 22, 2025
6b78fb0
fixed syntax error. outputs now missing in our json representation
GeigerJ2 Oct 22, 2025
9995215
Fix callable_name
superstar54 Oct 22, 2025
88ec724
Update environment.yml
jan-janssen Oct 22, 2025
678c7e1
Update pyproject.toml
jan-janssen Oct 22, 2025
e40adbd
wip
GeigerJ2 Oct 22, 2025
295c39e
push for xing to test locally
GeigerJ2 Oct 23, 2025
d1f48c4
Fix the
superstar54 Oct 23, 2025
c829333
reset notebooks to `main` state
GeigerJ2 Oct 23, 2025
6548eda
Merge remote-tracking branch 'upstream/main' into aw
GeigerJ2 Oct 23, 2025
d82ad85
black on aiida.py
GeigerJ2 Oct 23, 2025
008230c
re-introduce plumpy pin and fix qe aiida.ipynb example
GeigerJ2 Oct 23, 2025
891de62
fix `get_bulk_structure1` references in wg instances
GeigerJ2 Oct 23, 2025
dd30832
cleanup
GeigerJ2 Oct 23, 2025
27a1751
more cleanup
GeigerJ2 Oct 23, 2025
5d705ad
fix `wg.nodes` access
GeigerJ2 Oct 23, 2025
1ecb3f5
add nbstripout via pre-commit and strip all notebooks
GeigerJ2 Oct 23, 2025
21e9df9
Revert "add nbstripout via pre-commit and strip all notebooks"
GeigerJ2 Oct 23, 2025
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2 changes: 1 addition & 1 deletion .gitignore
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Original file line numberDiff line numberDiff line change
Expand Up@@ -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
2 changes: 1 addition & 1 deletion binder/environment.yml
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Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -10,7 +10,7 @@ dependencies:
- pyiron_base =0.12.0
- pyiron_workflow =0.13.0
- pygraphviz =1.14
- aiida-workgraph =0.5.2
- aiida-workgraph =0.7.4
- plumpy =0.25.0
- conda_subprocess =0.0.7
- networkx =3.5
Expand Down
5,800 changes: 5,799 additions & 1 deletion example_workflows/quantum_espresso/aiida.ipynb
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4,994 changes: 4,993 additions & 1 deletion example_workflows/quantum_espresso/pyiron_base.ipynb
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6,016 changes: 6,015 additions & 1 deletion example_workflows/quantum_espresso/pyiron_workflow.ipynb
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2 changes: 1 addition & 1 deletion pyproject.toml
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -22,7 +22,7 @@ dependencies = [

[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",
Expand Down
54 changes: 30 additions & 24 deletions src/python_workflow_definition/aiida.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -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,
Expand All@@ -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 = {}
Expand All@@ -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
Expand All@@ -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)
Expand All@@ -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

Expand DownExpand Up@@ -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))
Expand Down
Loading
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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Test with aiida-workgraph 0.7.4#136

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 Merged

GeigerJ2
merged 19 commits into

from

Oct 23, 2025
 Merged


Test with aiida-workgraph 0.7.4
#136
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9b38c17

Update pyproject.toml


jan-janssen Oct 22, 2025
79c8edf

Update environment.yml


jan-janssen Oct 22, 2025
6b78fb0

fixed syntax error. outputs now missing in our json representation


GeigerJ2 Oct 22, 2025
9995215

Fix callable_name


superstar54 Oct 22, 2025
88ec724

Update environment.yml


jan-janssen Oct 22, 2025
678c7e1

Update pyproject.toml


jan-janssen Oct 22, 2025
e40adbd

wip


GeigerJ2 Oct 22, 2025
295c39e

push for xing to test locally


GeigerJ2 Oct 23, 2025
d1f48c4

Fix the


superstar54 Oct 23, 2025
c829333

reset notebooks to `main` state


GeigerJ2 Oct 23, 2025
6548eda

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


GeigerJ2 Oct 23, 2025
d82ad85

black on aiida.py


GeigerJ2 Oct 23, 2025
008230c

re-introduce plumpy pin and fix qe aiida.ipynb example


GeigerJ2 Oct 23, 2025
891de62

fix `get_bulk_structure1` references in wg instances


GeigerJ2 Oct 23, 2025
dd30832

cleanup


GeigerJ2 Oct 23, 2025
27a1751

more cleanup


GeigerJ2 Oct 23, 2025
5d705ad

fix `wg.nodes` access


GeigerJ2 Oct 23, 2025
1ecb3f5

add nbstripout via pre-commit and strip all notebooks


GeigerJ2 Oct 23, 2025
21e9df9

Revert "add nbstripout via pre-commit and strip all notebooks"


GeigerJ2 Oct 23, 2025

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2 changes: 1 addition & 1 deletion
.gitignore

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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

2 changes: 1 addition & 1 deletion
binder/environment.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -10,7 +10,7 @@ dependencies:
- pyiron_base =0.12.0
- pyiron_workflow =0.13.0
- pygraphviz =1.14
- aiida-workgraph =0.5.2
- aiida-workgraph =0.7.4
- plumpy =0.25.0
- conda_subprocess =0.0.7
- networkx =3.5
Expand Down

5,800 changes: 5,799 additions & 1 deletion
example_workflows/quantum_espresso/aiida.ipynb

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example_workflows/quantum_espresso/jobflow.ipynb

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4,994 changes: 4,993 additions & 1 deletion
example_workflows/quantum_espresso/pyiron_base.ipynb

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6,016 changes: 6,015 additions & 1 deletion
example_workflows/quantum_espresso/pyiron_workflow.ipynb

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2 changes: 1 addition & 1 deletion
pyproject.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -22,7 +22,7 @@ dependencies = [

[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",
Expand Down

54 changes: 30 additions & 24 deletions
src/python_workflow_definition/aiida.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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,
Expand All@@ -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 = {}
Expand All@@ -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
Expand All@@ -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)
Expand All@@ -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

Expand DownExpand Up@@ -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))
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Test with aiida-workgraph 0.7.4#136

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 Merged

GeigerJ2
merged 19 commits into

from

Oct 23, 2025
 Merged


Test with aiida-workgraph 0.7.4
#136
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9b38c17

Update pyproject.toml


jan-janssen Oct 22, 2025
79c8edf

Update environment.yml


jan-janssen Oct 22, 2025
6b78fb0

fixed syntax error. outputs now missing in our json representation


GeigerJ2 Oct 22, 2025
9995215

Fix callable_name


superstar54 Oct 22, 2025
88ec724

Update environment.yml


jan-janssen Oct 22, 2025
678c7e1

Update pyproject.toml


jan-janssen Oct 22, 2025
e40adbd

wip


GeigerJ2 Oct 22, 2025
295c39e

push for xing to test locally


GeigerJ2 Oct 23, 2025
d1f48c4

Fix the


superstar54 Oct 23, 2025
c829333

reset notebooks to `main` state


GeigerJ2 Oct 23, 2025
6548eda

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


GeigerJ2 Oct 23, 2025
d82ad85

black on aiida.py


GeigerJ2 Oct 23, 2025
008230c

re-introduce plumpy pin and fix qe aiida.ipynb example


GeigerJ2 Oct 23, 2025
891de62

fix `get_bulk_structure1` references in wg instances


GeigerJ2 Oct 23, 2025
dd30832

cleanup


GeigerJ2 Oct 23, 2025
27a1751

more cleanup


GeigerJ2 Oct 23, 2025
5d705ad

fix `wg.nodes` access


GeigerJ2 Oct 23, 2025
1ecb3f5

add nbstripout via pre-commit and strip all notebooks


GeigerJ2 Oct 23, 2025
21e9df9

Revert "add nbstripout via pre-commit and strip all notebooks"


GeigerJ2 Oct 23, 2025

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2 changes: 1 addition & 1 deletion
.gitignore

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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

2 changes: 1 addition & 1 deletion
binder/environment.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -10,7 +10,7 @@ dependencies:
- pyiron_base =0.12.0
- pyiron_workflow =0.13.0
- pygraphviz =1.14
- aiida-workgraph =0.5.2
- aiida-workgraph =0.7.4
- plumpy =0.25.0
- conda_subprocess =0.0.7
- networkx =3.5
Expand Down

5,800 changes: 5,799 additions & 1 deletion
example_workflows/quantum_espresso/aiida.ipynb

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example_workflows/quantum_espresso/jobflow.ipynb

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4,994 changes: 4,993 additions & 1 deletion
example_workflows/quantum_espresso/pyiron_base.ipynb

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6,016 changes: 6,015 additions & 1 deletion
example_workflows/quantum_espresso/pyiron_workflow.ipynb

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2 changes: 1 addition & 1 deletion
pyproject.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -22,7 +22,7 @@ dependencies = [

[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",
Expand Down

54 changes: 30 additions & 24 deletions
src/python_workflow_definition/aiida.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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,
Expand All@@ -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 = {}
Expand All@@ -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
Expand All@@ -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)
Expand All@@ -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

Expand DownExpand Up@@ -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))
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Test with aiida-workgraph 0.7.4#136

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 Merged

GeigerJ2
merged 19 commits into

from

Oct 23, 2025
 Merged


Test with aiida-workgraph 0.7.4
#136
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9b38c17

Update pyproject.toml


jan-janssen Oct 22, 2025
79c8edf

Update environment.yml


jan-janssen Oct 22, 2025
6b78fb0

fixed syntax error. outputs now missing in our json representation


GeigerJ2 Oct 22, 2025
9995215

Fix callable_name


superstar54 Oct 22, 2025
88ec724

Update environment.yml


jan-janssen Oct 22, 2025
678c7e1

Update pyproject.toml


jan-janssen Oct 22, 2025
e40adbd

wip


GeigerJ2 Oct 22, 2025
295c39e

push for xing to test locally


GeigerJ2 Oct 23, 2025
d1f48c4

Fix the


superstar54 Oct 23, 2025
c829333

reset notebooks to `main` state


GeigerJ2 Oct 23, 2025
6548eda

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


GeigerJ2 Oct 23, 2025
d82ad85

black on aiida.py


GeigerJ2 Oct 23, 2025
008230c

re-introduce plumpy pin and fix qe aiida.ipynb example


GeigerJ2 Oct 23, 2025
891de62

fix `get_bulk_structure1` references in wg instances


GeigerJ2 Oct 23, 2025
dd30832

cleanup


GeigerJ2 Oct 23, 2025
27a1751

more cleanup


GeigerJ2 Oct 23, 2025
5d705ad

fix `wg.nodes` access


GeigerJ2 Oct 23, 2025
1ecb3f5

add nbstripout via pre-commit and strip all notebooks


GeigerJ2 Oct 23, 2025
21e9df9

Revert "add nbstripout via pre-commit and strip all notebooks"


GeigerJ2 Oct 23, 2025

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2 changes: 1 addition & 1 deletion
.gitignore

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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

2 changes: 1 addition & 1 deletion
binder/environment.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -10,7 +10,7 @@ dependencies:
- pyiron_base =0.12.0
- pyiron_workflow =0.13.0
- pygraphviz =1.14
- aiida-workgraph =0.5.2
- aiida-workgraph =0.7.4
- plumpy =0.25.0
- conda_subprocess =0.0.7
- networkx =3.5
Expand Down

5,800 changes: 5,799 additions & 1 deletion
example_workflows/quantum_espresso/aiida.ipynb

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example_workflows/quantum_espresso/jobflow.ipynb

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4,994 changes: 4,993 additions & 1 deletion
example_workflows/quantum_espresso/pyiron_base.ipynb

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6,016 changes: 6,015 additions & 1 deletion
example_workflows/quantum_espresso/pyiron_workflow.ipynb

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2 changes: 1 addition & 1 deletion
pyproject.toml

View file


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Original file line numberDiff line numberDiff line change
Expand Up@@ -22,7 +22,7 @@ dependencies = [

[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",
Expand Down

54 changes: 30 additions & 24 deletions
src/python_workflow_definition/aiida.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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,
Expand All@@ -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 = {}
Expand All@@ -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
Expand All@@ -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)
Expand All@@ -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

Expand DownExpand Up@@ -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))
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
Test with aiida-workgraph 0.7.4#136

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Already on GitHub?
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to your account

 Merged

GeigerJ2
merged 19 commits into

from

Oct 23, 2025
 Merged


Test with aiida-workgraph 0.7.4
#136
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9b38c17

Update pyproject.toml


jan-janssen Oct 22, 2025
79c8edf

Update environment.yml


jan-janssen Oct 22, 2025
6b78fb0

fixed syntax error. outputs now missing in our json representation


GeigerJ2 Oct 22, 2025
9995215

Fix callable_name


superstar54 Oct 22, 2025
88ec724

Update environment.yml


jan-janssen Oct 22, 2025
678c7e1

Update pyproject.toml


jan-janssen Oct 22, 2025
e40adbd

wip


GeigerJ2 Oct 22, 2025
295c39e

push for xing to test locally


GeigerJ2 Oct 23, 2025
d1f48c4

Fix the


superstar54 Oct 23, 2025
c829333

reset notebooks to `main` state


GeigerJ2 Oct 23, 2025
6548eda

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


GeigerJ2 Oct 23, 2025
d82ad85

black on aiida.py


GeigerJ2 Oct 23, 2025
008230c

re-introduce plumpy pin and fix qe aiida.ipynb example


GeigerJ2 Oct 23, 2025
891de62

fix `get_bulk_structure1` references in wg instances


GeigerJ2 Oct 23, 2025
dd30832

cleanup


GeigerJ2 Oct 23, 2025
27a1751

more cleanup


GeigerJ2 Oct 23, 2025
5d705ad

fix `wg.nodes` access


GeigerJ2 Oct 23, 2025
1ecb3f5

add nbstripout via pre-commit and strip all notebooks


GeigerJ2 Oct 23, 2025
21e9df9

Revert "add nbstripout via pre-commit and strip all notebooks"


GeigerJ2 Oct 23, 2025

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2 changes: 1 addition & 1 deletion
.gitignore

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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

2 changes: 1 addition & 1 deletion
binder/environment.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -10,7 +10,7 @@ dependencies:
- pyiron_base =0.12.0
- pyiron_workflow =0.13.0
- pygraphviz =1.14
- aiida-workgraph =0.5.2
- aiida-workgraph =0.7.4
- plumpy =0.25.0
- conda_subprocess =0.0.7
- networkx =3.5
Expand Down

5,800 changes: 5,799 additions & 1 deletion
example_workflows/quantum_espresso/aiida.ipynb

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5,748 changes: 5,747 additions & 1 deletion
example_workflows/quantum_espresso/jobflow.ipynb

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4,994 changes: 4,993 additions & 1 deletion
example_workflows/quantum_espresso/pyiron_base.ipynb

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6,016 changes: 6,015 additions & 1 deletion
example_workflows/quantum_espresso/pyiron_workflow.ipynb

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2 changes: 1 addition & 1 deletion
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -22,7 +22,7 @@ dependencies = [

[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",
Expand Down

54 changes: 30 additions & 24 deletions
src/python_workflow_definition/aiida.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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,
Expand All@@ -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 = {}
Expand All@@ -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
Expand All@@ -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)
Expand All@@ -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

Expand DownExpand Up@@ -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))
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Test with aiida-workgraph 0.7.4#136

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 Merged

GeigerJ2
merged 19 commits into

from

Oct 23, 2025
 Merged


Test with aiida-workgraph 0.7.4
#136
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9b38c17

Update pyproject.toml


jan-janssen Oct 22, 2025
79c8edf

Update environment.yml


jan-janssen Oct 22, 2025
6b78fb0

fixed syntax error. outputs now missing in our json representation


GeigerJ2 Oct 22, 2025
9995215

Fix callable_name


superstar54 Oct 22, 2025
88ec724

Update environment.yml


jan-janssen Oct 22, 2025
678c7e1

Update pyproject.toml


jan-janssen Oct 22, 2025
e40adbd

wip


GeigerJ2 Oct 22, 2025
295c39e

push for xing to test locally


GeigerJ2 Oct 23, 2025
d1f48c4

Fix the


superstar54 Oct 23, 2025
c829333

reset notebooks to `main` state


GeigerJ2 Oct 23, 2025
6548eda

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


GeigerJ2 Oct 23, 2025
d82ad85

black on aiida.py


GeigerJ2 Oct 23, 2025
008230c

re-introduce plumpy pin and fix qe aiida.ipynb example


GeigerJ2 Oct 23, 2025
891de62

fix `get_bulk_structure1` references in wg instances


GeigerJ2 Oct 23, 2025
dd30832

cleanup


GeigerJ2 Oct 23, 2025
27a1751

more cleanup


GeigerJ2 Oct 23, 2025
5d705ad

fix `wg.nodes` access


GeigerJ2 Oct 23, 2025
1ecb3f5

add nbstripout via pre-commit and strip all notebooks


GeigerJ2 Oct 23, 2025
21e9df9

Revert "add nbstripout via pre-commit and strip all notebooks"


GeigerJ2 Oct 23, 2025

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2 changes: 1 addition & 1 deletion
.gitignore

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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

2 changes: 1 addition & 1 deletion
binder/environment.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -10,7 +10,7 @@ dependencies:
- pyiron_base =0.12.0
- pyiron_workflow =0.13.0
- pygraphviz =1.14
- aiida-workgraph =0.5.2
- aiida-workgraph =0.7.4
- plumpy =0.25.0
- conda_subprocess =0.0.7
- networkx =3.5
Expand Down

5,800 changes: 5,799 additions & 1 deletion
example_workflows/quantum_espresso/aiida.ipynb

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example_workflows/quantum_espresso/jobflow.ipynb

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4,994 changes: 4,993 additions & 1 deletion
example_workflows/quantum_espresso/pyiron_base.ipynb

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6,016 changes: 6,015 additions & 1 deletion
example_workflows/quantum_espresso/pyiron_workflow.ipynb

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2 changes: 1 addition & 1 deletion
pyproject.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -22,7 +22,7 @@ dependencies = [

[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",
Expand Down

54 changes: 30 additions & 24 deletions
src/python_workflow_definition/aiida.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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,
Expand All@@ -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 = {}
Expand All@@ -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
Expand All@@ -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)
Expand All@@ -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

Expand DownExpand Up@@ -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))
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Test with aiida-workgraph 0.7.4#136

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 Merged

GeigerJ2
merged 19 commits into

from

Oct 23, 2025
 Merged


Test with aiida-workgraph 0.7.4
#136
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9b38c17

Update pyproject.toml


jan-janssen Oct 22, 2025
79c8edf

Update environment.yml


jan-janssen Oct 22, 2025
6b78fb0

fixed syntax error. outputs now missing in our json representation


GeigerJ2 Oct 22, 2025
9995215

Fix callable_name


superstar54 Oct 22, 2025
88ec724

Update environment.yml


jan-janssen Oct 22, 2025
678c7e1

Update pyproject.toml


jan-janssen Oct 22, 2025
e40adbd

wip


GeigerJ2 Oct 22, 2025
295c39e

push for xing to test locally


GeigerJ2 Oct 23, 2025
d1f48c4

Fix the


superstar54 Oct 23, 2025
c829333

reset notebooks to `main` state


GeigerJ2 Oct 23, 2025
6548eda

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


GeigerJ2 Oct 23, 2025
d82ad85

black on aiida.py


GeigerJ2 Oct 23, 2025
008230c

re-introduce plumpy pin and fix qe aiida.ipynb example


GeigerJ2 Oct 23, 2025
891de62

fix `get_bulk_structure1` references in wg instances


GeigerJ2 Oct 23, 2025
dd30832

cleanup


GeigerJ2 Oct 23, 2025
27a1751

more cleanup


GeigerJ2 Oct 23, 2025
5d705ad

fix `wg.nodes` access


GeigerJ2 Oct 23, 2025
1ecb3f5

add nbstripout via pre-commit and strip all notebooks


GeigerJ2 Oct 23, 2025
21e9df9

Revert "add nbstripout via pre-commit and strip all notebooks"


GeigerJ2 Oct 23, 2025

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2 changes: 1 addition & 1 deletion
.gitignore

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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

2 changes: 1 addition & 1 deletion
binder/environment.yml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -10,7 +10,7 @@ dependencies:
- pyiron_base =0.12.0
- pyiron_workflow =0.13.0
- pygraphviz =1.14
- aiida-workgraph =0.5.2
- aiida-workgraph =0.7.4
- plumpy =0.25.0
- conda_subprocess =0.0.7
- networkx =3.5
Expand Down

5,800 changes: 5,799 additions & 1 deletion
example_workflows/quantum_espresso/aiida.ipynb

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5,748 changes: 5,747 additions & 1 deletion
example_workflows/quantum_espresso/jobflow.ipynb

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4,994 changes: 4,993 additions & 1 deletion
example_workflows/quantum_espresso/pyiron_base.ipynb

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6,016 changes: 6,015 additions & 1 deletion
example_workflows/quantum_espresso/pyiron_workflow.ipynb

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2 changes: 1 addition & 1 deletion
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -22,7 +22,7 @@ dependencies = [

[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",
Expand Down

54 changes: 30 additions & 24 deletions
src/python_workflow_definition/aiida.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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,
Expand All@@ -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 = {}
Expand All@@ -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
Expand All@@ -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)
Expand All@@ -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

Expand DownExpand Up@@ -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))
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
Test with aiida-workgraph 0.7.4#136

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privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

GeigerJ2
merged 19 commits into

from

Oct 23, 2025
 Merged


Test with aiida-workgraph 0.7.4
#136
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9b38c17

Update pyproject.toml


jan-janssen Oct 22, 2025
79c8edf

Update environment.yml


jan-janssen Oct 22, 2025
6b78fb0

fixed syntax error. outputs now missing in our json representation


GeigerJ2 Oct 22, 2025
9995215

Fix callable_name


superstar54 Oct 22, 2025
88ec724

Update environment.yml


jan-janssen Oct 22, 2025
678c7e1

Update pyproject.toml


jan-janssen Oct 22, 2025
e40adbd

wip


GeigerJ2 Oct 22, 2025
295c39e

push for xing to test locally


GeigerJ2 Oct 23, 2025
d1f48c4

Fix the


superstar54 Oct 23, 2025
c829333

reset notebooks to `main` state


GeigerJ2 Oct 23, 2025
6548eda

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


GeigerJ2 Oct 23, 2025
d82ad85

black on aiida.py


GeigerJ2 Oct 23, 2025
008230c

re-introduce plumpy pin and fix qe aiida.ipynb example


GeigerJ2 Oct 23, 2025
891de62

fix `get_bulk_structure1` references in wg instances


GeigerJ2 Oct 23, 2025
dd30832

cleanup


GeigerJ2 Oct 23, 2025
27a1751

more cleanup


GeigerJ2 Oct 23, 2025
5d705ad

fix `wg.nodes` access


GeigerJ2 Oct 23, 2025
1ecb3f5

add nbstripout via pre-commit and strip all notebooks


GeigerJ2 Oct 23, 2025
21e9df9

Revert "add nbstripout via pre-commit and strip all notebooks"


GeigerJ2 Oct 23, 2025

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2 changes: 1 addition & 1 deletion
.gitignore

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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

2 changes: 1 addition & 1 deletion
binder/environment.yml

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Expand Up@@ -10,7 +10,7 @@ dependencies:
- pyiron_base =0.12.0
- pyiron_workflow =0.13.0
- pygraphviz =1.14
- aiida-workgraph =0.5.2
- aiida-workgraph =0.7.4
- plumpy =0.25.0
- conda_subprocess =0.0.7
- networkx =3.5
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5,800 changes: 5,799 additions & 1 deletion
example_workflows/quantum_espresso/aiida.ipynb

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5,748 changes: 5,747 additions & 1 deletion
example_workflows/quantum_espresso/jobflow.ipynb

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4,994 changes: 4,993 additions & 1 deletion
example_workflows/quantum_espresso/pyiron_base.ipynb

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6,016 changes: 6,015 additions & 1 deletion
example_workflows/quantum_espresso/pyiron_workflow.ipynb

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2 changes: 1 addition & 1 deletion
pyproject.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -22,7 +22,7 @@ dependencies = [

[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",
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54 changes: 30 additions & 24 deletions
src/python_workflow_definition/aiida.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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,
Expand All@@ -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 = {}
Expand All@@ -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
Expand All@@ -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)
Expand All@@ -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

Expand DownExpand Up@@ -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))
Expand Down
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