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Merged
merged 2 commits into from
May 24, 2025
Merged

Update notebooks #113

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43dfa38
Update notebooks
jan-janssen May 24, 2025
9e208ad
add a space in every notebook
jan-janssen May 24, 2025
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388 changes: 91 additions & 297 deletions example_workflows/arithmetic/aiida.ipynb
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4 changes: 2 additions & 2 deletions example_workflows/arithmetic/cwl.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,7 @@
{
"name": "stdout",
"output_type": "stream",
"text": "/srv/conda/envs/notebook/bin/cwltool:11: DeprecationWarning: Nesting argument groups is deprecated.\n sys.exit(run())\n\u001B[1;30mINFO\u001B[0m /srv/conda/envs/notebook/bin/cwltool 3.1.20250110105449\n\u001B[1;30mINFO\u001B[0m Resolved 'workflow.cwl' to 'file:///home/jovyan/example_workflows/arithmetic/workflow.cwl'\n\u001B[1;30mINFO\u001B[0m [workflow ] start\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_prod_and_div_0\n\u001B[1;30mINFO\u001B[0m [step get_prod_and_div_0] start\n\u001B[1;30mINFO\u001B[0m [job get_prod_and_div_0] /tmp/hig0p5dd$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/0xeme5n4/stgba321752-0a06-41dd-95c0-f5890f1dfaae/workflow.py \\\n --function=workflow.get_prod_and_div \\\n --arg_y=/tmp/0xeme5n4/stg9f21530f-2f98-44e6-80b6-afa2aac5a083/y.pickle \\\n --arg_x=/tmp/0xeme5n4/stg2e35a78a-a776-48de-b82f-8075d3284a3c/x.pickle\n\u001B[1;30mINFO\u001B[0m [job get_prod_and_div_0] completed success\n\u001B[1;30mINFO\u001B[0m [step get_prod_and_div_0] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_sum_1\n\u001B[1;30mINFO\u001B[0m [step get_sum_1] start\n\u001B[1;30mINFO\u001B[0m [job get_sum_1] /tmp/u07nctrs$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/sa53wz5h/stg686b1324-0030-4bfd-bdab-64fc9ee4d491/workflow.py \\\n --function=workflow.get_sum \\\n --arg_y=/tmp/sa53wz5h/stg1679a702-ac89-4c84-8cb5-7a57ae9e1834/div.pickle \\\n --arg_x=/tmp/sa53wz5h/stg6ab588fe-2723-416e-a7b8-648b1a63406e/prod.pickle\n\u001B[1;30mINFO\u001B[0m [job get_sum_1] completed success\n\u001B[1;30mINFO\u001B[0m [step get_sum_1] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] completed success\n{\n \"result_file\": {\n \"location\": \"file:///home/jovyan/example_workflows/arithmetic/result.pickle\",\n \"basename\": \"result.pickle\",\n \"class\": \"File\",\n \"checksum\": \"sha1$3dfd802cefb317cc7138af1e3a299f565c74ddec\",\n \"size\": 21,\n \"path\": \"/home/jovyan/example_workflows/arithmetic/result.pickle\"\n }\n}\u001B[1;30mINFO\u001B[0m Final process status is success\n"
"text": "/srv/conda/envs/notebook/bin/cwltool:11: DeprecationWarning: Nesting argument groups is deprecated.\n sys.exit(run())\n\u001B[1;30mINFO\u001B[0m /srv/conda/envs/notebook/bin/cwltool 3.1.20250110105449\n\u001B[1;30mINFO\u001B[0m Resolved 'workflow.cwl' to 'file:///home/jovyan/example_workflows/arithmetic/workflow.cwl'\n\u001B[1;30mINFO\u001B[0m [workflow ] start\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_prod_and_div_0\n\u001B[1;30mINFO\u001B[0m [step get_prod_and_div_0] start\n\u001B[1;30mINFO\u001B[0m [job get_prod_and_div_0] /tmp/_1apt559$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/dyuxg6ka/stgf337bac5-2f8e-4489-bd51-83491b1d5f0e/workflow.py \\\n --function=workflow.get_prod_and_div \\\n --arg_x=/tmp/dyuxg6ka/stgd87c2fe4-ca8e-4031-9af0-751d6944cbe7/x.pickle \\\n --arg_y=/tmp/dyuxg6ka/stg7bcb8ced-0e5b-442e-a0e0-2b3117afe2d8/y.pickle\n\u001B[1;30mINFO\u001B[0m [job get_prod_and_div_0] completed success\n\u001B[1;30mINFO\u001B[0m [step get_prod_and_div_0] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_sum_1\n\u001B[1;30mINFO\u001B[0m [step get_sum_1] start\n\u001B[1;30mINFO\u001B[0m [job get_sum_1] /tmp/ysau_yra$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/rm6c9qek/stgfef68b90-5d69-4da9-a952-b9c2f2a1eb76/workflow.py \\\n --function=workflow.get_sum \\\n --arg_x=/tmp/rm6c9qek/stg35728be7-5a6d-487b-bd02-345581007663/prod.pickle \\\n --arg_y=/tmp/rm6c9qek/stgc0992786-237e-4308-9d9e-814ebbfb0319/div.pickle\n\u001B[1;30mINFO\u001B[0m [job get_sum_1] completed success\n\u001B[1;30mINFO\u001B[0m [step get_sum_1] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_square_2\n\u001B[1;30mINFO\u001B[0m [step get_square_2] start\n\u001B[1;30mINFO\u001B[0m [job get_square_2] /tmp/o3gzya8t$ python \\\n -m \\\n python_workflow_definition.cwl \\\n --workflowfile=/tmp/6a3sltnz/stg58ccf048-a5c3-4ba3-a24f-c64adfff84cd/workflow.py \\\n --function=workflow.get_square \\\n --arg_x=/tmp/6a3sltnz/stg70203cec-cbd4-4fea-a3de-70e9373d9c9d/result.pickle\n\u001B[1;30mINFO\u001B[0m [job get_square_2] completed success\n\u001B[1;30mINFO\u001B[0m [step get_square_2] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] completed success\n{\n \"result_file\": {\n \"location\": \"file:///home/jovyan/example_workflows/arithmetic/result.pickle\",\n \"basename\": \"result.pickle\",\n \"class\": \"File\",\n \"checksum\": \"sha1$1fd8f217331336b1226b84e351c56fb9a8d93685\",\n \"size\": 21,\n \"path\": \"/home/jovyan/example_workflows/arithmetic/result.pickle\"\n }\n}\u001B[1;30mINFO\u001B[0m Final process status is success\n"
}
],
"execution_count": 4
Expand All @@ -78,7 +78,7 @@
{
"name": "stdout",
"output_type": "stream",
"text": "2.5\n"
"text": "6.25\n"
}
],
"execution_count": 5
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