871 lines
46 KiB
Text
871 lines
46 KiB
Text
{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# SocioPatterns"
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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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"metadata": {
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"autoscroll": false,
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"collapsed": false,
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"ein.tags": "worksheet-0",
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"slideshow": {
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"slide_type": "-"
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}
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},
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"outputs": [],
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"source": [
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"import numpy as np\n",
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"import pandas as pd\n",
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"import matplotlib.pyplot as plt\n",
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"%matplotlib inline"
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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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"metadata": {
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"autoscroll": false,
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"collapsed": false,
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"ein.tags": "worksheet-0",
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"slideshow": {
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"slide_type": "-"
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}
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},
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"outputs": [],
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"source": [
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"import igraph as ig\n",
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"import dionysus as d"
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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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"metadata": {},
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"outputs": [],
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"source": [
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"plt.style.use(\"fivethirtyeight\")\n",
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"plt.rcParams[\"figure.figsize\"] = 10, 6"
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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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"metadata": {},
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"outputs": [],
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"source": [
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"%load_ext autoreload\n",
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"%autoreload 2"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Data import"
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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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"metadata": {},
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"outputs": [],
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"source": [
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"g = ig.read(\"data/sociopatterns/infectious/infectious.graphml\")"
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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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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"'IGRAPH UN-- 10972 415912 -- \\n+ attr: id (v), name (v), id (e), time (e)'"
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]
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},
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"execution_count": 7,
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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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"g.summary()"
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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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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"76944"
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]
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},
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"execution_count": 8,
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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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"len(np.unique(g.es[\"time\"]))"
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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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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"[(12, 11), (10, 9), (0, 2), (3, 4), (5, 8), (6, 7), (1, 2, 8)]"
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]
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},
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"execution_count": 9,
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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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"edges = g.es.select(time_eq=1240916059)\n",
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"g.subgraph_edges(edges).maximal_cliques()"
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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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"metadata": {},
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"outputs": [],
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"source": [
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"cliques = []\n",
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"for t in np.unique(g.es[\"time\"]):\n",
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" edges = g.es.select(time_eq=t)\n",
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" cliques.append(g.subgraph_edges(edges).maximal_cliques())"
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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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"metadata": {},
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"outputs": [],
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"source": [
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"maxcliques = g.maximal_cliques()"
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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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"metadata": {},
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"outputs": [],
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"source": [
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"def filt_subgraph(t):\n",
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" edges = g.es.select(time_eq=t)\n",
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" cliques = g.subgraph_edges(edges).maximal_cliques()\n",
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" return d.Filtration(cliques)"
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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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"metadata": {},
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"outputs": [],
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"source": [
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"times = np.sort(np.unique(g.es[\"time\"]))"
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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": 27,
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"metadata": {},
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"outputs": [],
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"source": [
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"import multiprocessing"
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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": 29,
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"metadata": {},
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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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"Process ForkPoolWorker-73:\n",
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"Process ForkPoolWorker-89:\n",
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"Process ForkPoolWorker-90:\n",
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"Process ForkPoolWorker-72:\n",
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"Process ForkPoolWorker-78:\n",
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"Process ForkPoolWorker-79:\n",
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"Process ForkPoolWorker-67:\n",
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"Process ForkPoolWorker-76:\n",
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"Process ForkPoolWorker-81:\n",
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"Process ForkPoolWorker-70:\n",
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"Process ForkPoolWorker-95:\n",
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"Process ForkPoolWorker-68:\n",
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"Process ForkPoolWorker-71:\n",
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"Process ForkPoolWorker-94:\n",
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" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
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" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
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"Process ForkPoolWorker-66:\n",
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"Process ForkPoolWorker-91:\n",
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"Process ForkPoolWorker-65:\n",
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"Process ForkPoolWorker-75:\n",
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"Process ForkPoolWorker-74:\n",
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"Process ForkPoolWorker-96:\n",
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"Traceback (most recent call last):\n",
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"Traceback (most recent call last):\n",
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"Traceback (most recent call last):\n",
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"Traceback (most recent call last):\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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"Traceback (most recent call last):\n",
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"Traceback (most recent call last):\n",
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"Traceback (most recent call last):\n",
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"Traceback (most recent call last):\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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"Traceback (most recent call last):\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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"Process ForkPoolWorker-80:\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
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" self._target(*self._args, **self._kwargs)\n",
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"Traceback (most recent call last):\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
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" self._target(*self._args, **self._kwargs)\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
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" self._target(*self._args, **self._kwargs)\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
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" result = (True, func(*args, **kwds))\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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"Traceback (most recent call last):\n",
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"Traceback (most recent call last):\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
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" self._target(*self._args, **self._kwargs)\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
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" return list(map(*args))\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
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" self._target(*self._args, **self._kwargs)\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
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" result = (True, func(*args, **kwds))\n",
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"Traceback (most recent call last):\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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"Process ForkPoolWorker-92:\n",
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"Traceback (most recent call last):\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
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" result = (True, func(*args, **kwds))\n",
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"Traceback (most recent call last):\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
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" self._target(*self._args, **self._kwargs)\n",
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"Traceback (most recent call last):\n",
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" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3849, in select\n",
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" es = es.select(filtered_idxs)\n",
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"Traceback (most recent call last):\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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"Traceback (most recent call last):\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
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" return list(map(*args))\n",
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"Traceback (most recent call last):\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
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" result = (True, func(*args, **kwds))\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
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" self._target(*self._args, **self._kwargs)\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
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" self._target(*self._args, **self._kwargs)\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
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" result = (True, func(*args, **kwds))\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
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" self._target(*self._args, **self._kwargs)\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
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" result = (True, func(*args, **kwds))\n",
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"Traceback (most recent call last):\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
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" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
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"Traceback (most recent call last):\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
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" return list(map(*args))\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3753, in select\n",
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" es = _igraph.EdgeSeq.select(self, *args)\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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"Traceback (most recent call last):\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
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" self._target(*self._args, **self._kwargs)\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
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" self._target(*self._args, **self._kwargs)\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
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" result = (True, func(*args, **kwds))\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
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" self._target(*self._args, **self._kwargs)\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
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" self._target(*self._args, **self._kwargs)\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
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" filtered_idxs=[i for i, v in enumerate(values) \\\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
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" result = (True, func(*args, **kwds))\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
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" return list(map(*args))\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
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" self._target(*self._args, **self._kwargs)\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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"Process ForkPoolWorker-88:\n",
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"KeyboardInterrupt\n",
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" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
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" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
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" result = (True, func(*args, **kwds))\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
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" self._target(*self._args, **self._kwargs)\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
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" self._target(*self._args, **self._kwargs)\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
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" result = (True, func(*args, **kwds))\n",
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" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
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" if func(v, value)]\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
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" return list(map(*args))\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
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" return list(map(*args))\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
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" return list(map(*args))\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
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" self._target(*self._args, **self._kwargs)\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
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" result = (True, func(*args, **kwds))\n",
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" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
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" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
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" return list(map(*args))\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
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" self._target(*self._args, **self._kwargs)\n",
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"Process ForkPoolWorker-93:\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
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" self._target(*self._args, **self._kwargs)\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
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" result = (True, func(*args, **kwds))\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
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" self.run()\n",
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" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
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" self._target(*self._args, **self._kwargs)\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
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" result = (True, func(*args, **kwds))\n",
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"KeyboardInterrupt\n",
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"Traceback (most recent call last):\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
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" result = (True, func(*args, **kwds))\n",
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" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
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|
" return list(map(*args))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
|
|
" result = (True, func(*args, **kwds))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
|
|
" self._target(*self._args, **self._kwargs)\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
|
|
" result = (True, func(*args, **kwds))\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
|
|
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
|
|
" result = (True, func(*args, **kwds))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
|
|
" self.run()\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
|
|
" result = (True, func(*args, **kwds))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
|
|
" result = (True, func(*args, **kwds))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3849, in select\n",
|
|
" es = es.select(filtered_idxs)\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
|
|
" result = (True, func(*args, **kwds))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
|
|
" result = (True, func(*args, **kwds))\n",
|
|
"Traceback (most recent call last):\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
|
|
" self._target(*self._args, **self._kwargs)\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
|
|
" self._target(*self._args, **self._kwargs)\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
|
|
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
|
|
" result = (True, func(*args, **kwds))\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3849, in select\n",
|
|
" es = es.select(filtered_idxs)\n"
|
|
]
|
|
},
|
|
{
|
|
"ename": "KeyboardInterrupt",
|
|
"evalue": "",
|
|
"output_type": "error",
|
|
"traceback": [
|
|
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
|
|
"\u001b[0;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)",
|
|
"\u001b[0;32m<ipython-input-29-64fed6fd3c57>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0mpool\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmultiprocessing\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mPool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mprocesses\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmultiprocessing\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcpu_count\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mcliques\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpool\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmap\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mclique_subgraph\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtimes\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
|
|
"\u001b[0;32m/usr/lib/python3.5/multiprocessing/pool.py\u001b[0m in \u001b[0;36mmap\u001b[0;34m(self, func, iterable, chunksize)\u001b[0m\n\u001b[1;32m 258\u001b[0m \u001b[0;32min\u001b[0m \u001b[0ma\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mthat\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0mreturned\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 259\u001b[0m '''\n\u001b[0;32m--> 260\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_map_async\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfunc\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0miterable\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmapstar\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mchunksize\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 261\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 262\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mstarmap\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0miterable\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mchunksize\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
|
|
"\u001b[0;32m/usr/lib/python3.5/multiprocessing/pool.py\u001b[0m in \u001b[0;36mget\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 600\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 601\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtimeout\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 602\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwait\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtimeout\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 603\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mready\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 604\u001b[0m \u001b[0;32mraise\u001b[0m \u001b[0mTimeoutError\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
|
|
"\u001b[0;32m/usr/lib/python3.5/multiprocessing/pool.py\u001b[0m in \u001b[0;36mwait\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 597\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 598\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mwait\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtimeout\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 599\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_event\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwait\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtimeout\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 600\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 601\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtimeout\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
|
|
"\u001b[0;32m/usr/lib/python3.5/threading.py\u001b[0m in \u001b[0;36mwait\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 547\u001b[0m \u001b[0msignaled\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_flag\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 548\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0msignaled\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 549\u001b[0;31m \u001b[0msignaled\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_cond\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwait\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtimeout\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 550\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0msignaled\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 551\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
|
|
"\u001b[0;32m/usr/lib/python3.5/threading.py\u001b[0m in \u001b[0;36mwait\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 291\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;31m# restore state no matter what (e.g., KeyboardInterrupt)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 292\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mtimeout\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 293\u001b[0;31m \u001b[0mwaiter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0macquire\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 294\u001b[0m \u001b[0mgotit\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 295\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
|
|
"\u001b[0;31mKeyboardInterrupt\u001b[0m: "
|
|
]
|
|
},
|
|
{
|
|
"name": "stderr",
|
|
"output_type": "stream",
|
|
"text": [
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
|
|
" self.run()\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
"Process ForkPoolWorker-77:\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in <listcomp>\n",
|
|
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
|
|
" if func(v, value)]\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3753, in select\n",
|
|
" es = _igraph.EdgeSeq.select(self, *args)\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
|
|
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
|
|
" self._target(*self._args, **self._kwargs)\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3753, in select\n",
|
|
" es = _igraph.EdgeSeq.select(self, *args)\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
|
|
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
|
|
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
"Traceback (most recent call last):\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
|
|
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
|
|
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3841, in select\n",
|
|
" values = es[attr]\n",
|
|
"Process ForkPoolWorker-84:\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
|
|
" result = (True, func(*args, **kwds))\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
|
|
" result = (True, func(*args, **kwds))\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
|
|
" if func(v, value)]\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
|
|
" if func(v, value)]\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
|
|
" if func(v, value)]\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
|
|
" self.run()\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
|
|
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
|
|
" if func(v, value)]\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in <listcomp>\n",
|
|
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
|
|
"KeyboardInterrupt\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
|
|
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
|
|
"Traceback (most recent call last):\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
|
|
" self._target(*self._args, **self._kwargs)\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
"Process ForkPoolWorker-69:\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
"Process ForkPoolWorker-86:\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
|
|
" result = (True, func(*args, **kwds))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
|
|
" self.run()\n",
|
|
"KeyboardInterrupt\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3841, in select\n",
|
|
" values = es[attr]\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
|
|
" if func(v, value)]\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
|
|
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
|
|
" if func(v, value)]\n",
|
|
"Process ForkPoolWorker-85:\n",
|
|
"Process ForkPoolWorker-82:\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
"Process ForkPoolWorker-83:\n",
|
|
"Traceback (most recent call last):\n",
|
|
"Traceback (most recent call last):\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
|
|
" self._target(*self._args, **self._kwargs)\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
|
|
" if func(v, value)]\n",
|
|
"KeyboardInterrupt\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
|
|
" self.run()\n",
|
|
"Traceback (most recent call last):\n",
|
|
"Traceback (most recent call last):\n",
|
|
"KeyboardInterrupt\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
|
|
" result = (True, func(*args, **kwds))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
|
|
" self.run()\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
|
|
" self._target(*self._args, **self._kwargs)\n",
|
|
"Process ForkPoolWorker-87:\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
|
|
" self.run()\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
|
|
" self.run()\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
|
|
" self._target(*self._args, **self._kwargs)\n",
|
|
"Traceback (most recent call last):\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
|
|
" self._target(*self._args, **self._kwargs)\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
|
|
" result = (True, func(*args, **kwds))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
|
|
" result = (True, func(*args, **kwds))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
|
|
" self.run()\n",
|
|
"Traceback (most recent call last):\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
|
|
" self.run()\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
|
|
" result = (True, func(*args, **kwds))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
|
|
" self._target(*self._args, **self._kwargs)\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
|
|
" self._target(*self._args, **self._kwargs)\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
|
|
" self._target(*self._args, **self._kwargs)\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
|
|
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
|
|
" result = (True, func(*args, **kwds))\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
|
|
" result = (True, func(*args, **kwds))\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
|
|
" result = (True, func(*args, **kwds))\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in <listcomp>\n",
|
|
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
|
|
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
|
|
" return list(map(*args))\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
|
|
" if func(v, value)]\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
|
|
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
|
|
"KeyboardInterrupt\n",
|
|
"KeyboardInterrupt\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
|
|
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
|
|
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
|
|
" if func(v, value)]\n",
|
|
"KeyboardInterrupt\n"
|
|
]
|
|
}
|
|
],
|
|
"source": [
|
|
"pool = multiprocessing.Pool(processes=multiprocessing.cpu_count())\n",
|
|
"cliques = pool.map(clique_subgraph, times)"
|
|
]
|
|
},
|
|
{
|
|
"cell_type": "code",
|
|
"execution_count": 32,
|
|
"metadata": {},
|
|
"outputs": [],
|
|
"source": [
|
|
"pool.terminate()"
|
|
]
|
|
},
|
|
{
|
|
"cell_type": "code",
|
|
"execution_count": 13,
|
|
"metadata": {},
|
|
"outputs": [],
|
|
"source": [
|
|
"maxcliques = g.subgraph_edges(g.es.select(time_lt=times[30])).maximal_cliques()\n",
|
|
"filts = [filt_subgraph(t) for t in times[1:30]]"
|
|
]
|
|
},
|
|
{
|
|
"cell_type": "code",
|
|
"execution_count": 14,
|
|
"metadata": {},
|
|
"outputs": [
|
|
{
|
|
"name": "stdout",
|
|
"output_type": "stream",
|
|
"text": [
|
|
"<3,4,11> 0\n",
|
|
"<7,9,10> 0\n",
|
|
"<7,8,10> 0\n",
|
|
"<5,6,7,8> 0\n",
|
|
"<4,8> 0\n",
|
|
"<3,5> 0\n",
|
|
"<0,1,2> 0\n"
|
|
]
|
|
}
|
|
],
|
|
"source": [
|
|
"maxfilt = d.Filtration(maxcliques)\n",
|
|
"for s in maxfilt:\n",
|
|
" print(s)"
|
|
]
|
|
},
|
|
{
|
|
"cell_type": "code",
|
|
"execution_count": 15,
|
|
"metadata": {},
|
|
"outputs": [],
|
|
"source": [
|
|
"presences = [[s in filt for filt in filts] for s in maxfilt]"
|
|
]
|
|
},
|
|
{
|
|
"cell_type": "code",
|
|
"execution_count": 16,
|
|
"metadata": {},
|
|
"outputs": [
|
|
{
|
|
"data": {
|
|
"text/plain": [
|
|
"[False,\n",
|
|
" False,\n",
|
|
" False,\n",
|
|
" True,\n",
|
|
" False,\n",
|
|
" False,\n",
|
|
" True,\n",
|
|
" False,\n",
|
|
" False,\n",
|
|
" False,\n",
|
|
" True,\n",
|
|
" False,\n",
|
|
" False,\n",
|
|
" False,\n",
|
|
" False,\n",
|
|
" False,\n",
|
|
" False,\n",
|
|
" False,\n",
|
|
" True,\n",
|
|
" False,\n",
|
|
" True,\n",
|
|
" False,\n",
|
|
" False,\n",
|
|
" False,\n",
|
|
" False,\n",
|
|
" False,\n",
|
|
" False,\n",
|
|
" False,\n",
|
|
" False]"
|
|
]
|
|
},
|
|
"execution_count": 16,
|
|
"metadata": {},
|
|
"output_type": "execute_result"
|
|
}
|
|
],
|
|
"source": [
|
|
"presences[-1]"
|
|
]
|
|
},
|
|
{
|
|
"cell_type": "code",
|
|
"execution_count": 18,
|
|
"metadata": {},
|
|
"outputs": [
|
|
{
|
|
"data": {
|
|
"text/plain": [
|
|
"[[], [], [], [], [], [], [2, 3, 5, 6, 9, 10, 17, 18, 19, 20]]"
|
|
]
|
|
},
|
|
"execution_count": 18,
|
|
"metadata": {},
|
|
"output_type": "execute_result"
|
|
}
|
|
],
|
|
"source": [
|
|
"[np.argwhere(np.array(p)[1:] ^ np.array(p)[:-1]).flatten().tolist() for p in presences]"
|
|
]
|
|
},
|
|
{
|
|
"cell_type": "code",
|
|
"execution_count": null,
|
|
"metadata": {},
|
|
"outputs": [],
|
|
"source": []
|
|
}
|
|
],
|
|
"metadata": {
|
|
"kernelspec": {
|
|
"display_name": "Python 3",
|
|
"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": "3.5.2"
|
|
}
|
|
},
|
|
"nbformat": 4,
|
|
"nbformat_minor": 2
|
|
}
|