diff --git a/.jupyter_cache/executed/094517cf9b662d4b071537ec5ac80b62/base.ipynb b/.jupyter_cache/executed/094517cf9b662d4b071537ec5ac80b62/base.ipynb index e9406f42..5fe69373 100644 --- a/.jupyter_cache/executed/094517cf9b662d4b071537ec5ac80b62/base.ipynb +++ b/.jupyter_cache/executed/094517cf9b662d4b071537ec5ac80b62/base.ipynb @@ -135,7 +135,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 2, @@ -168,63 +168,63 @@ "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) Apr 25 10:41:51 AM - INFO : 2/2 inputs mapped to the graph\n" + "(CORNETO) Apr 25 10:48:19 AM - INFO : 2/2 inputs mapped to the graph\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) Apr 25 10:41:51 AM - INFO : 2/2 outputs mapped to the graph\n" + "(CORNETO) Apr 25 10:48:19 AM - INFO : 2/2 outputs mapped to the graph\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) Apr 25 10:41:51 AM - INFO : Pruning the graph with size: V x E = (6, 6)...\n" + "(CORNETO) Apr 25 10:48:19 AM - INFO : Pruning the graph with size: V x E = (6, 6)...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) Apr 25 10:41:51 AM - INFO : Finished. Final size: V x E = (6, 6).\n" + "(CORNETO) Apr 25 10:48:19 AM - INFO : Finished. Final size: V x E = (6, 6).\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) Apr 25 10:41:51 AM - INFO : 2/2 inputs after pruning.\n" + "(CORNETO) Apr 25 10:48:19 AM - INFO : 2/2 inputs after pruning.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) Apr 25 10:41:51 AM - INFO : 2/2 outputs after pruning.\n" + "(CORNETO) Apr 25 10:48:19 AM - INFO : 2/2 outputs after pruning.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) Apr 25 10:41:51 AM - INFO : Converting into a flow graph...\n" + "(CORNETO) Apr 25 10:48:19 AM - INFO : Converting into a flow graph...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) Apr 25 10:41:51 AM - INFO : Creating a network flow problem...\n" + "(CORNETO) Apr 25 10:48:19 AM - INFO : Creating a network flow problem...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) Apr 25 10:41:51 AM - INFO : Preprocess completed.\n" + "(CORNETO) Apr 25 10:48:19 AM - INFO : Preprocess completed.\n" ] }, { @@ -235,35 +235,35 @@ " CVXPY \n", " v1.4.3 \n", "===============================================================================\n", - "(CVXPY) Apr 25 10:41:51 AM: Your problem has 86 variables, 20 constraints, and 0 parameters.\n" + "(CVXPY) Apr 25 10:48:19 AM: Your problem has 86 variables, 20 constraints, and 0 parameters.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: It is compliant with the following grammars: DCP, DQCP\n" + "(CVXPY) Apr 25 10:48:19 AM: It is compliant with the following grammars: DCP, DQCP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" + "(CVXPY) Apr 25 10:48:19 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" + "(CVXPY) Apr 25 10:48:19 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: Your problem is compiled with the CPP canonicalization backend.\n" + "(CVXPY) Apr 25 10:48:19 AM: Your problem is compiled with the CPP canonicalization backend.\n" ] }, { @@ -273,49 +273,49 @@ "-------------------------------------------------------------------------------\n", " Compilation \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:51 AM: Compiling problem (target solver=SCIP).\n" + "(CVXPY) Apr 25 10:48:19 AM: Compiling problem (target solver=SCIP).\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP\n" + "(CVXPY) Apr 25 10:48:19 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: Applying reduction Dcp2Cone\n" + "(CVXPY) Apr 25 10:48:19 AM: Applying reduction Dcp2Cone\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: Applying reduction CvxAttr2Constr\n" + "(CVXPY) Apr 25 10:48:19 AM: Applying reduction CvxAttr2Constr\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: Applying reduction ConeMatrixStuffing\n" + "(CVXPY) Apr 25 10:48:19 AM: Applying reduction ConeMatrixStuffing\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: Applying reduction SCIP\n" + "(CVXPY) Apr 25 10:48:19 AM: Applying reduction SCIP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: Finished problem compilation (took 2.805e-02 seconds).\n" + "(CVXPY) Apr 25 10:48:19 AM: Finished problem compilation (took 3.197e-02 seconds).\n" ] }, { @@ -325,7 +325,7 @@ "-------------------------------------------------------------------------------\n", " Numerical solver \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:51 AM: Invoking solver SCIP to obtain a solution.\n" + "(CVXPY) Apr 25 10:48:19 AM: Invoking solver SCIP to obtain a solution.\n" ] }, { @@ -334,9 +334,7 @@ "text": [ "-------------------------------------------------------------------------------\n", " Summary \n", - "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:51 AM: Problem status: optimal\n", - "presolving:\n", + "-------------------------------------------------------------------------------presolving:\n", "(round 1, fast) 36 del vars, 95 del conss, 0 add conss, 48 chg bounds, 1 chg sides, 23 chg coeffs, 0 upgd conss, 0 impls, 28 clqs\n", "(round 2, fast) 54 del vars, 129 del conss, 0 add conss, 52 chg bounds, 9 chg sides, 31 chg coeffs, 0 upgd conss, 0 impls, 20 clqs\n", "(round 3, fast) 63 del vars, 145 del conss, 0 add conss, 52 chg bounds, 11 chg sides, 33 chg coeffs, 0 upgd conss, 0 impls, 18 clqs\n", @@ -367,49 +365,50 @@ "Presolving Time: 0.00\n", "\n", " time | node | left |LP iter|LP it/n|mem/heur|mdpt |vars |cons |rows |cuts |sepa|confs|strbr| dualbound | primalbound | gap | compl. \n", - "p 0.0s| 1 | 0 | 1 | - | clique| 0 | 27 | 45 | 42 | 0 | 0 | 0 | 0 |-3.500000e+00 | 1.000000e-01 | Inf | unknown\n", - "p 0.0s| 1 | 0 | 1 | - | locks| 0 | 27 | 45 | 42 | 0 | 0 | 0 | 0 |-3.500000e+00 |-6.000000e-01 | 483.33%| unknown\n", - "p 0.0s| 1 | 0 | 1 | - | vbounds| 0 | 27 | 46 | 42 | 0 | 0 | 1 | 0 |-3.500000e+00 |-1.600000e+00 | 118.75%| unknown\n", - "p 0.0s| 1 | 0 | 1 | - | vbounds| 0 | 27 | 48 | 42 | 0 | 0 | 3 | 0 |-3.500000e+00 |-3.200000e+00 | 9.37%| unknown\n", - " 0.0s| 1 | 0 | 16 | - | 1789k | 0 | 27 | 29 | 42 | 0 | 0 | 9 | 0 |-3.300000e+00 |-3.200000e+00 | 3.13%| unknown\n", - " 0.0s| 1 | 0 | 21 | - | 1810k | 0 | 27 | 29 | 45 | 3 | 1 | 9 | 0 |-3.300000e+00 |-3.200000e+00 | 3.13%| unknown\n", - "r 0.0s| 1 | 0 | 21 | - |rounding| 0 | 27 | 29 | 45 | 3 | 1 | 9 | 0 |-3.300000e+00 |-3.300000e+00 | 0.00%| unknown\n", - " 0.0s| 1 | 0 | 21 | - | 1810k | 0 | 27 | 29 | 45 | 3 | 1 | 9 | 0 |-3.300000e+00 |-3.300000e+00 | 0.00%| unknown\n", + "p 0.0s| 1 | 0 | 0 | - | clique| 0 | 27 | 45 | 42 | 0 | 0 | 0 | 0 |-3.500000e+00 | 1.000000e-01 | Inf | unknown\n", + "p 0.0s| 1 | 0 | 0 | - | locks| 0 | 27 | 45 | 42 | 0 | 0 | 0 | 0 |-3.500000e+00 |-6.000000e-01 | 483.33%| unknown\n", + "p 0.0s| 1 | 0 | 0 | - | vbounds| 0 | 27 | 45 | 42 | 0 | 0 | 0 | 0 |-3.500000e+00 |-1.600000e+00 | 118.75%| unknown\n", + "p 0.0s| 1 | 0 | 0 | - | vbounds| 0 | 27 | 46 | 42 | 0 | 0 | 1 | 0 |-3.500000e+00 |-3.200000e+00 | 9.37%| unknown\n", + " 0.0s| 1 | 0 | 14 | - | 1786k | 0 | 27 | 29 | 42 | 0 | 0 | 7 | 0 |-3.300000e+00 |-3.200000e+00 | 3.13%| unknown\n", + "r 0.0s| 1 | 0 | 14 | - |rounding| 0 | 27 | 29 | 42 | 0 | 0 | 7 | 0 |-3.300000e+00 |-3.300000e+00 | 0.00%| unknown\n", + " 0.0s| 1 | 0 | 14 | - | 1786k | 0 | 27 | 29 | 42 | 0 | 0 | 7 | 0 |-3.300000e+00 |-3.300000e+00 | 0.00%| unknown\n", "\n", "SCIP Status : problem is solved [optimal solution found]\n", "Solving Time (sec) : 0.00\n", "Solving Nodes : 1\n", "Primal Bound : -3.30000000000000e+00 (5 solutions)\n", "Dual Bound : -3.30000000000000e+00\n", - "Gap : 0.00 %\n" + "Gap : 0.00 %\n", + "\n", + "(CVXPY) Apr 25 10:48:19 AM: Problem status: optimal\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: Optimal value: 7.000e-01\n" + "(CVXPY) Apr 25 10:48:19 AM: Optimal value: 7.000e-01\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: Compilation took 2.805e-02 seconds\n" + "(CVXPY) Apr 25 10:48:19 AM: Compilation took 3.197e-02 seconds\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: Solver (including time spent in interface) took 1.459e-02 seconds\n" + "(CVXPY) Apr 25 10:48:19 AM: Solver (including time spent in interface) took 1.419e-02 seconds\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) Apr 25 10:41:51 AM - INFO : Finished in 0.07 s.\n" + "(CORNETO) Apr 25 10:48:19 AM - INFO : Finished in 0.07 s.\n" ] } ], @@ -551,7 +550,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 5, @@ -601,32 +600,32 @@ " \n", " \n", " 0\n", - " I2\n", + " M2\n", " 1.0\n", " \n", " \n", " 1\n", - " M1\n", + " I1\n", " 1.0\n", " \n", " \n", " 2\n", - " N1\n", - " 0.0\n", + " N2\n", + " -1.0\n", " \n", " \n", " 3\n", - " N2\n", - " -1.0\n", + " N1\n", + " 0.0\n", " \n", " \n", " 4\n", - " I1\n", + " M1\n", " 1.0\n", " \n", " \n", " 5\n", - " M2\n", + " I2\n", " 1.0\n", " \n", " \n", @@ -655,12 +654,12 @@ ], "text/plain": [ " V value\n", - "0 I2 1.0\n", - "1 M1 1.0\n", - "2 N1 0.0\n", - "3 N2 -1.0\n", - "4 I1 1.0\n", - "5 M2 1.0\n", + "0 M2 1.0\n", + "1 I1 1.0\n", + "2 N2 -1.0\n", + "3 N1 0.0\n", + "4 M1 1.0\n", + "5 I2 1.0\n", "6 _s 1.0\n", "7 _pert_c0 1.0\n", "8 _meas_c0 0.0\n", @@ -955,7 +954,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 8, diff --git a/.jupyter_cache/executed/25bf812442150df0e2133bc8edc87bd9/base.ipynb b/.jupyter_cache/executed/25bf812442150df0e2133bc8edc87bd9/base.ipynb index 7fc1b7e1..cbd50efb 100644 --- a/.jupyter_cache/executed/25bf812442150df0e2133bc8edc87bd9/base.ipynb +++ b/.jupyter_cache/executed/25bf812442150df0e2133bc8edc87bd9/base.ipynb @@ -200,7 +200,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 5, diff --git a/.jupyter_cache/executed/43db6d99b10aae7002b43157110f8d59/base.ipynb b/.jupyter_cache/executed/43db6d99b10aae7002b43157110f8d59/base.ipynb index f8b21b86..f59d419b 100644 --- a/.jupyter_cache/executed/43db6d99b10aae7002b43157110f8d59/base.ipynb +++ b/.jupyter_cache/executed/43db6d99b10aae7002b43157110f8d59/base.ipynb @@ -42,7 +42,7 @@ " NameBiomass Objective Function with GAM\n", " \n", " Memory address\n", - " 0x7f4ff9f4e350\n", + " 0x7fefbc1edfd0\n", " \n", " Stoichiometry\n", " \n", @@ -60,7 +60,7 @@ " " ], "text/plain": [ - "" + "" ] }, "execution_count": 2, @@ -83,7 +83,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "\n" + "\n" ] } ], @@ -210,35 +210,35 @@ "output_type": "stream", "text": [ "Warning: node 'acald_c', graph '%3' size too small for label\n", - "Warning: node 'nad_c', graph '%3' size too small for label\n", "Warning: node 'coa_c', graph '%3' size too small for label\n", + "Warning: node 'nad_c', graph '%3' size too small for label\n", "Warning: node 'accoa_c', graph '%3' size too small for label\n", "Warning: node 'nadh_c', graph '%3' size too small for label\n", "Warning: node 'acald_e', graph '%3' size too small for label\n", "Warning: node 'atp_c', graph '%3' size too small for label\n", - "Warning: node 'adp_c', graph '%3' size too small for label\n", "Warning: node 'actp_c', graph '%3' size too small for label\n", + "Warning: node 'adp_c', graph '%3' size too small for label\n", "Warning: node 'acon_C_c', graph '%3' size too small for label\n", "Warning: node 'h2o_c', graph '%3' size too small for label\n", "Warning: node 'icit_c', graph '%3' size too small for label\n", "Warning: node 'amp_c', graph '%3' size too small for label\n", "Warning: node 'akg_c', graph '%3' size too small for label\n", - "Warning: node 'succoa_c', graph '%3' size too small for label\n", "Warning: node 'co2_c', graph '%3' size too small for label\n", + "Warning: node 'succoa_c', graph '%3' size too small for label\n", "Warning: node 'akg_e', graph '%3' size too small for label\n", "Warning: node 'etoh_c', graph '%3' size too small for label\n", - "Warning: node 'r5p_c', graph '%3' size too small for label\n", - "Warning: node '3pg_c', graph '%3' size too small for label\n", - "Warning: node 'gln__L_c', graph '%3' size too small for label\n", + "Warning: node 'nadph_c', graph '%3' size too small for label\n", + "Warning: node 'g3p_c', graph '%3' size too small for label\n", "Warning: node 'glu__L_c', graph '%3' size too small for label\n", - "Warning: node 'f6p_c', graph '%3' size too small for label\n", - "Warning: node 'pyr_c', graph '%3' size too small for label\n", "Warning: node 'oaa_c', graph '%3' size too small for label\n", - "Warning: node 'pep_c', graph '%3' size too small for label\n", - "Warning: node 'nadph_c', graph '%3' size too small for label\n", + "Warning: node 'pyr_c', graph '%3' size too small for label\n", "Warning: node 'e4p_c', graph '%3' size too small for label\n", - "Warning: node 'g3p_c', graph '%3' size too small for label\n", + "Warning: node 'r5p_c', graph '%3' size too small for label\n", + "Warning: node 'gln__L_c', graph '%3' size too small for label\n", "Warning: node 'g6p_c', graph '%3' size too small for label\n", + "Warning: node 'pep_c', graph '%3' size too small for label\n", + "Warning: node 'f6p_c', graph '%3' size too small for label\n", + "Warning: node '3pg_c', graph '%3' size too small for label\n", "Warning: node 'nadp_c', graph '%3' size too small for label\n", "Warning: node 'co2_e', graph '%3' size too small for label\n", "Warning: node 'q8h2_c', graph '%3' size too small for label\n", @@ -280,2805 +280,2805 @@ "\n", "\n", - "\n", - "\n", + "\n", + "\n", "%3\n", - "\n", + "\n", "\n", "\n", "acald_c\n", - "\n", - "acald_c\n", + "\n", + "acald_c\n", "\n", "\n", "\n", "e_0_center\n", - "\n", + "\n", "\n", "\n", "\n", "acald_c->e_0_center\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "nad_c\n", - "\n", - "nad_c\n", + "coa_c\n", + "\n", + "coa_c\n", "\n", - "\n", + "\n", "\n", - "nad_c->e_0_center\n", - "\n", + "coa_c->e_0_center\n", + "\n", "\n", "\n", "\n", "e_7_center\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", + "coa_c->e_7_center\n", + "\n", + "\n", + "\n", + "\n", + "e_70_center\n", + "\n", + "\n", + "\n", + "\n", + "coa_c->e_70_center\n", + "\n", + "\n", + "\n", + "\n", + "e_72_center\n", + "\n", + "\n", + "\n", + "\n", + "coa_c->e_72_center\n", + "\n", + "\n", + "\n", + "\n", + "e_89_center\n", + "\n", + "\n", + "\n", + "\n", + "coa_c->e_89_center\n", + "\n", + "\n", + "\n", + "\n", + "nad_c\n", + "\n", + "nad_c\n", + "\n", + "\n", + "\n", + "nad_c->e_0_center\n", + "\n", + "\n", + "\n", + "\n", "nad_c->e_7_center\n", - "\n", + "\n", "\n", "\n", "\n", "e_9_center\n", - "\n", + "\n", "\n", "\n", - "\n", + "\n", "nad_c->e_9_center\n", - "\n", + "\n", "\n", "\n", "\n", "e_12_center\n", - "\n", + "\n", "\n", "\n", - "\n", + "\n", "nad_c->e_12_center\n", - "\n", + "\n", "\n", "\n", "\n", "e_48_center\n", - "\n", + "\n", "\n", "\n", - "\n", + "\n", "nad_c->e_48_center\n", - "\n", + "\n", "\n", "\n", "\n", "e_60_center\n", - "\n", + "\n", "\n", "\n", "\n", "nad_c->e_60_center\n", - "\n", + "\n", "\n", "\n", "\n", "e_63_center\n", - "\n", + "\n", "\n", "\n", - "\n", + "\n", "nad_c->e_63_center\n", - "\n", + "\n", "\n", "\n", "\n", "e_64_center\n", - "\n", + "\n", "\n", "\n", - "\n", + "\n", "nad_c->e_64_center\n", - "\n", + "\n", "\n", "\n", "\n", "e_67_center\n", - "\n", + "\n", "\n", "\n", "\n", "nad_c->e_67_center\n", - "\n", - "\n", - "\n", - "\n", - "e_70_center\n", - "\n", + "\n", "\n", "\n", - "\n", - "nad_c->e_70_center\n", - "\n", - "\n", - "\n", - "\n", - "coa_c\n", - "\n", - "coa_c\n", - "\n", - "\n", - "\n", - "coa_c->e_0_center\n", - "\n", - "\n", - "\n", - "\n", - "coa_c->e_7_center\n", - "\n", - "\n", - "\n", "\n", - "coa_c->e_70_center\n", - "\n", - "\n", - "\n", - "\n", - "e_72_center\n", - "\n", - "\n", - "\n", - "\n", - "coa_c->e_72_center\n", - "\n", - "\n", - "\n", - "\n", - "e_89_center\n", - "\n", - "\n", - "\n", - "\n", - "coa_c->e_89_center\n", - "\n", - "\n", - "\n", - "\n", - "h_c\n", - "\n", - "h_c\n", - "\n", - "\n", - "\n", - "e_15_center\n", - 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small for label\n", - "Warning: node 'adp_c', graph '%3' size too small for label\n", "Warning: node 'actp_c', graph '%3' size too small for label\n", + "Warning: node 'adp_c', graph '%3' size too small for label\n", "Warning: node 'acon_C_c', graph '%3' size too small for label\n", "Warning: node 'h2o_c', graph '%3' size too small for label\n", "Warning: node 'icit_c', graph '%3' size too small for label\n", "Warning: node 'amp_c', graph '%3' size too small for label\n", "Warning: node 'akg_c', graph '%3' size too small for label\n", - "Warning: node 'succoa_c', graph '%3' size too small for label\n", "Warning: node 'co2_c', graph '%3' size too small for label\n", + "Warning: node 'succoa_c', graph '%3' size too small for label\n", "Warning: node 'akg_e', graph '%3' size too small for label\n", "Warning: node 'etoh_c', graph '%3' size too small for label\n", - "Warning: node 'r5p_c', graph '%3' size too small for label\n", - "Warning: node '3pg_c', graph '%3' size too small for label\n", - "Warning: node 'gln__L_c', graph '%3' size too small for label\n", + "Warning: node 'nadph_c', graph '%3' size too small for label\n", + "Warning: node 'g3p_c', graph '%3' size too small for label\n", "Warning: node 'glu__L_c', graph '%3' size too small for label\n", - "Warning: node 'f6p_c', graph '%3' size too small for label\n", - "Warning: node 'pyr_c', graph '%3' size too small for label\n", "Warning: node 'oaa_c', graph '%3' size too small for label\n", - "Warning: node 'pep_c', graph '%3' size too small for label\n", - "Warning: node 'nadph_c', graph '%3' size too small for label\n", + "Warning: node 'pyr_c', graph '%3' size too small for label\n", "Warning: node 'e4p_c', graph '%3' size too small for label\n", - "Warning: node 'g3p_c', graph '%3' size too small for label\n", + "Warning: node 'r5p_c', graph '%3' size too small for label\n", + "Warning: node 'gln__L_c', graph '%3' size too small for label\n", "Warning: node 'g6p_c', graph '%3' size too small for label\n", + "Warning: node 'pep_c', graph '%3' size too small for label\n", + "Warning: node 'f6p_c', graph '%3' size too small for label\n", + "Warning: node '3pg_c', graph '%3' size too small for label\n", "Warning: node 'nadp_c', graph '%3' size too small for label\n", "Warning: node 'co2_e', graph '%3' size too small for label\n", "Warning: node 'q8h2_c', graph '%3' size too small for label\n", @@ -3195,2805 +3195,2805 @@ "\n", "\n", - "\n", - "\n", + "\n", + "\n", "%3\n", - "\n", + "\n", "\n", "\n", "acald_c\n", - "\n", - "acald_c\n", + "\n", + "acald_c\n", "\n", "\n", "\n", "e_0_center\n", - "\n", + "\n", "\n", "\n", "\n", "acald_c->e_0_center\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "nad_c\n", - "\n", - "nad_c\n", + "coa_c\n", + "\n", + "coa_c\n", "\n", - "\n", + "\n", "\n", - "nad_c->e_0_center\n", - "\n", + "coa_c->e_0_center\n", + "\n", "\n", "\n", "\n", "e_7_center\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", + "coa_c->e_7_center\n", + "\n", + "\n", + "\n", + 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"\n", + "\n", "\n", - "\n", + "\n", "\n", - "e_93_center->f6p_c\n", - "\n", - "\n", + "e_93_center->g3p_c\n", + "\n", + "\n", "\n", - "\n", + "\n", "\n", - "e_93_center->g3p_c\n", - "\n", - "\n", + "e_93_center->f6p_c\n", + "\n", + "\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 9, diff --git a/.jupyter_cache/executed/4b6c60c42f20e0738189935b8e87f5a1/base.ipynb b/.jupyter_cache/executed/4b6c60c42f20e0738189935b8e87f5a1/base.ipynb index 03bf4ad5..fe7943b3 100644 --- a/.jupyter_cache/executed/4b6c60c42f20e0738189935b8e87f5a1/base.ipynb +++ b/.jupyter_cache/executed/4b6c60c42f20e0738189935b8e87f5a1/base.ipynb @@ -51,35 +51,35 @@ " CVXPY \n", " v1.4.3 \n", "===============================================================================\n", - "(CVXPY) Apr 25 10:40:00 AM: Your problem has 5 variables, 2 constraints, and 0 parameters.\n" + "(CVXPY) Apr 25 10:46:24 AM: Your problem has 5 variables, 2 constraints, and 0 parameters.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: It is compliant with the following grammars: DCP, DQCP\n" + "(CVXPY) Apr 25 10:46:24 AM: It is compliant with the following grammars: DCP, DQCP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" + "(CVXPY) Apr 25 10:46:24 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" + "(CVXPY) Apr 25 10:46:24 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: Your problem is compiled with the CPP canonicalization backend.\n" + "(CVXPY) Apr 25 10:46:24 AM: Your problem is compiled with the CPP canonicalization backend.\n" ] }, { @@ -89,49 +89,49 @@ "-------------------------------------------------------------------------------\n", " Compilation \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:00 AM: Compiling problem (target solver=OSQP).\n" + "(CVXPY) Apr 25 10:46:24 AM: Compiling problem (target solver=OSQP).\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: Reduction chain: CvxAttr2Constr -> Qp2SymbolicQp -> QpMatrixStuffing -> OSQP\n" + "(CVXPY) Apr 25 10:46:24 AM: Reduction chain: CvxAttr2Constr -> Qp2SymbolicQp -> QpMatrixStuffing -> OSQP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: Applying reduction CvxAttr2Constr\n" + "(CVXPY) Apr 25 10:46:24 AM: Applying reduction CvxAttr2Constr\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: Applying reduction Qp2SymbolicQp\n" + "(CVXPY) Apr 25 10:46:24 AM: Applying reduction Qp2SymbolicQp\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: Applying reduction QpMatrixStuffing\n" + "(CVXPY) Apr 25 10:46:24 AM: Applying reduction QpMatrixStuffing\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: Applying reduction OSQP\n" + "(CVXPY) Apr 25 10:46:24 AM: Applying reduction OSQP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: Finished problem compilation (took 9.753e-03 seconds).\n" + "(CVXPY) Apr 25 10:46:24 AM: Finished problem compilation (took 9.047e-03 seconds).\n" ] }, { @@ -141,7 +141,7 @@ "-------------------------------------------------------------------------------\n", " Numerical solver \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:00 AM: Invoking solver OSQP to obtain a solution.\n" + "(CVXPY) Apr 25 10:46:24 AM: Invoking solver OSQP to obtain a solution.\n" ] }, { @@ -165,42 +165,42 @@ " warm start: on, polish: on, time_limit: off\n", "\n", "iter objective pri res dua res rho time\n", - " 1 -5.2220e+00 3.68e+00 1.70e+02 1.00e-01 4.35e-05s\n", - " 150 6.9994e-01 1.96e-05 7.82e-06 4.77e+00 9.17e-05s\n", - "plsh 7.0000e-01 1.95e-30 0.00e+00 -------- 1.20e-04s\n", + " 1 -5.2220e+00 3.68e+00 1.70e+02 1.00e-01 4.43e-05s\n", + " 150 6.9994e-01 1.96e-05 7.82e-06 4.77e+00 9.01e-05s\n", + "plsh 7.0000e-01 1.95e-30 0.00e+00 -------- 1.23e-04s\n", "\n", "status: solved\n", "solution polish: successful\n", "number of iterations: 150\n", "optimal objective: 0.7000\n", - "run time: 1.20e-04s\n", + "run time: 1.23e-04s\n", "optimal rho estimate: 9.81e+00\n", "\n", "-------------------------------------------------------------------------------\n", " Summary \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:00 AM: Problem status: optimal\n" + "(CVXPY) Apr 25 10:46:24 AM: Problem status: optimal\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: Optimal value: -3.000e-01\n" + "(CVXPY) Apr 25 10:46:24 AM: Optimal value: -3.000e-01\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: Compilation took 9.753e-03 seconds\n" + "(CVXPY) Apr 25 10:46:24 AM: Compilation took 9.047e-03 seconds\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: Solver (including time spent in interface) took 2.524e-03 seconds\n" + "(CVXPY) Apr 25 10:46:24 AM: Solver (including time spent in interface) took 1.582e-03 seconds\n" ] } ], diff --git a/.jupyter_cache/executed/517c8075025ade78e95139e2b291eb2c/base.ipynb b/.jupyter_cache/executed/517c8075025ade78e95139e2b291eb2c/base.ipynb index 7e6bb587..6cd7e148 100644 --- a/.jupyter_cache/executed/517c8075025ade78e95139e2b291eb2c/base.ipynb +++ b/.jupyter_cache/executed/517c8075025ade78e95139e2b291eb2c/base.ipynb @@ -135,7 +135,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 2, @@ -286,7 +286,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 3, @@ -386,35 +386,35 @@ " CVXPY \n", " v1.4.3 \n", "===============================================================================\n", - "(CVXPY) Apr 25 10:40:10 AM: Your problem has 20 variables, 5 constraints, and 0 parameters.\n" + "(CVXPY) Apr 25 10:46:33 AM: Your problem has 20 variables, 5 constraints, and 0 parameters.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: It is compliant with the following grammars: DCP, DQCP\n" + "(CVXPY) Apr 25 10:46:33 AM: It is compliant with the following grammars: DCP, DQCP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" + "(CVXPY) Apr 25 10:46:33 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" + "(CVXPY) Apr 25 10:46:33 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: Your problem is compiled with the CPP canonicalization backend.\n" + "(CVXPY) Apr 25 10:46:33 AM: Your problem is compiled with the CPP canonicalization backend.\n" ] }, { @@ -424,49 +424,49 @@ "-------------------------------------------------------------------------------\n", " Compilation \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:10 AM: Compiling problem (target solver=SCIP).\n" + "(CVXPY) Apr 25 10:46:33 AM: Compiling problem (target solver=SCIP).\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP\n" + "(CVXPY) Apr 25 10:46:33 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: Applying reduction Dcp2Cone\n" + "(CVXPY) Apr 25 10:46:33 AM: Applying reduction Dcp2Cone\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: Applying reduction CvxAttr2Constr\n" + "(CVXPY) Apr 25 10:46:33 AM: Applying reduction CvxAttr2Constr\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: Applying reduction ConeMatrixStuffing\n" + "(CVXPY) Apr 25 10:46:33 AM: Applying reduction ConeMatrixStuffing\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: Applying reduction SCIP\n" + "(CVXPY) Apr 25 10:46:33 AM: Applying reduction SCIP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: Finished problem compilation (took 1.412e-02 seconds).\n" + "(CVXPY) Apr 25 10:46:33 AM: Finished problem compilation (took 1.440e-02 seconds).\n" ] }, { @@ -476,7 +476,7 @@ "-------------------------------------------------------------------------------\n", " Numerical solver \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:10 AM: Invoking solver SCIP to obtain a solution.\n" + "(CVXPY) Apr 25 10:46:33 AM: Invoking solver SCIP to obtain a solution.\n" ] }, { @@ -486,7 +486,13 @@ "-------------------------------------------------------------------------------\n", " Summary \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:10 AM: Problem status: optimal\n", + "(CVXPY) Apr 25 10:46:33 AM: Problem status: optimal\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ "presolving:\n", " (0.0s) symmetry computation started: requiring (bin +, int +, cont +), (fixed: bin -, int -, cont -)\n", " (0.0s) no symmetry present (symcode time: 0.00)\n", @@ -506,28 +512,22 @@ "Solving Nodes : 1\n", "Primal Bound : -1.90000000000000e+02 (1 solutions)\n", "Dual Bound : -1.90000000000000e+02\n", - "Gap : 0.00 %\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "(CVXPY) Apr 25 10:40:10 AM: Optimal value: -1.900e+02\n" + "Gap : 0.00 %\n", + "(CVXPY) Apr 25 10:46:33 AM: Optimal value: -1.900e+02\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: Compilation took 1.412e-02 seconds\n" + "(CVXPY) Apr 25 10:46:33 AM: Compilation took 1.440e-02 seconds\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: Solver (including time spent in interface) took 6.421e-03 seconds\n" + "(CVXPY) Apr 25 10:46:33 AM: Solver (including time spent in interface) took 6.373e-03 seconds\n" ] }, { diff --git a/.jupyter_cache/executed/5d6f361d9e37c70dcbca3b8f4d6e510d/base.ipynb b/.jupyter_cache/executed/5d6f361d9e37c70dcbca3b8f4d6e510d/base.ipynb index f353c42f..451a196b 100644 --- a/.jupyter_cache/executed/5d6f361d9e37c70dcbca3b8f4d6e510d/base.ipynb +++ b/.jupyter_cache/executed/5d6f361d9e37c70dcbca3b8f4d6e510d/base.ipynb @@ -93,7 +93,7 @@ "Solver claims optimal solution for feasible problem.\n", "Applying the solution.\n", "Applied solution is primal feasible.\n", - "Search 1.4e-02s, solve 1.9e-02s, overhead 31%.\n", + "Search 1.4e-02s, solve 1.9e-02s, overhead 34%.\n", "=============[ PICOS ]=============\n" ] } diff --git a/.jupyter_cache/executed/5e0662f0c002e3e51fbb7e377567e03e/base.ipynb b/.jupyter_cache/executed/5e0662f0c002e3e51fbb7e377567e03e/base.ipynb index 19029588..75d2cc58 100644 --- a/.jupyter_cache/executed/5e0662f0c002e3e51fbb7e377567e03e/base.ipynb +++ b/.jupyter_cache/executed/5e0662f0c002e3e51fbb7e377567e03e/base.ipynb @@ -96,7 +96,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 2, @@ -190,7 +190,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 3, @@ -286,7 +286,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 4, @@ -514,7 +514,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 12, @@ -666,7 +666,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 16, @@ -699,31 +699,31 @@ "\n", "%3\n", "\n", - "\n", + "\n", "\n", - "A\n", + "B\n", "\n", - "A\n", + "B\n", "\n", "\n", "\n", "e_0_center\n", "\n", "\n", - "\n", + "\n", "\n", - "A->e_0_center\n", + "B->e_0_center\n", "\n", "\n", - "\n", + "\n", "\n", - "B\n", + "A\n", "\n", - "B\n", + "A\n", "\n", - "\n", + "\n", "\n", - "B->e_0_center\n", + "A->e_0_center\n", "\n", "\n", "\n", @@ -810,30 +810,30 @@ "\n", "\n", "e_2_source\n", - "\n", + "\n", "\n", "\n", "\n", "e_2_source->A\n", - "\n", - "\n", + "\n", + "\n", "\n", "\n", "\n", "e_3_source\n", - "\n", + "\n", "\n", "\n", "\n", "e_3_source->B\n", - "\n", - "\n", + "\n", + "\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 17, diff --git a/.jupyter_cache/executed/675e77349578388ccf114552ebd1c801/base.ipynb b/.jupyter_cache/executed/675e77349578388ccf114552ebd1c801/base.ipynb index a4040bae..8cce109c 100644 --- a/.jupyter_cache/executed/675e77349578388ccf114552ebd1c801/base.ipynb +++ b/.jupyter_cache/executed/675e77349578388ccf114552ebd1c801/base.ipynb @@ -228,7 +228,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 2, @@ -385,7 +385,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 5, diff --git a/.jupyter_cache/executed/9207a79194e6c46831386d8e051393f9/base.ipynb b/.jupyter_cache/executed/9207a79194e6c46831386d8e051393f9/base.ipynb index b2ed73d6..d95ad2dc 100644 --- a/.jupyter_cache/executed/9207a79194e6c46831386d8e051393f9/base.ipynb +++ b/.jupyter_cache/executed/9207a79194e6c46831386d8e051393f9/base.ipynb @@ -142,36 +142,36 @@ "name": "stderr", "output_type": "stream", "text": [ - "Warning: node 'nad_c', graph '%3' size too small for label\n", "Warning: node 'coa_c', graph '%3' size too small for label\n", "Warning: node 'acald_c', graph '%3' size too small for label\n", + "Warning: node 'nad_c', graph '%3' size too small for label\n", "Warning: node 'nadh_c', graph '%3' size too small for label\n", "Warning: node 'accoa_c', graph '%3' size too small for label\n", "Warning: node 'acald_e', graph '%3' size too small for label\n", "Warning: node 'atp_c', graph '%3' size too small for label\n", "Warning: node 'adp_c', graph '%3' size too small for label\n", "Warning: node 'actp_c', graph '%3' size too small for label\n", - "Warning: node 'acon_C_c', graph '%3' size too small for label\n", "Warning: node 'h2o_c', graph '%3' size too small for label\n", + "Warning: node 'acon_C_c', graph '%3' size too small for label\n", "Warning: node 'icit_c', graph '%3' size too small for label\n", "Warning: node 'amp_c', graph '%3' size too small for label\n", "Warning: node 'akg_c', graph '%3' size too small for label\n", - "Warning: node 'succoa_c', graph '%3' size too small for label\n", "Warning: node 'co2_c', graph '%3' size too small for label\n", + "Warning: node 'succoa_c', graph '%3' size too small for label\n", "Warning: node 'akg_e', graph '%3' size too small for label\n", "Warning: node 'etoh_c', graph '%3' size too small for label\n", - "Warning: node 'e4p_c', graph '%3' size too small for label\n", - "Warning: node 'glu__L_c', graph '%3' size too small for label\n", - "Warning: node 'pep_c', graph '%3' size too small for label\n", + "Warning: node 'gln__L_c', graph '%3' size too small for label\n", "Warning: node '3pg_c', graph '%3' size too small for label\n", + "Warning: node 'f6p_c', graph '%3' size too small for label\n", "Warning: node 'pyr_c', graph '%3' size too small for label\n", + "Warning: node 'r5p_c', graph '%3' size too small for label\n", + "Warning: node 'e4p_c', graph '%3' size too small for label\n", + "Warning: node 'g3p_c', graph '%3' size too small for label\n", "Warning: node 'g6p_c', graph '%3' size too small for label\n", + "Warning: node 'pep_c', graph '%3' size too small for label\n", "Warning: node 'oaa_c', graph '%3' size too small for label\n", - "Warning: node 'f6p_c', graph '%3' size too small for label\n", - "Warning: node 'g3p_c', graph '%3' size too small for label\n", "Warning: node 'nadph_c', graph '%3' size too small for label\n", - "Warning: node 'r5p_c', graph '%3' size too small for label\n", - "Warning: node 'gln__L_c', graph '%3' size too small for label\n", + "Warning: node 'glu__L_c', graph '%3' size too small for label\n", "Warning: node 'nadp_c', graph '%3' size too small for label\n", "Warning: node 'co2_e', graph '%3' size too small for label\n", "Warning: node 'q8h2_c', graph '%3' size too small for label\n", @@ -213,2805 +213,2805 @@ "\n", "\n", - "\n", - "\n", + "\n", + "\n", "%3\n", - "\n", - "\n", + "\n", + "\n", "\n", - "nad_c\n", - "\n", - "nad_c\n", + "coa_c\n", + "\n", + "coa_c\n", "\n", "\n", "\n", "e_0_center\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "nad_c->e_0_center\n", - "\n", + "coa_c->e_0_center\n", + "\n", "\n", "\n", "\n", "e_7_center\n", - "\n", + "\n", + "\n", + "\n", + "\n", + "coa_c->e_7_center\n", + "\n", + "\n", + "\n", + "\n", + "e_70_center\n", + "\n", + "\n", + "\n", + "\n", + "coa_c->e_70_center\n", + "\n", + "\n", + "\n", + "\n", + "e_72_center\n", + "\n", + "\n", + "\n", + "\n", + "coa_c->e_72_center\n", + "\n", + "\n", + "\n", + "\n", + "e_89_center\n", + "\n", + "\n", + "\n", + "\n", + "coa_c->e_89_center\n", + "\n", + "\n", + "\n", + "\n", + "acald_c\n", + "\n", + "acald_c\n", + "\n", + "\n", + "\n", + "acald_c->e_0_center\n", + "\n", + "\n", + "\n", + "\n", + "nad_c\n", + "\n", + "nad_c\n", + "\n", + "\n", + "\n", + "nad_c->e_0_center\n", + "\n", "\n", "\n", "\n", "nad_c->e_7_center\n", - "\n", + "\n", "\n", "\n", "\n", "e_9_center\n", - "\n", + "\n", "\n", "\n", "\n", "nad_c->e_9_center\n", - "\n", + "\n", "\n", "\n", "\n", "e_12_center\n", - "\n", + "\n", "\n", "\n", - "\n", + "\n", "nad_c->e_12_center\n", - "\n", + "\n", "\n", "\n", "\n", "e_48_center\n", - "\n", + "\n", "\n", "\n", "\n", "nad_c->e_48_center\n", - "\n", + "\n", "\n", "\n", "\n", "e_60_center\n", - "\n", + "\n", "\n", "\n", - "\n", + "\n", "nad_c->e_60_center\n", - "\n", + "\n", "\n", "\n", "\n", "e_63_center\n", - "\n", + "\n", "\n", "\n", "\n", "nad_c->e_63_center\n", - "\n", + "\n", "\n", "\n", "\n", "e_64_center\n", - "\n", + "\n", "\n", "\n", "\n", "nad_c->e_64_center\n", - "\n", + "\n", "\n", "\n", "\n", "e_67_center\n", - 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'%3' size too small for label\n", + "Warning: node 'succoa_c', graph '%3' size too small for label\n", "Warning: node 'akg_e', graph '%3' size too small for label\n", "Warning: node 'etoh_c', graph '%3' size too small for label\n", - "Warning: node 'e4p_c', graph '%3' size too small for label\n", - "Warning: node 'glu__L_c', graph '%3' size too small for label\n", - "Warning: node 'pep_c', graph '%3' size too small for label\n", + "Warning: node 'gln__L_c', graph '%3' size too small for label\n", "Warning: node '3pg_c', graph '%3' size too small for label\n", + "Warning: node 'f6p_c', graph '%3' size too small for label\n", "Warning: node 'pyr_c', graph '%3' size too small for label\n", + "Warning: node 'r5p_c', graph '%3' size too small for label\n", + "Warning: node 'e4p_c', graph '%3' size too small for label\n", + "Warning: node 'g3p_c', graph '%3' size too small for label\n", "Warning: node 'g6p_c', graph '%3' size too small for label\n", + "Warning: node 'pep_c', graph '%3' size 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"\n", "\n", "\n", "\n", "e_93_center->f6p_c\n", - "\n", - "\n", + "\n", + "\n", "\n", "\n", "\n", "e_93_center->g3p_c\n", - "\n", - "\n", + "\n", + "\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 10, diff --git a/.jupyter_cache/executed/a6f4873eacabb963a97b021f7c0cbd92/base.ipynb b/.jupyter_cache/executed/a6f4873eacabb963a97b021f7c0cbd92/base.ipynb index daa74c69..12d1f3df 100644 --- a/.jupyter_cache/executed/a6f4873eacabb963a97b021f7c0cbd92/base.ipynb +++ b/.jupyter_cache/executed/a6f4873eacabb963a97b021f7c0cbd92/base.ipynb @@ -45,7 +45,7 @@ { "data": { "text/plain": [ - "" + "" ] }, "execution_count": 2, @@ -99,7 +99,7 @@ { "data": { "text/plain": [ - "" + "" ] }, "execution_count": 4, @@ -198,35 +198,35 @@ " CVXPY \n", " v1.4.3 \n", "===============================================================================\n", - "(CVXPY) Apr 25 10:40:09 AM: Your problem has 50 variables, 1 constraints, and 0 parameters.\n" + "(CVXPY) Apr 25 10:46:32 AM: Your problem has 50 variables, 1 constraints, and 0 parameters.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: It is compliant with the following grammars: DCP, DQCP\n" + "(CVXPY) Apr 25 10:46:32 AM: It is compliant with the following grammars: DCP, DQCP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" + "(CVXPY) Apr 25 10:46:32 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" + "(CVXPY) Apr 25 10:46:32 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Your problem is compiled with the CPP canonicalization backend.\n" + "(CVXPY) Apr 25 10:46:32 AM: Your problem is compiled with the CPP canonicalization backend.\n" ] }, { @@ -236,56 +236,56 @@ "-------------------------------------------------------------------------------\n", " Compilation \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:09 AM: Compiling problem (target solver=SCIP).\n" + "(CVXPY) Apr 25 10:46:32 AM: Compiling problem (target solver=SCIP).\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Reduction chain: FlipObjective -> Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP\n" + "(CVXPY) Apr 25 10:46:32 AM: Reduction chain: FlipObjective -> Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Applying reduction FlipObjective\n" + "(CVXPY) Apr 25 10:46:32 AM: Applying reduction FlipObjective\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Applying reduction Dcp2Cone\n" + "(CVXPY) Apr 25 10:46:32 AM: Applying reduction Dcp2Cone\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Applying reduction CvxAttr2Constr\n" + "(CVXPY) Apr 25 10:46:32 AM: Applying reduction CvxAttr2Constr\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Applying reduction ConeMatrixStuffing\n" + "(CVXPY) Apr 25 10:46:32 AM: Applying reduction ConeMatrixStuffing\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Applying reduction SCIP\n" + "(CVXPY) Apr 25 10:46:32 AM: Applying reduction SCIP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Finished problem compilation (took 8.441e-03 seconds).\n" + "(CVXPY) Apr 25 10:46:32 AM: Finished problem compilation (took 8.368e-03 seconds).\n" ] }, { @@ -295,7 +295,7 @@ "-------------------------------------------------------------------------------\n", " Numerical solver \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:09 AM: Invoking solver SCIP to obtain a solution.\n" + "(CVXPY) Apr 25 10:46:32 AM: Invoking solver SCIP to obtain a solution.\n" ] }, { @@ -304,7 +304,9 @@ "text": [ "-------------------------------------------------------------------------------\n", " Summary \n", - "-------------------------------------------------------------------------------feasible solution found by trivial heuristic after 0.0 seconds, objective value -6.000000e+02\n", + "-------------------------------------------------------------------------------\n", + "(CVXPY) Apr 25 10:46:32 AM: Problem status: optimal\n", + "feasible solution found by trivial heuristic after 0.0 seconds, objective value -6.000000e+02\n", "presolving:\n", "(round 1, fast) 4 del vars, 0 del conss, 0 add conss, 0 chg bounds, 0 chg sides, 0 chg coeffs, 0 upgd conss, 0 impls, 0 clqs\n", "(round 2, exhaustive) 4 del vars, 0 del conss, 0 add conss, 0 chg bounds, 0 chg sides, 0 chg coeffs, 1 upgd conss, 0 impls, 0 clqs\n", @@ -320,30 +322,28 @@ "Solving Nodes : 0\n", "Primal Bound : -7.53400000000000e+03 (3 solutions)\n", "Dual Bound : -7.53400000000000e+03\n", - "Gap : 0.00 %\n", - "\n", - "(CVXPY) Apr 25 10:40:09 AM: Problem status: optimal\n" + "Gap : 0.00 %\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Optimal value: 7.534e+03\n" + "(CVXPY) Apr 25 10:46:32 AM: Optimal value: 7.534e+03\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Compilation took 8.441e-03 seconds\n" + "(CVXPY) Apr 25 10:46:32 AM: Compilation took 8.368e-03 seconds\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Solver (including time spent in interface) took 3.624e-03 seconds\n" + "(CVXPY) Apr 25 10:46:32 AM: Solver (including time spent in interface) took 3.592e-03 seconds\n" ] }, { diff --git a/.jupyter_cache/executed/aa636f5a6eecef6aa2002893edcd864a/base.ipynb b/.jupyter_cache/executed/aa636f5a6eecef6aa2002893edcd864a/base.ipynb index de69c079..69e10ee4 100644 --- a/.jupyter_cache/executed/aa636f5a6eecef6aa2002893edcd864a/base.ipynb +++ b/.jupyter_cache/executed/aa636f5a6eecef6aa2002893edcd864a/base.ipynb @@ -176,7 +176,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 2, @@ -363,7 +363,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 3, @@ -530,7 +530,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 6, @@ -782,7 +782,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 8, @@ -951,7 +951,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 11, diff --git a/.jupyter_cache/executed/ca40e9dde7623740cf208b495fee7220/base.ipynb b/.jupyter_cache/executed/ca40e9dde7623740cf208b495fee7220/base.ipynb index 65cda87b..a1e1302f 100644 --- a/.jupyter_cache/executed/ca40e9dde7623740cf208b495fee7220/base.ipynb +++ b/.jupyter_cache/executed/ca40e9dde7623740cf208b495fee7220/base.ipynb @@ -259,7 +259,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 2, @@ -460,7 +460,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 5, @@ -693,7 +693,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 6, diff --git a/.jupyter_cache/executed/e27b680013be7d7e49baa0fa27adc652/base.ipynb b/.jupyter_cache/executed/e27b680013be7d7e49baa0fa27adc652/base.ipynb index 4c35b012..49f02f39 100644 --- a/.jupyter_cache/executed/e27b680013be7d7e49baa0fa27adc652/base.ipynb +++ b/.jupyter_cache/executed/e27b680013be7d7e49baa0fa27adc652/base.ipynb @@ -146,7 +146,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 2, @@ -244,7 +244,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 3, @@ -314,7 +314,7 @@ { "data": { "text/plain": [ - "[1748, 812, 151, 583, 314, 3092]" + "[3439, 125, 38, 32, 676, 1125, 3066, 1511, 3629]" ] }, "execution_count": 6, @@ -335,7 +335,7 @@ { "data": { "text/plain": [ - "21.2781776291676" + "13.777606294870285" ] }, "execution_count": 7, @@ -366,7 +366,7 @@ { "data": { "text/plain": [ - "21.2781776291676" + "13.777606294870285" ] }, "execution_count": 9, @@ -389,8 +389,11 @@ "name": "stderr", "output_type": "stream", "text": [ - "Warning: node '3092', graph '%3' size too small for label\n", - "Warning: node '1748', graph '%3' size too small for label\n" + "Warning: node '3066', graph '%3' size too small for label\n", + "Warning: node '1511', graph '%3' size too small for label\n", + "Warning: node '1125', graph '%3' size too small for label\n", + "Warning: node '3439', graph '%3' size too small for label\n", + "Warning: node '3629', graph '%3' size too small for label\n" ] }, { @@ -402,104 +405,140 @@ "\n", "\n", - "\n", - "\n", + "\n", + "\n", "%3\n", - "\n", - "\n", + "\n", + "\n", "\n", - "314\n", - "\n", - "314\n", + "3066\n", + "\n", + "3066\n", "\n", - "\n", + "\n", "\n", - "3092\n", - "\n", - "3092\n", + "1511\n", + "\n", + "1511\n", "\n", - "\n", + "\n", "\n", - "314->3092\n", - "\n", - "\n", + "3066->1511\n", + "\n", + "\n", "\n", - "\n", - "\n", - "e_6_target\n", - "\n", + "\n", + "\n", + "3629\n", + "\n", + "3629\n", "\n", - "\n", - "\n", - "3092->e_6_target\n", - "\n", - "\n", + "\n", + "\n", + "1511->3629\n", + "\n", + "\n", "\n", - "\n", + "\n", "\n", - "583\n", - "\n", - "583\n", - "\n", - "\n", - "\n", - "583->314\n", - "\n", - "\n", + "32\n", + "\n", + "32\n", "\n", - "\n", + "\n", "\n", - "812\n", + "676\n", "\n", - "812\n", + "676\n", "\n", - "\n", + "\n", + "\n", + "32->676\n", + "\n", + "\n", + "\n", + "\n", "\n", - "151\n", + "1125\n", "\n", - "151\n", + "1125\n", "\n", - "\n", + "\n", "\n", - "812->151\n", + "676->1125\n", "\n", "\n", "\n", - "\n", - "\n", - "151->583\n", + "\n", + "\n", + "1125->3066\n", "\n", "\n", "\n", - "\n", + "\n", "\n", - "1748\n", - "\n", - "1748\n", + "3439\n", + "\n", + "3439\n", + "\n", + "\n", + "\n", + "125\n", + "\n", + "125\n", "\n", - "\n", + "\n", "\n", - "1748->812\n", - "\n", - "\n", + "3439->125\n", + "\n", + "\n", "\n", - "\n", - "\n", - "e_5_source\n", - "\n", + "\n", + "\n", + "38\n", + "\n", + "38\n", "\n", - "\n", + "\n", "\n", - "e_5_source->1748\n", - "\n", - "\n", + "125->38\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "38->32\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "e_9_target\n", + "\n", + "\n", + "\n", + "\n", + "3629->e_9_target\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "e_8_source\n", + "\n", + "\n", + "\n", + "\n", + "e_8_source->3439\n", + "\n", + "\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 10, diff --git a/.jupyter_cache/executed/eacafec4a2dc14df477fd155cfe3cc73/base.ipynb b/.jupyter_cache/executed/eacafec4a2dc14df477fd155cfe3cc73/base.ipynb index 12b41bfc..c9390f76 100644 --- a/.jupyter_cache/executed/eacafec4a2dc14df477fd155cfe3cc73/base.ipynb +++ b/.jupyter_cache/executed/eacafec4a2dc14df477fd155cfe3cc73/base.ipynb @@ -182,35 +182,35 @@ " CVXPY \n", " v1.4.3 \n", "===============================================================================\n", - "(CVXPY) Apr 25 10:40:58 AM: Your problem has 310 variables, 7 constraints, and 0 parameters.\n" + "(CVXPY) Apr 25 10:47:26 AM: Your problem has 310 variables, 7 constraints, and 0 parameters.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:58 AM: It is compliant with the following grammars: DCP, DQCP\n" + "(CVXPY) Apr 25 10:47:26 AM: It is compliant with the following grammars: DCP, DQCP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:58 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" + "(CVXPY) Apr 25 10:47:26 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:58 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" + "(CVXPY) Apr 25 10:47:26 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:58 AM: Your problem is compiled with the CPP canonicalization backend.\n" + "(CVXPY) Apr 25 10:47:26 AM: Your problem is compiled with the CPP canonicalization backend.\n" ] }, { @@ -220,49 +220,49 @@ "-------------------------------------------------------------------------------\n", " Compilation \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:58 AM: Compiling problem (target solver=SCIPY).\n" + "(CVXPY) Apr 25 10:47:26 AM: Compiling problem (target solver=SCIPY).\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:58 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIPY\n" + "(CVXPY) Apr 25 10:47:26 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIPY\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:58 AM: Applying reduction Dcp2Cone\n" + "(CVXPY) Apr 25 10:47:26 AM: Applying reduction Dcp2Cone\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:58 AM: Applying reduction CvxAttr2Constr\n" + "(CVXPY) Apr 25 10:47:26 AM: Applying reduction CvxAttr2Constr\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:58 AM: Applying reduction ConeMatrixStuffing\n" + "(CVXPY) Apr 25 10:47:26 AM: Applying reduction ConeMatrixStuffing\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:58 AM: Applying reduction SCIPY\n" + "(CVXPY) Apr 25 10:47:26 AM: Applying reduction SCIPY\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:58 AM: Finished problem compilation (took 1.355e-02 seconds).\n" + "(CVXPY) Apr 25 10:47:26 AM: Finished problem compilation (took 1.438e-02 seconds).\n" ] }, { @@ -272,7 +272,7 @@ "-------------------------------------------------------------------------------\n", " Numerical solver \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:58 AM: Invoking solver SCIPY to obtain a solution.\n" + "(CVXPY) Apr 25 10:47:26 AM: Invoking solver SCIPY to obtain a solution.\n" ] }, { @@ -283,28 +283,28 @@ "-------------------------------------------------------------------------------\n", " Summary \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:32 AM: Problem status: optimal\n" + "(CVXPY) Apr 25 10:48:00 AM: Problem status: optimal\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: Optimal value: 4.100e+01\n" + "(CVXPY) Apr 25 10:48:00 AM: Optimal value: 4.100e+01\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: Compilation took 1.355e-02 seconds\n" + "(CVXPY) Apr 25 10:48:00 AM: Compilation took 1.438e-02 seconds\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: Solver (including time spent in interface) took 3.391e+01 seconds\n" + "(CVXPY) Apr 25 10:48:00 AM: Solver (including time spent in interface) took 3.394e+01 seconds\n" ] }, { @@ -518,7 +518,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 6, @@ -567,35 +567,35 @@ " CVXPY \n", " v1.4.3 \n", "===============================================================================\n", - "(CVXPY) Apr 25 10:41:32 AM: Your problem has 670 variables, 17 constraints, and 0 parameters.\n" + "(CVXPY) Apr 25 10:48:00 AM: Your problem has 670 variables, 17 constraints, and 0 parameters.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: It is compliant with the following grammars: DCP, DQCP\n" + "(CVXPY) Apr 25 10:48:00 AM: It is compliant with the following grammars: DCP, DQCP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" + "(CVXPY) Apr 25 10:48:00 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" + "(CVXPY) Apr 25 10:48:00 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: Your problem is compiled with the CPP canonicalization backend.\n" + "(CVXPY) Apr 25 10:48:00 AM: Your problem is compiled with the CPP canonicalization backend.\n" ] }, { @@ -605,49 +605,49 @@ "-------------------------------------------------------------------------------\n", " Compilation \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:32 AM: Compiling problem (target solver=SCIPY).\n" + "(CVXPY) Apr 25 10:48:00 AM: Compiling problem (target solver=SCIPY).\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIPY\n" + "(CVXPY) Apr 25 10:48:00 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIPY\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: Applying reduction Dcp2Cone\n" + "(CVXPY) Apr 25 10:48:00 AM: Applying reduction Dcp2Cone\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: Applying reduction CvxAttr2Constr\n" + "(CVXPY) Apr 25 10:48:00 AM: Applying reduction CvxAttr2Constr\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: Applying reduction ConeMatrixStuffing\n" + "(CVXPY) Apr 25 10:48:00 AM: Applying reduction ConeMatrixStuffing\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: Applying reduction SCIPY\n" + "(CVXPY) Apr 25 10:48:00 AM: Applying reduction SCIPY\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: Finished problem compilation (took 2.558e-02 seconds).\n" + "(CVXPY) Apr 25 10:48:00 AM: Finished problem compilation (took 2.385e-02 seconds).\n" ] }, { @@ -657,7 +657,7 @@ "-------------------------------------------------------------------------------\n", " Numerical solver \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:32 AM: Invoking solver SCIPY to obtain a solution.\n" + "(CVXPY) Apr 25 10:48:00 AM: Invoking solver SCIPY to obtain a solution.\n" ] }, { @@ -668,28 +668,28 @@ "-------------------------------------------------------------------------------\n", " Summary \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:49 AM: Problem status: optimal\n" + "(CVXPY) Apr 25 10:48:17 AM: Problem status: optimal\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:49 AM: Optimal value: 4.100e+01\n" + "(CVXPY) Apr 25 10:48:17 AM: Optimal value: 4.100e+01\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:49 AM: Compilation took 2.558e-02 seconds\n" + "(CVXPY) Apr 25 10:48:17 AM: Compilation took 2.385e-02 seconds\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:49 AM: Solver (including time spent in interface) took 1.722e+01 seconds\n" + "(CVXPY) Apr 25 10:48:17 AM: Solver (including time spent in interface) took 1.726e+01 seconds\n" ] }, { @@ -888,7 +888,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 8, diff --git a/.jupyter_cache/global.db b/.jupyter_cache/global.db index 67ed97b4..bcbe5a79 100644 Binary files a/.jupyter_cache/global.db and b/.jupyter_cache/global.db differ diff --git a/jupyter_execute/5dde94a20152e8d2cd3e92c6015a2b3508059abdc232cb0e202f2ac4d7beb885.svg b/jupyter_execute/5dde94a20152e8d2cd3e92c6015a2b3508059abdc232cb0e202f2ac4d7beb885.svg new file mode 100644 index 00000000..e6a182fa --- /dev/null +++ b/jupyter_execute/5dde94a20152e8d2cd3e92c6015a2b3508059abdc232cb0e202f2ac4d7beb885.svg @@ -0,0 +1,2802 @@ + + + + + + +%3 + + + +acald_c + +acald_c 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a/jupyter_execute/guide/interoperability/cvxpy.ipynb +++ b/jupyter_execute/guide/interoperability/cvxpy.ipynb @@ -70,25 +70,25 @@ " CVXPY \n", " v1.4.3 \n", "===============================================================================\n", - "(CVXPY) Apr 25 10:40:00 AM: Your problem has 5 variables, 2 constraints, and 0 parameters.\n", - "(CVXPY) Apr 25 10:40:00 AM: It is compliant with the following grammars: DCP, DQCP\n", - "(CVXPY) Apr 25 10:40:00 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n", - "(CVXPY) Apr 25 10:40:00 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n", - "(CVXPY) Apr 25 10:40:00 AM: Your problem is compiled with the CPP canonicalization backend.\n", + "(CVXPY) Apr 25 10:46:24 AM: Your problem has 5 variables, 2 constraints, and 0 parameters.\n", + "(CVXPY) Apr 25 10:46:24 AM: It is compliant with the following grammars: DCP, DQCP\n", + "(CVXPY) Apr 25 10:46:24 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n", + "(CVXPY) Apr 25 10:46:24 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n", + "(CVXPY) Apr 25 10:46:24 AM: Your problem is compiled with the CPP canonicalization backend.\n", "-------------------------------------------------------------------------------\n", " Compilation \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:00 AM: Compiling problem (target solver=OSQP).\n", - "(CVXPY) Apr 25 10:40:00 AM: Reduction chain: CvxAttr2Constr -> Qp2SymbolicQp -> QpMatrixStuffing -> OSQP\n", - "(CVXPY) Apr 25 10:40:00 AM: Applying reduction CvxAttr2Constr\n", - "(CVXPY) Apr 25 10:40:00 AM: Applying reduction Qp2SymbolicQp\n", - "(CVXPY) Apr 25 10:40:00 AM: Applying reduction QpMatrixStuffing\n", - "(CVXPY) Apr 25 10:40:00 AM: Applying reduction OSQP\n", - "(CVXPY) Apr 25 10:40:00 AM: Finished problem compilation (took 9.753e-03 seconds).\n", + "(CVXPY) Apr 25 10:46:24 AM: Compiling problem (target solver=OSQP).\n", + "(CVXPY) Apr 25 10:46:24 AM: Reduction chain: CvxAttr2Constr -> Qp2SymbolicQp -> QpMatrixStuffing -> OSQP\n", + "(CVXPY) Apr 25 10:46:24 AM: Applying reduction CvxAttr2Constr\n", + "(CVXPY) Apr 25 10:46:24 AM: Applying reduction Qp2SymbolicQp\n", + "(CVXPY) Apr 25 10:46:24 AM: Applying reduction QpMatrixStuffing\n", + "(CVXPY) Apr 25 10:46:24 AM: Applying reduction OSQP\n", + "(CVXPY) Apr 25 10:46:24 AM: Finished problem compilation (took 9.047e-03 seconds).\n", "-------------------------------------------------------------------------------\n", " Numerical solver \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:00 AM: Invoking solver OSQP to obtain a solution.\n", + "(CVXPY) Apr 25 10:46:24 AM: Invoking solver OSQP to obtain a solution.\n", "-----------------------------------------------------------------\n", " OSQP v0.6.3 - Operator Splitting QP Solver\n", " (c) Bartolomeo Stellato, Goran Banjac\n", @@ -106,52 +106,52 @@ " warm start: on, polish: on, time_limit: off\n", "\n", "iter objective pri res dua res rho time\n", - " 1 -5.2220e+00 3.68e+00 1.70e+02 1.00e-01 4.35e-05s\n", - " 150 6.9994e-01 1.96e-05 7.82e-06 4.77e+00 9.17e-05s\n", - "plsh 7.0000e-01 1.95e-30 0.00e+00 -------- 1.20e-04s\n", + " 1 -5.2220e+00 3.68e+00 1.70e+02 1.00e-01 4.43e-05s\n", + " 150 6.9994e-01 1.96e-05 7.82e-06 4.77e+00 9.01e-05s\n", + "plsh 7.0000e-01 1.95e-30 0.00e+00 -------- 1.23e-04s\n", "\n", "status: solved\n", "solution polish: successful\n", "number of iterations: 150\n", "optimal objective: 0.7000\n", - "run time: 1.20e-04s\n", + "run time: 1.23e-04s\n", "optimal rho estimate: 9.81e+00\n", "\n", "-------------------------------------------------------------------------------\n", " Summary \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:00 AM: Problem status: optimal\n", - "(CVXPY) Apr 25 10:40:00 AM: Optimal value: -3.000e-01\n", - "(CVXPY) Apr 25 10:40:00 AM: Compilation took 9.753e-03 seconds\n", - "(CVXPY) Apr 25 10:40:00 AM: Solver (including time spent in interface) took 2.524e-03 seconds\n" + "(CVXPY) Apr 25 10:46:24 AM: Problem status: optimal\n", + "(CVXPY) Apr 25 10:46:24 AM: Optimal value: -3.000e-01\n", + "(CVXPY) Apr 25 10:46:24 AM: Compilation took 9.047e-03 seconds\n", + "(CVXPY) Apr 25 10:46:24 AM: Solver (including time spent in interface) took 1.582e-03 seconds\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: It is compliant with the following grammars: DCP, DQCP\n" + "(CVXPY) Apr 25 10:46:24 AM: It is compliant with the following grammars: DCP, DQCP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" + "(CVXPY) Apr 25 10:46:24 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" + "(CVXPY) Apr 25 10:46:24 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: Your problem is compiled with the CPP canonicalization backend.\n" + "(CVXPY) Apr 25 10:46:24 AM: Your problem is compiled with the CPP canonicalization backend.\n" ] }, { @@ -161,49 +161,49 @@ "-------------------------------------------------------------------------------\n", " Compilation \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:00 AM: Compiling problem (target solver=OSQP).\n" + "(CVXPY) Apr 25 10:46:24 AM: Compiling problem (target solver=OSQP).\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: Reduction chain: CvxAttr2Constr -> Qp2SymbolicQp -> QpMatrixStuffing -> OSQP\n" + "(CVXPY) Apr 25 10:46:24 AM: Reduction chain: CvxAttr2Constr -> Qp2SymbolicQp -> QpMatrixStuffing -> OSQP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: Applying reduction CvxAttr2Constr\n" + "(CVXPY) Apr 25 10:46:24 AM: Applying reduction CvxAttr2Constr\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: Applying reduction Qp2SymbolicQp\n" + "(CVXPY) Apr 25 10:46:24 AM: Applying reduction Qp2SymbolicQp\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: Applying reduction QpMatrixStuffing\n" + "(CVXPY) Apr 25 10:46:24 AM: Applying reduction QpMatrixStuffing\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: Applying reduction OSQP\n" + "(CVXPY) Apr 25 10:46:24 AM: Applying reduction OSQP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: Finished problem compilation (took 9.753e-03 seconds).\n" + "(CVXPY) Apr 25 10:46:24 AM: Finished problem compilation (took 9.047e-03 seconds).\n" ] }, { @@ -213,7 +213,7 @@ "-------------------------------------------------------------------------------\n", " Numerical solver \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:00 AM: Invoking solver OSQP to obtain a solution.\n" + "(CVXPY) Apr 25 10:46:24 AM: Invoking solver OSQP to obtain a solution.\n" ] }, { @@ -237,42 +237,42 @@ " warm start: on, polish: on, time_limit: off\n", "\n", "iter objective pri res dua res rho time\n", - " 1 -5.2220e+00 3.68e+00 1.70e+02 1.00e-01 4.35e-05s\n", - " 150 6.9994e-01 1.96e-05 7.82e-06 4.77e+00 9.17e-05s\n", - "plsh 7.0000e-01 1.95e-30 0.00e+00 -------- 1.20e-04s\n", + " 1 -5.2220e+00 3.68e+00 1.70e+02 1.00e-01 4.43e-05s\n", + " 150 6.9994e-01 1.96e-05 7.82e-06 4.77e+00 9.01e-05s\n", + "plsh 7.0000e-01 1.95e-30 0.00e+00 -------- 1.23e-04s\n", "\n", "status: solved\n", "solution polish: successful\n", "number of iterations: 150\n", "optimal objective: 0.7000\n", - "run time: 1.20e-04s\n", + "run time: 1.23e-04s\n", "optimal rho estimate: 9.81e+00\n", "\n", "-------------------------------------------------------------------------------\n", " Summary \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:00 AM: Problem status: optimal\n" + "(CVXPY) Apr 25 10:46:24 AM: Problem status: optimal\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: Optimal value: -3.000e-01\n" + "(CVXPY) Apr 25 10:46:24 AM: Optimal value: -3.000e-01\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: Compilation took 9.753e-03 seconds\n" + "(CVXPY) Apr 25 10:46:24 AM: Compilation took 9.047e-03 seconds\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:00 AM: Solver (including time spent in interface) took 2.524e-03 seconds\n" + "(CVXPY) Apr 25 10:46:24 AM: Solver (including time spent in interface) took 1.582e-03 seconds\n" ] } ], diff --git a/jupyter_execute/guide/interoperability/networkx.ipynb b/jupyter_execute/guide/interoperability/networkx.ipynb index f0b8612f..f5bce1b1 100644 --- a/jupyter_execute/guide/interoperability/networkx.ipynb +++ b/jupyter_execute/guide/interoperability/networkx.ipynb @@ -230,7 +230,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 5, diff --git a/jupyter_execute/guide/interoperability/picos.ipynb b/jupyter_execute/guide/interoperability/picos.ipynb index 2e6cd2c3..26a22e22 100644 --- a/jupyter_execute/guide/interoperability/picos.ipynb +++ b/jupyter_execute/guide/interoperability/picos.ipynb @@ -102,7 +102,7 @@ "Solver claims optimal solution for feasible problem.\n", "Applying the solution.\n", "Applied solution is primal feasible.\n", - "Search 1.4e-02s, solve 1.9e-02s, overhead 31%.\n", + "Search 1.4e-02s, solve 1.9e-02s, overhead 34%.\n", "=============[ PICOS ]=============\n" ] }, @@ -147,7 +147,7 @@ "Solver claims optimal solution for feasible problem.\n", "Applying the solution.\n", "Applied solution is primal feasible.\n", - "Search 1.4e-02s, solve 1.9e-02s, overhead 31%.\n", + "Search 1.4e-02s, solve 1.9e-02s, overhead 34%.\n", "=============[ PICOS ]=============\n" ] } diff --git a/jupyter_execute/guide/intro/acyclic-flows.ipynb b/jupyter_execute/guide/intro/acyclic-flows.ipynb index 4a474269..3df6fb43 100644 --- a/jupyter_execute/guide/intro/acyclic-flows.ipynb +++ b/jupyter_execute/guide/intro/acyclic-flows.ipynb @@ -204,7 +204,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 2, @@ -405,7 +405,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 3, @@ -592,7 +592,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 6, @@ -864,7 +864,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 8, @@ -1043,7 +1043,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 11, diff --git a/jupyter_execute/guide/intro/constrained-optimization.ipynb b/jupyter_execute/guide/intro/constrained-optimization.ipynb index 62f4bb22..77511c89 100644 --- a/jupyter_execute/guide/intro/constrained-optimization.ipynb +++ b/jupyter_execute/guide/intro/constrained-optimization.ipynb @@ -93,7 +93,7 @@ { "data": { "text/plain": [ - "" + "" ] }, "execution_count": 2, @@ -147,7 +147,7 @@ { "data": { "text/plain": [ - "" + "" ] }, "execution_count": 4, @@ -254,29 +254,31 @@ " CVXPY \n", " v1.4.3 \n", "===============================================================================\n", - "(CVXPY) Apr 25 10:40:09 AM: Your problem has 50 variables, 1 constraints, and 0 parameters.\n", - "(CVXPY) Apr 25 10:40:09 AM: It is compliant with the following grammars: DCP, DQCP\n", - "(CVXPY) Apr 25 10:40:09 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n", - "(CVXPY) Apr 25 10:40:09 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n", - "(CVXPY) Apr 25 10:40:09 AM: Your problem is compiled with the CPP canonicalization backend.\n", + "(CVXPY) Apr 25 10:46:32 AM: Your problem has 50 variables, 1 constraints, and 0 parameters.\n", + "(CVXPY) Apr 25 10:46:32 AM: It is compliant with the following grammars: DCP, DQCP\n", + "(CVXPY) Apr 25 10:46:32 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n", + "(CVXPY) Apr 25 10:46:32 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n", + "(CVXPY) Apr 25 10:46:32 AM: Your problem is compiled with the CPP canonicalization backend.\n", "-------------------------------------------------------------------------------\n", " Compilation \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:09 AM: Compiling problem (target solver=SCIP).\n", - "(CVXPY) Apr 25 10:40:09 AM: Reduction chain: FlipObjective -> Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP\n", - "(CVXPY) Apr 25 10:40:09 AM: Applying reduction FlipObjective\n", - "(CVXPY) Apr 25 10:40:09 AM: Applying reduction Dcp2Cone\n", - "(CVXPY) Apr 25 10:40:09 AM: Applying reduction CvxAttr2Constr\n", - "(CVXPY) Apr 25 10:40:09 AM: Applying reduction ConeMatrixStuffing\n", - "(CVXPY) Apr 25 10:40:09 AM: Applying reduction SCIP\n", - "(CVXPY) Apr 25 10:40:09 AM: Finished problem compilation (took 8.441e-03 seconds).\n", + "(CVXPY) Apr 25 10:46:32 AM: Compiling problem (target solver=SCIP).\n", + "(CVXPY) Apr 25 10:46:32 AM: Reduction chain: FlipObjective -> Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP\n", + "(CVXPY) Apr 25 10:46:32 AM: Applying reduction FlipObjective\n", + "(CVXPY) Apr 25 10:46:32 AM: Applying reduction Dcp2Cone\n", + "(CVXPY) Apr 25 10:46:32 AM: Applying reduction CvxAttr2Constr\n", + "(CVXPY) Apr 25 10:46:32 AM: Applying reduction ConeMatrixStuffing\n", + "(CVXPY) Apr 25 10:46:32 AM: Applying reduction SCIP\n", + "(CVXPY) Apr 25 10:46:32 AM: Finished problem compilation (took 8.368e-03 seconds).\n", "-------------------------------------------------------------------------------\n", " Numerical solver \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:09 AM: Invoking solver SCIP to obtain a solution.\n", + "(CVXPY) Apr 25 10:46:32 AM: Invoking solver SCIP to obtain a solution.\n", "-------------------------------------------------------------------------------\n", " Summary \n", - "-------------------------------------------------------------------------------feasible solution found by trivial heuristic after 0.0 seconds, objective value -6.000000e+02\n", + "-------------------------------------------------------------------------------\n", + "(CVXPY) Apr 25 10:46:32 AM: Problem status: optimal\n", + "feasible solution found by trivial heuristic after 0.0 seconds, objective value -6.000000e+02\n", "presolving:\n", "(round 1, fast) 4 del vars, 0 del conss, 0 add conss, 0 chg bounds, 0 chg sides, 0 chg coeffs, 0 upgd conss, 0 impls, 0 clqs\n", "(round 2, exhaustive) 4 del vars, 0 del conss, 0 add conss, 0 chg bounds, 0 chg sides, 0 chg coeffs, 1 upgd conss, 0 impls, 0 clqs\n", @@ -293,39 +295,37 @@ "Primal Bound : -7.53400000000000e+03 (3 solutions)\n", "Dual Bound : -7.53400000000000e+03\n", "Gap : 0.00 %\n", - "\n", - "(CVXPY) Apr 25 10:40:09 AM: Problem status: optimal\n", - "(CVXPY) Apr 25 10:40:09 AM: Optimal value: 7.534e+03\n", - "(CVXPY) Apr 25 10:40:09 AM: Compilation took 8.441e-03 seconds\n", - "(CVXPY) Apr 25 10:40:09 AM: Solver (including time spent in interface) took 3.624e-03 seconds\n" + "(CVXPY) Apr 25 10:46:32 AM: Optimal value: 7.534e+03\n", + "(CVXPY) Apr 25 10:46:32 AM: Compilation took 8.368e-03 seconds\n", + "(CVXPY) Apr 25 10:46:32 AM: Solver (including time spent in interface) took 3.592e-03 seconds\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: It is compliant with the following grammars: DCP, DQCP\n" + "(CVXPY) Apr 25 10:46:32 AM: It is compliant with the following grammars: DCP, DQCP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" + "(CVXPY) Apr 25 10:46:32 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" + "(CVXPY) Apr 25 10:46:32 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Your problem is compiled with the CPP canonicalization backend.\n" + "(CVXPY) Apr 25 10:46:32 AM: Your problem is compiled with the CPP canonicalization backend.\n" ] }, { @@ -335,56 +335,56 @@ "-------------------------------------------------------------------------------\n", " Compilation \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:09 AM: Compiling problem (target solver=SCIP).\n" + "(CVXPY) Apr 25 10:46:32 AM: Compiling problem (target solver=SCIP).\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Reduction chain: FlipObjective -> Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP\n" + "(CVXPY) Apr 25 10:46:32 AM: Reduction chain: FlipObjective -> Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Applying reduction FlipObjective\n" + "(CVXPY) Apr 25 10:46:32 AM: Applying reduction FlipObjective\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Applying reduction Dcp2Cone\n" + "(CVXPY) Apr 25 10:46:32 AM: Applying reduction Dcp2Cone\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Applying reduction CvxAttr2Constr\n" + "(CVXPY) Apr 25 10:46:32 AM: Applying reduction CvxAttr2Constr\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Applying reduction ConeMatrixStuffing\n" + "(CVXPY) Apr 25 10:46:32 AM: Applying reduction ConeMatrixStuffing\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Applying reduction SCIP\n" + "(CVXPY) Apr 25 10:46:32 AM: Applying reduction SCIP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Finished problem compilation (took 8.441e-03 seconds).\n" + "(CVXPY) Apr 25 10:46:32 AM: Finished problem compilation (took 8.368e-03 seconds).\n" ] }, { @@ -394,7 +394,7 @@ "-------------------------------------------------------------------------------\n", " Numerical solver \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:09 AM: Invoking solver SCIP to obtain a solution.\n" + "(CVXPY) Apr 25 10:46:32 AM: Invoking solver SCIP to obtain a solution.\n" ] }, { @@ -403,7 +403,9 @@ "text": [ "-------------------------------------------------------------------------------\n", " Summary \n", - "-------------------------------------------------------------------------------feasible solution found by trivial heuristic after 0.0 seconds, objective value -6.000000e+02\n", + "-------------------------------------------------------------------------------\n", + "(CVXPY) Apr 25 10:46:32 AM: Problem status: optimal\n", + "feasible solution found by trivial heuristic after 0.0 seconds, objective value -6.000000e+02\n", "presolving:\n", "(round 1, fast) 4 del vars, 0 del conss, 0 add conss, 0 chg bounds, 0 chg sides, 0 chg coeffs, 0 upgd conss, 0 impls, 0 clqs\n", "(round 2, exhaustive) 4 del vars, 0 del conss, 0 add conss, 0 chg bounds, 0 chg sides, 0 chg coeffs, 1 upgd conss, 0 impls, 0 clqs\n", @@ -419,30 +421,28 @@ "Solving Nodes : 0\n", "Primal Bound : -7.53400000000000e+03 (3 solutions)\n", "Dual Bound : -7.53400000000000e+03\n", - "Gap : 0.00 %\n", - "\n", - "(CVXPY) Apr 25 10:40:09 AM: Problem status: optimal\n" + "Gap : 0.00 %\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Optimal value: 7.534e+03\n" + "(CVXPY) Apr 25 10:46:32 AM: Optimal value: 7.534e+03\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Compilation took 8.441e-03 seconds\n" + "(CVXPY) Apr 25 10:46:32 AM: Compilation took 8.368e-03 seconds\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:09 AM: Solver (including time spent in interface) took 3.624e-03 seconds\n" + "(CVXPY) Apr 25 10:46:32 AM: Solver (including time spent in interface) took 3.592e-03 seconds\n" ] }, { diff --git a/jupyter_execute/guide/intro/multi-commodity-network-flows.ipynb b/jupyter_execute/guide/intro/multi-commodity-network-flows.ipynb index 65db58cb..e98057a6 100644 --- a/jupyter_execute/guide/intro/multi-commodity-network-flows.ipynb +++ b/jupyter_execute/guide/intro/multi-commodity-network-flows.ipynb @@ -145,7 +145,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 2, @@ -304,7 +304,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 3, @@ -404,29 +404,29 @@ " CVXPY \n", " v1.4.3 \n", "===============================================================================\n", - "(CVXPY) Apr 25 10:40:10 AM: Your problem has 20 variables, 5 constraints, and 0 parameters.\n", - "(CVXPY) Apr 25 10:40:10 AM: It is compliant with the following grammars: DCP, DQCP\n", - "(CVXPY) Apr 25 10:40:10 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n", - "(CVXPY) Apr 25 10:40:10 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n", - "(CVXPY) Apr 25 10:40:10 AM: Your problem is compiled with the CPP canonicalization backend.\n", + "(CVXPY) Apr 25 10:46:33 AM: Your problem has 20 variables, 5 constraints, and 0 parameters.\n", + "(CVXPY) Apr 25 10:46:33 AM: It is compliant with the following grammars: DCP, DQCP\n", + "(CVXPY) Apr 25 10:46:33 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n", + "(CVXPY) Apr 25 10:46:33 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n", + "(CVXPY) Apr 25 10:46:33 AM: Your problem is compiled with the CPP canonicalization backend.\n", "-------------------------------------------------------------------------------\n", " Compilation \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:10 AM: Compiling problem (target solver=SCIP).\n", - "(CVXPY) Apr 25 10:40:10 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP\n", - "(CVXPY) Apr 25 10:40:10 AM: Applying reduction Dcp2Cone\n", - "(CVXPY) Apr 25 10:40:10 AM: Applying reduction CvxAttr2Constr\n", - "(CVXPY) Apr 25 10:40:10 AM: Applying reduction ConeMatrixStuffing\n", - "(CVXPY) Apr 25 10:40:10 AM: Applying reduction SCIP\n", - "(CVXPY) Apr 25 10:40:10 AM: Finished problem compilation (took 1.412e-02 seconds).\n", + "(CVXPY) Apr 25 10:46:33 AM: Compiling problem (target solver=SCIP).\n", + "(CVXPY) Apr 25 10:46:33 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP\n", + "(CVXPY) Apr 25 10:46:33 AM: Applying reduction Dcp2Cone\n", + "(CVXPY) Apr 25 10:46:33 AM: Applying reduction CvxAttr2Constr\n", + "(CVXPY) Apr 25 10:46:33 AM: Applying reduction ConeMatrixStuffing\n", + "(CVXPY) Apr 25 10:46:33 AM: Applying reduction SCIP\n", + "(CVXPY) Apr 25 10:46:33 AM: Finished problem compilation (took 1.440e-02 seconds).\n", "-------------------------------------------------------------------------------\n", " Numerical solver \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:10 AM: Invoking solver SCIP to obtain a solution.\n", + "(CVXPY) Apr 25 10:46:33 AM: Invoking solver SCIP to obtain a solution.\n", "-------------------------------------------------------------------------------\n", " Summary \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:10 AM: Problem status: optimal\n", + "(CVXPY) Apr 25 10:46:33 AM: Problem status: optimal\n", "presolving:\n", " (0.0s) symmetry computation started: requiring (bin +, int +, cont +), (fixed: bin -, int -, cont -)\n", " (0.0s) no symmetry present (symcode time: 0.00)\n", @@ -447,37 +447,37 @@ "Primal Bound : -1.90000000000000e+02 (1 solutions)\n", "Dual Bound : -1.90000000000000e+02\n", "Gap : 0.00 %\n", - "(CVXPY) Apr 25 10:40:10 AM: Optimal value: -1.900e+02\n", - "(CVXPY) Apr 25 10:40:10 AM: Compilation took 1.412e-02 seconds\n", - "(CVXPY) Apr 25 10:40:10 AM: Solver (including time spent in interface) took 6.421e-03 seconds\n" + "(CVXPY) Apr 25 10:46:33 AM: Optimal value: -1.900e+02\n", + "(CVXPY) Apr 25 10:46:33 AM: Compilation took 1.440e-02 seconds\n", + "(CVXPY) Apr 25 10:46:33 AM: Solver (including time spent in interface) took 6.373e-03 seconds\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: It is compliant with the following grammars: DCP, DQCP\n" + "(CVXPY) Apr 25 10:46:33 AM: It is compliant with the following grammars: DCP, DQCP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" + "(CVXPY) Apr 25 10:46:33 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" + "(CVXPY) Apr 25 10:46:33 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: Your problem is compiled with the CPP canonicalization backend.\n" + "(CVXPY) Apr 25 10:46:33 AM: Your problem is compiled with the CPP canonicalization backend.\n" ] }, { @@ -487,49 +487,49 @@ "-------------------------------------------------------------------------------\n", " Compilation \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:10 AM: Compiling problem (target solver=SCIP).\n" + "(CVXPY) Apr 25 10:46:33 AM: Compiling problem (target solver=SCIP).\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP\n" + "(CVXPY) Apr 25 10:46:33 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: Applying reduction Dcp2Cone\n" + "(CVXPY) Apr 25 10:46:33 AM: Applying reduction Dcp2Cone\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: Applying reduction CvxAttr2Constr\n" + "(CVXPY) Apr 25 10:46:33 AM: Applying reduction CvxAttr2Constr\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: Applying reduction ConeMatrixStuffing\n" + "(CVXPY) Apr 25 10:46:33 AM: Applying reduction ConeMatrixStuffing\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: Applying reduction SCIP\n" + "(CVXPY) Apr 25 10:46:33 AM: Applying reduction SCIP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: Finished problem compilation (took 1.412e-02 seconds).\n" + "(CVXPY) Apr 25 10:46:33 AM: Finished problem compilation (took 1.440e-02 seconds).\n" ] }, { @@ -539,7 +539,7 @@ "-------------------------------------------------------------------------------\n", " Numerical solver \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:10 AM: Invoking solver SCIP to obtain a solution.\n" + "(CVXPY) Apr 25 10:46:33 AM: Invoking solver SCIP to obtain a solution.\n" ] }, { @@ -549,7 +549,13 @@ "-------------------------------------------------------------------------------\n", " Summary \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:10 AM: Problem status: optimal\n", + "(CVXPY) Apr 25 10:46:33 AM: Problem status: optimal\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ "presolving:\n", " (0.0s) symmetry computation started: requiring (bin +, int +, cont +), (fixed: bin -, int -, cont -)\n", " (0.0s) no symmetry present (symcode time: 0.00)\n", @@ -569,28 +575,22 @@ "Solving Nodes : 1\n", "Primal Bound : -1.90000000000000e+02 (1 solutions)\n", "Dual Bound : -1.90000000000000e+02\n", - "Gap : 0.00 %\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "(CVXPY) Apr 25 10:40:10 AM: Optimal value: -1.900e+02\n" + "Gap : 0.00 %\n", + "(CVXPY) Apr 25 10:46:33 AM: Optimal value: -1.900e+02\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: Compilation took 1.412e-02 seconds\n" + "(CVXPY) Apr 25 10:46:33 AM: Compilation took 1.440e-02 seconds\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:10 AM: Solver (including time spent in interface) took 6.421e-03 seconds\n" + "(CVXPY) Apr 25 10:46:33 AM: Solver (including time spent in interface) took 6.373e-03 seconds\n" ] }, { diff --git a/jupyter_execute/guide/intro/prior-knowledge.ipynb b/jupyter_execute/guide/intro/prior-knowledge.ipynb index 14e81205..a2041141 100644 --- a/jupyter_execute/guide/intro/prior-knowledge.ipynb +++ b/jupyter_execute/guide/intro/prior-knowledge.ipynb @@ -125,7 +125,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 2, @@ -227,7 +227,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 3, @@ -331,7 +331,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 4, @@ -595,7 +595,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 12, @@ -757,7 +757,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 16, @@ -806,31 +806,31 @@ "\n", "%3\n", "\n", - "\n", + "\n", "\n", - "A\n", + "B\n", "\n", - "A\n", + "B\n", "\n", "\n", "\n", "e_0_center\n", "\n", "\n", - "\n", + "\n", "\n", - "A->e_0_center\n", + "B->e_0_center\n", "\n", "\n", - "\n", + "\n", "\n", - "B\n", + "A\n", "\n", - "B\n", + "A\n", "\n", - "\n", + "\n", "\n", - "B->e_0_center\n", + "A->e_0_center\n", "\n", "\n", "\n", @@ -917,30 +917,30 @@ "\n", "\n", "e_2_source\n", - "\n", + "\n", "\n", "\n", "\n", "e_2_source->A\n", - "\n", - "\n", + "\n", + "\n", "\n", "\n", "\n", "e_3_source\n", - "\n", + "\n", "\n", "\n", "\n", "e_3_source->B\n", - "\n", - "\n", + "\n", + "\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 17, diff --git a/jupyter_execute/guide/metabolism/flux-balance-analysis.ipynb b/jupyter_execute/guide/metabolism/flux-balance-analysis.ipynb index 3c9de426..25e56615 100644 --- a/jupyter_execute/guide/metabolism/flux-balance-analysis.ipynb +++ b/jupyter_execute/guide/metabolism/flux-balance-analysis.ipynb @@ -97,7 +97,7 @@ " NameBiomass Objective Function with GAM\n", " \n", " Memory address\n", - " 0x7f4ff9f4e350\n", + " 0x7fefbc1edfd0\n", " \n", " Stoichiometry\n", " \n", @@ -115,7 +115,7 @@ " " ], "text/plain": [ - "" + "" ] }, "execution_count": 2, @@ -138,7 +138,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "\n" + "\n" ] } ], @@ -265,35 +265,35 @@ "output_type": "stream", "text": [ "Warning: node 'acald_c', graph '%3' size too small for label\n", - "Warning: node 'nad_c', graph '%3' size too small for label\n", "Warning: node 'coa_c', graph '%3' size too small for label\n", + "Warning: node 'nad_c', graph '%3' size too small for label\n", "Warning: node 'accoa_c', graph '%3' size too small for label\n", "Warning: node 'nadh_c', graph '%3' size too small for label\n", "Warning: node 'acald_e', graph '%3' size too small for label\n", "Warning: node 'atp_c', graph '%3' size too small for label\n", - "Warning: node 'adp_c', graph '%3' size too small for label\n", "Warning: node 'actp_c', graph '%3' size too small for label\n", + "Warning: node 'adp_c', graph '%3' size too small for label\n", "Warning: node 'acon_C_c', graph '%3' size too small for label\n", "Warning: node 'h2o_c', graph '%3' size too small for label\n", "Warning: node 'icit_c', graph '%3' size too small for label\n", "Warning: node 'amp_c', graph '%3' size too small for label\n", "Warning: node 'akg_c', graph '%3' size too small for label\n", - "Warning: node 'succoa_c', graph '%3' size too small for label\n", "Warning: node 'co2_c', graph '%3' size too small for label\n", + "Warning: node 'succoa_c', graph '%3' size too small for label\n", "Warning: node 'akg_e', graph '%3' size too small for label\n", "Warning: node 'etoh_c', graph '%3' size too small for label\n", - "Warning: node 'r5p_c', graph '%3' size too small for label\n", - "Warning: node '3pg_c', graph '%3' size too small for label\n", - "Warning: node 'gln__L_c', graph '%3' size too small for label\n", + "Warning: node 'nadph_c', graph '%3' size too small for label\n", + "Warning: node 'g3p_c', graph '%3' size too small for label\n", "Warning: node 'glu__L_c', graph '%3' size too small for label\n", - "Warning: node 'f6p_c', graph '%3' size too small for label\n", - "Warning: node 'pyr_c', graph '%3' size too small for label\n", "Warning: node 'oaa_c', graph '%3' size too small for label\n", - "Warning: node 'pep_c', graph '%3' size too small for label\n", - "Warning: node 'nadph_c', graph '%3' size too small for label\n", + "Warning: node 'pyr_c', graph '%3' size too small for label\n", "Warning: node 'e4p_c', graph '%3' size too small for label\n", - "Warning: node 'g3p_c', graph '%3' size too small for label\n", + "Warning: node 'r5p_c', graph '%3' size too small for label\n", + "Warning: node 'gln__L_c', graph '%3' size too small for label\n", "Warning: node 'g6p_c', graph '%3' size too small for label\n", + "Warning: node 'pep_c', graph '%3' size too small for label\n", + "Warning: node 'f6p_c', graph '%3' size too small for label\n", + "Warning: node '3pg_c', graph '%3' size too small for label\n", "Warning: node 'nadp_c', graph '%3' size too small for label\n", "Warning: node 'co2_e', graph '%3' size too small for label\n", "Warning: node 'q8h2_c', graph '%3' size too small for label\n", @@ -335,2805 +335,2805 @@ "\n", "\n", - "\n", - "\n", + "\n", + "\n", "%3\n", - "\n", + "\n", "\n", "\n", "acald_c\n", - "\n", - "acald_c\n", + "\n", + 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'co2_c', graph '%3' size too small for label\n", + "Warning: node 'succoa_c', graph '%3' size too small for label\n", "Warning: node 'akg_e', graph '%3' size too small for label\n", "Warning: node 'etoh_c', graph '%3' size too small for label\n", - "Warning: node 'r5p_c', graph '%3' size too small for label\n", - "Warning: node '3pg_c', graph '%3' size too small for label\n", - "Warning: node 'gln__L_c', graph '%3' size too small for label\n", + "Warning: node 'nadph_c', graph '%3' size too small for label\n", + "Warning: node 'g3p_c', graph '%3' size too small for label\n", "Warning: node 'glu__L_c', graph '%3' size too small for label\n", - "Warning: node 'f6p_c', graph '%3' size too small for label\n", - "Warning: node 'pyr_c', graph '%3' size too small for label\n", "Warning: node 'oaa_c', graph '%3' size too small for label\n", - "Warning: node 'pep_c', graph '%3' size too small for label\n", - "Warning: node 'nadph_c', graph '%3' size too small for label\n", + "Warning: node 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"text/plain": [ - "" + "" ] }, "execution_count": 2, @@ -490,7 +490,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 5, @@ -731,7 +731,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 6, diff --git a/jupyter_execute/guide/metabolism/sparse-fba.ipynb b/jupyter_execute/guide/metabolism/sparse-fba.ipynb index addb5942..62e608c4 100644 --- a/jupyter_execute/guide/metabolism/sparse-fba.ipynb +++ b/jupyter_execute/guide/metabolism/sparse-fba.ipynb @@ -158,36 +158,36 @@ "name": "stderr", "output_type": "stream", "text": [ - "Warning: node 'nad_c', graph '%3' size too small for label\n", "Warning: node 'coa_c', graph '%3' size too small for label\n", "Warning: node 'acald_c', graph '%3' size too small for label\n", + "Warning: node 'nad_c', graph '%3' size too small for label\n", "Warning: node 'nadh_c', graph '%3' size too small for label\n", "Warning: node 'accoa_c', graph '%3' size too small for label\n", "Warning: node 'acald_e', graph '%3' size too small for label\n", "Warning: node 'atp_c', graph '%3' size too small for label\n", "Warning: node 'adp_c', graph '%3' size too small for label\n", "Warning: node 'actp_c', graph '%3' size too small for label\n", - "Warning: node 'acon_C_c', graph '%3' size too small for label\n", "Warning: node 'h2o_c', graph '%3' size too small for label\n", + "Warning: node 'acon_C_c', graph '%3' size too small for label\n", "Warning: node 'icit_c', graph '%3' size too small for label\n", "Warning: node 'amp_c', graph '%3' size too small for label\n", "Warning: node 'akg_c', graph '%3' size too small for label\n", - "Warning: node 'succoa_c', graph '%3' size too small for label\n", "Warning: node 'co2_c', graph '%3' size too small for label\n", + "Warning: node 'succoa_c', graph '%3' size too small for label\n", "Warning: node 'akg_e', graph '%3' size too small for label\n", "Warning: node 'etoh_c', graph '%3' size too small for label\n", - "Warning: node 'e4p_c', graph '%3' size too small for label\n", - "Warning: node 'glu__L_c', graph '%3' size too small for label\n", - "Warning: node 'pep_c', graph '%3' size too small for label\n", + "Warning: node 'gln__L_c', graph '%3' size too small for label\n", "Warning: node '3pg_c', graph '%3' size too small for label\n", + "Warning: node 'f6p_c', graph '%3' size too small for label\n", "Warning: node 'pyr_c', graph '%3' size too small for label\n", + "Warning: node 'r5p_c', graph '%3' size too small for label\n", + "Warning: node 'e4p_c', graph '%3' size too small for label\n", + "Warning: node 'g3p_c', graph '%3' size too small for label\n", "Warning: node 'g6p_c', graph '%3' size too small for label\n", + "Warning: node 'pep_c', graph '%3' size too small for label\n", "Warning: node 'oaa_c', graph '%3' size too small for label\n", - "Warning: node 'f6p_c', graph '%3' size too small for label\n", - "Warning: node 'g3p_c', graph '%3' size too small for label\n", "Warning: node 'nadph_c', graph '%3' size too small for label\n", - "Warning: 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graph '%3' size too small for label\n", "Warning: node 'akg_c', graph '%3' size too small for label\n", - "Warning: node 'succoa_c', graph '%3' size too small for label\n", "Warning: node 'co2_c', graph '%3' size too small for label\n", + "Warning: node 'succoa_c', graph '%3' size too small for label\n", "Warning: node 'akg_e', graph '%3' size too small for label\n", "Warning: node 'etoh_c', graph '%3' size too small for label\n", - "Warning: node 'e4p_c', graph '%3' size too small for label\n", - "Warning: node 'glu__L_c', graph '%3' size too small for label\n", - "Warning: node 'pep_c', graph '%3' size too small for label\n", + "Warning: node 'gln__L_c', graph '%3' size too small for label\n", "Warning: node '3pg_c', graph '%3' size too small for label\n", + "Warning: node 'f6p_c', graph '%3' size too small for label\n", "Warning: node 'pyr_c', graph '%3' size too small for label\n", + "Warning: node 'r5p_c', graph '%3' size too small for label\n", + "Warning: node 'e4p_c', graph 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b/jupyter_execute/guide/networks/shortest-paths.ipynb @@ -172,7 +172,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 2, @@ -270,7 +270,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 3, @@ -348,7 +348,7 @@ { "data": { "text/plain": [ - "[1748, 812, 151, 583, 314, 3092]" + "[3439, 125, 38, 32, 676, 1125, 3066, 1511, 3629]" ] }, "execution_count": 6, @@ -369,7 +369,7 @@ { "data": { "text/plain": [ - "21.2781776291676" + "13.777606294870285" ] }, "execution_count": 7, @@ -400,7 +400,7 @@ { "data": { "text/plain": [ - "21.2781776291676" + "13.777606294870285" ] }, "execution_count": 9, @@ -423,8 +423,11 @@ "name": "stderr", "output_type": "stream", "text": [ - "Warning: node '3092', graph '%3' size too small for label\n", - "Warning: node '1748', graph '%3' size too small for label\n" + "Warning: node '3066', graph '%3' size too small for label\n", + "Warning: node '1511', graph '%3' size too small for label\n", + "Warning: node '1125', graph '%3' size too small for label\n", + "Warning: node '3439', graph '%3' size too small for label\n", + "Warning: node '3629', graph '%3' size too small for label\n" ] }, { @@ -436,104 +439,140 @@ "\n", "\n", - "\n", - "\n", + "\n", + "\n", "%3\n", - "\n", - "\n", + "\n", + "\n", "\n", - "314\n", - "\n", - "314\n", + "3066\n", + "\n", + "3066\n", "\n", - "\n", + "\n", "\n", - "3092\n", - "\n", - "3092\n", + "1511\n", + "\n", + "1511\n", "\n", - "\n", + "\n", "\n", - "314->3092\n", - "\n", - "\n", + "3066->1511\n", + "\n", + "\n", "\n", - "\n", - "\n", - "e_6_target\n", - "\n", + "\n", + "\n", + "3629\n", + "\n", + "3629\n", "\n", - "\n", - "\n", - "3092->e_6_target\n", - "\n", - "\n", + "\n", + "\n", + "1511->3629\n", + "\n", + "\n", "\n", - "\n", + "\n", "\n", - "583\n", - "\n", - "583\n", - "\n", - "\n", - "\n", - "583->314\n", - "\n", - "\n", + "32\n", + "\n", + "32\n", "\n", - "\n", + "\n", "\n", - "812\n", + "676\n", "\n", - "812\n", + "676\n", "\n", - "\n", + "\n", + "\n", + "32->676\n", + "\n", 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}, "execution_count": 10, diff --git a/jupyter_execute/guide/networks/steiner-trees.ipynb b/jupyter_execute/guide/networks/steiner-trees.ipynb index e977c2c7..e46d0e38 100644 --- a/jupyter_execute/guide/networks/steiner-trees.ipynb +++ b/jupyter_execute/guide/networks/steiner-trees.ipynb @@ -254,61 +254,61 @@ " CVXPY \n", " v1.4.3 \n", "===============================================================================\n", - "(CVXPY) Apr 25 10:40:58 AM: Your problem has 310 variables, 7 constraints, and 0 parameters.\n", - "(CVXPY) Apr 25 10:40:58 AM: It is compliant with the following grammars: DCP, DQCP\n", - "(CVXPY) Apr 25 10:40:58 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n", - "(CVXPY) Apr 25 10:40:58 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n", - "(CVXPY) Apr 25 10:40:58 AM: Your problem is compiled with the CPP canonicalization backend.\n", + "(CVXPY) Apr 25 10:47:26 AM: Your problem has 310 variables, 7 constraints, and 0 parameters.\n", + "(CVXPY) Apr 25 10:47:26 AM: It is compliant with the following grammars: DCP, DQCP\n", + "(CVXPY) Apr 25 10:47:26 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n", + "(CVXPY) Apr 25 10:47:26 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n", + "(CVXPY) Apr 25 10:47:26 AM: Your problem is compiled with the CPP canonicalization backend.\n", "-------------------------------------------------------------------------------\n", " Compilation \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:58 AM: Compiling problem (target solver=SCIPY).\n", - "(CVXPY) Apr 25 10:40:58 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIPY\n", - "(CVXPY) Apr 25 10:40:58 AM: Applying reduction Dcp2Cone\n", - "(CVXPY) Apr 25 10:40:58 AM: Applying reduction CvxAttr2Constr\n", - "(CVXPY) Apr 25 10:40:58 AM: Applying reduction ConeMatrixStuffing\n", - "(CVXPY) Apr 25 10:40:58 AM: Applying reduction SCIPY\n", - "(CVXPY) Apr 25 10:40:58 AM: Finished problem compilation (took 1.355e-02 seconds).\n", + "(CVXPY) Apr 25 10:47:26 AM: Compiling problem (target solver=SCIPY).\n", + "(CVXPY) Apr 25 10:47:26 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIPY\n", + "(CVXPY) Apr 25 10:47:26 AM: Applying reduction Dcp2Cone\n", + "(CVXPY) Apr 25 10:47:26 AM: Applying reduction CvxAttr2Constr\n", + "(CVXPY) Apr 25 10:47:26 AM: Applying reduction ConeMatrixStuffing\n", + "(CVXPY) Apr 25 10:47:26 AM: Applying reduction SCIPY\n", + "(CVXPY) Apr 25 10:47:26 AM: Finished problem compilation (took 1.438e-02 seconds).\n", "-------------------------------------------------------------------------------\n", " Numerical solver \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:58 AM: Invoking solver SCIPY to obtain a solution.\n", + "(CVXPY) Apr 25 10:47:26 AM: Invoking solver SCIPY to obtain a solution.\n", "Solver terminated with message: Optimization terminated successfully. (HiGHS Status 7: Optimal)\n", "-------------------------------------------------------------------------------\n", " Summary \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:32 AM: Problem status: optimal\n", - "(CVXPY) Apr 25 10:41:32 AM: Optimal value: 4.100e+01\n", - "(CVXPY) Apr 25 10:41:32 AM: Compilation took 1.355e-02 seconds\n", - "(CVXPY) Apr 25 10:41:32 AM: Solver (including time spent in interface) took 3.391e+01 seconds\n" + "(CVXPY) Apr 25 10:48:00 AM: Problem status: optimal\n", + "(CVXPY) Apr 25 10:48:00 AM: Optimal value: 4.100e+01\n", + "(CVXPY) Apr 25 10:48:00 AM: Compilation took 1.438e-02 seconds\n", + "(CVXPY) Apr 25 10:48:00 AM: Solver (including time spent in interface) took 3.394e+01 seconds\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:58 AM: It is compliant with the following grammars: DCP, DQCP\n" + "(CVXPY) Apr 25 10:47:26 AM: It is compliant with the following grammars: DCP, DQCP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:58 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" + "(CVXPY) Apr 25 10:47:26 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:58 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" + "(CVXPY) Apr 25 10:47:26 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:58 AM: Your problem is compiled with the CPP canonicalization backend.\n" + "(CVXPY) Apr 25 10:47:26 AM: Your problem is compiled with the CPP canonicalization backend.\n" ] }, { @@ -318,49 +318,49 @@ "-------------------------------------------------------------------------------\n", " Compilation \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:58 AM: Compiling problem (target solver=SCIPY).\n" + "(CVXPY) Apr 25 10:47:26 AM: Compiling problem (target solver=SCIPY).\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:58 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIPY\n" + "(CVXPY) Apr 25 10:47:26 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIPY\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:58 AM: Applying reduction Dcp2Cone\n" + "(CVXPY) Apr 25 10:47:26 AM: Applying reduction Dcp2Cone\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:58 AM: Applying reduction CvxAttr2Constr\n" + "(CVXPY) Apr 25 10:47:26 AM: Applying reduction CvxAttr2Constr\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:58 AM: Applying reduction ConeMatrixStuffing\n" + "(CVXPY) Apr 25 10:47:26 AM: Applying reduction ConeMatrixStuffing\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:58 AM: Applying reduction SCIPY\n" + "(CVXPY) Apr 25 10:47:26 AM: Applying reduction SCIPY\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:40:58 AM: Finished problem compilation (took 1.355e-02 seconds).\n" + "(CVXPY) Apr 25 10:47:26 AM: Finished problem compilation (took 1.438e-02 seconds).\n" ] }, { @@ -370,7 +370,7 @@ "-------------------------------------------------------------------------------\n", " Numerical solver \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:40:58 AM: Invoking solver SCIPY to obtain a solution.\n" + "(CVXPY) Apr 25 10:47:26 AM: Invoking solver SCIPY to obtain a solution.\n" ] }, { @@ -381,28 +381,28 @@ "-------------------------------------------------------------------------------\n", " Summary \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:32 AM: Problem status: optimal\n" + "(CVXPY) Apr 25 10:48:00 AM: Problem status: optimal\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: Optimal value: 4.100e+01\n" + "(CVXPY) Apr 25 10:48:00 AM: Optimal value: 4.100e+01\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: Compilation took 1.355e-02 seconds\n" + "(CVXPY) Apr 25 10:48:00 AM: Compilation took 1.438e-02 seconds\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: Solver (including time spent in interface) took 3.391e+01 seconds\n" + "(CVXPY) Apr 25 10:48:00 AM: Solver (including time spent in interface) took 3.394e+01 seconds\n" ] }, { @@ -616,7 +616,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 6, @@ -673,33 +673,33 @@ " CVXPY \n", " v1.4.3 \n", "===============================================================================\n", - "(CVXPY) Apr 25 10:41:32 AM: Your problem has 670 variables, 17 constraints, and 0 parameters.\n", - "(CVXPY) Apr 25 10:41:32 AM: It is compliant with the following grammars: DCP, DQCP\n", - "(CVXPY) Apr 25 10:41:32 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n", - "(CVXPY) Apr 25 10:41:32 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n", - "(CVXPY) Apr 25 10:41:32 AM: Your problem is compiled with the CPP canonicalization backend.\n", + "(CVXPY) Apr 25 10:48:00 AM: Your problem has 670 variables, 17 constraints, and 0 parameters.\n", + "(CVXPY) Apr 25 10:48:00 AM: It is compliant with the following grammars: DCP, DQCP\n", + "(CVXPY) Apr 25 10:48:00 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n", + "(CVXPY) Apr 25 10:48:00 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n", + "(CVXPY) Apr 25 10:48:00 AM: Your problem is compiled with the CPP canonicalization backend.\n", "-------------------------------------------------------------------------------\n", " Compilation \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:32 AM: Compiling problem (target solver=SCIPY).\n", - "(CVXPY) Apr 25 10:41:32 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIPY\n", - "(CVXPY) Apr 25 10:41:32 AM: Applying reduction Dcp2Cone\n", - "(CVXPY) Apr 25 10:41:32 AM: Applying reduction CvxAttr2Constr\n", - "(CVXPY) Apr 25 10:41:32 AM: Applying reduction ConeMatrixStuffing\n", - "(CVXPY) Apr 25 10:41:32 AM: Applying reduction SCIPY\n", - "(CVXPY) Apr 25 10:41:32 AM: Finished problem compilation (took 2.558e-02 seconds).\n", + "(CVXPY) Apr 25 10:48:00 AM: Compiling problem (target solver=SCIPY).\n", + "(CVXPY) Apr 25 10:48:00 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIPY\n", + "(CVXPY) Apr 25 10:48:00 AM: Applying reduction Dcp2Cone\n", + "(CVXPY) Apr 25 10:48:00 AM: Applying reduction CvxAttr2Constr\n", + "(CVXPY) Apr 25 10:48:00 AM: Applying reduction ConeMatrixStuffing\n", + "(CVXPY) Apr 25 10:48:00 AM: Applying reduction SCIPY\n", + "(CVXPY) Apr 25 10:48:00 AM: Finished problem compilation (took 2.385e-02 seconds).\n", "-------------------------------------------------------------------------------\n", " Numerical solver \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:32 AM: Invoking solver SCIPY to obtain a solution.\n", + "(CVXPY) Apr 25 10:48:00 AM: Invoking solver SCIPY to obtain a solution.\n", "Solver terminated with message: Optimization terminated successfully. (HiGHS Status 7: Optimal)\n", "-------------------------------------------------------------------------------\n", " Summary \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:49 AM: Problem status: optimal\n", - "(CVXPY) Apr 25 10:41:49 AM: Optimal value: 4.100e+01\n", - "(CVXPY) Apr 25 10:41:49 AM: Compilation took 2.558e-02 seconds\n", - "(CVXPY) Apr 25 10:41:49 AM: Solver (including time spent in interface) took 1.722e+01 seconds\n", + "(CVXPY) Apr 25 10:48:17 AM: Problem status: optimal\n", + "(CVXPY) Apr 25 10:48:17 AM: Optimal value: 4.100e+01\n", + "(CVXPY) Apr 25 10:48:17 AM: Compilation took 2.385e-02 seconds\n", + "(CVXPY) Apr 25 10:48:17 AM: Solver (including time spent in interface) took 1.726e+01 seconds\n", "Optimal value: 41.0\n" ] }, @@ -707,28 +707,28 @@ "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: It is compliant with the following grammars: DCP, DQCP\n" + "(CVXPY) Apr 25 10:48:00 AM: It is compliant with the following grammars: DCP, DQCP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" + "(CVXPY) Apr 25 10:48:00 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" + "(CVXPY) Apr 25 10:48:00 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: Your problem is compiled with the CPP canonicalization backend.\n" + "(CVXPY) Apr 25 10:48:00 AM: Your problem is compiled with the CPP canonicalization backend.\n" ] }, { @@ -738,49 +738,49 @@ "-------------------------------------------------------------------------------\n", " Compilation \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:32 AM: Compiling problem (target solver=SCIPY).\n" + "(CVXPY) Apr 25 10:48:00 AM: Compiling problem (target solver=SCIPY).\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIPY\n" + "(CVXPY) Apr 25 10:48:00 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIPY\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: Applying reduction Dcp2Cone\n" + "(CVXPY) Apr 25 10:48:00 AM: Applying reduction Dcp2Cone\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: Applying reduction CvxAttr2Constr\n" + "(CVXPY) Apr 25 10:48:00 AM: Applying reduction CvxAttr2Constr\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: Applying reduction ConeMatrixStuffing\n" + "(CVXPY) Apr 25 10:48:00 AM: Applying reduction ConeMatrixStuffing\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: Applying reduction SCIPY\n" + "(CVXPY) Apr 25 10:48:00 AM: Applying reduction SCIPY\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:32 AM: Finished problem compilation (took 2.558e-02 seconds).\n" + "(CVXPY) Apr 25 10:48:00 AM: Finished problem compilation (took 2.385e-02 seconds).\n" ] }, { @@ -790,7 +790,7 @@ "-------------------------------------------------------------------------------\n", " Numerical solver \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:32 AM: Invoking solver SCIPY to obtain a solution.\n" + "(CVXPY) Apr 25 10:48:00 AM: Invoking solver SCIPY to obtain a solution.\n" ] }, { @@ -801,28 +801,28 @@ "-------------------------------------------------------------------------------\n", " Summary \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:49 AM: Problem status: optimal\n" + "(CVXPY) Apr 25 10:48:17 AM: Problem status: optimal\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:49 AM: Optimal value: 4.100e+01\n" + "(CVXPY) Apr 25 10:48:17 AM: Optimal value: 4.100e+01\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:49 AM: Compilation took 2.558e-02 seconds\n" + "(CVXPY) Apr 25 10:48:17 AM: Compilation took 2.385e-02 seconds\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:49 AM: Solver (including time spent in interface) took 1.722e+01 seconds\n" + "(CVXPY) Apr 25 10:48:17 AM: Solver (including time spent in interface) took 1.726e+01 seconds\n" ] }, { @@ -1021,7 +1021,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 8, diff --git a/jupyter_execute/guide/signaling/carnival.ipynb b/jupyter_execute/guide/signaling/carnival.ipynb index fdaf7d19..0eab26ac 100644 --- a/jupyter_execute/guide/signaling/carnival.ipynb +++ b/jupyter_execute/guide/signaling/carnival.ipynb @@ -171,7 +171,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 2, @@ -204,43 +204,41 @@ "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) Apr 25 10:41:51 AM - INFO : 2/2 inputs mapped to the graph\n", - "(CORNETO) Apr 25 10:41:51 AM - INFO : 2/2 outputs mapped to the graph\n", - "(CORNETO) Apr 25 10:41:51 AM - INFO : Pruning the graph with size: V x E = (6, 6)...\n", - "(CORNETO) Apr 25 10:41:51 AM - INFO : Finished. Final size: V x E = (6, 6).\n", - "(CORNETO) Apr 25 10:41:51 AM - INFO : 2/2 inputs after pruning.\n", - "(CORNETO) Apr 25 10:41:51 AM - INFO : 2/2 outputs after pruning.\n", - "(CORNETO) Apr 25 10:41:51 AM - INFO : Converting into a flow graph...\n", - "(CORNETO) Apr 25 10:41:51 AM - INFO : Creating a network flow problem...\n", - "(CORNETO) Apr 25 10:41:51 AM - INFO : Preprocess completed.\n", + "(CORNETO) Apr 25 10:48:19 AM - INFO : 2/2 inputs mapped to the graph\n", + "(CORNETO) Apr 25 10:48:19 AM - INFO : 2/2 outputs mapped to the graph\n", + "(CORNETO) Apr 25 10:48:19 AM - INFO : Pruning the graph with size: V x E = (6, 6)...\n", + "(CORNETO) Apr 25 10:48:19 AM - INFO : Finished. Final size: V x E = (6, 6).\n", + "(CORNETO) Apr 25 10:48:19 AM - INFO : 2/2 inputs after pruning.\n", + "(CORNETO) Apr 25 10:48:19 AM - INFO : 2/2 outputs after pruning.\n", + "(CORNETO) Apr 25 10:48:19 AM - INFO : Converting into a flow graph...\n", + "(CORNETO) Apr 25 10:48:19 AM - INFO : Creating a network flow problem...\n", + "(CORNETO) Apr 25 10:48:19 AM - INFO : Preprocess completed.\n", "===============================================================================\n", " CVXPY \n", " v1.4.3 \n", "===============================================================================\n", - "(CVXPY) Apr 25 10:41:51 AM: Your problem has 86 variables, 20 constraints, and 0 parameters.\n", - "(CVXPY) Apr 25 10:41:51 AM: It is compliant with the following grammars: DCP, DQCP\n", - "(CVXPY) Apr 25 10:41:51 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n", - "(CVXPY) Apr 25 10:41:51 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n", - "(CVXPY) Apr 25 10:41:51 AM: Your problem is compiled with the CPP canonicalization backend.\n", + "(CVXPY) Apr 25 10:48:19 AM: Your problem has 86 variables, 20 constraints, and 0 parameters.\n", + "(CVXPY) Apr 25 10:48:19 AM: It is compliant with the following grammars: DCP, DQCP\n", + "(CVXPY) Apr 25 10:48:19 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n", + "(CVXPY) Apr 25 10:48:19 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n", + "(CVXPY) Apr 25 10:48:19 AM: Your problem is compiled with the CPP canonicalization backend.\n", "-------------------------------------------------------------------------------\n", " Compilation \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:51 AM: Compiling problem (target solver=SCIP).\n", - "(CVXPY) Apr 25 10:41:51 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP\n", - "(CVXPY) Apr 25 10:41:51 AM: Applying reduction Dcp2Cone\n", - "(CVXPY) Apr 25 10:41:51 AM: Applying reduction CvxAttr2Constr\n", - "(CVXPY) Apr 25 10:41:51 AM: Applying reduction ConeMatrixStuffing\n", - "(CVXPY) Apr 25 10:41:51 AM: Applying reduction SCIP\n", - "(CVXPY) Apr 25 10:41:51 AM: Finished problem compilation (took 2.805e-02 seconds).\n", + "(CVXPY) Apr 25 10:48:19 AM: Compiling problem (target solver=SCIP).\n", + "(CVXPY) Apr 25 10:48:19 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP\n", + "(CVXPY) Apr 25 10:48:19 AM: Applying reduction Dcp2Cone\n", + "(CVXPY) Apr 25 10:48:19 AM: Applying reduction CvxAttr2Constr\n", + "(CVXPY) Apr 25 10:48:19 AM: Applying reduction ConeMatrixStuffing\n", + "(CVXPY) Apr 25 10:48:19 AM: Applying reduction SCIP\n", + "(CVXPY) Apr 25 10:48:19 AM: Finished problem compilation (took 3.197e-02 seconds).\n", "-------------------------------------------------------------------------------\n", " Numerical solver \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:51 AM: Invoking solver SCIP to obtain a solution.\n", + "(CVXPY) Apr 25 10:48:19 AM: Invoking solver SCIP to obtain a solution.\n", "-------------------------------------------------------------------------------\n", " Summary \n", - "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:51 AM: Problem status: optimal\n", - "presolving:\n", + "-------------------------------------------------------------------------------presolving:\n", "(round 1, fast) 36 del vars, 95 del conss, 0 add conss, 48 chg bounds, 1 chg sides, 23 chg coeffs, 0 upgd conss, 0 impls, 28 clqs\n", "(round 2, fast) 54 del vars, 129 del conss, 0 add conss, 52 chg bounds, 9 chg sides, 31 chg coeffs, 0 upgd conss, 0 impls, 20 clqs\n", "(round 3, fast) 63 del vars, 145 del conss, 0 add conss, 52 chg bounds, 11 chg sides, 33 chg coeffs, 0 upgd conss, 0 impls, 18 clqs\n", @@ -271,14 +269,13 @@ "Presolving Time: 0.00\n", "\n", " time | node | left |LP iter|LP it/n|mem/heur|mdpt |vars |cons |rows |cuts |sepa|confs|strbr| dualbound | primalbound | gap | compl. \n", - "p 0.0s| 1 | 0 | 1 | - | clique| 0 | 27 | 45 | 42 | 0 | 0 | 0 | 0 |-3.500000e+00 | 1.000000e-01 | Inf | unknown\n", - "p 0.0s| 1 | 0 | 1 | - | locks| 0 | 27 | 45 | 42 | 0 | 0 | 0 | 0 |-3.500000e+00 |-6.000000e-01 | 483.33%| unknown\n", - "p 0.0s| 1 | 0 | 1 | - | vbounds| 0 | 27 | 46 | 42 | 0 | 0 | 1 | 0 |-3.500000e+00 |-1.600000e+00 | 118.75%| unknown\n", - "p 0.0s| 1 | 0 | 1 | - | vbounds| 0 | 27 | 48 | 42 | 0 | 0 | 3 | 0 |-3.500000e+00 |-3.200000e+00 | 9.37%| unknown\n", - " 0.0s| 1 | 0 | 16 | - | 1789k | 0 | 27 | 29 | 42 | 0 | 0 | 9 | 0 |-3.300000e+00 |-3.200000e+00 | 3.13%| unknown\n", - " 0.0s| 1 | 0 | 21 | - | 1810k | 0 | 27 | 29 | 45 | 3 | 1 | 9 | 0 |-3.300000e+00 |-3.200000e+00 | 3.13%| unknown\n", - "r 0.0s| 1 | 0 | 21 | - |rounding| 0 | 27 | 29 | 45 | 3 | 1 | 9 | 0 |-3.300000e+00 |-3.300000e+00 | 0.00%| unknown\n", - " 0.0s| 1 | 0 | 21 | - | 1810k | 0 | 27 | 29 | 45 | 3 | 1 | 9 | 0 |-3.300000e+00 |-3.300000e+00 | 0.00%| unknown\n", + "p 0.0s| 1 | 0 | 0 | - | clique| 0 | 27 | 45 | 42 | 0 | 0 | 0 | 0 |-3.500000e+00 | 1.000000e-01 | Inf | unknown\n", + "p 0.0s| 1 | 0 | 0 | - | locks| 0 | 27 | 45 | 42 | 0 | 0 | 0 | 0 |-3.500000e+00 |-6.000000e-01 | 483.33%| unknown\n", + "p 0.0s| 1 | 0 | 0 | - | vbounds| 0 | 27 | 45 | 42 | 0 | 0 | 0 | 0 |-3.500000e+00 |-1.600000e+00 | 118.75%| unknown\n", + "p 0.0s| 1 | 0 | 0 | - | vbounds| 0 | 27 | 46 | 42 | 0 | 0 | 1 | 0 |-3.500000e+00 |-3.200000e+00 | 9.37%| unknown\n", + " 0.0s| 1 | 0 | 14 | - | 1786k | 0 | 27 | 29 | 42 | 0 | 0 | 7 | 0 |-3.300000e+00 |-3.200000e+00 | 3.13%| unknown\n", + "r 0.0s| 1 | 0 | 14 | - |rounding| 0 | 27 | 29 | 42 | 0 | 0 | 7 | 0 |-3.300000e+00 |-3.300000e+00 | 0.00%| unknown\n", + " 0.0s| 1 | 0 | 14 | - | 1786k | 0 | 27 | 29 | 42 | 0 | 0 | 7 | 0 |-3.300000e+00 |-3.300000e+00 | 0.00%| unknown\n", "\n", "SCIP Status : problem is solved [optimal solution found]\n", "Solving Time (sec) : 0.00\n", @@ -286,66 +283,68 @@ "Primal Bound : -3.30000000000000e+00 (5 solutions)\n", "Dual Bound : -3.30000000000000e+00\n", "Gap : 0.00 %\n", - "(CVXPY) Apr 25 10:41:51 AM: Optimal value: 7.000e-01\n", - "(CVXPY) Apr 25 10:41:51 AM: Compilation took 2.805e-02 seconds\n", - "(CVXPY) Apr 25 10:41:51 AM: Solver (including time spent in interface) took 1.459e-02 seconds\n", - "(CORNETO) Apr 25 10:41:51 AM - INFO : Finished in 0.07 s.\n" + "\n", + "(CVXPY) Apr 25 10:48:19 AM: Problem status: optimal\n", + "(CVXPY) Apr 25 10:48:19 AM: Optimal value: 7.000e-01\n", + "(CVXPY) Apr 25 10:48:19 AM: Compilation took 3.197e-02 seconds\n", + "(CVXPY) Apr 25 10:48:19 AM: Solver (including time spent in interface) took 1.419e-02 seconds\n", + "(CORNETO) Apr 25 10:48:19 AM - INFO : Finished in 0.07 s.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) Apr 25 10:41:51 AM - INFO : 2/2 outputs mapped to the graph\n" + "(CORNETO) Apr 25 10:48:19 AM - INFO : 2/2 outputs mapped to the graph\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) Apr 25 10:41:51 AM - INFO : Pruning the graph with size: V x E = (6, 6)...\n" + "(CORNETO) Apr 25 10:48:19 AM - INFO : Pruning the graph with size: V x E = (6, 6)...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) Apr 25 10:41:51 AM - INFO : Finished. Final size: V x E = (6, 6).\n" + "(CORNETO) Apr 25 10:48:19 AM - INFO : Finished. Final size: V x E = (6, 6).\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) Apr 25 10:41:51 AM - INFO : 2/2 inputs after pruning.\n" + "(CORNETO) Apr 25 10:48:19 AM - INFO : 2/2 inputs after pruning.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) Apr 25 10:41:51 AM - INFO : 2/2 outputs after pruning.\n" + "(CORNETO) Apr 25 10:48:19 AM - INFO : 2/2 outputs after pruning.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) Apr 25 10:41:51 AM - INFO : Converting into a flow graph...\n" + "(CORNETO) Apr 25 10:48:19 AM - INFO : Converting into a flow graph...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) Apr 25 10:41:51 AM - INFO : Creating a network flow problem...\n" + "(CORNETO) Apr 25 10:48:19 AM - INFO : Creating a network flow problem...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) Apr 25 10:41:51 AM - INFO : Preprocess completed.\n" + "(CORNETO) Apr 25 10:48:19 AM - INFO : Preprocess completed.\n" ] }, { @@ -356,35 +355,35 @@ " CVXPY \n", " v1.4.3 \n", "===============================================================================\n", - "(CVXPY) Apr 25 10:41:51 AM: Your problem has 86 variables, 20 constraints, and 0 parameters.\n" + "(CVXPY) Apr 25 10:48:19 AM: Your problem has 86 variables, 20 constraints, and 0 parameters.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: It is compliant with the following grammars: DCP, DQCP\n" + "(CVXPY) Apr 25 10:48:19 AM: It is compliant with the following grammars: DCP, DQCP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" + "(CVXPY) Apr 25 10:48:19 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" + "(CVXPY) Apr 25 10:48:19 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: Your problem is compiled with the CPP canonicalization backend.\n" + "(CVXPY) Apr 25 10:48:19 AM: Your problem is compiled with the CPP canonicalization backend.\n" ] }, { @@ -394,49 +393,49 @@ "-------------------------------------------------------------------------------\n", " Compilation \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:51 AM: Compiling problem (target solver=SCIP).\n" + "(CVXPY) Apr 25 10:48:19 AM: Compiling problem (target solver=SCIP).\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP\n" + "(CVXPY) Apr 25 10:48:19 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: Applying reduction Dcp2Cone\n" + "(CVXPY) Apr 25 10:48:19 AM: Applying reduction Dcp2Cone\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: Applying reduction CvxAttr2Constr\n" + "(CVXPY) Apr 25 10:48:19 AM: Applying reduction CvxAttr2Constr\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: Applying reduction ConeMatrixStuffing\n" + "(CVXPY) Apr 25 10:48:19 AM: Applying reduction ConeMatrixStuffing\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: Applying reduction SCIP\n" + "(CVXPY) Apr 25 10:48:19 AM: Applying reduction SCIP\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: Finished problem compilation (took 2.805e-02 seconds).\n" + "(CVXPY) Apr 25 10:48:19 AM: Finished problem compilation (took 3.197e-02 seconds).\n" ] }, { @@ -446,7 +445,7 @@ "-------------------------------------------------------------------------------\n", " Numerical solver \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:51 AM: Invoking solver SCIP to obtain a solution.\n" + "(CVXPY) Apr 25 10:48:19 AM: Invoking solver SCIP to obtain a solution.\n" ] }, { @@ -455,9 +454,7 @@ "text": [ "-------------------------------------------------------------------------------\n", " Summary \n", - "-------------------------------------------------------------------------------\n", - "(CVXPY) Apr 25 10:41:51 AM: Problem status: optimal\n", - "presolving:\n", + "-------------------------------------------------------------------------------presolving:\n", "(round 1, fast) 36 del vars, 95 del conss, 0 add conss, 48 chg bounds, 1 chg sides, 23 chg coeffs, 0 upgd conss, 0 impls, 28 clqs\n", "(round 2, fast) 54 del vars, 129 del conss, 0 add conss, 52 chg bounds, 9 chg sides, 31 chg coeffs, 0 upgd conss, 0 impls, 20 clqs\n", "(round 3, fast) 63 del vars, 145 del conss, 0 add conss, 52 chg bounds, 11 chg sides, 33 chg coeffs, 0 upgd conss, 0 impls, 18 clqs\n", @@ -488,49 +485,50 @@ "Presolving Time: 0.00\n", "\n", " time | node | left |LP iter|LP it/n|mem/heur|mdpt |vars |cons |rows |cuts |sepa|confs|strbr| dualbound | primalbound | gap | compl. \n", - "p 0.0s| 1 | 0 | 1 | - | clique| 0 | 27 | 45 | 42 | 0 | 0 | 0 | 0 |-3.500000e+00 | 1.000000e-01 | Inf | unknown\n", - "p 0.0s| 1 | 0 | 1 | - | locks| 0 | 27 | 45 | 42 | 0 | 0 | 0 | 0 |-3.500000e+00 |-6.000000e-01 | 483.33%| unknown\n", - "p 0.0s| 1 | 0 | 1 | - | vbounds| 0 | 27 | 46 | 42 | 0 | 0 | 1 | 0 |-3.500000e+00 |-1.600000e+00 | 118.75%| unknown\n", - "p 0.0s| 1 | 0 | 1 | - | vbounds| 0 | 27 | 48 | 42 | 0 | 0 | 3 | 0 |-3.500000e+00 |-3.200000e+00 | 9.37%| unknown\n", - " 0.0s| 1 | 0 | 16 | - | 1789k | 0 | 27 | 29 | 42 | 0 | 0 | 9 | 0 |-3.300000e+00 |-3.200000e+00 | 3.13%| unknown\n", - " 0.0s| 1 | 0 | 21 | - | 1810k | 0 | 27 | 29 | 45 | 3 | 1 | 9 | 0 |-3.300000e+00 |-3.200000e+00 | 3.13%| unknown\n", - "r 0.0s| 1 | 0 | 21 | - |rounding| 0 | 27 | 29 | 45 | 3 | 1 | 9 | 0 |-3.300000e+00 |-3.300000e+00 | 0.00%| unknown\n", - " 0.0s| 1 | 0 | 21 | - | 1810k | 0 | 27 | 29 | 45 | 3 | 1 | 9 | 0 |-3.300000e+00 |-3.300000e+00 | 0.00%| unknown\n", + "p 0.0s| 1 | 0 | 0 | - | clique| 0 | 27 | 45 | 42 | 0 | 0 | 0 | 0 |-3.500000e+00 | 1.000000e-01 | Inf | unknown\n", + "p 0.0s| 1 | 0 | 0 | - | locks| 0 | 27 | 45 | 42 | 0 | 0 | 0 | 0 |-3.500000e+00 |-6.000000e-01 | 483.33%| unknown\n", + "p 0.0s| 1 | 0 | 0 | - | vbounds| 0 | 27 | 45 | 42 | 0 | 0 | 0 | 0 |-3.500000e+00 |-1.600000e+00 | 118.75%| unknown\n", + "p 0.0s| 1 | 0 | 0 | - | vbounds| 0 | 27 | 46 | 42 | 0 | 0 | 1 | 0 |-3.500000e+00 |-3.200000e+00 | 9.37%| unknown\n", + " 0.0s| 1 | 0 | 14 | - | 1786k | 0 | 27 | 29 | 42 | 0 | 0 | 7 | 0 |-3.300000e+00 |-3.200000e+00 | 3.13%| unknown\n", + "r 0.0s| 1 | 0 | 14 | - |rounding| 0 | 27 | 29 | 42 | 0 | 0 | 7 | 0 |-3.300000e+00 |-3.300000e+00 | 0.00%| unknown\n", + " 0.0s| 1 | 0 | 14 | - | 1786k | 0 | 27 | 29 | 42 | 0 | 0 | 7 | 0 |-3.300000e+00 |-3.300000e+00 | 0.00%| unknown\n", "\n", "SCIP Status : problem is solved [optimal solution found]\n", "Solving Time (sec) : 0.00\n", "Solving Nodes : 1\n", "Primal Bound : -3.30000000000000e+00 (5 solutions)\n", "Dual Bound : -3.30000000000000e+00\n", - "Gap : 0.00 %\n" + "Gap : 0.00 %\n", + "\n", + "(CVXPY) Apr 25 10:48:19 AM: Problem status: optimal\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: Optimal value: 7.000e-01\n" + "(CVXPY) Apr 25 10:48:19 AM: Optimal value: 7.000e-01\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: Compilation took 2.805e-02 seconds\n" + "(CVXPY) Apr 25 10:48:19 AM: Compilation took 3.197e-02 seconds\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CVXPY) Apr 25 10:41:51 AM: Solver (including time spent in interface) took 1.459e-02 seconds\n" + "(CVXPY) Apr 25 10:48:19 AM: Solver (including time spent in interface) took 1.419e-02 seconds\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) Apr 25 10:41:51 AM - INFO : Finished in 0.07 s.\n" + "(CORNETO) Apr 25 10:48:19 AM - INFO : Finished in 0.07 s.\n" ] } ], @@ -672,7 +670,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 5, @@ -722,32 +720,32 @@ " \n", " \n", " 0\n", - " I2\n", + " M2\n", " 1.0\n", " \n", " \n", " 1\n", - " M1\n", + " I1\n", " 1.0\n", " \n", " \n", " 2\n", - " N1\n", - " 0.0\n", + " N2\n", + " -1.0\n", " \n", " \n", " 3\n", - " N2\n", - " -1.0\n", + " N1\n", + " 0.0\n", " \n", " \n", " 4\n", - " I1\n", + " M1\n", " 1.0\n", " \n", " \n", " 5\n", - " M2\n", + " I2\n", " 1.0\n", " \n", " \n", @@ -776,12 +774,12 @@ ], "text/plain": [ " V value\n", - "0 I2 1.0\n", - "1 M1 1.0\n", - "2 N1 0.0\n", - "3 N2 -1.0\n", - "4 I1 1.0\n", - "5 M2 1.0\n", + "0 M2 1.0\n", + "1 I1 1.0\n", + "2 N2 -1.0\n", + "3 N1 0.0\n", + "4 M1 1.0\n", + "5 I2 1.0\n", "6 _s 1.0\n", "7 _pert_c0 1.0\n", "8 _meas_c0 0.0\n", @@ -1076,7 +1074,7 @@ "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 8, diff --git a/main/.buildinfo b/main/.buildinfo index b9fc0c85..6a5ea8ec 100644 --- a/main/.buildinfo +++ b/main/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. 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b/main/_static/switcher.json index c82c96ef..70481cd2 100644 --- a/main/_static/switcher.json +++ b/main/_static/switcher.json @@ -1,12 +1,12 @@ [ { "name": "latest (dev)", - "version": "dev", + "version": "1.0.0-alpha.0", "url": "https://saezlab.github.io/corneto/dev/" }, { "name": "v1.0.0-alpha.0", - "version": "v1.0.0-alpha.0", + "version": "1.0.0-alpha.0", "url": "https://saezlab.github.io/corneto/main/" } ] \ No newline at end of file diff --git a/main/api/corneto.backend.html b/main/api/corneto.backend.html index f1c97fbc..21ba7d5c 100644 --- a/main/api/corneto.backend.html +++ b/main/api/corneto.backend.html @@ -63,7 +63,7 @@ diff --git a/main/api/corneto.html b/main/api/corneto.html index ef437254..7d8645ac 100644 --- a/main/api/corneto.html +++ b/main/api/corneto.html @@ -63,7 +63,7 @@ diff --git a/main/api/corneto.methods.html b/main/api/corneto.methods.html index 4a17ce44..db84cdc5 100644 --- a/main/api/corneto.methods.html +++ b/main/api/corneto.methods.html @@ -63,7 +63,7 @@ diff --git a/main/api/corneto.methods.metabolism.html b/main/api/corneto.methods.metabolism.html index 39010a60..23b62efd 100644 --- a/main/api/corneto.methods.metabolism.html +++ b/main/api/corneto.methods.metabolism.html @@ -63,7 +63,7 @@ diff --git a/main/api/corneto.utils.html b/main/api/corneto.utils.html index d3b76ac6..6a35a695 100644 --- a/main/api/corneto.utils.html +++ b/main/api/corneto.utils.html @@ -63,7 +63,7 @@ diff --git a/main/api/index.html b/main/api/index.html index 8d941b40..4d78883c 100644 --- a/main/api/index.html +++ b/main/api/index.html @@ -63,7 +63,7 @@ diff --git a/main/api/modules.html b/main/api/modules.html index e194b1a4..5199d613 100644 --- a/main/api/modules.html +++ b/main/api/modules.html @@ -63,7 +63,7 @@ diff --git a/main/genindex.html b/main/genindex.html index 4a786eff..523425fe 100644 --- a/main/genindex.html +++ b/main/genindex.html @@ -64,7 +64,7 @@ diff --git a/main/guide/index.html b/main/guide/index.html index 69966dbd..49c59f3e 100644 --- a/main/guide/index.html +++ b/main/guide/index.html @@ -63,7 +63,7 @@ diff --git a/main/guide/interactomics/index.html b/main/guide/interactomics/index.html index 3fb60485..d9558461 100644 --- a/main/guide/interactomics/index.html +++ b/main/guide/interactomics/index.html @@ -63,7 +63,7 @@ diff --git a/main/guide/interoperability/cobrapy.html b/main/guide/interoperability/cobrapy.html index 533b5f07..2f2bed9c 100644 --- a/main/guide/interoperability/cobrapy.html +++ b/main/guide/interoperability/cobrapy.html @@ -63,7 +63,7 @@ diff --git a/main/guide/interoperability/cvxpy.html b/main/guide/interoperability/cvxpy.html index 01978933..422cfd73 100644 --- a/main/guide/interoperability/cvxpy.html +++ b/main/guide/interoperability/cvxpy.html @@ -63,7 +63,7 @@ @@ -503,25 +503,25 @@

CVXPY: Convex optimization, for everyone diff --git a/main/guide/interoperability/index.html b/main/guide/interoperability/index.html index 7f32fca3..cd035a9a 100644 --- a/main/guide/interoperability/index.html +++ b/main/guide/interoperability/index.html @@ -63,7 +63,7 @@ diff --git a/main/guide/interoperability/liana.html b/main/guide/interoperability/liana.html index dbed236b..6887d77e 100644 --- a/main/guide/interoperability/liana.html +++ b/main/guide/interoperability/liana.html @@ -63,7 +63,7 @@ diff --git a/main/guide/interoperability/networkx.html b/main/guide/interoperability/networkx.html index e189bd25..975ebdd7 100644 --- a/main/guide/interoperability/networkx.html +++ b/main/guide/interoperability/networkx.html @@ -63,7 +63,7 @@ diff --git a/main/guide/interoperability/omnipath.html b/main/guide/interoperability/omnipath.html index bf0885b0..8b18f853 100644 --- a/main/guide/interoperability/omnipath.html +++ b/main/guide/interoperability/omnipath.html @@ -63,7 +63,7 @@ diff --git a/main/guide/interoperability/picos.html b/main/guide/interoperability/picos.html index cbe272d1..45c62f1a 100644 --- a/main/guide/interoperability/picos.html +++ b/main/guide/interoperability/picos.html @@ -63,7 +63,7 @@ @@ -528,7 +528,7 @@

PICOS: A Python interface to conic optimization solvers diff --git a/main/guide/intro/acyclic-flows.html b/main/guide/intro/acyclic-flows.html index 7def2943..4d9c856a 100644 --- a/main/guide/intro/acyclic-flows.html +++ b/main/guide/intro/acyclic-flows.html @@ -63,7 +63,7 @@ diff --git a/main/guide/intro/constrained-optimization.html b/main/guide/intro/constrained-optimization.html index 0e3ba959..1418a9fd 100644 --- a/main/guide/intro/constrained-optimization.html +++ b/main/guide/intro/constrained-optimization.html @@ -63,7 +63,7 @@ @@ -505,7 +505,7 @@

The Knapsack Problem
-
Problem(Maximize(Expression(AFFINE, NONNEGATIVE, ())), [Inequality(Expression(AFFINE, NONNEGATIVE, ()))])
diff --git a/main/guide/intro/index.html b/main/guide/intro/index.html
index 195fdac1..87aa7ea0 100644
--- a/main/guide/intro/index.html
+++ b/main/guide/intro/index.html
@@ -63,7 +63,7 @@
     
     
diff --git a/main/guide/intro/multi-commodity-network-flows.html b/main/guide/intro/multi-commodity-network-flows.html
index 68136de2..b5b41e34 100644
--- a/main/guide/intro/multi-commodity-network-flows.html
+++ b/main/guide/intro/multi-commodity-network-flows.html
@@ -63,7 +63,7 @@
     
     
@@ -572,29 +572,29 @@ 

Multi-commodity Network Flows +../../_images/a305e411a464dd625dc1df4c8647ec72bb0be3b3a4762b097911a491fa13c376.svg

diff --git a/main/guide/metabolism/flux-balance-analysis.html b/main/guide/metabolism/flux-balance-analysis.html index 5b80ea2f..8976e57e 100644 --- a/main/guide/metabolism/flux-balance-analysis.html +++ b/main/guide/metabolism/flux-balance-analysis.html @@ -63,7 +63,7 @@ @@ -513,7 +513,7 @@

Using COBRApy - +../../_images/5dde94a20152e8d2cd3e92c6015a2b3508059abdc232cb0e202f2ac4d7beb885.svg

diff --git a/main/guide/metabolism/imat.html b/main/guide/metabolism/imat.html index 65ec335f..5edee452 100644 --- a/main/guide/metabolism/imat.html +++ b/main/guide/metabolism/imat.html @@ -63,7 +63,7 @@ diff --git a/main/guide/metabolism/index.html b/main/guide/metabolism/index.html index 3f414ae9..67001d26 100644 --- a/main/guide/metabolism/index.html +++ b/main/guide/metabolism/index.html @@ -63,7 +63,7 @@ diff --git a/main/guide/metabolism/multicondition-imat.html b/main/guide/metabolism/multicondition-imat.html index 2d0c133f..6bcd7680 100644 --- a/main/guide/metabolism/multicondition-imat.html +++ b/main/guide/metabolism/multicondition-imat.html @@ -63,7 +63,7 @@ diff --git a/main/guide/metabolism/multicondition-sfba.html b/main/guide/metabolism/multicondition-sfba.html index 96a239c5..77499bea 100644 --- a/main/guide/metabolism/multicondition-sfba.html +++ b/main/guide/metabolism/multicondition-sfba.html @@ -63,7 +63,7 @@ diff --git a/main/guide/metabolism/sparse-fba.html b/main/guide/metabolism/sparse-fba.html index 767ea128..51cb3249 100644 --- a/main/guide/metabolism/sparse-fba.html +++ b/main/guide/metabolism/sparse-fba.html @@ -63,7 +63,7 @@ @@ -546,7 +546,7 @@

Manual implementation of sparse FBA -../../_images/ff9706e23f6cb627d889958fceacccd827e539b11fa6d9410e77e91936cfdcb2.svg +../../_images/66ec3dbd2d4149b75be0407118008cbd8c54d4d16f6cc666b9a7938a007211b1.svg

Now we are going to see how to use specialized building blocks from CORNETO to automatically add indicators for the presence of reactions in a model. Indicators are binary variables associated to a continuous variable: when the indicator is 0, the continuous variable is 0; and when the indicator is 1, the continuous variable is unconstrained.

By creating indicators for flow, we can try for example to minimize the number of reactions with flux in the model, by minimizing the total number of ones in the indicator vector.

@@ -603,7 +603,7 @@

Manual implementation of sparse FBA -../../_images/0828d8cd5b477206d583eeda9a084f5f4488743bfd1ff3f65ffcde6a3fd3804c.svg +../../_images/c0a2bcef604ae3b0817afcfb97fcec57469cdf598b7734ff90c891e19dea50fa.svg
diff --git a/main/guide/networks/index.html b/main/guide/networks/index.html index 2ca2b773..05aa7119 100644 --- a/main/guide/networks/index.html +++ b/main/guide/networks/index.html @@ -63,7 +63,7 @@ diff --git a/main/guide/networks/pcst.html b/main/guide/networks/pcst.html index b90d988b..9820b1e3 100644 --- a/main/guide/networks/pcst.html +++ b/main/guide/networks/pcst.html @@ -63,7 +63,7 @@ diff --git a/main/guide/networks/shortest-paths.html b/main/guide/networks/shortest-paths.html index 5e129eb1..bbfc6bac 100644 --- a/main/guide/networks/shortest-paths.html +++ b/main/guide/networks/shortest-paths.html @@ -63,7 +63,7 @@ @@ -558,7 +558,7 @@

Random graphs -

diff --git a/main/guide/networks/steiner-trees.html b/main/guide/networks/steiner-trees.html index 856a2b9c..cec88012 100644 --- a/main/guide/networks/steiner-trees.html +++ b/main/guide/networks/steiner-trees.html @@ -63,7 +63,7 @@ @@ -599,33 +599,33 @@

Exact Steiner Trees with CORNETO @@ -658,33 +658,33 @@

Exact Steiner Trees with CORNETO @@ -532,43 +532,41 @@

A toy example -
(CORNETO) Apr 25 10:41:51 AM - INFO    : 2/2 inputs mapped to the graph
-(CORNETO) Apr 25 10:41:51 AM - INFO    : 2/2 outputs mapped to the graph
-(CORNETO) Apr 25 10:41:51 AM - INFO    : Pruning the graph with size: V x E = (6, 6)...
-(CORNETO) Apr 25 10:41:51 AM - INFO    : Finished. Final size: V x E = (6, 6).
-(CORNETO) Apr 25 10:41:51 AM - INFO    : 2/2 inputs after pruning.
-(CORNETO) Apr 25 10:41:51 AM - INFO    : 2/2 outputs after pruning.
-(CORNETO) Apr 25 10:41:51 AM - INFO    : Converting into a flow graph...
-(CORNETO) Apr 25 10:41:51 AM - INFO    : Creating a network flow problem...
-(CORNETO) Apr 25 10:41:51 AM - INFO    : Preprocess completed.
+
(CORNETO) Apr 25 10:48:19 AM - INFO    : 2/2 inputs mapped to the graph
+(CORNETO) Apr 25 10:48:19 AM - INFO    : 2/2 outputs mapped to the graph
+(CORNETO) Apr 25 10:48:19 AM - INFO    : Pruning the graph with size: V x E = (6, 6)...
+(CORNETO) Apr 25 10:48:19 AM - INFO    : Finished. Final size: V x E = (6, 6).
+(CORNETO) Apr 25 10:48:19 AM - INFO    : 2/2 inputs after pruning.
+(CORNETO) Apr 25 10:48:19 AM - INFO    : 2/2 outputs after pruning.
+(CORNETO) Apr 25 10:48:19 AM - INFO    : Converting into a flow graph...
+(CORNETO) Apr 25 10:48:19 AM - INFO    : Creating a network flow problem...
+(CORNETO) Apr 25 10:48:19 AM - INFO    : Preprocess completed.
 ===============================================================================
                                      CVXPY                                     
                                      v1.4.3                                    
 ===============================================================================
-(CVXPY) Apr 25 10:41:51 AM: Your problem has 86 variables, 20 constraints, and 0 parameters.
-(CVXPY) Apr 25 10:41:51 AM: It is compliant with the following grammars: DCP, DQCP
-(CVXPY) Apr 25 10:41:51 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)
-(CVXPY) Apr 25 10:41:51 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.
-(CVXPY) Apr 25 10:41:51 AM: Your problem is compiled with the CPP canonicalization backend.
+(CVXPY) Apr 25 10:48:19 AM: Your problem has 86 variables, 20 constraints, and 0 parameters.
+(CVXPY) Apr 25 10:48:19 AM: It is compliant with the following grammars: DCP, DQCP
+(CVXPY) Apr 25 10:48:19 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)
+(CVXPY) Apr 25 10:48:19 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.
+(CVXPY) Apr 25 10:48:19 AM: Your problem is compiled with the CPP canonicalization backend.
 -------------------------------------------------------------------------------
                                   Compilation                                  
 -------------------------------------------------------------------------------
-(CVXPY) Apr 25 10:41:51 AM: Compiling problem (target solver=SCIP).
-(CVXPY) Apr 25 10:41:51 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP
-(CVXPY) Apr 25 10:41:51 AM: Applying reduction Dcp2Cone
-(CVXPY) Apr 25 10:41:51 AM: Applying reduction CvxAttr2Constr
-(CVXPY) Apr 25 10:41:51 AM: Applying reduction ConeMatrixStuffing
-(CVXPY) Apr 25 10:41:51 AM: Applying reduction SCIP
-(CVXPY) Apr 25 10:41:51 AM: Finished problem compilation (took 2.805e-02 seconds).
+(CVXPY) Apr 25 10:48:19 AM: Compiling problem (target solver=SCIP).
+(CVXPY) Apr 25 10:48:19 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP
+(CVXPY) Apr 25 10:48:19 AM: Applying reduction Dcp2Cone
+(CVXPY) Apr 25 10:48:19 AM: Applying reduction CvxAttr2Constr
+(CVXPY) Apr 25 10:48:19 AM: Applying reduction ConeMatrixStuffing
+(CVXPY) Apr 25 10:48:19 AM: Applying reduction SCIP
+(CVXPY) Apr 25 10:48:19 AM: Finished problem compilation (took 3.197e-02 seconds).
 -------------------------------------------------------------------------------
                                 Numerical solver                               
 -------------------------------------------------------------------------------
-(CVXPY) Apr 25 10:41:51 AM: Invoking solver SCIP  to obtain a solution.
+(CVXPY) Apr 25 10:48:19 AM: Invoking solver SCIP  to obtain a solution.
 -------------------------------------------------------------------------------
                                     Summary                                    
--------------------------------------------------------------------------------
-(CVXPY) Apr 25 10:41:51 AM: Problem status: optimal
-presolving:
+-------------------------------------------------------------------------------presolving:
 (round 1, fast)       36 del vars, 95 del conss, 0 add conss, 48 chg bounds, 1 chg sides, 23 chg coeffs, 0 upgd conss, 0 impls, 28 clqs
 (round 2, fast)       54 del vars, 129 del conss, 0 add conss, 52 chg bounds, 9 chg sides, 31 chg coeffs, 0 upgd conss, 0 impls, 20 clqs
 (round 3, fast)       63 del vars, 145 del conss, 0 add conss, 52 chg bounds, 11 chg sides, 33 chg coeffs, 0 upgd conss, 0 impls, 18 clqs
@@ -599,14 +597,13 @@ 

A toy example diff --git a/main/guide/signaling/multicondition-carnival.html b/main/guide/signaling/multicondition-carnival.html index e9e8f12d..ab454897 100644 --- a/main/guide/signaling/multicondition-carnival.html +++ b/main/guide/signaling/multicondition-carnival.html @@ -63,7 +63,7 @@ diff --git a/main/index.html b/main/index.html index 74763f1b..c87c9182 100644 --- a/main/index.html +++ b/main/index.html @@ -63,7 +63,7 @@ diff --git a/main/py-modindex.html b/main/py-modindex.html index be358970..ead15f00 100644 --- a/main/py-modindex.html +++ b/main/py-modindex.html @@ -64,7 +64,7 @@ diff --git a/main/search.html b/main/search.html index ddeda689..5283e599 100644 --- a/main/search.html +++ b/main/search.html @@ -63,7 +63,7 @@ diff --git a/main/searchindex.js b/main/searchindex.js index 104396bd..b0ea0a50 100644 --- a/main/searchindex.js +++ b/main/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["api/corneto", "api/corneto.backend", "api/corneto.methods", "api/corneto.methods.metabolism", "api/corneto.utils", "api/index", "api/modules", "guide/index", "guide/interactomics/index", "guide/interoperability/cobrapy", "guide/interoperability/cvxpy", "guide/interoperability/decoupler", "guide/interoperability/index", "guide/interoperability/liana", "guide/interoperability/networkx", "guide/interoperability/omnipath", "guide/interoperability/picos", "guide/intro/acyclic-flows", "guide/intro/constrained-optimization", "guide/intro/index", "guide/intro/multi-commodity-network-flows", "guide/intro/prior-knowledge", "guide/metabolism/flux-balance-analysis", "guide/metabolism/imat", "guide/metabolism/index", "guide/metabolism/multicondition-imat", "guide/metabolism/multicondition-sfba", "guide/metabolism/sparse-fba", "guide/networks/index", "guide/networks/pcst", "guide/networks/shortest-paths", "guide/networks/steiner-trees", "guide/signaling/carnival", "guide/signaling/index", "guide/signaling/multicondition-carnival", "index", 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