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Add pyiron_base_to_aiida_simple.ipynb
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‎pyiron_base_to_aiida_simple.ipynb‎

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"id": "000bbd4a-f53c-4eea-9d85-76f0aa2ca10b",
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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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"data": {
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"text/plain": [
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"Profile<uuid='d106cde233334800a702a20040a6b629' name='adis'>"
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]
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},
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"execution_count": 1,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"from aiida import load_profile\n",
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"\n",
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"load_profile()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"id": "b4a78447-e87c-4fb4-8d17-d9a280eb7254",
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"metadata": {
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"trusted": true
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},
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"outputs": [],
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"source": [
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"from pyiron_base import Project, job"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"id": "06c2bd9e-b2ac-4b88-9158-fa37331c3418",
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"metadata": {
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"trusted": true
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},
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"outputs": [],
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"source": [
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"from python_workflow_definition.pyiron_base import write_workflow_json"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"id": "fb6dbdaa-8cab-48b2-8307-448003eca3f5",
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"metadata": {
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"trusted": true
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},
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"outputs": [],
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"source": [
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"from python_workflow_definition.aiida import load_workflow_json"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"id": "fb847d49-7bf9-4839-9b99-c116d1b0e9ee",
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"metadata": {
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"trusted": true
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},
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"outputs": [],
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"source": [
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"from simple_workflow import (\n",
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" add_x_and_y as _add_x_and_y, \n",
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" add_x_and_y_and_z as _add_x_and_y_and_z,\n",
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")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"id": "8f95244e",
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"metadata": {},
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"outputs": [],
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"source": [
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"workflow_json_filename = \"workflow_simple_pyiron_base.json\""
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]
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"id": "07598344-0f75-433b-8902-bea21a42088c",
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"metadata": {
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"trusted": true
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},
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"outputs": [],
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"source": [
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"add_x_and_y = job(_add_x_and_y, output_key_lst=[\"x\", \"y\", \"z\"])\n",
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"add_x_and_y_and_z = job(_add_x_and_y_and_z)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"id": "ecef1ed5-a8d3-48c3-9e01-4a40e55c1153",
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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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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "080b31b1d2ff47bfbabda6d012fc9e14",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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" 0%| | 0/17 [00:00<?, ?it/s]"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"source": [
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"pr = Project(\"test\")\n",
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"pr.remove_jobs(recursive=True, silently=True)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"id": "2b88a30a-e26b-4802-89b7-79ca08cc0af9",
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"metadata": {
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"trusted": true
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},
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"outputs": [],
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"source": [
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"obj = add_x_and_y(x=1, y=2, pyiron_project=pr)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 10,
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"id": "a5e5ca63-2906-47c9-bac6-adebf8643cba",
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"metadata": {
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"trusted": true
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},
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"outputs": [],
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"source": [
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"w = add_x_and_y_and_z(x=obj.output.x, y=obj.output.y, z=obj.output.z, pyiron_project=pr)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 11,
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"id": "e464da97-16a1-4772-9a07-0a47f152781d",
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"metadata": {
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"trusted": true
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},
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"outputs": [],
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"source": [
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"write_workflow_json(delayed_object=w, file_name=workflow_json_filename)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 12,
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"id": "bca646b2-0a9a-4271-966a-e5903a8c9031",
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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": [
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"\u001b[38;5;238m───────┬────────────────────────────────────────────────────────────────────────\u001b[0m\n",
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" \u001b[38;5;238m│ \u001b[0mFile: \u001b[1mworkflow_simple_pyiron_base.json\u001b[0m\n",
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"\u001b[38;5;238m───────┼────────────────────────────────────────────────────────────────────────\u001b[0m\n",
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"\u001b[38;5;238m 1\u001b[0m \u001b[38;5;238m│\u001b[0m \u001b[38;5;231m{\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208mnodes\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;231m{\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208m0\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;186m\"\u001b[0m\u001b[38;5;186msimple_workflow.add_x_and_y_and_z\u001b[0m\u001b[38;5;186m\"\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208m1\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;186m\"\u001b[0m\u001b[38;5;186msimple_workf\u001b[0m\n",
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"\u001b[38;5;238m \u001b[0m \u001b[38;5;238m│\u001b[0m \u001b[38;5;186mlow.add_x_and_y\u001b[0m\u001b[38;5;186m\"\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208m2\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;141m1\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208m3\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;141m2\u001b[0m\u001b[38;5;231m}\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208medges\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;231m[\u001b[0m\u001b[38;5;231m{\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208mtarget\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;141m0\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208mtargetHandl\u001b[0m\n",
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"\u001b[38;5;238m \u001b[0m \u001b[38;5;238m│\u001b[0m \u001b[38;5;208me\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;186m\"\u001b[0m\u001b[38;5;186mx\u001b[0m\u001b[38;5;186m\"\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208msource\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;141m1\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208msourceHandle\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;186m\"\u001b[0m\u001b[38;5;186mx\u001b[0m\u001b[38;5;186m\"\u001b[0m\u001b[38;5;231m}\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;231m{\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208mtarget\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;141m1\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208mtargetHandle\u001b[0m\n",
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"\u001b[38;5;238m \u001b[0m \u001b[38;5;238m│\u001b[0m \u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;186m\"\u001b[0m\u001b[38;5;186mx\u001b[0m\u001b[38;5;186m\"\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208msource\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;141m2\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208msourceHandle\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;141mnull\u001b[0m\u001b[38;5;231m}\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;231m{\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208mtarget\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;141m1\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208mtargetHandle\u001b[0m\n",
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"\u001b[38;5;238m \u001b[0m \u001b[38;5;238m│\u001b[0m \u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;186m\"\u001b[0m\u001b[38;5;186my\u001b[0m\u001b[38;5;186m\"\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208msource\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;141m3\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208msourceHandle\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;141mnull\u001b[0m\u001b[38;5;231m}\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;231m{\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208mtarget\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;141m0\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208mtargetHandle\u001b[0m\n",
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"\u001b[38;5;238m \u001b[0m \u001b[38;5;238m│\u001b[0m \u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;186m\"\u001b[0m\u001b[38;5;186my\u001b[0m\u001b[38;5;186m\"\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208msource\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;141m1\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208msourceHandle\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;186m\"\u001b[0m\u001b[38;5;186my\u001b[0m\u001b[38;5;186m\"\u001b[0m\u001b[38;5;231m}\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;231m{\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208mtarget\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;141m0\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208mtargetHandle\u001b[0m\u001b[38;5;208m\"\u001b[0m\n",
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"\u001b[38;5;238m \u001b[0m \u001b[38;5;238m│\u001b[0m \u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;186m\"\u001b[0m\u001b[38;5;186mz\u001b[0m\u001b[38;5;186m\"\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208msource\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;141m1\u001b[0m\u001b[38;5;231m,\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;208msourceHandle\u001b[0m\u001b[38;5;208m\"\u001b[0m\u001b[38;5;231m:\u001b[0m\u001b[38;5;231m \u001b[0m\u001b[38;5;186m\"\u001b[0m\u001b[38;5;186mz\u001b[0m\u001b[38;5;186m\"\u001b[0m\u001b[38;5;231m}\u001b[0m\u001b[38;5;231m]\u001b[0m\u001b[38;5;231m}\u001b[0m\n",
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"\u001b[38;5;238m───────┴────────────────────────────────────────────────────────────────────────\u001b[0m\n"
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]
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}
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],
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"source": [
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"!cat {workflow_json_filename}"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 13,
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"id": "8f2a621d-b533-4ddd-8bcd-c22db2f922ec",
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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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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "757587875b9b4d64ab8edadd59a31058",
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"version_major": 2,
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"version_minor": 1
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},
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"text/plain": [
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"NodeGraphWidget(settings={'minimap': True}, style={'width': '90%', 'height': '600px'}, value={'name': 'WorkGra…"
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]
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},
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"execution_count": 13,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"wg = load_workflow_json(filename=workflow_json_filename)\n",
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"wg"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "cf80267d-c2b0-4236-bf1d-a57596985fc1",
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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": "stderr",
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"output_type": "stream",
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"text": [
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"03/21/2025 12:36:41 PM <3704092> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [12791|WorkGraphEngine|continue_workgraph]: Continue workgraph.\n",
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"03/21/2025 12:36:41 PM <3704092> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [12791|WorkGraphEngine|continue_workgraph]: tasks ready to run: pickle_node3,pickle_node4\n",
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"03/21/2025 12:36:41 PM <3704092> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [12791|WorkGraphEngine|run_tasks]: Run task: pickle_node3, type: PYTHONJOB\n"
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"03/21/2025 12:36:42 PM <3704092> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [12791|WorkGraphEngine|run_tasks]: Run task: pickle_node4, type: PYTHONJOB\n"
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"text": [
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"03/21/2025 12:36:43 PM <3704092> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [12791|WorkGraphEngine|on_wait]: Process status: Waiting for child processes: 12799, 12807\n",
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"03/21/2025 12:36:46 PM <3704092> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [12791|WorkGraphEngine|update_task_state]: Task: pickle_node3 finished.\n",
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"03/21/2025 12:36:46 PM <3704092> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [12791|WorkGraphEngine|update_task_state]: Task: pickle_node4 finished.\n",
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"03/21/2025 12:36:47 PM <3704092> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [12791|WorkGraphEngine|continue_workgraph]: Continue workgraph.\n",
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"03/21/2025 12:36:47 PM <3704092> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [12791|WorkGraphEngine|continue_workgraph]: tasks ready to run: add_x_and_y2\n",
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"03/21/2025 12:36:47 PM <3704092> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [12791|WorkGraphEngine|run_tasks]: Run task: add_x_and_y2, type: PYTHONJOB\n"
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"text": [
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"kwargs: {'register_pickle_by_value': True, 'x': <Int: uuid: a197c161-4f9c-4b77-840a-78e0f5fda92a (pk: 12814) value: 1>, 'y': <Int: uuid: bbd7b68e-1a28-43e6-aea1-01884c7ac644 (pk: 12815) value: 2>}\n"
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"03/21/2025 12:36:48 PM <3704092> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [12791|WorkGraphEngine|on_wait]: Process status: Waiting for child processes: 12822\n",
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"03/21/2025 12:36:50 PM <3704092> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [12791|WorkGraphEngine|update_task_state]: Task: add_x_and_y2 finished.\n",
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"03/21/2025 12:36:51 PM <3704092> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [12791|WorkGraphEngine|continue_workgraph]: Continue workgraph.\n",
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"03/21/2025 12:36:51 PM <3704092> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [12791|WorkGraphEngine|continue_workgraph]: tasks ready to run: add_x_and_y_and_z1\n",
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"03/21/2025 12:36:51 PM <3704092> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [12791|WorkGraphEngine|run_tasks]: Run task: add_x_and_y_and_z1, type: PYTHONJOB\n"
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"text": [
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"------------------------------------------------------------\n",
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"kwargs: {'register_pickle_by_value': True, 'x': <Int: uuid: 2318418c-c5c0-4b15-81db-13f22402c82d (pk: 12826) value: 1>, 'y': <Int: uuid: 8736ff13-a51f-4e90-9253-54538c58b40a (pk: 12827) value: 2>, 'z': <Int: uuid: a8b70753-79e0-48e6-a39b-b2c6501bac2c (pk: 12828) value: 3>}\n"
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{
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"output_type": "stream",
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"text": [
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"03/21/2025 12:36:51 PM <3704092> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [12791|WorkGraphEngine|on_wait]: Process status: Waiting for child processes: 12835\n"
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}
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],
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"source": [
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"\n",
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"wg.run()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "10c2a6c3",
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"metadata": {},
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"outputs": [],
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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": "ADIS",
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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": "3.10.12"
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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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