diff --git a/README.md b/README.md
index 1e0cd35..a2f70ea 100644
--- a/README.md
+++ b/README.md
@@ -17,17 +17,15 @@ different workflow engines to enable interoperability.
As a first example we define two Python functions which add multiple inputs:
```python
def add_x_and_y(x, y):
- z = x + y
- return x, y, z
-
-def add_x_and_y_and_z(x, y, z):
- w = x + y + z
- return w
+ return x + y
+
+def get_prod_and_div(x: float, y: float) -> dict:
+ return {"prod": x * y, "div": x / y}
```
These two Python functions are combined in the following example workflow:
```python
-x, y, z = add_x_and_y(x=1, y=2)
-w = add_x_and_y_and_z(x=x, y=y, z=z)
+tmp_dict = get_prod_and_div(x=1, y=2)
+result = add_x_and_y(x=tmp_dict["prod"], y=tmp_dict["div"])
```
For the workflow representation of these Python functions the Python functions are stored in the [simple_workflow.py](simple_workflow.py)
Python module. The connection of the Python functions are stored in the [workflow_simple.json](workflow_simple.json)
@@ -35,23 +33,16 @@ JSON file:
```
{
"nodes": [
- {"id": 0, "function": "simple_workflow.add_x_and_y_and_z"},
+ {"id": 0, "function": "simple_workflow.get_prod_and_div"},
{"id": 1, "function": "simple_workflow.add_x_and_y"},
- {"id": 2, "function": "simple_workflow.add_x_and_y"},
- {"id": 3, "function": "simple_workflow.add_x_and_y"},
- {"id": 4, "value": 1},
- {"id": 5, "value": 2}
+ {"id": 2, "value": 1},
+ {"id": 3, "value": 2}
],
"edges": [
- {"target": 0, "targetPort": "x", "source": 1, "sourcePort": "x"},
- {"target": 1, "targetPort": "x", "source": 4, "sourcePort": null},
- {"target": 1, "targetPort": "y", "source": 5, "sourcePort": null},
- {"target": 0, "targetPort": "y", "source": 2, "sourcePort": "y"},
- {"target": 2, "targetPort": "x", "source": 4, "sourcePort": null},
- {"target": 2, "targetPort": "y", "source": 5, "sourcePort": null},
- {"target": 0, "targetPort": "z", "source": 3, "sourcePort": "z"},
- {"target": 3, "targetPort": "x", "source": 4, "sourcePort": null},
- {"target": 3, "targetPort": "y", "source": 5, "sourcePort": null}
+ {"target": 0, "targetPort": "x", "source": 2, "sourcePort": null},
+ {"target": 0, "targetPort": "y", "source": 3, "sourcePort": null},
+ {"target": 1, "targetPort": "x", "source": 0, "sourcePort": "prod"},
+ {"target": 1, "targetPort": "y", "source": 0, "sourcePort": "div"}
]
}
```
diff --git a/aiida_simple.ipynb b/aiida_simple.ipynb
index 9503b1b..e938ac4 100644
--- a/aiida_simple.ipynb
+++ b/aiida_simple.ipynb
@@ -1 +1,279 @@
-{"metadata":{"kernelspec":{"display_name":"Python 3 (ipykernel)","language":"python","name":"python3"},"language_info":{"codemirror_mode":{"name":"ipython","version":3},"file_extension":".py","mimetype":"text/x-python","name":"python","nbconvert_exporter":"python","pygments_lexer":"ipython3","version":"3.12.8"}},"nbformat_minor":4,"nbformat":4,"cells":[{"cell_type":"markdown","source":"# Aiida","metadata":{}},{"cell_type":"markdown","source":"## Define workflow with aiida","metadata":{}},{"cell_type":"code","source":"from python_workflow_definition.aiida import write_workflow_json\n\nfrom aiida_workgraph import WorkGraph, task\nfrom aiida import orm, load_profile\nload_profile()\n\nworkflow_json_filename = \"aiida_simple.json\"","metadata":{"trusted":false},"outputs":[],"execution_count":1},{"cell_type":"code","source":"from simple_workflow import add_x_and_y as _add_x_and_y\nfrom simple_workflow import add_x_and_y_and_z as _add_x_and_y_and_z","metadata":{"trusted":false},"outputs":[],"execution_count":2},{"cell_type":"code","source":"wg = WorkGraph(\"wg-simple\")","metadata":{"trusted":false},"outputs":[],"execution_count":4},{"cell_type":"code","source":"add_x_and_y_task = wg.add_task(\n task(outputs=['x', 'y', 'z'])(_add_x_and_y),\n name=\"add_x_and_y\",\n x=orm.Int(1),\n y=orm.Int(2),\n)","metadata":{"trusted":false},"outputs":[],"execution_count":5},{"cell_type":"code","source":"add_x_and_y_and_z_task = wg.add_task(\n _add_x_and_y_and_z,\n name=\"add_x_and_y_and_z\",\n x=add_x_and_y_task.outputs.x,\n y=add_x_and_y_task.outputs.y,\n z=add_x_and_y_task.outputs.z,\n)","metadata":{"trusted":false},"outputs":[],"execution_count":6},{"cell_type":"code","source":"write_workflow_json(wg=wg, file_name=workflow_json_filename)","metadata":{"trusted":false},"outputs":[{"data":{"text/plain":"{'nodes': {'0': 'simple_workflow.add_x_and_y',\n '1': 'simple_workflow.add_x_and_y_and_z',\n '2': 1,\n '3': 2},\n 'edges': [{'tn': 1, 'th': 'x', 'sn': 0, 'sh': 'x'},\n {'tn': 1, 'th': 'y', 'sn': 0, 'sh': 'y'},\n {'tn': 1, 'th': 'z', 'sn': 0, 'sh': 'z'},\n {'tn': 0, 'th': 'x', 'sn': 2, 'sh': None},\n {'tn': 0, 'th': 'y', 'sn': 3, 'sh': None}]}"},"execution_count":7,"metadata":{},"output_type":"execute_result"}],"execution_count":7},{"cell_type":"code","source":"!cat {workflow_json_filename}","metadata":{"trusted":false},"outputs":[{"name":"stdout","output_type":"stream","text":"{\n \"nodes\": {\n \"0\": \"simple_workflow.add_x_and_y\",\n \"1\": \"simple_workflow.add_x_and_y_and_z\",\n \"2\": 1,\n \"3\": 2\n },\n \"edges\": [\n {\n \"tn\": 1,\n \"th\": \"x\",\n \"sn\": 0,\n \"sh\": \"x\"\n },\n {\n \"tn\": 1,\n \"th\": \"y\",\n \"sn\": 0,\n \"sh\": \"y\"\n },\n {\n \"tn\": 1,\n \"th\": \"z\",\n \"sn\": 0,\n \"sh\": \"z\"\n },\n {\n \"tn\": 0,\n \"th\": \"x\",\n \"sn\": 2,\n \"sh\": null\n },\n {\n \"tn\": 0,\n \"th\": \"y\",\n \"sn\": 3,\n \"sh\": null\n }\n ]\n}"}],"execution_count":8},{"cell_type":"markdown","source":"## Load Workflow with jobflow","metadata":{}},{"cell_type":"code","source":"from python_workflow_definition.jobflow import load_workflow_json","metadata":{"trusted":false},"outputs":[{"name":"stderr","output_type":"stream","text":"/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/pkey.py:82: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"cipher\": algorithms.TripleDES,\n/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/transport.py:253: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"class\": algorithms.TripleDES,\n"}],"execution_count":9},{"cell_type":"code","source":"from jobflow.managers.local import run_locally","metadata":{"trusted":false},"outputs":[],"execution_count":10},{"cell_type":"code","source":"flow = load_workflow_json(file_name=workflow_json_filename)","metadata":{"trusted":false},"outputs":[],"execution_count":11},{"cell_type":"code","source":"result = run_locally(flow)\nresult","metadata":{"trusted":false},"outputs":[{"name":"stdout","output_type":"stream","text":"2025-04-02 14:36:37,425 INFO Started executing jobs locally\n2025-04-02 14:36:37,751 INFO Starting job - add_x_and_y (4bcb90c8-2c19-4981-a88e-56d5d24b5df9)\n2025-04-02 14:36:37,754 INFO Finished job - add_x_and_y (4bcb90c8-2c19-4981-a88e-56d5d24b5df9)\n2025-04-02 14:36:37,755 INFO Starting job - add_x_and_y_and_z (88bc90e5-09a0-443d-b24e-673cc6bc0819)\n2025-04-02 14:36:37,756 INFO Finished job - add_x_and_y_and_z (88bc90e5-09a0-443d-b24e-673cc6bc0819)\n2025-04-02 14:36:37,756 INFO Finished executing jobs locally\n"},{"data":{"text/plain":"{'4bcb90c8-2c19-4981-a88e-56d5d24b5df9': {1: Response(output={'x': 1, 'y': 2, 'z': 3}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '88bc90e5-09a0-443d-b24e-673cc6bc0819': {1: Response(output=6, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))}}"},"execution_count":12,"metadata":{},"output_type":"execute_result"}],"execution_count":12},{"cell_type":"markdown","source":"## Load Workflow with pyiron_base","metadata":{}},{"cell_type":"code","source":"from pyiron_base import Project","metadata":{"trusted":false},"outputs":[],"execution_count":13},{"cell_type":"code","source":"from python_workflow_definition.pyiron_base import load_workflow_json","metadata":{"trusted":false},"outputs":[],"execution_count":14},{"cell_type":"code","source":"pr = Project(\"test\")\npr.remove_jobs(recursive=True, silently=True)","metadata":{"trusted":false},"outputs":[{"data":{"application/vnd.jupyter.widget-view+json":{"model_id":"278f490ab20c4eaf9d39a75a7ee5231d","version_major":2,"version_minor":0},"text/plain":"0it [00:00, ?it/s]"},"metadata":{},"output_type":"display_data"}],"execution_count":15},{"cell_type":"code","source":"delayed_object = load_workflow_json(project=pr, file_name=workflow_json_filename)\ndelayed_object.draw()","metadata":{"trusted":false},"outputs":[{"data":{"image/svg+xml":"","text/plain":""},"metadata":{},"output_type":"display_data"}],"execution_count":16},{"cell_type":"code","source":"delayed_object.pull()","metadata":{"trusted":false},"outputs":[{"name":"stdout","output_type":"stream","text":"The job add_x_and_y_68901482a2c5221cc845f828aabebd27 was saved and received the ID: 1\nThe job add_x_and_y_and_z_b671e81aaa4670d81d7eee509650af8d was saved and received the ID: 2\n"},{"data":{"text/plain":"6"},"execution_count":17,"metadata":{},"output_type":"execute_result"}],"execution_count":17}]}
\ No newline at end of file
+{
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3 (ipykernel)",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.12.8"
+ }
+ },
+ "nbformat_minor": 4,
+ "nbformat": 4,
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "source": "# Aiida",
+ "metadata": {}
+ },
+ {
+ "cell_type": "markdown",
+ "source": "## Define workflow with aiida",
+ "metadata": {}
+ },
+ {
+ "cell_type": "code",
+ "source": "from python_workflow_definition.aiida import write_workflow_json\n\nfrom aiida_workgraph import WorkGraph, task\nfrom aiida import orm, load_profile\nload_profile()\n\nworkflow_json_filename = \"aiida_simple.json\"",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 1
+ },
+ {
+ "cell_type": "code",
+ "source": [
+ "from simple_workflow import (\n",
+ " add_x_and_y as _add_x_and_y,\n",
+ " get_prod_and_div as _get_prod_and_div,\n",
+ ")"
+ ],
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 2
+ },
+ {
+ "cell_type": "code",
+ "source": "wg = WorkGraph(\"wg-simple\")",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 4
+ },
+ {
+ "cell_type": "code",
+ "source": [
+ "get_prod_and_div_task = wg.add_task(\n",
+ " task(outputs=['prod', 'div'])(_get_prod_and_div),\n",
+ " name=\"get_prod_and_div\",\n",
+ " x=orm.Float(1),\n",
+ " y=orm.Float(2),\n",
+ ")"
+ ],
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 5
+ },
+ {
+ "cell_type": "code",
+ "source": [
+ "add_x_and_y_task = wg.add_task(\n",
+ " _add_x_and_y,\n",
+ " name=\"add_x_and_y\",\n",
+ " x=get_prod_and_div_task.outputs.prod,\n",
+ " y=get_prod_and_div_task.outputs.div,\n",
+ ")"
+ ],
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 6
+ },
+ {
+ "cell_type": "code",
+ "source": "write_workflow_json(wg=wg, file_name=workflow_json_filename)",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": "{'nodes': {'0': 'simple_workflow.add_x_and_y',\n '1': 'simple_workflow.add_x_and_y_and_z',\n '2': 1,\n '3': 2},\n 'edges': [{'tn': 1, 'th': 'x', 'sn': 0, 'sh': 'x'},\n {'tn': 1, 'th': 'y', 'sn': 0, 'sh': 'y'},\n {'tn': 1, 'th': 'z', 'sn': 0, 'sh': 'z'},\n {'tn': 0, 'th': 'x', 'sn': 2, 'sh': None},\n {'tn': 0, 'th': 'y', 'sn': 3, 'sh': None}]}"
+ },
+ "execution_count": 7,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "execution_count": 7
+ },
+ {
+ "cell_type": "code",
+ "source": "!cat {workflow_json_filename}",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": "{\n \"nodes\": {\n \"0\": \"simple_workflow.add_x_and_y\",\n \"1\": \"simple_workflow.add_x_and_y_and_z\",\n \"2\": 1,\n \"3\": 2\n },\n \"edges\": [\n {\n \"tn\": 1,\n \"th\": \"x\",\n \"sn\": 0,\n \"sh\": \"x\"\n },\n {\n \"tn\": 1,\n \"th\": \"y\",\n \"sn\": 0,\n \"sh\": \"y\"\n },\n {\n \"tn\": 1,\n \"th\": \"z\",\n \"sn\": 0,\n \"sh\": \"z\"\n },\n {\n \"tn\": 0,\n \"th\": \"x\",\n \"sn\": 2,\n \"sh\": null\n },\n {\n \"tn\": 0,\n \"th\": \"y\",\n \"sn\": 3,\n \"sh\": null\n }\n ]\n}"
+ }
+ ],
+ "execution_count": 8
+ },
+ {
+ "cell_type": "markdown",
+ "source": "## Load Workflow with jobflow",
+ "metadata": {}
+ },
+ {
+ "cell_type": "code",
+ "source": "from python_workflow_definition.jobflow import load_workflow_json",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": "/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/pkey.py:82: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"cipher\": algorithms.TripleDES,\n/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/transport.py:253: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"class\": algorithms.TripleDES,\n"
+ }
+ ],
+ "execution_count": 9
+ },
+ {
+ "cell_type": "code",
+ "source": "from jobflow.managers.local import run_locally",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 10
+ },
+ {
+ "cell_type": "code",
+ "source": "flow = load_workflow_json(file_name=workflow_json_filename)",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 11
+ },
+ {
+ "cell_type": "code",
+ "source": "result = run_locally(flow)\nresult",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": "2025-04-02 14:36:37,425 INFO Started executing jobs locally\n2025-04-02 14:36:37,751 INFO Starting job - add_x_and_y (4bcb90c8-2c19-4981-a88e-56d5d24b5df9)\n2025-04-02 14:36:37,754 INFO Finished job - add_x_and_y (4bcb90c8-2c19-4981-a88e-56d5d24b5df9)\n2025-04-02 14:36:37,755 INFO Starting job - add_x_and_y_and_z (88bc90e5-09a0-443d-b24e-673cc6bc0819)\n2025-04-02 14:36:37,756 INFO Finished job - add_x_and_y_and_z (88bc90e5-09a0-443d-b24e-673cc6bc0819)\n2025-04-02 14:36:37,756 INFO Finished executing jobs locally\n"
+ },
+ {
+ "data": {
+ "text/plain": "{'4bcb90c8-2c19-4981-a88e-56d5d24b5df9': {1: Response(output={'x': 1, 'y': 2, 'z': 3}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n '88bc90e5-09a0-443d-b24e-673cc6bc0819': {1: Response(output=6, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))}}"
+ },
+ "execution_count": 12,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "execution_count": 12
+ },
+ {
+ "cell_type": "markdown",
+ "source": "## Load Workflow with pyiron_base",
+ "metadata": {}
+ },
+ {
+ "cell_type": "code",
+ "source": "from pyiron_base import Project",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 13
+ },
+ {
+ "cell_type": "code",
+ "source": "from python_workflow_definition.pyiron_base import load_workflow_json",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 14
+ },
+ {
+ "cell_type": "code",
+ "source": "pr = Project(\"test\")\npr.remove_jobs(recursive=True, silently=True)",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "278f490ab20c4eaf9d39a75a7ee5231d",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": "0it [00:00, ?it/s]"
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "execution_count": 15
+ },
+ {
+ "cell_type": "code",
+ "source": "delayed_object = load_workflow_json(project=pr, file_name=workflow_json_filename)\ndelayed_object.draw()",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "image/svg+xml": "",
+ "text/plain": ""
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "execution_count": 16
+ },
+ {
+ "cell_type": "code",
+ "source": "delayed_object.pull()",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": "The job add_x_and_y_68901482a2c5221cc845f828aabebd27 was saved and received the ID: 1\nThe job add_x_and_y_and_z_b671e81aaa4670d81d7eee509650af8d was saved and received the ID: 2\n"
+ },
+ {
+ "data": {
+ "text/plain": "6"
+ },
+ "execution_count": 17,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "execution_count": 17
+ }
+ ]
+}
diff --git a/book/simple.md b/book/simple.md
index 2330b8d..41ae7bc 100644
--- a/book/simple.md
+++ b/book/simple.md
@@ -2,17 +2,15 @@
As a first example we define two Python functions which add multiple inputs:
```python
def add_x_and_y(x, y):
- z = x + y
- return x, y, z
-
-def add_x_and_y_and_z(x, y, z):
- w = x + y + z
- return w
+ return x + y
+
+def get_prod_and_div(x: float, y: float) -> dict:
+ return {"prod": x * y, "div": x / y}
```
These two Python functions are combined in the following example workflow:
```python
-x, y, z = add_x_and_y(x=1, y=2)
-w = add_x_and_y_and_z(x=x, y=y, z=z)
+tmp_dict = get_prod_and_div(x=1, y=2)
+result = add_x_and_y(x=tmp_dict["prod"], y=tmp_dict["div"])
```
For the workflow representation of these Python functions the Python functions are stored in the [simple_workflow.py](simple_workflow.py)
Python module. The connection of the Python functions are stored in the [workflow_simple.json](workflow_simple.json)
@@ -20,23 +18,16 @@ JSON file:
```
{
"nodes": [
- {"id": 0, "function": "simple_workflow.add_x_and_y_and_z"},
+ {"id": 0, "function": "simple_workflow.get_prod_and_div"},
{"id": 1, "function": "simple_workflow.add_x_and_y"},
- {"id": 2, "function": "simple_workflow.add_x_and_y"},
- {"id": 3, "function": "simple_workflow.add_x_and_y"},
- {"id": 4, "value": 1},
- {"id": 5, "value": 2}
+ {"id": 2, "value": 1},
+ {"id": 3, "value": 2}
],
"edges": [
- {"target": 0, "targetPort": "x", "source": 1, "sourcePort": "x"},
- {"target": 1, "targetPort": "x", "source": 4, "sourcePort": null},
- {"target": 1, "targetPort": "y", "source": 5, "sourcePort": null},
- {"target": 0, "targetPort": "y", "source": 2, "sourcePort": "y"},
- {"target": 2, "targetPort": "x", "source": 4, "sourcePort": null},
- {"target": 2, "targetPort": "y", "source": 5, "sourcePort": null},
- {"target": 0, "targetPort": "z", "source": 3, "sourcePort": "z"},
- {"target": 3, "targetPort": "x", "source": 4, "sourcePort": null},
- {"target": 3, "targetPort": "y", "source": 5, "sourcePort": null}
+ {"target": 0, "targetPort": "x", "source": 2, "sourcePort": null},
+ {"target": 0, "targetPort": "y", "source": 3, "sourcePort": null},
+ {"target": 1, "targetPort": "x", "source": 0, "sourcePort": "prod"},
+ {"target": 1, "targetPort": "y", "source": 0, "sourcePort": "div"}
]
}
```
diff --git a/jobflow_simple.ipynb b/jobflow_simple.ipynb
index ea246f0..d650e39 100644
--- a/jobflow_simple.ipynb
+++ b/jobflow_simple.ipynb
@@ -1 +1,334 @@
-{"metadata":{"kernelspec":{"display_name":"Python 3 (ipykernel)","language":"python","name":"python3"},"language_info":{"name":"python","version":"3.12.8","mimetype":"text/x-python","codemirror_mode":{"name":"ipython","version":3},"pygments_lexer":"ipython3","nbconvert_exporter":"python","file_extension":".py"}},"nbformat_minor":5,"nbformat":4,"cells":[{"id":"982a4fbe-7cf9-45dd-84ae-9854149db0b9","cell_type":"markdown","source":"# jobflow","metadata":{}},{"id":"e6180712-d081-45c7-ba41-fc5191f10427","cell_type":"markdown","source":"## Define workflow with jobflow","metadata":{}},{"id":"000bbd4a-f53c-4eea-9d85-76f0aa2ca10b","cell_type":"code","source":"from jobflow import job, Flow","metadata":{"trusted":false},"outputs":[{"name":"stderr","output_type":"stream","text":"/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/pkey.py:82: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"cipher\": algorithms.TripleDES,\n/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/transport.py:253: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"class\": algorithms.TripleDES,\n"}],"execution_count":1},{"id":"06c2bd9e-b2ac-4b88-9158-fa37331c3418","cell_type":"code","source":"from python_workflow_definition.jobflow import write_workflow_json","metadata":{"trusted":false},"outputs":[],"execution_count":2},{"id":"fb847d49-7bf9-4839-9b99-c116d1b0e9ee","cell_type":"code","source":"from simple_workflow import (\n add_x_and_y as _add_x_and_y, \n add_x_and_y_and_z as _add_x_and_y_and_z,\n)","metadata":{"trusted":false},"outputs":[],"execution_count":3},{"id":"8f95244e","cell_type":"code","source":"workflow_json_filename = \"jobflow_simple.json\"","metadata":{"trusted":false},"outputs":[],"execution_count":4},{"id":"07598344-0f75-433b-8902-bea21a42088c","cell_type":"code","source":"add_x_and_y = job(_add_x_and_y, data=[\"x\", \"y\", \"z\"])\nadd_x_and_y_and_z = job(_add_x_and_y_and_z)","metadata":{"trusted":false},"outputs":[],"execution_count":5},{"id":"ecef1ed5-a8d3-48c3-9e01-4a40e55c1153","cell_type":"code","source":"obj = add_x_and_y(x=1, y=2)","metadata":{"trusted":false},"outputs":[],"execution_count":6},{"id":"2b88a30a-e26b-4802-89b7-79ca08cc0af9","cell_type":"code","source":"w = add_x_and_y_and_z(x=obj.output.x, y=obj.output.y, z=obj.output.z)","metadata":{"trusted":false},"outputs":[],"execution_count":7},{"id":"a5e5ca63-2906-47c9-bac6-adebf8643cba","cell_type":"code","source":"flow = Flow([obj, w])","metadata":{"trusted":false},"outputs":[],"execution_count":8},{"id":"e464da97-16a1-4772-9a07-0a47f152781d","cell_type":"code","source":"write_workflow_json(flow=flow, file_name=workflow_json_filename)","metadata":{"trusted":false},"outputs":[],"execution_count":9},{"id":"bca646b2-0a9a-4271-966a-e5903a8c9031","cell_type":"code","source":"!cat {workflow_json_filename}","metadata":{"trusted":false},"outputs":[{"name":"stdout","output_type":"stream","text":"{\"nodes\": {\"0\": \"simple_workflow.add_x_and_y\", \"1\": \"simple_workflow.add_x_and_y_and_z\", \"2\": 1, \"3\": 2}, \"edges\": [{\"tn\": 0, \"th\": \"x\", \"sn\": 2, \"sh\": null}, {\"tn\": 0, \"th\": \"y\", \"sn\": 3, \"sh\": null}, {\"tn\": 1, \"th\": \"x\", \"sn\": 0, \"sh\": \"x\"}, {\"tn\": 1, \"th\": \"y\", \"sn\": 0, \"sh\": \"y\"}, {\"tn\": 1, \"th\": \"z\", \"sn\": 0, \"sh\": \"z\"}]}"}],"execution_count":10},{"id":"87a27540-c390-4d34-ae75-4739bfc4c1b7","cell_type":"markdown","source":"## Load Workflow with aiida","metadata":{}},{"id":"66a1b3a6-3d3b-4caa-b58f-d8bc089b1074","cell_type":"code","source":"from aiida import load_profile\n\nload_profile()","metadata":{"trusted":false},"outputs":[{"execution_count":11,"output_type":"execute_result","data":{"text/plain":"Profile"},"metadata":{}}],"execution_count":11},{"id":"4679693b-039b-45cf-8c67-5b2b3d705a83","cell_type":"code","source":"from python_workflow_definition.aiida import load_workflow_json","metadata":{"trusted":false},"outputs":[],"execution_count":12},{"id":"68c41a61-d185-47e8-ba31-eeff71d8b2c6","cell_type":"code","source":"wg = load_workflow_json(file_name=workflow_json_filename)\nwg","metadata":{"trusted":false},"outputs":[{"execution_count":13,"output_type":"execute_result","data":{"text/plain":"NodeGraphWidget(settings={'minimap': True}, style={'width': '90%', 'height': '600px'}, value={'name': 'WorkGra…","application/vnd.jupyter.widget-view+json":{"version_major":2,"version_minor":1,"model_id":"14e9a03e426b468dbfe338d7f734a41a"}},"metadata":{}}],"execution_count":13},{"id":"05228ece-643c-420c-8df8-4ce3df379515","cell_type":"code","source":"wg.run()","metadata":{"trusted":false},"outputs":[{"name":"stderr","output_type":"stream","text":"04/02/2025 02:37:38 PM <422> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [16|WorkGraphEngine|continue_workgraph]: tasks ready to run: add_x_and_y1\n04/02/2025 02:37:38 PM <422> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [16|WorkGraphEngine|update_task_state]: Task: add_x_and_y1, type: PyFunction, finished.\n04/02/2025 02:37:38 PM <422> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [16|WorkGraphEngine|continue_workgraph]: tasks ready to run: add_x_and_y_and_z2\n04/02/2025 02:37:39 PM <422> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [16|WorkGraphEngine|update_task_state]: Task: add_x_and_y_and_z2, type: PyFunction, finished.\n04/02/2025 02:37:39 PM <422> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [16|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n04/02/2025 02:37:39 PM <422> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [16|WorkGraphEngine|finalize]: Finalize workgraph.\n"}],"execution_count":14},{"id":"2c942094-61b4-4e94-859a-64f87b5bec64","cell_type":"markdown","source":"## Load Workflow with pyiron_base","metadata":{}},{"id":"40672826-23bf-4c24-84e2-a6b9d87e2a3f","cell_type":"code","source":"from pyiron_base import Project","metadata":{"trusted":false},"outputs":[],"execution_count":15},{"id":"ea102341-84f7-4156-a7d1-c3ab1ea613a5","cell_type":"code","source":"from python_workflow_definition.pyiron_base import load_workflow_json","metadata":{"trusted":false},"outputs":[],"execution_count":16},{"id":"f45684a8-2613-415a-ab0a-5cb2bafaffea","cell_type":"code","source":"pr = Project(\"test\")\npr.remove_jobs(recursive=True, silently=True)","metadata":{"trusted":false},"outputs":[{"output_type":"display_data","data":{"text/plain":"0it [00:00, ?it/s]","application/vnd.jupyter.widget-view+json":{"version_major":2,"version_minor":0,"model_id":"f4514974ee9546f788ea311ec80db1c9"}},"metadata":{}}],"execution_count":17},{"id":"8f2a621d-b533-4ddd-8bcd-c22db2f922ec","cell_type":"code","source":"delayed_object = load_workflow_json(project=pr, file_name=workflow_json_filename)\ndelayed_object.draw()","metadata":{"trusted":false},"outputs":[{"output_type":"display_data","data":{"text/plain":"","image/svg+xml":""},"metadata":{}}],"execution_count":18},{"id":"cf80267d-c2b0-4236-bf1d-a57596985fc1","cell_type":"code","source":"delayed_object.pull()","metadata":{"trusted":false},"outputs":[{"name":"stdout","output_type":"stream","text":"The job add_x_and_y_68901482a2c5221cc845f828aabebd27 was saved and received the ID: 1\nThe job add_x_and_y_and_z_b671e81aaa4670d81d7eee509650af8d was saved and received the ID: 2\n"},{"execution_count":19,"output_type":"execute_result","data":{"text/plain":"6"},"metadata":{}}],"execution_count":19},{"id":"9d819ed0-689c-46a7-9eff-0afb5ed66efc","cell_type":"code","source":"","metadata":{"trusted":false},"outputs":[],"execution_count":null}]}
\ No newline at end of file
+{
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3 (ipykernel)",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "name": "python",
+ "version": "3.12.8",
+ "mimetype": "text/x-python",
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "pygments_lexer": "ipython3",
+ "nbconvert_exporter": "python",
+ "file_extension": ".py"
+ }
+ },
+ "nbformat_minor": 5,
+ "nbformat": 4,
+ "cells": [
+ {
+ "id": "982a4fbe-7cf9-45dd-84ae-9854149db0b9",
+ "cell_type": "markdown",
+ "source": "# jobflow",
+ "metadata": {}
+ },
+ {
+ "id": "e6180712-d081-45c7-ba41-fc5191f10427",
+ "cell_type": "markdown",
+ "source": "## Define workflow with jobflow",
+ "metadata": {}
+ },
+ {
+ "id": "000bbd4a-f53c-4eea-9d85-76f0aa2ca10b",
+ "cell_type": "code",
+ "source": "from jobflow import job, Flow",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": "/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/pkey.py:82: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"cipher\": algorithms.TripleDES,\n/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/transport.py:253: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"class\": algorithms.TripleDES,\n"
+ }
+ ],
+ "execution_count": 1
+ },
+ {
+ "id": "06c2bd9e-b2ac-4b88-9158-fa37331c3418",
+ "cell_type": "code",
+ "source": "from python_workflow_definition.jobflow import write_workflow_json",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 2
+ },
+ {
+ "id": "fb847d49-7bf9-4839-9b99-c116d1b0e9ee",
+ "cell_type": "code",
+ "source": [
+ "from simple_workflow import (\n",
+ " add_x_and_y as _add_x_and_y, \n",
+ " get_prod_and_div as _get_prod_and_div,\n",
+ ")"
+ ],
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 3
+ },
+ {
+ "id": "8f95244e",
+ "cell_type": "code",
+ "source": "workflow_json_filename = \"jobflow_simple.json\"",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 4
+ },
+ {
+ "id": "07598344-0f75-433b-8902-bea21a42088c",
+ "cell_type": "code",
+ "source": [
+ "add_x_and_y = job(_add_x_and_y)\n",
+ "get_prod_and_div = job(_get_prod_and_div, data=[\"prod\", \"div\"])"
+ ],
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 5
+ },
+ {
+ "id": "ecef1ed5-a8d3-48c3-9e01-4a40e55c1153",
+ "cell_type": "code",
+ "source": "obj = get_prod_and_div(x=1, y=2)",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 6
+ },
+ {
+ "id": "2b88a30a-e26b-4802-89b7-79ca08cc0af9",
+ "cell_type": "code",
+ "source": "w = add_x_and_y(x=obj.output.prod, y=obj.output.div)",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 7
+ },
+ {
+ "id": "a5e5ca63-2906-47c9-bac6-adebf8643cba",
+ "cell_type": "code",
+ "source": "flow = Flow([obj, w])",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 8
+ },
+ {
+ "id": "e464da97-16a1-4772-9a07-0a47f152781d",
+ "cell_type": "code",
+ "source": "write_workflow_json(flow=flow, file_name=workflow_json_filename)",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 9
+ },
+ {
+ "id": "bca646b2-0a9a-4271-966a-e5903a8c9031",
+ "cell_type": "code",
+ "source": "!cat {workflow_json_filename}",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": "{\"nodes\": {\"0\": \"simple_workflow.add_x_and_y\", \"1\": \"simple_workflow.add_x_and_y_and_z\", \"2\": 1, \"3\": 2}, \"edges\": [{\"tn\": 0, \"th\": \"x\", \"sn\": 2, \"sh\": null}, {\"tn\": 0, \"th\": \"y\", \"sn\": 3, \"sh\": null}, {\"tn\": 1, \"th\": \"x\", \"sn\": 0, \"sh\": \"x\"}, {\"tn\": 1, \"th\": \"y\", \"sn\": 0, \"sh\": \"y\"}, {\"tn\": 1, \"th\": \"z\", \"sn\": 0, \"sh\": \"z\"}]}"
+ }
+ ],
+ "execution_count": 10
+ },
+ {
+ "id": "87a27540-c390-4d34-ae75-4739bfc4c1b7",
+ "cell_type": "markdown",
+ "source": "## Load Workflow with aiida",
+ "metadata": {}
+ },
+ {
+ "id": "66a1b3a6-3d3b-4caa-b58f-d8bc089b1074",
+ "cell_type": "code",
+ "source": "from aiida import load_profile\n\nload_profile()",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [
+ {
+ "execution_count": 11,
+ "output_type": "execute_result",
+ "data": {
+ "text/plain": "Profile"
+ },
+ "metadata": {}
+ }
+ ],
+ "execution_count": 11
+ },
+ {
+ "id": "4679693b-039b-45cf-8c67-5b2b3d705a83",
+ "cell_type": "code",
+ "source": "from python_workflow_definition.aiida import load_workflow_json",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 12
+ },
+ {
+ "id": "68c41a61-d185-47e8-ba31-eeff71d8b2c6",
+ "cell_type": "code",
+ "source": "wg = load_workflow_json(file_name=workflow_json_filename)\nwg",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [
+ {
+ "execution_count": 13,
+ "output_type": "execute_result",
+ "data": {
+ "text/plain": "NodeGraphWidget(settings={'minimap': True}, style={'width': '90%', 'height': '600px'}, value={'name': 'WorkGra…",
+ "application/vnd.jupyter.widget-view+json": {
+ "version_major": 2,
+ "version_minor": 1,
+ "model_id": "14e9a03e426b468dbfe338d7f734a41a"
+ }
+ },
+ "metadata": {}
+ }
+ ],
+ "execution_count": 13
+ },
+ {
+ "id": "05228ece-643c-420c-8df8-4ce3df379515",
+ "cell_type": "code",
+ "source": "wg.run()",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": "04/02/2025 02:37:38 PM <422> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [16|WorkGraphEngine|continue_workgraph]: tasks ready to run: add_x_and_y1\n04/02/2025 02:37:38 PM <422> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [16|WorkGraphEngine|update_task_state]: Task: add_x_and_y1, type: PyFunction, finished.\n04/02/2025 02:37:38 PM <422> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [16|WorkGraphEngine|continue_workgraph]: tasks ready to run: add_x_and_y_and_z2\n04/02/2025 02:37:39 PM <422> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [16|WorkGraphEngine|update_task_state]: Task: add_x_and_y_and_z2, type: PyFunction, finished.\n04/02/2025 02:37:39 PM <422> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [16|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n04/02/2025 02:37:39 PM <422> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [16|WorkGraphEngine|finalize]: Finalize workgraph.\n"
+ }
+ ],
+ "execution_count": 14
+ },
+ {
+ "id": "2c942094-61b4-4e94-859a-64f87b5bec64",
+ "cell_type": "markdown",
+ "source": "## Load Workflow with pyiron_base",
+ "metadata": {}
+ },
+ {
+ "id": "40672826-23bf-4c24-84e2-a6b9d87e2a3f",
+ "cell_type": "code",
+ "source": "from pyiron_base import Project",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 15
+ },
+ {
+ "id": "ea102341-84f7-4156-a7d1-c3ab1ea613a5",
+ "cell_type": "code",
+ "source": "from python_workflow_definition.pyiron_base import load_workflow_json",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 16
+ },
+ {
+ "id": "f45684a8-2613-415a-ab0a-5cb2bafaffea",
+ "cell_type": "code",
+ "source": "pr = Project(\"test\")\npr.remove_jobs(recursive=True, silently=True)",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [
+ {
+ "output_type": "display_data",
+ "data": {
+ "text/plain": "0it [00:00, ?it/s]",
+ "application/vnd.jupyter.widget-view+json": {
+ "version_major": 2,
+ "version_minor": 0,
+ "model_id": "f4514974ee9546f788ea311ec80db1c9"
+ }
+ },
+ "metadata": {}
+ }
+ ],
+ "execution_count": 17
+ },
+ {
+ "id": "8f2a621d-b533-4ddd-8bcd-c22db2f922ec",
+ "cell_type": "code",
+ "source": "delayed_object = load_workflow_json(project=pr, file_name=workflow_json_filename)\ndelayed_object.draw()",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [
+ {
+ "output_type": "display_data",
+ "data": {
+ "text/plain": "",
+ "image/svg+xml": ""
+ },
+ "metadata": {}
+ }
+ ],
+ "execution_count": 18
+ },
+ {
+ "id": "cf80267d-c2b0-4236-bf1d-a57596985fc1",
+ "cell_type": "code",
+ "source": "delayed_object.pull()",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": "The job add_x_and_y_68901482a2c5221cc845f828aabebd27 was saved and received the ID: 1\nThe job add_x_and_y_and_z_b671e81aaa4670d81d7eee509650af8d was saved and received the ID: 2\n"
+ },
+ {
+ "execution_count": 19,
+ "output_type": "execute_result",
+ "data": {
+ "text/plain": "6"
+ },
+ "metadata": {}
+ }
+ ],
+ "execution_count": 19
+ },
+ {
+ "id": "9d819ed0-689c-46a7-9eff-0afb5ed66efc",
+ "cell_type": "code",
+ "source": "",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": null
+ }
+ ]
+}
diff --git a/pyiron_base_simple.ipynb b/pyiron_base_simple.ipynb
index 090c80d..8f2044c 100644
--- a/pyiron_base_simple.ipynb
+++ b/pyiron_base_simple.ipynb
@@ -1 +1,315 @@
-{"metadata":{"kernelspec":{"display_name":"Python 3 (ipykernel)","language":"python","name":"python3"},"language_info":{"name":"python","version":"3.12.8","mimetype":"text/x-python","codemirror_mode":{"name":"ipython","version":3},"pygments_lexer":"ipython3","nbconvert_exporter":"python","file_extension":".py"}},"nbformat_minor":5,"nbformat":4,"cells":[{"id":"c39b76fb-259f-4e16-a44d-02a295c82386","cell_type":"markdown","source":"# pyiron","metadata":{}},{"id":"3638419b-a0cb-49e2-b157-7fbb1acde90f","cell_type":"markdown","source":"## Define workflow with pyiron_base","metadata":{}},{"id":"b4a78447-e87c-4fb4-8d17-d9a280eb7254","cell_type":"code","source":"from pyiron_base import Project, job","metadata":{"trusted":false},"outputs":[],"execution_count":1},{"id":"06c2bd9e-b2ac-4b88-9158-fa37331c3418","cell_type":"code","source":"from python_workflow_definition.pyiron_base import write_workflow_json","metadata":{"trusted":false},"outputs":[],"execution_count":2},{"id":"fb847d49-7bf9-4839-9b99-c116d1b0e9ee","cell_type":"code","source":"from simple_workflow import (\n add_x_and_y as _add_x_and_y, \n add_x_and_y_and_z as _add_x_and_y_and_z,\n)","metadata":{"trusted":false},"outputs":[],"execution_count":3},{"id":"8f95244e","cell_type":"code","source":"workflow_json_filename = \"pyiron_base_simple.json\"","metadata":{"trusted":false},"outputs":[],"execution_count":4},{"id":"07598344-0f75-433b-8902-bea21a42088c","cell_type":"code","source":"add_x_and_y = job(_add_x_and_y, output_key_lst=[\"x\", \"y\", \"z\"])\nadd_x_and_y_and_z = job(_add_x_and_y_and_z)","metadata":{"trusted":false},"outputs":[],"execution_count":5},{"id":"ecef1ed5-a8d3-48c3-9e01-4a40e55c1153","cell_type":"code","source":"pr = Project(\"test\")\npr.remove_jobs(recursive=True, silently=True)","metadata":{"trusted":false},"outputs":[{"output_type":"display_data","data":{"text/plain":" 0%| | 0/2 [00:00"},"metadata":{}}],"execution_count":11},{"id":"68a56b32-9f99-43d7-aaee-0c1cd9522681","cell_type":"code","source":"from python_workflow_definition.aiida import load_workflow_json","metadata":{"trusted":false},"outputs":[],"execution_count":12},{"id":"8f2a621d-b533-4ddd-8bcd-c22db2f922ec","cell_type":"code","source":"wg = load_workflow_json(file_name=workflow_json_filename)\nwg","metadata":{"trusted":false},"outputs":[{"execution_count":13,"output_type":"execute_result","data":{"text/plain":"NodeGraphWidget(settings={'minimap': True}, style={'width': '90%', 'height': '600px'}, value={'name': 'WorkGra…","application/vnd.jupyter.widget-view+json":{"version_major":2,"version_minor":1,"model_id":"dcfa2451385b4eb2b9204f7e196eeda4"}},"metadata":{}}],"execution_count":13},{"id":"cf80267d-c2b0-4236-bf1d-a57596985fc1","cell_type":"code","source":"\nwg.run()","metadata":{"trusted":false},"outputs":[{"name":"stderr","output_type":"stream","text":"04/02/2025 02:36:58 PM <248> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|continue_workgraph]: tasks ready to run: add_x_and_y2\n04/02/2025 02:36:59 PM <248> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|update_task_state]: Task: add_x_and_y2, type: PyFunction, finished.\n04/02/2025 02:36:59 PM <248> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|continue_workgraph]: tasks ready to run: add_x_and_y_and_z1\n04/02/2025 02:37:00 PM <248> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|update_task_state]: Task: add_x_and_y_and_z1, type: PyFunction, finished.\n04/02/2025 02:37:00 PM <248> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n04/02/2025 02:37:00 PM <248> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|finalize]: Finalize workgraph.\n"}],"execution_count":14},{"id":"0c3503e1-0a32-40e1-845d-3fd9ec3c4c19","cell_type":"markdown","source":"## Load Workflow with jobflow","metadata":{}},{"id":"4abb0481-8e38-479d-ae61-6c46d091653e","cell_type":"code","source":"from python_workflow_definition.jobflow import load_workflow_json","metadata":{"trusted":false},"outputs":[{"name":"stderr","output_type":"stream","text":"/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/pkey.py:82: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"cipher\": algorithms.TripleDES,\n/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/transport.py:253: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"class\": algorithms.TripleDES,\n"}],"execution_count":15},{"id":"8253dd7c283bf3f7","cell_type":"code","source":"from jobflow.managers.local import run_locally","metadata":{"trusted":false},"outputs":[],"execution_count":16},{"id":"4b45e83b-945f-48c5-8e20-9df0ce0a14a1","cell_type":"code","source":"flow = load_workflow_json(file_name=workflow_json_filename)","metadata":{"trusted":false},"outputs":[],"execution_count":17},{"id":"8665c39c-220c-4982-b738-c31f6460530f","cell_type":"code","source":"result = run_locally(flow)\nresult","metadata":{"trusted":false},"outputs":[{"name":"stdout","output_type":"stream","text":"2025-04-02 14:37:00,813 INFO Started executing jobs locally\n2025-04-02 14:37:01,234 INFO Starting job - add_x_and_y (3cb63b3e-289b-4c08-a9e4-0ba051181adb)\n2025-04-02 14:37:01,238 INFO Finished job - add_x_and_y (3cb63b3e-289b-4c08-a9e4-0ba051181adb)\n2025-04-02 14:37:01,239 INFO Starting job - add_x_and_y_and_z (bff452ed-d3b3-4d6c-8162-feaa188b5660)\n2025-04-02 14:37:01,242 INFO Finished job - add_x_and_y_and_z (bff452ed-d3b3-4d6c-8162-feaa188b5660)\n2025-04-02 14:37:01,243 INFO Finished executing jobs locally\n"},{"execution_count":18,"output_type":"execute_result","data":{"text/plain":"{'3cb63b3e-289b-4c08-a9e4-0ba051181adb': {1: Response(output={'x': 1, 'y': 2, 'z': 3}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n 'bff452ed-d3b3-4d6c-8162-feaa188b5660': {1: Response(output=6, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))}}"},"metadata":{}}],"execution_count":18},{"id":"cf76f305-24de-45a7-be8e-cfe45cd6458e","cell_type":"code","source":"","metadata":{"trusted":false},"outputs":[],"execution_count":null}]}
\ No newline at end of file
+{
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3 (ipykernel)",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "name": "python",
+ "version": "3.12.8",
+ "mimetype": "text/x-python",
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "pygments_lexer": "ipython3",
+ "nbconvert_exporter": "python",
+ "file_extension": ".py"
+ }
+ },
+ "nbformat_minor": 5,
+ "nbformat": 4,
+ "cells": [
+ {
+ "id": "c39b76fb-259f-4e16-a44d-02a295c82386",
+ "cell_type": "markdown",
+ "source": "# pyiron",
+ "metadata": {}
+ },
+ {
+ "id": "3638419b-a0cb-49e2-b157-7fbb1acde90f",
+ "cell_type": "markdown",
+ "source": "## Define workflow with pyiron_base",
+ "metadata": {}
+ },
+ {
+ "id": "b4a78447-e87c-4fb4-8d17-d9a280eb7254",
+ "cell_type": "code",
+ "source": "from pyiron_base import Project, job",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 1
+ },
+ {
+ "id": "06c2bd9e-b2ac-4b88-9158-fa37331c3418",
+ "cell_type": "code",
+ "source": "from python_workflow_definition.pyiron_base import write_workflow_json",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 2
+ },
+ {
+ "id": "fb847d49-7bf9-4839-9b99-c116d1b0e9ee",
+ "cell_type": "code",
+ "source": [
+ "from simple_workflow import (\n",
+ " add_x_and_y as _add_x_and_y, \n",
+ " get_prod_and_div as _get_prod_and_div,\n",
+ ")"
+ ],
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 3
+ },
+ {
+ "id": "8f95244e",
+ "cell_type": "code",
+ "source": "workflow_json_filename = \"pyiron_base_simple.json\"",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 4
+ },
+ {
+ "id": "07598344-0f75-433b-8902-bea21a42088c",
+ "cell_type": "code",
+ "source": [
+ "add_x_and_y = job(_add_x_and_y)\n",
+ "get_prod_and_div = job(_get_prod_and_div, output_key_lst=[\"prod\", \"div\"])"
+ ],
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 5
+ },
+ {
+ "id": "ecef1ed5-a8d3-48c3-9e01-4a40e55c1153",
+ "cell_type": "code",
+ "source": "pr = Project(\"test\")\npr.remove_jobs(recursive=True, silently=True)",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [
+ {
+ "output_type": "display_data",
+ "data": {
+ "text/plain": " 0%| | 0/2 [00:00"
+ },
+ "metadata": {}
+ }
+ ],
+ "execution_count": 11
+ },
+ {
+ "id": "68a56b32-9f99-43d7-aaee-0c1cd9522681",
+ "cell_type": "code",
+ "source": "from python_workflow_definition.aiida import load_workflow_json",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 12
+ },
+ {
+ "id": "8f2a621d-b533-4ddd-8bcd-c22db2f922ec",
+ "cell_type": "code",
+ "source": "wg = load_workflow_json(file_name=workflow_json_filename)\nwg",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [
+ {
+ "execution_count": 13,
+ "output_type": "execute_result",
+ "data": {
+ "text/plain": "NodeGraphWidget(settings={'minimap': True}, style={'width': '90%', 'height': '600px'}, value={'name': 'WorkGra…",
+ "application/vnd.jupyter.widget-view+json": {
+ "version_major": 2,
+ "version_minor": 1,
+ "model_id": "dcfa2451385b4eb2b9204f7e196eeda4"
+ }
+ },
+ "metadata": {}
+ }
+ ],
+ "execution_count": 13
+ },
+ {
+ "id": "cf80267d-c2b0-4236-bf1d-a57596985fc1",
+ "cell_type": "code",
+ "source": "\nwg.run()",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": "04/02/2025 02:36:58 PM <248> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|continue_workgraph]: tasks ready to run: add_x_and_y2\n04/02/2025 02:36:59 PM <248> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|update_task_state]: Task: add_x_and_y2, type: PyFunction, finished.\n04/02/2025 02:36:59 PM <248> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|continue_workgraph]: tasks ready to run: add_x_and_y_and_z1\n04/02/2025 02:37:00 PM <248> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|update_task_state]: Task: add_x_and_y_and_z1, type: PyFunction, finished.\n04/02/2025 02:37:00 PM <248> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n04/02/2025 02:37:00 PM <248> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [3|WorkGraphEngine|finalize]: Finalize workgraph.\n"
+ }
+ ],
+ "execution_count": 14
+ },
+ {
+ "id": "0c3503e1-0a32-40e1-845d-3fd9ec3c4c19",
+ "cell_type": "markdown",
+ "source": "## Load Workflow with jobflow",
+ "metadata": {}
+ },
+ {
+ "id": "4abb0481-8e38-479d-ae61-6c46d091653e",
+ "cell_type": "code",
+ "source": "from python_workflow_definition.jobflow import load_workflow_json",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": "/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/pkey.py:82: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"cipher\": algorithms.TripleDES,\n/srv/conda/envs/notebook/lib/python3.12/site-packages/paramiko/transport.py:253: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.\n \"class\": algorithms.TripleDES,\n"
+ }
+ ],
+ "execution_count": 15
+ },
+ {
+ "id": "8253dd7c283bf3f7",
+ "cell_type": "code",
+ "source": "from jobflow.managers.local import run_locally",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 16
+ },
+ {
+ "id": "4b45e83b-945f-48c5-8e20-9df0ce0a14a1",
+ "cell_type": "code",
+ "source": "flow = load_workflow_json(file_name=workflow_json_filename)",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": 17
+ },
+ {
+ "id": "8665c39c-220c-4982-b738-c31f6460530f",
+ "cell_type": "code",
+ "source": "result = run_locally(flow)\nresult",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": "2025-04-02 14:37:00,813 INFO Started executing jobs locally\n2025-04-02 14:37:01,234 INFO Starting job - add_x_and_y (3cb63b3e-289b-4c08-a9e4-0ba051181adb)\n2025-04-02 14:37:01,238 INFO Finished job - add_x_and_y (3cb63b3e-289b-4c08-a9e4-0ba051181adb)\n2025-04-02 14:37:01,239 INFO Starting job - add_x_and_y_and_z (bff452ed-d3b3-4d6c-8162-feaa188b5660)\n2025-04-02 14:37:01,242 INFO Finished job - add_x_and_y_and_z (bff452ed-d3b3-4d6c-8162-feaa188b5660)\n2025-04-02 14:37:01,243 INFO Finished executing jobs locally\n"
+ },
+ {
+ "execution_count": 18,
+ "output_type": "execute_result",
+ "data": {
+ "text/plain": "{'3cb63b3e-289b-4c08-a9e4-0ba051181adb': {1: Response(output={'x': 1, 'y': 2, 'z': 3}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))},\n 'bff452ed-d3b3-4d6c-8162-feaa188b5660': {1: Response(output=6, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/jovyan'))}}"
+ },
+ "metadata": {}
+ }
+ ],
+ "execution_count": 18
+ },
+ {
+ "id": "cf76f305-24de-45a7-be8e-cfe45cd6458e",
+ "cell_type": "code",
+ "source": "",
+ "metadata": {
+ "trusted": false
+ },
+ "outputs": [],
+ "execution_count": null
+ }
+ ]
+}
diff --git a/simple_workflow.py b/simple_workflow.py
index a686a81..afc4d72 100644
--- a/simple_workflow.py
+++ b/simple_workflow.py
@@ -1,8 +1,7 @@
-def add_x_and_y(x, y):
- z = x + y
- return {"x": x, "y": y, "z": z}
+def get_prod_and_div(x, y):
+ return {"prod": x * y, "div": x / y}
-def add_x_and_y_and_z(x, y, z):
- w = x + y + z
+def add_x_and_y(x, y):
+ w = x + y
return w
\ No newline at end of file
diff --git a/workflow_simple.json b/workflow_simple.json
index 69b6e00..7e3bdcc 100644
--- a/workflow_simple.json
+++ b/workflow_simple.json
@@ -1,15 +1,14 @@
{
"nodes": [
- {"id": 0, "function": "simple_workflow.add_x_and_y"},
- {"id": 1, "function": "simple_workflow.add_x_and_y_and_z"},
+ {"id": 0, "function": "simple_workflow.get_prod_and_div"},
+ {"id": 1, "function": "simple_workflow.add_x_and_y"},
{"id": 2, "value": 1},
{"id": 3, "value": 2}
],
"edges": [
{"target": 0, "targetPort": "x", "source": 2, "sourcePort": null},
{"target": 0, "targetPort": "y", "source": 3, "sourcePort": null},
- {"target": 1, "targetPort": "x", "source": 0, "sourcePort": "x"},
- {"target": 1, "targetPort": "y", "source": 0, "sourcePort": "y"},
- {"target": 1, "targetPort": "z", "source": 0, "sourcePort": "z"}
+ {"target": 1, "targetPort": "x", "source": 0, "sourcePort": "prod"},
+ {"target": 1, "targetPort": "y", "source": 0, "sourcePort": "div"}
]
}