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Merged
jan-janssen merged 3 commits into from
Mar 13, 2025
Merged

The simple workflow produced from pyiron_base is broken #10

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jan-janssen Mar 12, 2025
85960e5
Update pyiron_base.py
jan-janssen Mar 13, 2025
cb5b33e
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jan-janssen Mar 13, 2025
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jan-janssen authored Mar 13, 2025
commit cb5b33e92b7210a932697b15a64def9254ea3daa
2 changes: 1 addition & 1 deletion pyiron_base_to_jobflow_qe.ipynb
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2 changes: 1 addition & 1 deletion pyiron_base_to_jobflow_simple.ipynb
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{"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":5,"nbformat":4,"cells":[{"id":"28d69730-d8cb-4174-ae3f-aa70da8a8108","cell_type":"code","source":"import numpy as np","metadata":{"trusted":true},"outputs":[],"execution_count":1},{"id":"cacaa0a8-27c8-44de-9e37-69cd3d13408b","cell_type":"code","source":"from jobflow.managers.local import run_locally","metadata":{"trusted":true},"outputs":[],"execution_count":2},{"id":"78ca455d-d0b8-4814-81fa-6039f6adb4c4","cell_type":"code","source":"from python_workflow_definition.jobflow import load_workflow_json","metadata":{"trusted":true},"outputs":[],"execution_count":3},{"id":"14d87342-706e-4120-99e6-b5363f724601","cell_type":"code","source":"from pyiron_base import Project, job","metadata":{"trusted":true},"outputs":[],"execution_count":4},{"id":"a2ed2608-9e1b-4a81-81cb-5079573ea2d1","cell_type":"code","source":"from python_workflow_definition.pyiron_base import write_workflow_json","metadata":{"trusted":true},"outputs":[],"execution_count":5},{"id":"444347b0-d5ba-4903-b8d4-a9d7fc35d268","cell_type":"code","source":"from python_workflow_definition.jobflow import load_workflow_json","metadata":{"trusted":true},"outputs":[],"execution_count":6},{"id":"b75c2530-9b89-4185-838f-a17e517fa68f","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":true},"outputs":[],"execution_count":7},{"id":"208ddfb8-dfda-4227-aa1f-3dc29e34ea82","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":true},"outputs":[],"execution_count":8},{"id":"13debfcd-362d-4fd0-a91f-5ab33632fceb","cell_type":"code","source":"pr = Project(\"test\")\npr.remove_jobs(recursive=True, silently=True)","metadata":{"trusted":true},"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":"7c918be13b6a448c8a85eb140d71ae02"}},"metadata":{}}],"execution_count":9},{"id":"1f1cb12f-4001-478d-8ea0-b369f4f2981a","cell_type":"code","source":"obj = add_x_and_y(x=1, y=2, pyiron_project=pr)","metadata":{"trusted":true},"outputs":[],"execution_count":10},{"id":"4140f07b-af54-41ef-be22-df6b5b53bf95","cell_type":"code","source":"w = add_x_and_y_and_z(x=obj.output.x, y=obj.output.y, z=obj.output.z, pyiron_project=pr)","metadata":{"trusted":true},"outputs":[],"execution_count":11},{"id":"52646121-335f-48e6-bd5e-a1d69d00e8bc","cell_type":"code","source":"write_workflow_json(delayed_object=w, file_name=\"workflow_pyiron.json\")","metadata":{"trusted":true},"outputs":[],"execution_count":12},{"id":"72c8e6e6-8e60-4a4f-81f3-968b4b5f36ee","cell_type":"code","source":"!cat workflow_pyiron.json","metadata":{"trusted":true},"outputs":[{"name":"stdout","output_type":"stream","text":"{\"nodes\": {\"0\": \"simple_workflow.add_x_and_y_and_z\", \"1\": \"simple_workflow.add_x_and_y\", \"2\": \"simple_workflow.add_x_and_y\", \"3\": \"simple_workflow.add_x_and_y\", \"4\": 1, \"5\": 2}, \"edges\": [{\"target\": 0, \"targetHandle\": \"x\", \"source\": 1, \"sourceHandle\": \"x\"}, {\"target\": 1, \"targetHandle\": \"x\", \"source\": 4, \"sourceHandle\": null}, {\"target\": 1, \"targetHandle\": \"y\", \"source\": 5, \"sourceHandle\": null}, {\"target\": 0, \"targetHandle\": \"y\", \"source\": 2, \"sourceHandle\": \"y\"}, {\"target\": 2, \"targetHandle\": \"x\", \"source\": 4, \"sourceHandle\": null}, {\"target\": 2, \"targetHandle\": \"y\", \"source\": 5, \"sourceHandle\": null}, {\"target\": 0, \"targetHandle\": \"z\", \"source\": 3, \"sourceHandle\": \"z\"}, {\"target\": 3, \"targetHandle\": \"x\", \"source\": 4, \"sourceHandle\": null}, {\"target\": 3, \"targetHandle\": \"y\", \"source\": 5, \"sourceHandle\": null}]}"}],"execution_count":13},{"id":"32fcd4b2-4f0a-442d-b098-827672823796","cell_type":"code","source":"flow = load_workflow_json(file_name=\"workflow_pyiron.json\")","metadata":{"trusted":true},"outputs":[],"execution_count":14},{"id":"a80b59bd-fe30-49c6-92ca-35ef2d77a6fb","cell_type":"code","source":"result = run_locally(flow)\nresult","metadata":{"trusted":true},"outputs":[{"name":"stdout","output_type":"stream","text":"2025-03-12 10:37:54,131 INFO Started executing jobs locally\n2025-03-12 10:37:54,427 INFO Starting job - add_x_and_y (567c1da3-2bfd-4fb6-a6ae-d1d156cc9383)\n2025-03-12 10:37:54,429 INFO Finished job - add_x_and_y (567c1da3-2bfd-4fb6-a6ae-d1d156cc9383)\n2025-03-12 10:37:54,430 INFO Starting job - add_x_and_y (375ed1ca-2163-48a9-93a9-1323bd788a11)\n2025-03-12 10:37:54,430 INFO Finished job - add_x_and_y (375ed1ca-2163-48a9-93a9-1323bd788a11)\n2025-03-12 10:37:54,431 INFO Starting job - add_x_and_y (ebbb4aa0-3db0-4a5a-8b3c-dfacc56a7421)\n2025-03-12 10:37:54,431 INFO Finished job - add_x_and_y (ebbb4aa0-3db0-4a5a-8b3c-dfacc56a7421)\n2025-03-12 10:37:54,433 INFO Starting job - add_x_and_y_and_z (9a6590d4-4355-4d71-b521-ebee3381f1c8)\n2025-03-12 10:37:54,435 INFO Finished job - add_x_and_y_and_z (9a6590d4-4355-4d71-b521-ebee3381f1c8)\n2025-03-12 10:37:54,435 INFO Finished executing jobs locally\n"},{"execution_count":15,"output_type":"execute_result","data":{"text/plain":"{'567c1da3-2bfd-4fb6-a6ae-d1d156cc9383': {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 '375ed1ca-2163-48a9-93a9-1323bd788a11': {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 'ebbb4aa0-3db0-4a5a-8b3c-dfacc56a7421': {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 '9a6590d4-4355-4d71-b521-ebee3381f1c8': {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":15},{"id":"6a8d1a17-3698-4873-8937-616e9e7dc7ca","cell_type":"code","source":"","metadata":{"trusted":true},"outputs":[],"execution_count":null}]}
{"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":5,"nbformat":4,"cells":[{"id":"28d69730-d8cb-4174-ae3f-aa70da8a8108","cell_type":"code","source":"import numpy as np","metadata":{"trusted":true},"outputs":[],"execution_count":1},{"id":"cacaa0a8-27c8-44de-9e37-69cd3d13408b","cell_type":"code","source":"from jobflow.managers.local import run_locally","metadata":{"trusted":true},"outputs":[],"execution_count":2},{"id":"78ca455d-d0b8-4814-81fa-6039f6adb4c4","cell_type":"code","source":"from python_workflow_definition.jobflow import load_workflow_json","metadata":{"trusted":true},"outputs":[],"execution_count":3},{"id":"14d87342-706e-4120-99e6-b5363f724601","cell_type":"code","source":"from pyiron_base import Project, job","metadata":{"trusted":true},"outputs":[],"execution_count":4},{"id":"a2ed2608-9e1b-4a81-81cb-5079573ea2d1","cell_type":"code","source":"from python_workflow_definition.pyiron_base import write_workflow_json","metadata":{"trusted":true},"outputs":[],"execution_count":5},{"id":"444347b0-d5ba-4903-b8d4-a9d7fc35d268","cell_type":"code","source":"from python_workflow_definition.jobflow import load_workflow_json","metadata":{"trusted":true},"outputs":[],"execution_count":6},{"id":"b75c2530-9b89-4185-838f-a17e517fa68f","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":true},"outputs":[],"execution_count":7},{"id":"208ddfb8-dfda-4227-aa1f-3dc29e34ea82","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":true},"outputs":[],"execution_count":8},{"id":"13debfcd-362d-4fd0-a91f-5ab33632fceb","cell_type":"code","source":"pr = Project(\"test\")\npr.remove_jobs(recursive=True, silently=True)","metadata":{"trusted":true},"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":"1bcb58b981944c688403d1eaca7b3598"}},"metadata":{}}],"execution_count":9},{"id":"1f1cb12f-4001-478d-8ea0-b369f4f2981a","cell_type":"code","source":"obj = add_x_and_y(x=1, y=2, pyiron_project=pr)","metadata":{"trusted":true},"outputs":[],"execution_count":10},{"id":"4140f07b-af54-41ef-be22-df6b5b53bf95","cell_type":"code","source":"w = add_x_and_y_and_z(x=obj.output.x, y=obj.output.y, z=obj.output.z, pyiron_project=pr)","metadata":{"trusted":true},"outputs":[],"execution_count":11},{"id":"52646121-335f-48e6-bd5e-a1d69d00e8bc","cell_type":"code","source":"write_workflow_json(delayed_object=w, file_name=\"workflow_pyiron.json\")","metadata":{"trusted":true},"outputs":[],"execution_count":12},{"id":"72c8e6e6-8e60-4a4f-81f3-968b4b5f36ee","cell_type":"code","source":"!cat workflow_pyiron.json","metadata":{"trusted":true},"outputs":[{"name":"stdout","output_type":"stream","text":"{\"nodes\": {\"0\": \"simple_workflow.add_x_and_y_and_z\", \"1\": \"simple_workflow.add_x_and_y\", \"2\": 1, \"3\": 2}, \"edges\": [{\"target\": 0, \"targetHandle\": \"x\", \"source\": 1, \"sourceHandle\": \"x\"}, {\"target\": 1, \"targetHandle\": \"x\", \"source\": 2, \"sourceHandle\": null}, {\"target\": 1, \"targetHandle\": \"y\", \"source\": 3, \"sourceHandle\": null}, {\"target\": 0, \"targetHandle\": \"y\", \"source\": 1, \"sourceHandle\": \"y\"}, {\"target\": 0, \"targetHandle\": \"z\", \"source\": 1, \"sourceHandle\": \"z\"}]}"}],"execution_count":13},{"id":"32fcd4b2-4f0a-442d-b098-827672823796","cell_type":"code","source":"flow = load_workflow_json(file_name=\"workflow_pyiron.json\")","metadata":{"trusted":true},"outputs":[],"execution_count":14},{"id":"a80b59bd-fe30-49c6-92ca-35ef2d77a6fb","cell_type":"code","source":"result = run_locally(flow)\nresult","metadata":{"trusted":true},"outputs":[{"name":"stdout","output_type":"stream","text":"2025-03-13 06:29:36,854 INFO Started executing jobs locally\n2025-03-13 06:29:37,166 INFO Starting job - add_x_and_y (75f3eb14-326b-46bb-848d-ef501b2d43b4)\n2025-03-13 06:29:37,169 INFO Finished job - add_x_and_y (75f3eb14-326b-46bb-848d-ef501b2d43b4)\n2025-03-13 06:29:37,170 INFO Starting job - add_x_and_y_and_z (609c1659-ec60-4211-8996-670770e4b36c)\n2025-03-13 06:29:37,172 INFO Finished job - add_x_and_y_and_z (609c1659-ec60-4211-8996-670770e4b36c)\n2025-03-13 06:29:37,172 INFO Finished executing jobs locally\n"},{"execution_count":15,"output_type":"execute_result","data":{"text/plain":"{'75f3eb14-326b-46bb-848d-ef501b2d43b4': {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 '609c1659-ec60-4211-8996-670770e4b36c': {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":15},{"id":"6a8d1a17-3698-4873-8937-616e9e7dc7ca","cell_type":"code","source":"","metadata":{"trusted":true},"outputs":[],"execution_count":null}]}