mirror of
https://github.com/gsi-upm/soil
synced 2025-08-24 03:52:20 +00:00
v0.20.8 fix bugs
This commit is contained in:
J. Fernando Sánchez
@@ -2,13 +2,12 @@
|
||||
"cells": [
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 4,
|
||||
"execution_count": 1,
|
||||
"metadata": {
|
||||
"ExecuteTime": {
|
||||
"end_time": "2017-11-08T16:22:30.732107Z",
|
||||
"start_time": "2017-11-08T17:22:30.059855+01:00"
|
||||
},
|
||||
"collapsed": true
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
@@ -28,24 +27,16 @@
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 5,
|
||||
"execution_count": 2,
|
||||
"metadata": {
|
||||
"ExecuteTime": {
|
||||
"end_time": "2017-11-08T16:22:35.580593Z",
|
||||
"start_time": "2017-11-08T17:22:35.542745+01:00"
|
||||
}
|
||||
},
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"Populating the interactive namespace from numpy and matplotlib\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"%pylab inline\n",
|
||||
"%matplotlib inline\n",
|
||||
"\n",
|
||||
"from soil import *"
|
||||
]
|
||||
@@ -66,7 +57,7 @@
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 6,
|
||||
"execution_count": 3,
|
||||
"metadata": {
|
||||
"ExecuteTime": {
|
||||
"end_time": "2017-11-08T16:22:37.242327Z",
|
||||
@@ -86,7 +77,7 @@
|
||||
" prob_neighbor_spread: 0.0\r\n",
|
||||
" prob_tv_spread: 0.01\r\n",
|
||||
"interval: 1\r\n",
|
||||
"max_time: 30\r\n",
|
||||
"max_time: 300\r\n",
|
||||
"name: Sim_all_dumb\r\n",
|
||||
"network_agents:\r\n",
|
||||
"- agent_type: DumbViewer\r\n",
|
||||
@@ -110,7 +101,7 @@
|
||||
" prob_neighbor_spread: 0.0\r\n",
|
||||
" prob_tv_spread: 0.01\r\n",
|
||||
"interval: 1\r\n",
|
||||
"max_time: 30\r\n",
|
||||
"max_time: 300\r\n",
|
||||
"name: Sim_half_herd\r\n",
|
||||
"network_agents:\r\n",
|
||||
"- agent_type: DumbViewer\r\n",
|
||||
@@ -142,18 +133,18 @@
|
||||
" prob_neighbor_spread: 0.0\r\n",
|
||||
" prob_tv_spread: 0.01\r\n",
|
||||
"interval: 1\r\n",
|
||||
"max_time: 30\r\n",
|
||||
"max_time: 300\r\n",
|
||||
"name: Sim_all_herd\r\n",
|
||||
"network_agents:\r\n",
|
||||
"- agent_type: HerdViewer\r\n",
|
||||
" state:\r\n",
|
||||
" has_tv: true\r\n",
|
||||
" id: neutral\r\n",
|
||||
" state_id: neutral\r\n",
|
||||
" weight: 1\r\n",
|
||||
"- agent_type: HerdViewer\r\n",
|
||||
" state:\r\n",
|
||||
" has_tv: true\r\n",
|
||||
" id: neutral\r\n",
|
||||
" state_id: neutral\r\n",
|
||||
" weight: 1\r\n",
|
||||
"network_params:\r\n",
|
||||
" generator: barabasi_albert_graph\r\n",
|
||||
@@ -169,13 +160,13 @@
|
||||
" prob_tv_spread: 0.01\r\n",
|
||||
" prob_neighbor_cure: 0.1\r\n",
|
||||
"interval: 1\r\n",
|
||||
"max_time: 30\r\n",
|
||||
"max_time: 300\r\n",
|
||||
"name: Sim_wise_herd\r\n",
|
||||
"network_agents:\r\n",
|
||||
"- agent_type: HerdViewer\r\n",
|
||||
" state:\r\n",
|
||||
" has_tv: true\r\n",
|
||||
" id: neutral\r\n",
|
||||
" state_id: neutral\r\n",
|
||||
" weight: 1\r\n",
|
||||
"- agent_type: WiseViewer\r\n",
|
||||
" state:\r\n",
|
||||
@@ -195,13 +186,13 @@
|
||||
" prob_tv_spread: 0.01\r\n",
|
||||
" prob_neighbor_cure: 0.1\r\n",
|
||||
"interval: 1\r\n",
|
||||
"max_time: 30\r\n",
|
||||
"max_time: 300\r\n",
|
||||
"name: Sim_all_wise\r\n",
|
||||
"network_agents:\r\n",
|
||||
"- agent_type: WiseViewer\r\n",
|
||||
" state:\r\n",
|
||||
" has_tv: true\r\n",
|
||||
" id: neutral\r\n",
|
||||
" state_id: neutral\r\n",
|
||||
" weight: 1\r\n",
|
||||
"- agent_type: WiseViewer\r\n",
|
||||
" state:\r\n",
|
||||
@@ -225,7 +216,7 @@
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 22,
|
||||
"execution_count": 4,
|
||||
"metadata": {
|
||||
"ExecuteTime": {
|
||||
"end_time": "2017-11-08T18:07:46.781745Z",
|
||||
@@ -233,7 +224,24 @@
|
||||
},
|
||||
"scrolled": true
|
||||
},
|
||||
"outputs": [],
|
||||
"outputs": [
|
||||
{
|
||||
"ename": "ValueError",
|
||||
"evalue": "No objects to concatenate",
|
||||
"output_type": "error",
|
||||
"traceback": [
|
||||
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
|
||||
"\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)",
|
||||
"Cell \u001b[0;32mIn[4], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m evodumb \u001b[38;5;241m=\u001b[39m \u001b[43manalysis\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mread_data\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43msoil_output/Sim_all_dumb/\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mprocess\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43manalysis\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_count\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mgroup\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mkeys\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mid\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m)\u001b[49m;\n",
|
||||
"File \u001b[0;32m/mnt/data/home/j/git/lab.gsi/soil/soil/soil/analysis.py:14\u001b[0m, in \u001b[0;36mread_data\u001b[0;34m(group, *args, **kwargs)\u001b[0m\n\u001b[1;32m 12\u001b[0m iterable \u001b[38;5;241m=\u001b[39m _read_data(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 13\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m group:\n\u001b[0;32m---> 14\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mgroup_trials\u001b[49m\u001b[43m(\u001b[49m\u001b[43miterable\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 15\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 16\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mlist\u001b[39m(iterable)\n",
|
||||
"File \u001b[0;32m/mnt/data/home/j/git/lab.gsi/soil/soil/soil/analysis.py:201\u001b[0m, in \u001b[0;36mgroup_trials\u001b[0;34m(trials, aggfunc)\u001b[0m\n\u001b[1;32m 199\u001b[0m trials \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(trials)\n\u001b[1;32m 200\u001b[0m trials \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(\u001b[38;5;28mmap\u001b[39m(\u001b[38;5;28;01mlambda\u001b[39;00m x: x[\u001b[38;5;241m1\u001b[39m] \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(x, \u001b[38;5;28mtuple\u001b[39m) \u001b[38;5;28;01melse\u001b[39;00m x, trials))\n\u001b[0;32m--> 201\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mpd\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mconcat\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtrials\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241m.\u001b[39mgroupby(level\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m)\u001b[38;5;241m.\u001b[39magg(aggfunc)\u001b[38;5;241m.\u001b[39mreorder_levels([\u001b[38;5;241m2\u001b[39m, \u001b[38;5;241m0\u001b[39m,\u001b[38;5;241m1\u001b[39m] ,axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1\u001b[39m)\n",
|
||||
"File \u001b[0;32m/mnt/data/home/j/git/lab.gsi/soil/soil/.env-v0.20/lib/python3.8/site-packages/pandas/util/_decorators.py:331\u001b[0m, in \u001b[0;36mdeprecate_nonkeyword_arguments.<locals>.decorate.<locals>.wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 325\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlen\u001b[39m(args) \u001b[38;5;241m>\u001b[39m num_allow_args:\n\u001b[1;32m 326\u001b[0m warnings\u001b[38;5;241m.\u001b[39mwarn(\n\u001b[1;32m 327\u001b[0m msg\u001b[38;5;241m.\u001b[39mformat(arguments\u001b[38;5;241m=\u001b[39m_format_argument_list(allow_args)),\n\u001b[1;32m 328\u001b[0m \u001b[38;5;167;01mFutureWarning\u001b[39;00m,\n\u001b[1;32m 329\u001b[0m stacklevel\u001b[38;5;241m=\u001b[39mfind_stack_level(),\n\u001b[1;32m 330\u001b[0m )\n\u001b[0;32m--> 331\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n",
|
||||
"File \u001b[0;32m/mnt/data/home/j/git/lab.gsi/soil/soil/.env-v0.20/lib/python3.8/site-packages/pandas/core/reshape/concat.py:368\u001b[0m, in \u001b[0;36mconcat\u001b[0;34m(objs, axis, join, ignore_index, keys, levels, names, verify_integrity, sort, copy)\u001b[0m\n\u001b[1;32m 146\u001b[0m \u001b[38;5;129m@deprecate_nonkeyword_arguments\u001b[39m(version\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m, allowed_args\u001b[38;5;241m=\u001b[39m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mobjs\u001b[39m\u001b[38;5;124m\"\u001b[39m])\n\u001b[1;32m 147\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mconcat\u001b[39m(\n\u001b[1;32m 148\u001b[0m objs: Iterable[NDFrame] \u001b[38;5;241m|\u001b[39m Mapping[HashableT, NDFrame],\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 157\u001b[0m copy: \u001b[38;5;28mbool\u001b[39m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 158\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m DataFrame \u001b[38;5;241m|\u001b[39m Series:\n\u001b[1;32m 159\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 160\u001b[0m \u001b[38;5;124;03m Concatenate pandas objects along a particular axis.\u001b[39;00m\n\u001b[1;32m 161\u001b[0m \n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 366\u001b[0m \u001b[38;5;124;03m 1 3 4\u001b[39;00m\n\u001b[1;32m 367\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[0;32m--> 368\u001b[0m op \u001b[38;5;241m=\u001b[39m \u001b[43m_Concatenator\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 369\u001b[0m \u001b[43m \u001b[49m\u001b[43mobjs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 370\u001b[0m \u001b[43m \u001b[49m\u001b[43maxis\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43maxis\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 371\u001b[0m \u001b[43m \u001b[49m\u001b[43mignore_index\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mignore_index\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 372\u001b[0m \u001b[43m \u001b[49m\u001b[43mjoin\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mjoin\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 373\u001b[0m \u001b[43m \u001b[49m\u001b[43mkeys\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mkeys\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 374\u001b[0m \u001b[43m \u001b[49m\u001b[43mlevels\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mlevels\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 375\u001b[0m \u001b[43m \u001b[49m\u001b[43mnames\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mnames\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 376\u001b[0m \u001b[43m \u001b[49m\u001b[43mverify_integrity\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mverify_integrity\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 377\u001b[0m \u001b[43m \u001b[49m\u001b[43mcopy\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcopy\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 378\u001b[0m \u001b[43m \u001b[49m\u001b[43msort\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msort\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 379\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 381\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m op\u001b[38;5;241m.\u001b[39mget_result()\n",
|
||||
"File \u001b[0;32m/mnt/data/home/j/git/lab.gsi/soil/soil/.env-v0.20/lib/python3.8/site-packages/pandas/core/reshape/concat.py:425\u001b[0m, in \u001b[0;36m_Concatenator.__init__\u001b[0;34m(self, objs, axis, join, keys, levels, names, ignore_index, verify_integrity, copy, sort)\u001b[0m\n\u001b[1;32m 422\u001b[0m objs \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(objs)\n\u001b[1;32m 424\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlen\u001b[39m(objs) \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[0;32m--> 425\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNo objects to concatenate\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 427\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m keys \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 428\u001b[0m objs \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(com\u001b[38;5;241m.\u001b[39mnot_none(\u001b[38;5;241m*\u001b[39mobjs))\n",
|
||||
"\u001b[0;31mValueError\u001b[0m: No objects to concatenate"
|
||||
]
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"evodumb = analysis.read_data('soil_output/Sim_all_dumb/', process=analysis.get_count, group=True, keys=['id']);"
|
||||
]
|
||||
@@ -721,9 +729,9 @@
|
||||
],
|
||||
"metadata": {
|
||||
"kernelspec": {
|
||||
"display_name": "Python 3",
|
||||
"display_name": "venv-soil",
|
||||
"language": "python",
|
||||
"name": "python3"
|
||||
"name": "venv-soil"
|
||||
},
|
||||
"language_info": {
|
||||
"codemirror_mode": {
|
||||
@@ -735,7 +743,7 @@
|
||||
"name": "python",
|
||||
"nbconvert_exporter": "python",
|
||||
"pygments_lexer": "ipython3",
|
||||
"version": "3.6.2"
|
||||
"version": "3.8.10"
|
||||
},
|
||||
"toc": {
|
||||
"colors": {
|
||||
|
||||
Reference in New Issue
Block a user