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cwl.load_workflow_json -> cwl.pwd_to_cwl 
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‎example_workflows/arithmetic/cwl.ipynb‎

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{
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"name": "python",
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"version": "3.12.8",
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"mimetype": "text/x-python",
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"pygments_lexer": "ipython3",
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"nbconvert_exporter": "python",
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"file_extension": ".py"
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}
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},
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"nbformat_minor": 5,
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"nbformat": 4,
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"cells": [
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{
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"id": "377fef56-484d-491c-b19e-1be6931e44eb",
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"cell_type": "code",
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"source": "import pickle",
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"execution_count": 1,
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"id": "377fef56-484d-491c-b19e-1be6931e44eb",
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"metadata": {
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"trusted": true
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},
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"outputs": [],
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"execution_count": 1
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"source": [
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"import pickle"
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]
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},
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{
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"id": "92e3921b-2bb8-4333-8cfe-4bd27f785d24",
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"cell_type": "code",
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"source": "from python_workflow_definition.cwl import load_workflow_json",
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"execution_count": null,
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"id": "92e3921b-2bb8-4333-8cfe-4bd27f785d24",
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"metadata": {
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"trusted": true
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},
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"outputs": [],
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"execution_count": 2
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"source": [
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"from python_workflow_definition.cwl import pwd_to_cwl"
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]
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},
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{
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"id": "5303c059-8ae4-4557-858e-b4bd64eac711",
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"cell_type": "code",
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"source": "load_workflow_json(file_name=\"workflow.json\")",
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"execution_count": null,
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"id": "5303c059-8ae4-4557-858e-b4bd64eac711",
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"metadata": {
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"trusted": true
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},
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"outputs": [],
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"execution_count": 3
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"source": [
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"pwd_to_cwl(file_name=\"workflow.json\")"
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]
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},
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{
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"id": "df302bd2-e9b6-4595-979c-67c46414d986",
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"cell_type": "code",
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"source": "! cwltool workflow.cwl workflow.yml",
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"execution_count": 4,
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"id": "df302bd2-e9b6-4595-979c-67c46414d986",
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"metadata": {
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"trusted": true
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},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"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$3dfd802cefb317cc7138af1e3a299f565c74ddec\",\n \"size\": 21,\n \"path\": \"/home/jovyan/example_workflows/arithmetic/result.pickle\"\n }\n}\u001B[1;30mINFO\u001B[0m Final process status is success\n"
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"text": [
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"/srv/conda/envs/notebook/bin/cwltool:11: DeprecationWarning: Nesting argument groups is deprecated.\n",
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" sys.exit(run())\n",
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"\u001b[1;30mINFO\u001b[0m /srv/conda/envs/notebook/bin/cwltool 3.1.20250110105449\n",
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"\u001b[1;30mINFO\u001b[0m Resolved 'workflow.cwl' to 'file:///home/jovyan/example_workflows/arithmetic/workflow.cwl'\n",
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"\u001b[1;30mINFO\u001b[0m [workflow ] start\n",
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"\u001b[1;30mINFO\u001b[0m [workflow ] starting step get_prod_and_div_0\n",
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"\u001b[1;30mINFO\u001b[0m [step get_prod_and_div_0] start\n",
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"\u001b[1;30mINFO\u001b[0m [job get_prod_and_div_0] /tmp/hig0p5dd$ python \\\n",
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" -m \\\n",
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" python_workflow_definition.cwl \\\n",
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" --workflowfile=/tmp/0xeme5n4/stgba321752-0a06-41dd-95c0-f5890f1dfaae/workflow.py \\\n",
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" --function=workflow.get_prod_and_div \\\n",
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" --arg_y=/tmp/0xeme5n4/stg9f21530f-2f98-44e6-80b6-afa2aac5a083/y.pickle \\\n",
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" --arg_x=/tmp/0xeme5n4/stg2e35a78a-a776-48de-b82f-8075d3284a3c/x.pickle\n",
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"\u001b[1;30mINFO\u001b[0m [job get_prod_and_div_0] completed success\n",
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"\u001b[1;30mINFO\u001b[0m [step get_prod_and_div_0] completed success\n",
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"\u001b[1;30mINFO\u001b[0m [workflow ] starting step get_sum_1\n",
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"\u001b[1;30mINFO\u001b[0m [step get_sum_1] start\n",
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"\u001b[1;30mINFO\u001b[0m [job get_sum_1] /tmp/u07nctrs$ python \\\n",
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" -m \\\n",
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" python_workflow_definition.cwl \\\n",
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" --workflowfile=/tmp/sa53wz5h/stg686b1324-0030-4bfd-bdab-64fc9ee4d491/workflow.py \\\n",
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" --function=workflow.get_sum \\\n",
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" --arg_y=/tmp/sa53wz5h/stg1679a702-ac89-4c84-8cb5-7a57ae9e1834/div.pickle \\\n",
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" --arg_x=/tmp/sa53wz5h/stg6ab588fe-2723-416e-a7b8-648b1a63406e/prod.pickle\n",
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"\u001b[1;30mINFO\u001b[0m [job get_sum_1] completed success\n",
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"\u001b[1;30mINFO\u001b[0m [step get_sum_1] completed success\n",
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"\u001b[1;30mINFO\u001b[0m [workflow ] completed success\n",
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"{\n",
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" \"result_file\": {\n",
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" \"location\": \"file:///home/jovyan/example_workflows/arithmetic/result.pickle\",\n",
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" \"basename\": \"result.pickle\",\n",
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" \"class\": \"File\",\n",
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" \"checksum\": \"sha1$3dfd802cefb317cc7138af1e3a299f565c74ddec\",\n",
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" \"size\": 21,\n",
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" \"path\": \"/home/jovyan/example_workflows/arithmetic/result.pickle\"\n",
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" }\n",
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"}\u001b[1;30mINFO\u001b[0m Final process status is success\n"
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]
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}
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],
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"execution_count": 4
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"source": [
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"! cwltool workflow.cwl workflow.yml"
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]
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},
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{
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"id": "2942dbba-ea0a-4d20-be5c-ed9992d09ff8",
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"cell_type": "code",
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"source": "with open(\"result.pickle\", \"rb\") as f:\n print(pickle.load(f))",
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"execution_count": 5,
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"id": "2942dbba-ea0a-4d20-be5c-ed9992d09ff8",
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"metadata": {
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"trusted": true
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},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": "2.5\n"
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"text": [
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"2.5\n"
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]
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}
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],
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"execution_count": 5
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"source": [
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"with open(\"result.pickle\", \"rb\") as f:\n",
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" print(pickle.load(f))"
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]
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},
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{
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"id": "60e909ee-d0d0-4bd1-81c8-dd5274ae5834",
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"cell_type": "code",
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"source": "",
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"execution_count": null,
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"id": "60e909ee-d0d0-4bd1-81c8-dd5274ae5834",
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"metadata": {
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"trusted": true
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},
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"outputs": [],
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"execution_count": null
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.12.8"
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}
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]
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

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