diff --git a/docs/Basic Usage.ipynb b/docs/Basic Usage.ipynb index 055a039..e4ac131 100644 --- a/docs/Basic Usage.ipynb +++ b/docs/Basic Usage.ipynb @@ -14,28 +14,16 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 3, "metadata": {}, - "outputs": [ - { - "ename": "ImportError", - "evalue": "cannot import name 'BMSRegressor' from 'autora.theorist.bms' (C:\\Users\\cwill\\GitHub\\autora\\autora\\theorist\\bms\\__init__.py)", - "output_type": "error", - "traceback": [ - "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[1;31mImportError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[1;32mIn[1], line 3\u001b[0m\n\u001b[0;32m 1\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mnumpy\u001b[39;00m \u001b[39mas\u001b[39;00m \u001b[39mnp\u001b[39;00m\n\u001b[0;32m 2\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mmatplotlib\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mpyplot\u001b[39;00m \u001b[39mas\u001b[39;00m \u001b[39mplt\u001b[39;00m\n\u001b[1;32m----> 3\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39mautora\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mtheorist\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mbms\u001b[39;00m \u001b[39mimport\u001b[39;00m BMSRegressor; BMSRegressor()\n\u001b[0;32m 4\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39mautora\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mtheorist\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mbsr\u001b[39;00m \u001b[39mimport\u001b[39;00m BSRRegressor; BSRRegressor()\n\u001b[0;32m 5\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39mautora\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mtheorist\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mdarts\u001b[39;00m \u001b[39mimport\u001b[39;00m DARTSRegressor; DARTSRegressor()\n", - "\u001b[1;31mImportError\u001b[0m: cannot import name 'BMSRegressor' from 'autora.theorist.bms' (C:\\Users\\cwill\\GitHub\\autora\\autora\\theorist\\bms\\__init__.py)" - ] - } - ], + "outputs": [], "source": [ "import numpy as np\n", "import matplotlib.pyplot as plt\n", "from autora.theorist.bms import BMSRegressor; BMSRegressor()\n", "from autora.theorist.bsr import BSRRegressor; BSRRegressor()\n", "from autora.theorist.darts import DARTSRegressor; DARTSRegressor()\n", - "from autora.experimentalist.sampler.model_disagreement_sampler import model_disagreement_sampler" + "from autora.experimentalist.sampler.model_disagreement import model_disagreement_sampler" ] }, { @@ -54,7 +42,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 4, "metadata": {}, "outputs": [], "source": [ @@ -80,7 +68,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 5, "metadata": {}, "outputs": [ { @@ -113,17 +101,36 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "INFO:autora.skl.bms:BMS fitting started\n", - "INFO:autora.skl.bms:BMS fitting finished\n", - "INFO:autora.skl.darts:Starting fit initialization\n", - "INFO:autora.skl.darts:Starting fit.\n" + "INFO:autora.theorist.bms.regressor:BMS fitting started\n" + ] + }, + { + "ename": "KeyboardInterrupt", + "evalue": "", + "output_type": "error", + "traceback": [ + "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[1;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)", + "Cell \u001b[1;32mIn[6], line 7\u001b[0m\n\u001b[0;32m 4\u001b[0m darts_theorist \u001b[39m=\u001b[39m DARTSRegressor()\n\u001b[0;32m 6\u001b[0m \u001b[39m#Fit theorists\u001b[39;00m\n\u001b[1;32m----> 7\u001b[0m bms_theorist\u001b[39m.\u001b[39;49mfit(X,ground_truth(X))\n\u001b[0;32m 8\u001b[0m bsr_theorist\u001b[39m.\u001b[39mfit(X,ground_truth(X))\n\u001b[0;32m 9\u001b[0m darts_theorist\u001b[39m.\u001b[39mfit(X,ground_truth(X))\n", + "File \u001b[1;32mc:\\Users\\cwill\\GitHub\\virtualEnvs\\autoraEnv\\lib\\site-packages\\autora\\theorist\\bms\\regressor.py:133\u001b[0m, in \u001b[0;36mBMSRegressor.fit\u001b[1;34m(self, X, y, num_param, root, custom_ops, seed)\u001b[0m\n\u001b[0;32m 120\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39madd_primitive(root)\n\u001b[0;32m 121\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mpms \u001b[39m=\u001b[39m Parallel(\n\u001b[0;32m 122\u001b[0m Ts\u001b[39m=\u001b[39m\u001b[39mself\u001b[39m\u001b[39m.\u001b[39mts,\n\u001b[0;32m 123\u001b[0m variables\u001b[39m=\u001b[39m\u001b[39mself\u001b[39m\u001b[39m.\u001b[39mvariables,\n\u001b[1;32m (...)\u001b[0m\n\u001b[0;32m 131\u001b[0m seed\u001b[39m=\u001b[39mseed,\n\u001b[0;32m 132\u001b[0m )\n\u001b[1;32m--> 133\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mmodel_, \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mloss_, \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mcache_ \u001b[39m=\u001b[39m utils\u001b[39m.\u001b[39;49mrun(\u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mpms, \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mepochs)\n\u001b[0;32m 134\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mmodels_ \u001b[39m=\u001b[39m \u001b[39mlist\u001b[39m(\u001b[39mself\u001b[39m\u001b[39m.\u001b[39mpms\u001b[39m.\u001b[39mtrees\u001b[39m.\u001b[39mvalues())\n\u001b[0;32m 136\u001b[0m _logger\u001b[39m.\u001b[39minfo(\u001b[39m\"\u001b[39m\u001b[39mBMS fitting finished\u001b[39m\u001b[39m\"\u001b[39m)\n", + "File \u001b[1;32mc:\\Users\\cwill\\GitHub\\virtualEnvs\\autoraEnv\\lib\\site-packages\\autora\\theorist\\bms\\utils.py:35\u001b[0m, in \u001b[0;36mrun\u001b[1;34m(pms, num_steps, thinning)\u001b[0m\n\u001b[0;32m 33\u001b[0m desc_len, model, model_len \u001b[39m=\u001b[39m [], pms\u001b[39m.\u001b[39mt1, np\u001b[39m.\u001b[39minf\n\u001b[0;32m 34\u001b[0m \u001b[39mfor\u001b[39;00m n \u001b[39min\u001b[39;00m tqdm(\u001b[39mrange\u001b[39m(num_steps)):\n\u001b[1;32m---> 35\u001b[0m pms\u001b[39m.\u001b[39;49mmcmc_step()\n\u001b[0;32m 36\u001b[0m pms\u001b[39m.\u001b[39mtree_swap()\n\u001b[0;32m 37\u001b[0m \u001b[39mif\u001b[39;00m num_steps \u001b[39m%\u001b[39m thinning \u001b[39m==\u001b[39m \u001b[39m0\u001b[39m: \u001b[39m# sample less often if we thin more\u001b[39;00m\n", + "File \u001b[1;32mc:\\Users\\cwill\\GitHub\\virtualEnvs\\autoraEnv\\lib\\site-packages\\autora\\theorist\\bms\\parallel.py:102\u001b[0m, in \u001b[0;36mParallel.mcmc_step\u001b[1;34m(self, verbose, p_rr, p_long)\u001b[0m\n\u001b[0;32m 99\u001b[0m p_rr \u001b[39m=\u001b[39m \u001b[39m0.0\u001b[39m\n\u001b[0;32m 100\u001b[0m \u001b[39mfor\u001b[39;00m T, tree \u001b[39min\u001b[39;00m \u001b[39mlist\u001b[39m(\u001b[39mself\u001b[39m\u001b[39m.\u001b[39mtrees\u001b[39m.\u001b[39mitems()):\n\u001b[0;32m 101\u001b[0m \u001b[39m# MCMC step\u001b[39;00m\n\u001b[1;32m--> 102\u001b[0m tree\u001b[39m.\u001b[39;49mmcmc_step(verbose\u001b[39m=\u001b[39;49mverbose, p_rr\u001b[39m=\u001b[39;49mp_rr, p_long\u001b[39m=\u001b[39;49mp_long)\n\u001b[0;32m 103\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mt1 \u001b[39m=\u001b[39m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mtrees[\u001b[39m\"\u001b[39m\u001b[39m1.0\u001b[39m\u001b[39m\"\u001b[39m]\n", + "File \u001b[1;32mc:\\Users\\cwill\\GitHub\\virtualEnvs\\autoraEnv\\lib\\site-packages\\autora\\theorist\\bms\\mcmc.py:1251\u001b[0m, in \u001b[0;36mTree.mcmc_step\u001b[1;34m(self, verbose, p_rr, p_long)\u001b[0m\n\u001b[0;32m 1249\u001b[0m sf \u001b[39m=\u001b[39m \u001b[39mlen\u001b[39m(\u001b[39mself\u001b[39m\u001b[39m.\u001b[39met_space[ofin])\n\u001b[0;32m 1250\u001b[0m \u001b[39m# Probability of acceptance\u001b[39;00m\n\u001b[1;32m-> 1251\u001b[0m dE, dEB, dEP, par_valuesNew, nif, nfi \u001b[39m=\u001b[39m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mdE_et(\n\u001b[0;32m 1252\u001b[0m target, new, verbose\u001b[39m=\u001b[39;49mverbose\n\u001b[0;32m 1253\u001b[0m )\n\u001b[0;32m 1254\u001b[0m \u001b[39mtry\u001b[39;00m:\n\u001b[0;32m 1255\u001b[0m paccept \u001b[39m=\u001b[39m (\n\u001b[0;32m 1256\u001b[0m \u001b[39mfloat\u001b[39m(nif) \u001b[39m*\u001b[39m omegai \u001b[39m*\u001b[39m sf \u001b[39m*\u001b[39m np\u001b[39m.\u001b[39mexp(\u001b[39m-\u001b[39mdEB \u001b[39m/\u001b[39m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mBT \u001b[39m-\u001b[39m dEP \u001b[39m/\u001b[39m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mPT)\n\u001b[0;32m 1257\u001b[0m ) \u001b[39m/\u001b[39m (\u001b[39mfloat\u001b[39m(nfi) \u001b[39m*\u001b[39m omegaf \u001b[39m*\u001b[39m si)\n", + "File \u001b[1;32mc:\\Users\\cwill\\GitHub\\virtualEnvs\\autoraEnv\\lib\\site-packages\\autora\\theorist\\bms\\mcmc.py:886\u001b[0m, in \u001b[0;36mTree.dE_et\u001b[1;34m(self, target, new, verbose)\u001b[0m\n\u001b[0;32m 884\u001b[0m old \u001b[39m=\u001b[39m [target\u001b[39m.\u001b[39mvalue, [o\u001b[39m.\u001b[39mvalue \u001b[39mfor\u001b[39;00m o \u001b[39min\u001b[39;00m target\u001b[39m.\u001b[39moffspring]]\n\u001b[0;32m 885\u001b[0m \u001b[39m# replace\u001b[39;00m\n\u001b[1;32m--> 886\u001b[0m added \u001b[39m=\u001b[39m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49met_replace(target, new, update_gof\u001b[39m=\u001b[39;49m\u001b[39mTrue\u001b[39;49;00m, verbose\u001b[39m=\u001b[39;49mverbose)\n\u001b[0;32m 887\u001b[0m bicNew \u001b[39m=\u001b[39m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mbic\n\u001b[0;32m 888\u001b[0m par_valuesNew \u001b[39m=\u001b[39m deepcopy(\u001b[39mself\u001b[39m\u001b[39m.\u001b[39mpar_values)\n", + "File \u001b[1;32mc:\\Users\\cwill\\GitHub\\virtualEnvs\\autoraEnv\\lib\\site-packages\\autora\\theorist\\bms\\mcmc.py:596\u001b[0m, in \u001b[0;36mTree.et_replace\u001b[1;34m(self, target, new, update_gof, verbose)\u001b[0m\n\u001b[0;32m 594\u001b[0m \u001b[39mif\u001b[39;00m update_gof:\n\u001b[0;32m 595\u001b[0m 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\u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mget_sse(fit\u001b[39m=\u001b[39;49mfit, verbose\u001b[39m=\u001b[39;49mverbose)\n\u001b[0;32m 723\u001b[0m \u001b[39m# Calculate the BIC\u001b[39;00m\n\u001b[0;32m 724\u001b[0m parameters \u001b[39m=\u001b[39m \u001b[39mset\u001b[39m([p\u001b[39m.\u001b[39mvalue \u001b[39mfor\u001b[39;00m p \u001b[39min\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mets[\u001b[39m0\u001b[39m] \u001b[39mif\u001b[39;00m p\u001b[39m.\u001b[39mvalue \u001b[39min\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mparameters])\n", + "File \u001b[1;32mc:\\Users\\cwill\\GitHub\\virtualEnvs\\autoraEnv\\lib\\site-packages\\autora\\theorist\\bms\\mcmc.py:628\u001b[0m, in \u001b[0;36mTree.get_sse\u001b[1;34m(self, fit, verbose)\u001b[0m\n\u001b[0;32m 619\u001b[0m dic: \u001b[39mdict\u001b[39m \u001b[39m=\u001b[39m \u001b[39mdict\u001b[39m(\n\u001b[0;32m 620\u001b[0m {\n\u001b[0;32m 621\u001b[0m \u001b[39m\"\u001b[39m\u001b[39mfac\u001b[39m\u001b[39m\"\u001b[39m: scipy\u001b[39m.\u001b[39mspecial\u001b[39m.\u001b[39mfactorial,\n\u001b[1;32m (...)\u001b[0m\n\u001b[0;32m 625\u001b[0m \u001b[39m*\u001b[39m\u001b[39m*\u001b[39m\u001b[39mself\u001b[39m\u001b[39m.\u001b[39mcustom_ops\n\u001b[0;32m 626\u001b[0m )\n\u001b[0;32m 627\u001b[0m \u001b[39mtry\u001b[39;00m:\n\u001b[1;32m--> 628\u001b[0m flam \u001b[39m=\u001b[39m lambdify(\n\u001b[0;32m 629\u001b[0m variables \u001b[39m+\u001b[39;49m parameters,\n\u001b[0;32m 630\u001b[0m ex,\n\u001b[0;32m 631\u001b[0m [\n\u001b[0;32m 632\u001b[0m \u001b[39m\"\u001b[39;49m\u001b[39mnumpy\u001b[39;49m\u001b[39m\"\u001b[39;49m,\n\u001b[0;32m 633\u001b[0m dic,\n\u001b[0;32m 634\u001b[0m ],\n\u001b[0;32m 635\u001b[0m )\n\u001b[0;32m 636\u001b[0m \u001b[39mexcept\u001b[39;00m (\u001b[39mSyntaxError\u001b[39;00m, \u001b[39mKeyError\u001b[39;00m):\n\u001b[0;32m 637\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39msse \u001b[39m=\u001b[39m \u001b[39mdict\u001b[39m([(ds, np\u001b[39m.\u001b[39minf) \u001b[39mfor\u001b[39;00m ds \u001b[39min\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mx])\n", + "File \u001b[1;32mc:\\Users\\cwill\\GitHub\\virtualEnvs\\autoraEnv\\lib\\site-packages\\sympy\\utilities\\lambdify.py:830\u001b[0m, in \u001b[0;36mlambdify\u001b[1;34m(args, expr, modules, printer, use_imps, dummify, cse, docstring_limit)\u001b[0m\n\u001b[0;32m 828\u001b[0m \u001b[39mfor\u001b[39;00m k \u001b[39min\u001b[39;00m m:\n\u001b[0;32m 829\u001b[0m user_functions[k] \u001b[39m=\u001b[39m k\n\u001b[1;32m--> 830\u001b[0m printer \u001b[39m=\u001b[39m Printer({\u001b[39m'\u001b[39;49m\u001b[39mfully_qualified_modules\u001b[39;49m\u001b[39m'\u001b[39;49m: \u001b[39mFalse\u001b[39;49;00m, \u001b[39m'\u001b[39;49m\u001b[39minline\u001b[39;49m\u001b[39m'\u001b[39;49m: \u001b[39mTrue\u001b[39;49;00m,\n\u001b[0;32m 831\u001b[0m \u001b[39m'\u001b[39;49m\u001b[39mallow_unknown_functions\u001b[39;49m\u001b[39m'\u001b[39;49m: \u001b[39mTrue\u001b[39;49;00m,\n\u001b[0;32m 832\u001b[0m \u001b[39m'\u001b[39;49m\u001b[39muser_functions\u001b[39;49m\u001b[39m'\u001b[39;49m: user_functions})\n\u001b[0;32m 834\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39misinstance\u001b[39m(args, \u001b[39mset\u001b[39m):\n\u001b[0;32m 835\u001b[0m sympy_deprecation_warning(\n\u001b[0;32m 836\u001b[0m \u001b[39m \u001b[39m\u001b[39m\"\"\"\u001b[39;00m\n\u001b[0;32m 837\u001b[0m \u001b[39mPassing the function arguments to lambdify() as a set is deprecated. This\u001b[39;00m\n\u001b[1;32m (...)\u001b[0m\n\u001b[0;32m 842\u001b[0m active_deprecations_target\u001b[39m=\u001b[39m\u001b[39m\"\u001b[39m\u001b[39mdeprecated-lambdify-arguments-set\u001b[39m\u001b[39m\"\u001b[39m,\n\u001b[0;32m 843\u001b[0m )\n", + "File \u001b[1;32mc:\\Users\\cwill\\GitHub\\virtualEnvs\\autoraEnv\\lib\\site-packages\\sympy\\printing\\numpy.py:56\u001b[0m, in \u001b[0;36mNumPyPrinter.__init__\u001b[1;34m(self, settings)\u001b[0m\n\u001b[0;32m 52\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mprintmethod \u001b[39m=\u001b[39m \u001b[39m\"\u001b[39m\u001b[39m_\u001b[39m\u001b[39m{}\u001b[39;00m\u001b[39mcode\u001b[39m\u001b[39m\"\u001b[39m\u001b[39m.\u001b[39mformat(\u001b[39mself\u001b[39m\u001b[39m.\u001b[39m_module)\n\u001b[0;32m 54\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m_kf \u001b[39m=\u001b[39m {\u001b[39m*\u001b[39m\u001b[39m*\u001b[39mPythonCodePrinter\u001b[39m.\u001b[39m_kf, \u001b[39m*\u001b[39m\u001b[39m*\u001b[39m\u001b[39mself\u001b[39m\u001b[39m.\u001b[39m_kf}\n\u001b[1;32m---> 56\u001b[0m \u001b[39msuper\u001b[39;49m()\u001b[39m.\u001b[39;49m\u001b[39m__init__\u001b[39;49m(settings\u001b[39m=\u001b[39;49msettings)\n", + "File \u001b[1;32mc:\\Users\\cwill\\GitHub\\virtualEnvs\\autoraEnv\\lib\\site-packages\\sympy\\printing\\pycode.py:99\u001b[0m, in \u001b[0;36mAbstractPythonCodePrinter.__init__\u001b[1;34m(self, settings)\u001b[0m\n\u001b[0;32m 88\u001b[0m _operators \u001b[39m=\u001b[39m {\u001b[39m'\u001b[39m\u001b[39mand\u001b[39m\u001b[39m'\u001b[39m: \u001b[39m'\u001b[39m\u001b[39mand\u001b[39m\u001b[39m'\u001b[39m, \u001b[39m'\u001b[39m\u001b[39mor\u001b[39m\u001b[39m'\u001b[39m: \u001b[39m'\u001b[39m\u001b[39mor\u001b[39m\u001b[39m'\u001b[39m, \u001b[39m'\u001b[39m\u001b[39mnot\u001b[39m\u001b[39m'\u001b[39m: \u001b[39m'\u001b[39m\u001b[39mnot\u001b[39m\u001b[39m'\u001b[39m}\n\u001b[0;32m 89\u001b[0m _default_settings \u001b[39m=\u001b[39m \u001b[39mdict\u001b[39m(\n\u001b[0;32m 90\u001b[0m CodePrinter\u001b[39m.\u001b[39m_default_settings,\n\u001b[0;32m 91\u001b[0m user_functions\u001b[39m=\u001b[39m{},\n\u001b[1;32m (...)\u001b[0m\n\u001b[0;32m 96\u001b[0m standard\u001b[39m=\u001b[39m\u001b[39m'\u001b[39m\u001b[39mpython3\u001b[39m\u001b[39m'\u001b[39m,\n\u001b[0;32m 97\u001b[0m )\n\u001b[1;32m---> 99\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39m__init__\u001b[39m(\u001b[39mself\u001b[39m, settings\u001b[39m=\u001b[39m\u001b[39mNone\u001b[39;00m):\n\u001b[0;32m 100\u001b[0m \u001b[39msuper\u001b[39m()\u001b[39m.\u001b[39m\u001b[39m__init__\u001b[39m(settings)\n\u001b[0;32m 102\u001b[0m \u001b[39m# Python standard handler\u001b[39;00m\n", + "\u001b[1;31mKeyboardInterrupt\u001b[0m: " ] } ], diff --git a/tests/test_model_disagreement_sampler.py b/tests/test_model_disagreement_sampler.py index 7cc415b..510a2f9 100644 --- a/tests/test_model_disagreement_sampler.py +++ b/tests/test_model_disagreement_sampler.py @@ -1,4 +1,4 @@ -from autora.experimentalist.sampler.model_disagreement_sampler import model_disagreement_sampler +from autora.experimentalist.sampler.model_disagreement import model_disagreement_sampler from autora.theorist.bms import BMSRegressor; BMSRegressor() from autora.theorist.darts import DARTSRegressor; DARTSRegressor() import numpy as np