corneto.backend package
linear_or(x, axis=None, varname='or')#
-- Parameters:
-
+- Return type:
+ProblemDef
+- Parameters:
+
x (CExpression)
axis (int | None)
@@ -738,8 +741,11 @@ corneto.backend package
linear_and(x, axis=None, varname='and')#
-- Parameters:
-
+- Return type:
+ProblemDef
+- Parameters:
+
x (CExpression)
axis (int | None)
@@ -751,8 +757,11 @@ corneto.backend package
vstack(arg_list)#
-
@@ -761,8 +770,11 @@ corneto.backend package
hstack(arg_list)#
-
diff --git a/dev/api/corneto.methods.html b/dev/api/corneto.methods.html
index 75f6d31..dba8220 100644
--- a/dev/api/corneto.methods.html
+++ b/dev/api/corneto.methods.html
@@ -734,7 +734,7 @@ Submodulescorneto.methods.steiner module#
-
-corneto.methods.steiner.exact_steiner_tree(G, terminals, edge_weights=None, root=None, tolerance=0.001, strict_acyclic=False, flow_name='_flow', out_flow_edge_type=EdgeType.UNDIRECTED, backend=<corneto.backend._cvxpy_backend.CvxpyBackend object>)#
+corneto.methods.steiner.exact_steiner_tree(G, terminals, edge_weights=None, root=None, tolerance=0.001, strict_acyclic=False, flow_name='_flow', in_flow_edge_type=EdgeType.DIRECTED, out_flow_edge_type=EdgeType.DIRECTED, backend=<corneto.backend._cvxpy_backend.CvxpyBackend object>)#
- Parameters:
diff --git a/dev/guide/interoperability/cvxpy.html b/dev/guide/interoperability/cvxpy.html
index d04795f..24d4355 100644
--- a/dev/guide/interoperability/cvxpy.html
+++ b/dev/guide/interoperability/cvxpy.html
@@ -503,25 +503,25 @@ CVXPY: Convex optimization, for everyone
diff --git a/dev/guide/intro/acyclic-flows.html b/dev/guide/intro/acyclic-flows.html
index a79ae85..c0bb6b4 100644
--- a/dev/guide/intro/acyclic-flows.html
+++ b/dev/guide/intro/acyclic-flows.html
@@ -539,8 +539,8 @@ Largest DAG from a given source and sink vertex
{'_flow': Variable((14,), _flow),
- '_flow_ineg': Variable((14,), _flow_ineg, boolean=True),
'_flow_ipos': Variable((14,), _flow_ipos, boolean=True),
+ '_flow_ineg': Variable((14,), _flow_ineg, boolean=True),
'_dag_layer_pos': Variable((7,), _dag_layer_pos),
'positive_flow': Variable((14,), _flow_ipos, boolean=True),
'negative_flow': Variable((14,), _flow_ineg, boolean=True),
diff --git a/dev/guide/intro/constrained-optimization.html b/dev/guide/intro/constrained-optimization.html
index 7b44743..04eafbe 100644
--- a/dev/guide/intro/constrained-optimization.html
+++ b/dev/guide/intro/constrained-optimization.html
@@ -505,7 +505,7 @@ The Knapsack Problem
-<corneto.DeprecatedBackend at 0x7fced04c68d0>
+<corneto.DeprecatedBackend at 0x7fb898e1ab10>
@@ -543,7 +543,7 @@ The Knapsack Problem
-<corneto.backend._base.ProblemDef at 0x7fce80114fd0>
+<corneto.backend._base.ProblemDef at 0x7fb84dd2eed0>
@@ -557,9 +557,9 @@ The Knapsack Problem
{'obj5': Variable((1,), obj5, boolean=True),
'obj4': Variable((1,), obj4, boolean=True),
- 'obj3': Variable((1,), obj3, boolean=True),
'obj2': Variable((1,), obj2, boolean=True),
- 'obj1': Variable((1,), obj1, boolean=True)}
+ 'obj1': Variable((1,), obj1, boolean=True),
+ 'obj3': Variable((1,), obj3, boolean=True)}
@@ -723,26 +723,26 @@ A more complex knapsackA more complex knapsack
Problem(Maximize(Expression(AFFINE, NONNEGATIVE, ())), [Inequality(Expression(AFFINE, NONNEGATIVE, ()))])
diff --git a/dev/guide/intro/multi-commodity-network-flows.html b/dev/guide/intro/multi-commodity-network-flows.html
index 6acdb58..3b21c0d 100644
--- a/dev/guide/intro/multi-commodity-network-flows.html
+++ b/dev/guide/intro/multi-commodity-network-flows.html
@@ -572,25 +572,25 @@ Multi-commodity Network FlowsProblem(Minimize(Expression(AFFINE, UNKNOWN, ())), [Inequality(Constant(CONSTANT, ZERO, (10, 2))), Inequality(Variable((10, 2), _flow)), Equality(Expression(AFFINE, UNKNOWN, (5, 2)), Constant(CONSTANT, ZERO, ())), Inequality(Expression(AFFINE, UNKNOWN, (10,))), Inequality(Constant(CONSTANT, ZERO, (10,)))])
diff --git a/dev/guide/intro/prior-knowledge.html b/dev/guide/intro/prior-knowledge.html
index 2cb8473..b7d3fc3 100644
--- a/dev/guide/intro/prior-knowledge.html
+++ b/dev/guide/intro/prior-knowledge.html
@@ -736,7 +736,7 @@ Hypergraphs
-
+
@@ -745,7 +745,7 @@ Hypergraphs
-('B', 'A', 'C', 'D', 'F', 'E')
+('B', 'A', 'C', 'D', 'E', 'F')
diff --git a/dev/guide/metabolism/flux-balance-analysis.html b/dev/guide/metabolism/flux-balance-analysis.html
index 44edf28..07f7c54 100644
--- a/dev/guide/metabolism/flux-balance-analysis.html
+++ b/dev/guide/metabolism/flux-balance-analysis.html
@@ -511,7 +511,7 @@ Using COBRApy
-<Solution 0.874 at 0x7fa457ba20d0>
+<Solution 0.874 at 0x7f7408cf1a90>
@@ -624,7 +624,7 @@ Using COBRApy
-
+
@@ -651,7 +651,7 @@ Using COBRApy
-
+
diff --git a/dev/guide/metabolism/imat.html b/dev/guide/metabolism/imat.html
index 060b734..e300bed 100644
--- a/dev/guide/metabolism/imat.html
+++ b/dev/guide/metabolism/imat.html
@@ -512,7 +512,7 @@ Context-specific models (iMAT)
-
+
@@ -551,7 +551,7 @@ Context-specific models (iMAT)
-
+
We can make the plot to look more like the image from the original paper by drawing the reactions with fluxes above a certain threshold with a wider line:
@@ -563,7 +563,7 @@ Context-specific models (iMAT)
-
+
diff --git a/dev/guide/metabolism/sparse-fba.html b/dev/guide/metabolism/sparse-fba.html
index 955acb0..50363e6 100644
--- a/dev/guide/metabolism/sparse-fba.html
+++ b/dev/guide/metabolism/sparse-fba.html
@@ -545,7 +545,7 @@ Manual implementation of sparse FBA
-
+
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
-
+
diff --git a/dev/guide/networks/pcst.html b/dev/guide/networks/pcst.html
index d256694..72f343e 100644
--- a/dev/guide/networks/pcst.html
+++ b/dev/guide/networks/pcst.html
@@ -554,7 +554,7 @@ Prize-Collecting Steiner Trees (PCSTs)
-
+
diff --git a/dev/guide/networks/shortest-paths.html b/dev/guide/networks/shortest-paths.html
index e69dd8a..8a00092 100644
--- a/dev/guide/networks/shortest-paths.html
+++ b/dev/guide/networks/shortest-paths.html
@@ -560,7 +560,7 @@ Random graphs
-[2125, 3529, 71, 3705, 1596, 464, 1388]
+[4963, 361, 9, 38, 76, 285]
@@ -572,7 +572,7 @@ Random graphs
-14.367935129555612
+12.929288678466708
@@ -592,7 +592,7 @@ Random graphs
-14.367935129555613
+12.929288678466705
@@ -604,7 +604,7 @@ Random graphs
-
+
diff --git a/dev/guide/networks/steiner-trees.html b/dev/guide/networks/steiner-trees.html
index 2b6651c..465ceab 100644
--- a/dev/guide/networks/steiner-trees.html
+++ b/dev/guide/networks/steiner-trees.html
@@ -605,25 +605,25 @@ Exact Steiner Trees with CORNETO
@@ -835,37 +835,37 @@ Exact Steiner Trees with CORNETO
+
diff --git a/dev/guide/signaling/carnival.html b/dev/guide/signaling/carnival.html
index 91f0775..9fa8fba 100644
--- a/dev/guide/signaling/carnival.html
+++ b/dev/guide/signaling/carnival.html
@@ -531,48 +531,48 @@ A toy example
-(CORNETO) May 15 07:51:41 AM - INFO : 2/2 inputs mapped to the graph
-(CORNETO) May 15 07:51:41 AM - INFO : 2/2 outputs mapped to the graph
-(CORNETO) May 15 07:51:41 AM - INFO : Pruning the graph with size: V x E = (6, 6)...
-(CORNETO) May 15 07:51:41 AM - INFO : Finished. Final size: V x E = (6, 6).
-(CORNETO) May 15 07:51:41 AM - INFO : 2/2 inputs after pruning.
-(CORNETO) May 15 07:51:41 AM - INFO : 2/2 outputs after pruning.
-(CORNETO) May 15 07:51:41 AM - INFO : Converting into a flow graph...
-(CORNETO) May 15 07:51:41 AM - INFO : Creating a network flow problem...
-(CORNETO) May 15 07:51:41 AM - INFO : Preprocess completed.
+(CORNETO) May 21 03:51:04 PM - INFO : 2/2 inputs mapped to the graph
+(CORNETO) May 21 03:51:04 PM - INFO : 2/2 outputs mapped to the graph
+(CORNETO) May 21 03:51:04 PM - INFO : Pruning the graph with size: V x E = (6, 6)...
+(CORNETO) May 21 03:51:04 PM - INFO : Finished. Final size: V x E = (6, 6).
+(CORNETO) May 21 03:51:04 PM - INFO : 2/2 inputs after pruning.
+(CORNETO) May 21 03:51:04 PM - INFO : 2/2 outputs after pruning.
+(CORNETO) May 21 03:51:04 PM - INFO : Converting into a flow graph...
+(CORNETO) May 21 03:51:04 PM - INFO : Creating a network flow problem...
+(CORNETO) May 21 03:51:04 PM - INFO : Preprocess completed.
===============================================================================
CVXPY
v1.5.1
===============================================================================
-(CVXPY) May 15 07:51:41 AM: Your problem has 86 variables, 197 constraints, and 0 parameters.
-(CVXPY) May 15 07:51:41 AM: It is compliant with the following grammars: DCP, DQCP
-(CVXPY) May 15 07:51:41 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)
-(CVXPY) May 15 07:51:41 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.
-(CVXPY) May 15 07:51:41 AM: Your problem is compiled with the CPP canonicalization backend.
+(CVXPY) May 21 03:51:04 PM: Your problem has 86 variables, 197 constraints, and 0 parameters.
+(CVXPY) May 21 03:51:04 PM: It is compliant with the following grammars: DCP, DQCP
+(CVXPY) May 21 03:51:04 PM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)
+(CVXPY) May 21 03:51:04 PM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.
+(CVXPY) May 21 03:51:04 PM: Your problem is compiled with the CPP canonicalization backend.
-------------------------------------------------------------------------------
Compilation
-------------------------------------------------------------------------------
-(CVXPY) May 15 07:51:41 AM: Compiling problem (target solver=SCIP).
-(CVXPY) May 15 07:51:41 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP
-(CVXPY) May 15 07:51:41 AM: Applying reduction Dcp2Cone
-(CVXPY) May 15 07:51:41 AM: Applying reduction CvxAttr2Constr
-(CVXPY) May 15 07:51:41 AM: Applying reduction ConeMatrixStuffing
-(CVXPY) May 15 07:51:41 AM: Applying reduction SCIP
-(CVXPY) May 15 07:51:41 AM: Finished problem compilation (took 2.971e-02 seconds).
+(CVXPY) May 21 03:51:04 PM: Compiling problem (target solver=SCIP).
+(CVXPY) May 21 03:51:04 PM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP
+(CVXPY) May 21 03:51:04 PM: Applying reduction Dcp2Cone
+(CVXPY) May 21 03:51:04 PM: Applying reduction CvxAttr2Constr
+(CVXPY) May 21 03:51:04 PM: Applying reduction ConeMatrixStuffing
+(CVXPY) May 21 03:51:04 PM: Applying reduction SCIP
+(CVXPY) May 21 03:51:04 PM: Finished problem compilation (took 2.959e-02 seconds).
-------------------------------------------------------------------------------
Numerical solver
-------------------------------------------------------------------------------
-(CVXPY) May 15 07:51:41 AM: Invoking solver SCIP to obtain a solution.
+(CVXPY) May 21 03:51:04 PM: Invoking solver SCIP to obtain a solution.
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
-(round 4, fast) 65 del vars, 147 del conss, 0 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 0 upgd conss, 0 impls, 18 clqs
-(round 5, fast) 67 del vars, 151 del conss, 0 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 0 upgd conss, 0 impls, 18 clqs
-(round 6, exhaustive) 67 del vars, 151 del conss, 0 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 40 upgd conss, 0 impls, 18 clqs
+(round 2, fast) 54 del vars, 131 del conss, 0 add conss, 53 chg bounds, 10 chg sides, 32 chg coeffs, 0 upgd conss, 0 impls, 20 clqs
+(round 3, fast) 62 del vars, 145 del conss, 0 add conss, 53 chg bounds, 12 chg sides, 34 chg coeffs, 0 upgd conss, 0 impls, 18 clqs
+(round 4, fast) 64 del vars, 147 del conss, 0 add conss, 53 chg bounds, 16 chg sides, 38 chg coeffs, 0 upgd conss, 0 impls, 18 clqs
+(round 5, fast) 66 del vars, 151 del conss, 0 add conss, 53 chg bounds, 16 chg sides, 38 chg coeffs, 0 upgd conss, 0 impls, 18 clqs
+(round 6, exhaustive) 66 del vars, 151 del conss, 0 add conss, 53 chg bounds, 16 chg sides, 38 chg coeffs, 40 upgd conss, 0 impls, 18 clqs
(0.0s) probing cycle finished: starting next cycle
-(round 7, exhaustive) 69 del vars, 151 del conss, 0 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 40 upgd conss, 28 impls, 46 clqs
-(round 8, medium) 69 del vars, 155 del conss, 0 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 40 upgd conss, 28 impls, 46 clqs
+(round 7, exhaustive) 68 del vars, 151 del conss, 0 add conss, 53 chg bounds, 16 chg sides, 38 chg coeffs, 40 upgd conss, 28 impls, 46 clqs
+(round 8, medium) 68 del vars, 155 del conss, 0 add conss, 53 chg bounds, 16 chg sides, 38 chg coeffs, 40 upgd conss, 28 impls, 46 clqs
(0.0s) probing cycle finished: starting next cycle
(0.0s) symmetry computation started: requiring (bin +, int +, cont +), (fixed: bin -, int -, cont -)
(0.0s) symmetry computation finished: 2 generators found (max: 1500, log10 of symmetry group size: 0.6) (symcode time: 0.00)
@@ -581,9 +581,9 @@ A toy example
-
+
diff --git a/dev/reports/guide/signaling/carnival.err.log b/dev/reports/guide/signaling/carnival.err.log
index ed94aa4..cd650b6 100644
--- a/dev/reports/guide/signaling/carnival.err.log
+++ b/dev/reports/guide/signaling/carnival.err.log
@@ -34,49 +34,49 @@ Cell [0;32mIn[11], line 5[0m
[1;32m 4[0m [38;5;66;03m# to the old R function https://saezlab.github.io/CARNIVAL/reference/runVanillaCarnival.html[39;00m
[0;32m----> 5[0m P [38;5;241m=[39m [43mrunCARNIVAL_AcyclicFlow[49m[43m([49m[43mG2[49m[43m,[49m[43m [49m[43mexp_list[49m[43m,[49m[43m [49m[43msolver[49m[38;5;241;43m=[39;49m[38;5;124;43m"[39;49m[38;5;124;43mGUROBI[39;49m[38;5;124;43m"[39;49m[43m)[49m
-File [0;32m~/work/corneto/corneto/corneto/methods/carnival.py:553[0m, in [0;36mrunCARNIVAL_AcyclicFlow[0;34m(G, exp_list, betaWeight, solver, verbosity)[0m
-[1;32m 550[0m P[38;5;241m.[39madd_objectives([38;5;28msum[39m(Z[m_nodes_positions, iexp][38;5;241m.[39mmultiply([38;5;28mabs[39m(m_values))))
-[1;32m 551[0m P[38;5;241m.[39madd_objectives(betaWeight [38;5;241m*[39m [38;5;28msum[39m([38;5;28msum[39m(Eact [38;5;241m+[39m Einh)))
-[0;32m--> 553[0m [43mP[49m[38;5;241;43m.[39;49m[43msolve[49m[43m([49m[43msolver[49m[38;5;241;43m=[39;49m[43msolver[49m[43m,[49m[43m [49m[43mverbosity[49m[38;5;241;43m=[39;49m[43mverbosity[49m[43m)[49m
-[1;32m 554[0m [38;5;28;01mreturn[39;00m P
+File [0;32m~/work/corneto/corneto/corneto/methods/carnival.py:546[0m, in [0;36mrunCARNIVAL_AcyclicFlow[0;34m(G, exp_list, betaWeight, solver, verbosity)[0m
+[1;32m 543[0m P[38;5;241m.[39madd_objectives([38;5;28msum[39m(Z[m_nodes_positions, iexp][38;5;241m.[39mmultiply([38;5;28mabs[39m(m_values))))
+[1;32m 544[0m P[38;5;241m.[39madd_objectives(betaWeight [38;5;241m*[39m [38;5;28msum[39m([38;5;28msum[39m(Eact [38;5;241m+[39m Einh)))
+[0;32m--> 546[0m [43mP[49m[38;5;241;43m.[39;49m[43msolve[49m[43m([49m[43msolver[49m[38;5;241;43m=[39;49m[43msolver[49m[43m,[49m[43m [49m[43mverbosity[49m[38;5;241;43m=[39;49m[43mverbosity[49m[43m)[49m
+[1;32m 547[0m [38;5;28;01mreturn[39;00m P
-File [0;32m~/work/corneto/corneto/corneto/backend/_base.py:494[0m, in [0;36mProblemDef.solve[0;34m(self, solver, max_seconds, warm_start, verbosity, **options)[0m
-[1;32m 492[0m [38;5;28;01mif[39;00m [38;5;28mself[39m[38;5;241m.[39m_backend [38;5;129;01mis[39;00m [38;5;28;01mNone[39;00m:
-[1;32m 493[0m [38;5;28;01mraise[39;00m [38;5;167;01mValueError[39;00m([38;5;124m"[39m[38;5;124mNo backend assigned.[39m[38;5;124m"[39m)
-[0;32m--> 494[0m [38;5;28;01mreturn[39;00m [38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43m_backend[49m[38;5;241;43m.[39;49m[43msolve[49m[43m([49m
-[1;32m 495[0m [43m [49m[38;5;28;43mself[39;49m[43m,[49m
-[1;32m 496[0m [43m [49m[43msolver[49m[38;5;241;43m=[39;49m[43msolver[49m[43m,[49m
-[1;32m 497[0m [43m [49m[43mmax_seconds[49m[38;5;241;43m=[39;49m[43mmax_seconds[49m[43m,[49m
-[1;32m 498[0m [43m [49m[43mwarm_start[49m[38;5;241;43m=[39;49m[43mwarm_start[49m[43m,[49m
-[1;32m 499[0m [43m [49m[43mverbosity[49m[38;5;241;43m=[39;49m[43mverbosity[49m[43m,[49m
-[1;32m 500[0m [43m [49m[38;5;241;43m*[39;49m[38;5;241;43m*[39;49m[43moptions[49m[43m,[49m
-[1;32m 501[0m [43m[49m[43m)[49m
+File [0;32m~/work/corneto/corneto/corneto/backend/_base.py:553[0m, in [0;36mProblemDef.solve[0;34m(self, solver, max_seconds, warm_start, verbosity, **options)[0m
+[1;32m 551[0m [38;5;28;01mif[39;00m [38;5;28mself[39m[38;5;241m.[39m_backend [38;5;129;01mis[39;00m [38;5;28;01mNone[39;00m:
+[1;32m 552[0m [38;5;28;01mraise[39;00m [38;5;167;01mValueError[39;00m([38;5;124m"[39m[38;5;124mNo backend assigned.[39m[38;5;124m"[39m)
+[0;32m--> 553[0m [38;5;28;01mreturn[39;00m [38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43m_backend[49m[38;5;241;43m.[39;49m[43msolve[49m[43m([49m
+[1;32m 554[0m [43m [49m[38;5;28;43mself[39;49m[43m,[49m
+[1;32m 555[0m [43m [49m[43msolver[49m[38;5;241;43m=[39;49m[43msolver[49m[43m,[49m
+[1;32m 556[0m [43m [49m[43mmax_seconds[49m[38;5;241;43m=[39;49m[43mmax_seconds[49m[43m,[49m
+[1;32m 557[0m [43m [49m[43mwarm_start[49m[38;5;241;43m=[39;49m[43mwarm_start[49m[43m,[49m
+[1;32m 558[0m [43m [49m[43mverbosity[49m[38;5;241;43m=[39;49m[43mverbosity[49m[43m,[49m
+[1;32m 559[0m [43m [49m[38;5;241;43m*[39;49m[38;5;241;43m*[39;49m[43moptions[49m[43m,[49m
+[1;32m 560[0m [43m[49m[43m)[49m
-File [0;32m~/work/corneto/corneto/corneto/backend/_base.py:751[0m, in [0;36mBackend.solve[0;34m(self, p, solver, max_seconds, warm_start, verbosity, **options)[0m
-[1;32m 745[0m [38;5;28;01melse[39;00m:
-[1;32m 746[0m o [38;5;241m=[39m (
-[1;32m 747[0m p[38;5;241m.[39mweights[[38;5;241m0[39m] [38;5;241m*[39m p[38;5;241m.[39mobjectives[[38;5;241m0[39m]
-[1;32m 748[0m [38;5;28;01mif[39;00m p[38;5;241m.[39mobjectives [38;5;129;01mand[39;00m p[38;5;241m.[39mweights[[38;5;241m0[39m] [38;5;241m!=[39m [38;5;241m0[39m
-[1;32m 749[0m [38;5;28;01melse[39;00m [38;5;28;01mNone[39;00m
-[1;32m 750[0m )
-[0;32m--> 751[0m [38;5;28;01mreturn[39;00m [38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43m_solve[49m[43m([49m
-[1;32m 752[0m [43m [49m[43mp[49m[43m,[49m
-[1;32m 753[0m [43m [49m[43mobjective[49m[38;5;241;43m=[39;49m[43mo[49m[43m,[49m
-[1;32m 754[0m [43m [49m[43msolver[49m[38;5;241;43m=[39;49m[43msolver[49m[43m,[49m
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diff --git a/dev/searchindex.js b/dev/searchindex.js
index fbbe1d7..5497055 100644
--- a/dev/searchindex.js
+++ b/dev/searchindex.js
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\ No newline at end of file
+Search.setIndex({"alltitles": {"A more complex knapsack": [[18, "a-more-complex-knapsack"]], "A toy example": [[32, "a-toy-example"]], "API Reference": [[5, "api-reference"]], "Acknowledgements": [[35, "acknowledgements"]], "Acyclic Flows": [[17, "acyclic-flows"]], "CARNIVAL": [[32, "carnival"]], "CARNIVAL with Acyclic signaling": [[32, "carnival-with-acyclic-signaling"]], "CARNIVAL with acyclic flow - single condition": [[32, "carnival-with-acyclic-flow-single-condition"]], "CARNIVAL with acyclic flow - two conditions": [[32, "carnival-with-acyclic-flow-two-conditions"]], "COBRApy: Constraint-based metabolic modeling in Python": [[9, "cobrapy-constraint-based-metabolic-modeling-in-python"]], "CORNETO": [[5, "corneto"]], "CORNETO ": [[35, "corneto"]], "CVXPY: Convex optimization, for everyone": [[10, "cvxpy-convex-optimization-for-everyone"]], "Constrained Optimization": [[18, "constrained-optimization"]], "Contents:": [[5, null]], "Context-specific metabolic model from transcriptomics data": [[36, "context-specific-metabolic-model-from-transcriptomics-data"]], "Context-specific models (iMAT)": [[23, "context-specific-models-imat"]], "Creating a weighted graph": [[30, "creating-a-weighted-graph"]], "Decoupler: Ensemble of methods to infer biological activities": [[11, "decoupler-ensemble-of-methods-to-infer-biological-activities"]], "Edge attributes": [[21, "edge-attributes"]], "Exact Steiner Trees with CORNETO": [[31, "exact-steiner-trees-with-corneto"]], "FBA with CORNETO": [[22, "fba-with-corneto"]], "Flux Balance Analysis (FBA)": [[22, "flux-balance-analysis-fba"]], "Getting started": [[19, "getting-started"]], "Heuristic steiner tree from NetworkX": [[31, "heuristic-steiner-tree-from-networkx"]], "Hypergraphs": [[21, "hypergraphs"]], "Importing graphs": [[21, "importing-graphs"]], "Interactomics": [[8, "interactomics"]], "Interoperability": [[12, "interoperability"]], "LIANA+: An all-in-one cell-cell communication framework": [[13, "liana-an-all-in-one-cell-cell-communication-framework"]], "Largest DAG from a given source and sink vertex": [[17, "largest-dag-from-a-given-source-and-sink-vertex"]], "Largest DAG from any source to any sink": [[17, "largest-dag-from-any-source-to-any-sink"]], "Let\u2019s check the Acyclic on flow": [[32, "let-s-check-the-acyclic-on-flow"]], "Limitation of single flow CARNIVAL": [[32, "limitation-of-single-flow-carnival"]], "Manual implementation of sparse FBA": [[27, "manual-implementation-of-sparse-fba"]], "Manually creating a graph": [[21, "manually-creating-a-graph"]], "Metabolism": [[24, "metabolism"]], "Module contents": [[0, "module-corneto"], [1, "module-corneto.backend"], [2, "module-corneto.methods"], [3, "module-corneto.methods.metabolism"], [4, "module-corneto.utils"]], "Multi-commodity Network Flows": [[20, "multi-commodity-network-flows"]], "Multi-condition CARNIVAL": [[34, "multi-condition-carnival"]], "Multi-condition iMAT": [[25, "multi-condition-imat"]], "Multi-condition sparse FBA": [[26, "multi-condition-sparse-fba"]], "Network methods": [[28, "network-methods"]], "NetworkX: Network Analysis in Python": [[14, "networkx-network-analysis-in-python"]], "Omnipath: intra- & intercellular signaling knowledge": [[15, "omnipath-intra-intercellular-signaling-knowledge"]], "PICOS: A Python interface to conic optimization solvers": [[16, "picos-a-python-interface-to-conic-optimization-solvers"]], "Prior Knowledge and Graphs": [[21, "prior-knowledge-and-graphs"]], "Prize-Collecting Steiner Trees (PCSTs)": [[29, "prize-collecting-steiner-trees-pcsts"]], "Random graphs": [[30, "random-graphs"]], "Saving and reading": [[21, "saving-and-reading"]], "Shortest paths": [[30, "shortest-paths"]], "Signaling": [[33, "signaling"]], "Sparse FBA": [[27, "sparse-fba"]], "Sparse FBA with min. flux": [[27, "sparse-fba-with-min-flux"]], "Steiner Trees (STs)": [[31, "steiner-trees-sts"]], "Submodules": [[2, "submodules"], [3, "submodules"]], "Subpackages": [[0, 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30, 31, 32, 34, 35, 36], "scipi": [1, 9, 10, 16, 17, 18, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 34, 36], "score": [23, 32, 36], "scsgraphviz": [9, 10, 16, 17, 18, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 34, 36], "seamlessli": 10, "search": [16, 17], "sec": [18, 20, 31, 32], "second": [10, 18, 20, 31, 32], "see": [13, 14, 17, 18, 21, 22, 27, 30, 31, 32], "seed": [30, 31], "seek": 31, "seen": 16, "select": [1, 16, 17, 18, 31], "selected_react": 36, "self": [21, 32], "sepa": [20, 31, 32], "serv": 17, "set": [1, 10, 11, 17, 18, 21, 22, 31, 33], "set_attr": [0, 5, 6], "set_index": 36, "setppc": [31, 32], "shape": [1, 2, 9, 10, 14, 16, 20, 22, 23, 31, 36], "share": 20, "shared_bound": [1, 20], "shlomi": 23, "shortest": [7, 14, 21, 28, 31], "shortest_path": [0, 5, 6, 14, 30], "shortest_path_length": [14, 30], "should": 30, "show": [22, 23, 24], "side": [18, 20, 31, 32], "sif": 21, "sif_fil": 0, "sif_graph": 21, "sigma": 10, "sign": [11, 17, 32], "signal": [0, 1, 5, 6, 7, 12, 13, 17, 21], "signal_implies_flow": 2, "signflow": [0, 2], "signflow_constraint": [0, 2], "signific": 10, "similar": [16, 32], "simpler": 30, "simplero": 31, "simpli": 17, "simplifi": [10, 17, 32], "simultan": [20, 31], "sinc": [17, 23, 31, 32], "singl": [7, 13, 20, 33], "single_source_dijkstra_path": 14, "single_source_dijkstra_path_length": 14, "sink": [7, 19], "size": [31, 32], "skip_unsupported_edg": 14, "slower": 30, "small": [17, 20, 31], "so": [17, 18], "sol": [18, 30], "solut": [7, 10, 16, 17, 18, 20, 22, 30, 31, 32], "solv": [0, 1, 2, 10, 13, 16, 17, 18, 20, 22, 23, 27, 29, 30, 31, 32, 36], "solve_shortest_path": [0, 2, 30], "solver": [1, 2, 7, 9, 10, 12, 17, 18, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 34, 35, 36], "solver_kwarg": 2, "some": [12, 17, 18, 21, 29, 31], "someth": 21, "sort": 17, "sourc": [1, 2, 7, 10, 14, 16, 19, 21, 31, 35], "source_attr": [0, 5, 6, 21], "space": [17, 18, 31], "span": 31, "spars": [1, 7, 22, 24], "sparse_class": 1, "spatial": 13, "special": [14, 17, 18, 21, 27], "specif": [7, 10, 16, 17, 18, 20, 21, 22, 24, 30, 31, 37], "specifi": [2, 18], "spent": [10, 18, 20, 31, 32], "split": 10, "st": [7, 28], "stand": 31, "standard": [14, 31, 32], "stanford": 10, "star": 30, "start": [0, 1, 7, 10, 16, 17, 20, 21, 31, 32], "startswith": [3, 36], "state": [2, 22, 23], "static": [0, 1], "statist": [2, 11, 31, 32], "statu": [10, 18, 20, 31, 32], "steadi": [22, 23], "steiner": [0, 5, 6, 7, 28], "steiner_tre": 31, "stellato": 10, "stem": 31, "still": [21, 31], "stoichiometr": [22, 23], "stoichiometri": 22, "stop": 31, "store": 21, "str": [0, 1, 2, 3], "straightforward": 21, "strategi": 16, "strbr": [20, 31, 32], "stree": 31, "strict": [10, 31], "strict_acycl": [2, 31], "strictli": 31, "structur": [14, 17, 31], "studi": 9, "sub": [17, 32], "subject": 18, "submodul": [0, 5, 6], "subnetwork": 31, "subpackag": [5, 6], "subset": [18, 31, 32], "subset_edg": 2, "subseteq": 31, "substanc": 22, "success": [10, 31], "successfulli": 31, "suffix": 1, "suffix_neg": 1, "suffix_po": 1, "suit": 21, "suitabl": 16, "sum": [10, 16, 17, 18, 20, 22, 27, 31, 32, 36], "sum_": [18, 29], "summari": [10, 18, 20, 31, 32], "superior": 31, "support": [0, 7, 10, 12, 14, 16, 17, 21, 22, 31, 32, 35], "switch": 10, "symbol": [1, 16, 17, 23, 29, 31, 32], "symbol_valu": 3, "symbol_values_list": 3, "symcod": [20, 31, 32], "symmetri": [20, 31, 32], "system": [9, 10, 18, 22, 23, 31, 32], "systemat": 23, "t": [0, 2, 16, 22, 23, 30, 31], "tackl": [10, 31], "tailor": [10, 31], "take": [11, 16, 17, 18, 20, 21, 27], "tala": 36, "target": [1, 2, 10, 11, 14, 17, 18, 20, 21, 31, 32], "target_attr": [0, 5, 6], "task": [30, 31, 33], "techniqu": [17, 18, 22, 23], "telecommun": 20, "tempor": 22, "termin": [2, 17, 29, 31], "terminal_per_condit": 2, "test": [11, 13, 36], "text": [18, 29], "textbook": [9, 22, 27], "tf": 32, "than": [17, 23, 30, 31, 32], "thank": [18, 32], "thd2": 36, "thei": [22, 23, 30, 31], "them": [29, 31], "therefor": 13, "thermodynam": 23, "thi": [1, 10, 14, 16, 17, 18, 20, 21, 22, 23, 24, 30, 31, 32, 35], "think": 14, "those": [13, 17, 31], "though": 22, "thought": 13, "three": 2, "threshold": 23, "through": [12, 16, 18, 20, 21, 22, 23, 32], "throughput": 23, "thu": [17, 32], "tighten": [18, 20, 31, 32], "time": [10, 18, 20, 22, 31, 32], "time_limit": 10, "timefram": 31, "tissu": 23, "titl": 36, "tkt1": 36, "tkt2": 36, "to_dict": 36, "to_direct": 30, "to_graph": 31, "to_networkx": 21, "todo": [17, 30, 32], "togeth": 14, "toi": [7, 33], "toler": [1, 2, 17], "tolist": 36, "tomer": 23, "too": 29, "took": [10, 18, 20, 31, 32], "tool": [7, 9, 10, 12, 14, 21, 23, 30, 31, 32, 33, 35], "toolkit": 14, "top": [7, 21], "topolog": 17, "topologi": 32, "total": [14, 18, 20, 22, 27, 29, 31], "total_valu": 18, "total_weight": [18, 31], "toward": [14, 32], "tpi": 36, "traceback": 32, "tradit": 23, "trairatphisan": 32, "transcript": [11, 22, 23, 32], "transcriptom": [11, 37], "transform": [14, 17, 18, 21, 22, 31, 32], "translat": [7, 22, 23], "transpar": 31, "transport": 20, "tree": [7, 28], "trick": 17, "tripl": 21, "triplet": 21, "trivial": 18, "true": [0, 1, 2, 14, 17, 18, 20, 23, 27, 30, 31, 36], "try": 27, "tupl": [0, 1, 2], "turnov": 22, "tutori": [8, 13, 17, 21, 22, 24, 30, 31, 35], "two": [2, 7, 17, 18, 20, 29, 30, 31, 33], "type": [0, 1, 2, 3, 7, 10, 16, 18, 20, 21, 29, 31, 32], "typic": [18, 22, 31], "u": [21, 30, 31], "ub": [1, 17, 20], "ub_loss": 2, "unblock": 27, "unblocked_flow": 27, "unconstrain": 27, "under": [21, 22, 23, 35], "undergo": 23, "underli": 33, "underpin": 31, "understand": [13, 22, 31], "undirect": [0, 5, 6, 8, 14, 21, 29, 31], "unifi": [7, 11, 18, 35], "uniform": 30, "union": [1, 35], "uniqu": 31, "unit": 22, "univers": [7, 10, 35], "unknown": [20, 23, 27, 31, 32, 36], "unless": 17, "unlik": [10, 29, 31], "unobserv": 31, "until": 31, "up": [14, 32], "upgd": [18, 31, 32], "upon": 17, "upper": [1, 22], "upregul": 23, "upstream": [13, 32], "urban": 20, "us": [1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 23, 24, 27, 29, 30, 31, 32, 35], "use_flow_ind": 2, "use_unblocked_flux_ind": 3, "useless": 31, "user": [10, 16, 21, 31, 32, 35], "usual": 22, "util": [0, 5, 6], "v": [1, 17, 21, 29, 30, 31, 32], "v0": [9, 10, 16, 17, 18, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 34, 36], "v1": [9, 10, 16, 17, 18, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 34, 36], "v2": [9, 10, 16, 17, 18, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 34, 36], "v3": 17, "v4": 17, "v5": 17, "v6": 17, "v7": 17, "v_i": 18, "valid": [17, 31], "valu": [0, 1, 2, 5, 6, 10, 16, 17, 18, 20, 22, 23, 27, 29, 30, 31, 32, 36], "valuabl": 15, "valueerror": 32, "var": [18, 20, 31, 32], "var_dag": 1, "varbound": [31, 32], "variabl": [0, 1, 9, 10, 16, 17, 18, 20, 21, 23, 27, 29, 31, 32, 36], "varieti": [31, 32], "variou": [7, 12, 13, 16, 20, 23], "varnam": 1, "vartyp": [0, 1, 18], "vbound": 32, "ve": 31, "vector": [16, 27, 31], "verbos": [1, 2, 10, 16, 18, 20, 31, 32], "veri": [17, 18, 21, 31], "versatil": [10, 14, 30], "version": [0, 1, 9, 10, 16, 17, 18, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 34, 35, 36], "vertex": [2, 7, 19, 21, 29], "vertex_attr": 2, "vertex_lb_dist": 1, "vertex_styl": 32, "vertex_ub_dist": 1, "vertex_valu": 32, "vertex_values_c0": 32, "vertex_var": 32, "vertic": [0, 1, 2, 17, 20, 21, 29, 30, 31], "via": 16, "visit": 17, "visual": 14, "vivek": 22, "volum": 32, "vstack": [0, 1], "w": [3, 31], "w_i": 18, "wa": 32, "wai": [10, 17, 21, 22, 31], "want": [17, 31], "warm": 10, "warm_start": [1, 32], "warshal": 30, "we": [12, 14, 17, 18, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32], "weight": [1, 7, 11, 14, 17, 18, 20, 21, 22, 23, 27, 28, 29, 31, 32], "well": [21, 31, 32], "were": [17, 32], "what": [7, 17, 24, 35], "when": [14, 21, 22, 27, 30, 31], "where": [2, 17, 18, 21, 22, 29, 31, 32], "whether": 29, "which": [1, 10, 16, 17, 18, 21, 22, 23, 31, 32], "while": [12, 14, 16, 18, 20, 23, 31], "white": 23, "who": 21, "whose": 23, "wide": [18, 32], "wider": 23, "wip": 35, "wish": 31, "with_flow": [1, 17], "with_label": 31, "within": [10, 11, 18, 21, 27, 31], "without": [10, 32], "work": [12, 14, 21, 30, 32], "world": 35, "x": [1, 10, 16, 18, 32], "x_i": 18, "x_v": 29, "xor": [0, 1], "xz": 21, "y": 1, "y_e": 29, "yield": 31, "you": [10, 16, 17, 18, 20, 21, 22, 29, 30, 31, 32, 35], "your": [10, 18, 20, 31, 32], "z": 32, "z0": 3, "za": 3, "zero": [17, 20, 23, 27, 36], "zip": [2, 17, 29, 31, 36], "zip_path": 2, "zipfil": 2, "ziroundi": 31}, "titles": ["corneto package", "corneto.backend package", "corneto.methods package", "corneto.methods.metabolism package", "corneto.utils package", "API Reference", "corneto", "User guide", "Interactomics", "COBRApy: Constraint-based metabolic modeling in Python", "CVXPY: Convex optimization, for everyone", "Decoupler: Ensemble of methods to infer biological activities", "Interoperability", "LIANA+: An all-in-one cell-cell communication framework", "NetworkX: Network Analysis in Python", "Omnipath: intra- & intercellular signaling knowledge", "PICOS: A Python interface to conic optimization solvers", "Acyclic Flows", "Constrained Optimization", "Getting started", "Multi-commodity Network Flows", "Prior Knowledge and Graphs", "Flux Balance Analysis (FBA)", "Context-specific models (iMAT)", "Metabolism", "Multi-condition iMAT", "Multi-condition sparse FBA", "Sparse FBA", "Network methods", "Prize-Collecting Steiner Trees (PCSTs)", "Shortest paths", "Steiner Trees (STs)", "CARNIVAL", "Signaling", "Multi-condition CARNIVAL", "CORNETO ", "Context-specific metabolic model from transcriptomics data", "Tutorials"], "titleterms": {"": 32, "A": [16, 18, 32], "The": 18, "acknowledg": 35, "activ": 11, "acycl": [17, 32], "all": 13, "an": 13, "analysi": [14, 22], "ani": 17, "api": 5, "attribut": 21, "backend": 1, "balanc": 22, "base": 9, "biolog": 11, "carniv": [2, 32, 34], "cell": 13, "check": 32, "class": 35, "cobrapi": [9, 22], "collect": 29, "commod": 20, "commun": 13, "complex": 18, "condit": [25, 26, 32, 34], "conic": 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"optim": [10, 16, 18], "packag": [0, 1, 2, 3, 4], "path": 30, "pcst": 29, "pico": 16, "prior": 21, "prize": 29, "problem": 18, "python": [9, 14, 16], "random": 30, "read": 21, "refer": 5, "save": 21, "shortest": 30, "shortest_path": 2, "signal": [2, 15, 32, 33], "singl": 32, "sink": 17, "solver": 16, "sourc": 17, "span": 35, "spars": [26, 27], "specif": [23, 36], "st": 31, "start": 19, "steiner": [2, 29, 31], "submodul": [2, 3], "subpackag": [0, 2], "titl": 35, "toi": 32, "transcriptom": 36, "tree": [29, 31], "tutori": 37, "two": 32, "us": 22, "user": 7, "util": 4, "vertex": 17, "weight": 30, "what": 22}})
\ No newline at end of file
-
-
- Parameters: -
-
+
- Return type: +
+ProblemDef
+- Parameters: +
x (CExpression)
axis (int | None)
corneto.backend package linear_and(x, axis=None, varname='and')#
-
-
- Parameters: -
-
+
- Return type: +
+ProblemDef
+- Parameters: +
x (CExpression)
axis (int | None)
corneto.backend package vstack(arg_list)#
corneto.backend package hstack(arg_list)#
Submodulescorneto.methods.steiner module#
-
-corneto.methods.steiner.exact_steiner_tree(G, terminals, edge_weights=None, root=None, tolerance=0.001, strict_acyclic=False, flow_name='_flow', out_flow_edge_type=EdgeType.UNDIRECTED, backend=<corneto.backend._cvxpy_backend.CvxpyBackend object>)#
+corneto.methods.steiner.exact_steiner_tree(G, terminals, edge_weights=None, root=None, tolerance=0.001, strict_acyclic=False, flow_name='_flow', in_flow_edge_type=EdgeType.DIRECTED, out_flow_edge_type=EdgeType.DIRECTED, backend=<corneto.backend._cvxpy_backend.CvxpyBackend object>)#
- Parameters:
diff --git a/dev/guide/interoperability/cvxpy.html b/dev/guide/interoperability/cvxpy.html
index d04795f..24d4355 100644
--- a/dev/guide/interoperability/cvxpy.html
+++ b/dev/guide/interoperability/cvxpy.html
@@ -503,25 +503,25 @@ CVXPY: Convex optimization, for everyone
diff --git a/dev/guide/intro/acyclic-flows.html b/dev/guide/intro/acyclic-flows.html
index a79ae85..c0bb6b4 100644
--- a/dev/guide/intro/acyclic-flows.html
+++ b/dev/guide/intro/acyclic-flows.html
@@ -539,8 +539,8 @@ Largest DAG from a given source and sink vertex
{'_flow': Variable((14,), _flow),
- '_flow_ineg': Variable((14,), _flow_ineg, boolean=True),
'_flow_ipos': Variable((14,), _flow_ipos, boolean=True),
+ '_flow_ineg': Variable((14,), _flow_ineg, boolean=True),
'_dag_layer_pos': Variable((7,), _dag_layer_pos),
'positive_flow': Variable((14,), _flow_ipos, boolean=True),
'negative_flow': Variable((14,), _flow_ineg, boolean=True),
diff --git a/dev/guide/intro/constrained-optimization.html b/dev/guide/intro/constrained-optimization.html
index 7b44743..04eafbe 100644
--- a/dev/guide/intro/constrained-optimization.html
+++ b/dev/guide/intro/constrained-optimization.html
@@ -505,7 +505,7 @@ The Knapsack Problem
-<corneto.DeprecatedBackend at 0x7fced04c68d0>
+<corneto.DeprecatedBackend at 0x7fb898e1ab10>
@@ -543,7 +543,7 @@ The Knapsack Problem
-<corneto.backend._base.ProblemDef at 0x7fce80114fd0>
+<corneto.backend._base.ProblemDef at 0x7fb84dd2eed0>
@@ -557,9 +557,9 @@ The Knapsack Problem
{'obj5': Variable((1,), obj5, boolean=True),
'obj4': Variable((1,), obj4, boolean=True),
- 'obj3': Variable((1,), obj3, boolean=True),
'obj2': Variable((1,), obj2, boolean=True),
- 'obj1': Variable((1,), obj1, boolean=True)}
+ 'obj1': Variable((1,), obj1, boolean=True),
+ 'obj3': Variable((1,), obj3, boolean=True)}
@@ -723,26 +723,26 @@ A more complex knapsackA more complex knapsack
Problem(Maximize(Expression(AFFINE, NONNEGATIVE, ())), [Inequality(Expression(AFFINE, NONNEGATIVE, ()))])
diff --git a/dev/guide/intro/multi-commodity-network-flows.html b/dev/guide/intro/multi-commodity-network-flows.html
index 6acdb58..3b21c0d 100644
--- a/dev/guide/intro/multi-commodity-network-flows.html
+++ b/dev/guide/intro/multi-commodity-network-flows.html
@@ -572,25 +572,25 @@ Multi-commodity Network FlowsProblem(Minimize(Expression(AFFINE, UNKNOWN, ())), [Inequality(Constant(CONSTANT, ZERO, (10, 2))), Inequality(Variable((10, 2), _flow)), Equality(Expression(AFFINE, UNKNOWN, (5, 2)), Constant(CONSTANT, ZERO, ())), Inequality(Expression(AFFINE, UNKNOWN, (10,))), Inequality(Constant(CONSTANT, ZERO, (10,)))])
diff --git a/dev/guide/intro/prior-knowledge.html b/dev/guide/intro/prior-knowledge.html
index 2cb8473..b7d3fc3 100644
--- a/dev/guide/intro/prior-knowledge.html
+++ b/dev/guide/intro/prior-knowledge.html
@@ -736,7 +736,7 @@ Hypergraphs
-
+
@@ -745,7 +745,7 @@ Hypergraphs
-('B', 'A', 'C', 'D', 'F', 'E')
+('B', 'A', 'C', 'D', 'E', 'F')
diff --git a/dev/guide/metabolism/flux-balance-analysis.html b/dev/guide/metabolism/flux-balance-analysis.html
index 44edf28..07f7c54 100644
--- a/dev/guide/metabolism/flux-balance-analysis.html
+++ b/dev/guide/metabolism/flux-balance-analysis.html
@@ -511,7 +511,7 @@ Using COBRApy
-<Solution 0.874 at 0x7fa457ba20d0>
+<Solution 0.874 at 0x7f7408cf1a90>
@@ -624,7 +624,7 @@ Using COBRApy
-
+
@@ -651,7 +651,7 @@ Using COBRApy
-
+
diff --git a/dev/guide/metabolism/imat.html b/dev/guide/metabolism/imat.html
index 060b734..e300bed 100644
--- a/dev/guide/metabolism/imat.html
+++ b/dev/guide/metabolism/imat.html
@@ -512,7 +512,7 @@ Context-specific models (iMAT)
-
+
@@ -551,7 +551,7 @@ Context-specific models (iMAT)
-
+
We can make the plot to look more like the image from the original paper by drawing the reactions with fluxes above a certain threshold with a wider line:
@@ -563,7 +563,7 @@ Context-specific models (iMAT)
-
+
diff --git a/dev/guide/metabolism/sparse-fba.html b/dev/guide/metabolism/sparse-fba.html
index 955acb0..50363e6 100644
--- a/dev/guide/metabolism/sparse-fba.html
+++ b/dev/guide/metabolism/sparse-fba.html
@@ -545,7 +545,7 @@ Manual implementation of sparse FBA
-
+
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
-
+
diff --git a/dev/guide/networks/pcst.html b/dev/guide/networks/pcst.html
index d256694..72f343e 100644
--- a/dev/guide/networks/pcst.html
+++ b/dev/guide/networks/pcst.html
@@ -554,7 +554,7 @@ Prize-Collecting Steiner Trees (PCSTs)
-
+
diff --git a/dev/guide/networks/shortest-paths.html b/dev/guide/networks/shortest-paths.html
index e69dd8a..8a00092 100644
--- a/dev/guide/networks/shortest-paths.html
+++ b/dev/guide/networks/shortest-paths.html
@@ -560,7 +560,7 @@ Random graphs
-[2125, 3529, 71, 3705, 1596, 464, 1388]
+[4963, 361, 9, 38, 76, 285]
@@ -572,7 +572,7 @@ Random graphs
-14.367935129555612
+12.929288678466708
@@ -592,7 +592,7 @@ Random graphs
-14.367935129555613
+12.929288678466705
@@ -604,7 +604,7 @@ Random graphs
-
+
diff --git a/dev/guide/networks/steiner-trees.html b/dev/guide/networks/steiner-trees.html
index 2b6651c..465ceab 100644
--- a/dev/guide/networks/steiner-trees.html
+++ b/dev/guide/networks/steiner-trees.html
@@ -605,25 +605,25 @@ Exact Steiner Trees with CORNETO
@@ -835,37 +835,37 @@ Exact Steiner Trees with CORNETO
+
diff --git a/dev/guide/signaling/carnival.html b/dev/guide/signaling/carnival.html
index 91f0775..9fa8fba 100644
--- a/dev/guide/signaling/carnival.html
+++ b/dev/guide/signaling/carnival.html
@@ -531,48 +531,48 @@ A toy example
-(CORNETO) May 15 07:51:41 AM - INFO : 2/2 inputs mapped to the graph
-(CORNETO) May 15 07:51:41 AM - INFO : 2/2 outputs mapped to the graph
-(CORNETO) May 15 07:51:41 AM - INFO : Pruning the graph with size: V x E = (6, 6)...
-(CORNETO) May 15 07:51:41 AM - INFO : Finished. Final size: V x E = (6, 6).
-(CORNETO) May 15 07:51:41 AM - INFO : 2/2 inputs after pruning.
-(CORNETO) May 15 07:51:41 AM - INFO : 2/2 outputs after pruning.
-(CORNETO) May 15 07:51:41 AM - INFO : Converting into a flow graph...
-(CORNETO) May 15 07:51:41 AM - INFO : Creating a network flow problem...
-(CORNETO) May 15 07:51:41 AM - INFO : Preprocess completed.
+(CORNETO) May 21 03:51:04 PM - INFO : 2/2 inputs mapped to the graph
+(CORNETO) May 21 03:51:04 PM - INFO : 2/2 outputs mapped to the graph
+(CORNETO) May 21 03:51:04 PM - INFO : Pruning the graph with size: V x E = (6, 6)...
+(CORNETO) May 21 03:51:04 PM - INFO : Finished. Final size: V x E = (6, 6).
+(CORNETO) May 21 03:51:04 PM - INFO : 2/2 inputs after pruning.
+(CORNETO) May 21 03:51:04 PM - INFO : 2/2 outputs after pruning.
+(CORNETO) May 21 03:51:04 PM - INFO : Converting into a flow graph...
+(CORNETO) May 21 03:51:04 PM - INFO : Creating a network flow problem...
+(CORNETO) May 21 03:51:04 PM - INFO : Preprocess completed.
===============================================================================
CVXPY
v1.5.1
===============================================================================
-(CVXPY) May 15 07:51:41 AM: Your problem has 86 variables, 197 constraints, and 0 parameters.
-(CVXPY) May 15 07:51:41 AM: It is compliant with the following grammars: DCP, DQCP
-(CVXPY) May 15 07:51:41 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)
-(CVXPY) May 15 07:51:41 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.
-(CVXPY) May 15 07:51:41 AM: Your problem is compiled with the CPP canonicalization backend.
+(CVXPY) May 21 03:51:04 PM: Your problem has 86 variables, 197 constraints, and 0 parameters.
+(CVXPY) May 21 03:51:04 PM: It is compliant with the following grammars: DCP, DQCP
+(CVXPY) May 21 03:51:04 PM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)
+(CVXPY) May 21 03:51:04 PM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.
+(CVXPY) May 21 03:51:04 PM: Your problem is compiled with the CPP canonicalization backend.
-------------------------------------------------------------------------------
Compilation
-------------------------------------------------------------------------------
-(CVXPY) May 15 07:51:41 AM: Compiling problem (target solver=SCIP).
-(CVXPY) May 15 07:51:41 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP
-(CVXPY) May 15 07:51:41 AM: Applying reduction Dcp2Cone
-(CVXPY) May 15 07:51:41 AM: Applying reduction CvxAttr2Constr
-(CVXPY) May 15 07:51:41 AM: Applying reduction ConeMatrixStuffing
-(CVXPY) May 15 07:51:41 AM: Applying reduction SCIP
-(CVXPY) May 15 07:51:41 AM: Finished problem compilation (took 2.971e-02 seconds).
+(CVXPY) May 21 03:51:04 PM: Compiling problem (target solver=SCIP).
+(CVXPY) May 21 03:51:04 PM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP
+(CVXPY) May 21 03:51:04 PM: Applying reduction Dcp2Cone
+(CVXPY) May 21 03:51:04 PM: Applying reduction CvxAttr2Constr
+(CVXPY) May 21 03:51:04 PM: Applying reduction ConeMatrixStuffing
+(CVXPY) May 21 03:51:04 PM: Applying reduction SCIP
+(CVXPY) May 21 03:51:04 PM: Finished problem compilation (took 2.959e-02 seconds).
-------------------------------------------------------------------------------
Numerical solver
-------------------------------------------------------------------------------
-(CVXPY) May 15 07:51:41 AM: Invoking solver SCIP to obtain a solution.
+(CVXPY) May 21 03:51:04 PM: Invoking solver SCIP to obtain a solution.
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
-(round 4, fast) 65 del vars, 147 del conss, 0 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 0 upgd conss, 0 impls, 18 clqs
-(round 5, fast) 67 del vars, 151 del conss, 0 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 0 upgd conss, 0 impls, 18 clqs
-(round 6, exhaustive) 67 del vars, 151 del conss, 0 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 40 upgd conss, 0 impls, 18 clqs
+(round 2, fast) 54 del vars, 131 del conss, 0 add conss, 53 chg bounds, 10 chg sides, 32 chg coeffs, 0 upgd conss, 0 impls, 20 clqs
+(round 3, fast) 62 del vars, 145 del conss, 0 add conss, 53 chg bounds, 12 chg sides, 34 chg coeffs, 0 upgd conss, 0 impls, 18 clqs
+(round 4, fast) 64 del vars, 147 del conss, 0 add conss, 53 chg bounds, 16 chg sides, 38 chg coeffs, 0 upgd conss, 0 impls, 18 clqs
+(round 5, fast) 66 del vars, 151 del conss, 0 add conss, 53 chg bounds, 16 chg sides, 38 chg coeffs, 0 upgd conss, 0 impls, 18 clqs
+(round 6, exhaustive) 66 del vars, 151 del conss, 0 add conss, 53 chg bounds, 16 chg sides, 38 chg coeffs, 40 upgd conss, 0 impls, 18 clqs
(0.0s) probing cycle finished: starting next cycle
-(round 7, exhaustive) 69 del vars, 151 del conss, 0 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 40 upgd conss, 28 impls, 46 clqs
-(round 8, medium) 69 del vars, 155 del conss, 0 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 40 upgd conss, 28 impls, 46 clqs
+(round 7, exhaustive) 68 del vars, 151 del conss, 0 add conss, 53 chg bounds, 16 chg sides, 38 chg coeffs, 40 upgd conss, 28 impls, 46 clqs
+(round 8, medium) 68 del vars, 155 del conss, 0 add conss, 53 chg bounds, 16 chg sides, 38 chg coeffs, 40 upgd conss, 28 impls, 46 clqs
(0.0s) probing cycle finished: starting next cycle
(0.0s) symmetry computation started: requiring (bin +, int +, cont +), (fixed: bin -, int -, cont -)
(0.0s) symmetry computation finished: 2 generators found (max: 1500, log10 of symmetry group size: 0.6) (symcode time: 0.00)
@@ -581,9 +581,9 @@ A toy example
-
+
diff --git a/dev/reports/guide/signaling/carnival.err.log b/dev/reports/guide/signaling/carnival.err.log
index ed94aa4..cd650b6 100644
--- a/dev/reports/guide/signaling/carnival.err.log
+++ b/dev/reports/guide/signaling/carnival.err.log
@@ -34,49 +34,49 @@ Cell [0;32mIn[11], line 5[0m
[1;32m 4[0m [38;5;66;03m# to the old R function https://saezlab.github.io/CARNIVAL/reference/runVanillaCarnival.html[39;00m
[0;32m----> 5[0m P [38;5;241m=[39m [43mrunCARNIVAL_AcyclicFlow[49m[43m([49m[43mG2[49m[43m,[49m[43m [49m[43mexp_list[49m[43m,[49m[43m [49m[43msolver[49m[38;5;241;43m=[39;49m[38;5;124;43m"[39;49m[38;5;124;43mGUROBI[39;49m[38;5;124;43m"[39;49m[43m)[49m
-File [0;32m~/work/corneto/corneto/corneto/methods/carnival.py:553[0m, in [0;36mrunCARNIVAL_AcyclicFlow[0;34m(G, exp_list, betaWeight, solver, verbosity)[0m
-[1;32m 550[0m P[38;5;241m.[39madd_objectives([38;5;28msum[39m(Z[m_nodes_positions, iexp][38;5;241m.[39mmultiply([38;5;28mabs[39m(m_values))))
-[1;32m 551[0m P[38;5;241m.[39madd_objectives(betaWeight [38;5;241m*[39m [38;5;28msum[39m([38;5;28msum[39m(Eact [38;5;241m+[39m Einh)))
-[0;32m--> 553[0m [43mP[49m[38;5;241;43m.[39;49m[43msolve[49m[43m([49m[43msolver[49m[38;5;241;43m=[39;49m[43msolver[49m[43m,[49m[43m [49m[43mverbosity[49m[38;5;241;43m=[39;49m[43mverbosity[49m[43m)[49m
-[1;32m 554[0m [38;5;28;01mreturn[39;00m P
+File [0;32m~/work/corneto/corneto/corneto/methods/carnival.py:546[0m, in [0;36mrunCARNIVAL_AcyclicFlow[0;34m(G, exp_list, betaWeight, solver, verbosity)[0m
+[1;32m 543[0m P[38;5;241m.[39madd_objectives([38;5;28msum[39m(Z[m_nodes_positions, iexp][38;5;241m.[39mmultiply([38;5;28mabs[39m(m_values))))
+[1;32m 544[0m P[38;5;241m.[39madd_objectives(betaWeight [38;5;241m*[39m [38;5;28msum[39m([38;5;28msum[39m(Eact [38;5;241m+[39m Einh)))
+[0;32m--> 546[0m [43mP[49m[38;5;241;43m.[39;49m[43msolve[49m[43m([49m[43msolver[49m[38;5;241;43m=[39;49m[43msolver[49m[43m,[49m[43m [49m[43mverbosity[49m[38;5;241;43m=[39;49m[43mverbosity[49m[43m)[49m
+[1;32m 547[0m [38;5;28;01mreturn[39;00m P
-File [0;32m~/work/corneto/corneto/corneto/backend/_base.py:494[0m, in [0;36mProblemDef.solve[0;34m(self, solver, max_seconds, warm_start, verbosity, **options)[0m
-[1;32m 492[0m [38;5;28;01mif[39;00m [38;5;28mself[39m[38;5;241m.[39m_backend [38;5;129;01mis[39;00m [38;5;28;01mNone[39;00m:
-[1;32m 493[0m [38;5;28;01mraise[39;00m [38;5;167;01mValueError[39;00m([38;5;124m"[39m[38;5;124mNo backend assigned.[39m[38;5;124m"[39m)
-[0;32m--> 494[0m [38;5;28;01mreturn[39;00m [38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43m_backend[49m[38;5;241;43m.[39;49m[43msolve[49m[43m([49m
-[1;32m 495[0m [43m [49m[38;5;28;43mself[39;49m[43m,[49m
-[1;32m 496[0m [43m [49m[43msolver[49m[38;5;241;43m=[39;49m[43msolver[49m[43m,[49m
-[1;32m 497[0m [43m [49m[43mmax_seconds[49m[38;5;241;43m=[39;49m[43mmax_seconds[49m[43m,[49m
-[1;32m 498[0m [43m [49m[43mwarm_start[49m[38;5;241;43m=[39;49m[43mwarm_start[49m[43m,[49m
-[1;32m 499[0m [43m [49m[43mverbosity[49m[38;5;241;43m=[39;49m[43mverbosity[49m[43m,[49m
-[1;32m 500[0m [43m [49m[38;5;241;43m*[39;49m[38;5;241;43m*[39;49m[43moptions[49m[43m,[49m
-[1;32m 501[0m [43m[49m[43m)[49m
+File [0;32m~/work/corneto/corneto/corneto/backend/_base.py:553[0m, in [0;36mProblemDef.solve[0;34m(self, solver, max_seconds, warm_start, verbosity, **options)[0m
+[1;32m 551[0m [38;5;28;01mif[39;00m [38;5;28mself[39m[38;5;241m.[39m_backend [38;5;129;01mis[39;00m [38;5;28;01mNone[39;00m:
+[1;32m 552[0m [38;5;28;01mraise[39;00m [38;5;167;01mValueError[39;00m([38;5;124m"[39m[38;5;124mNo backend assigned.[39m[38;5;124m"[39m)
+[0;32m--> 553[0m [38;5;28;01mreturn[39;00m [38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43m_backend[49m[38;5;241;43m.[39;49m[43msolve[49m[43m([49m
+[1;32m 554[0m [43m [49m[38;5;28;43mself[39;49m[43m,[49m
+[1;32m 555[0m [43m [49m[43msolver[49m[38;5;241;43m=[39;49m[43msolver[49m[43m,[49m
+[1;32m 556[0m [43m [49m[43mmax_seconds[49m[38;5;241;43m=[39;49m[43mmax_seconds[49m[43m,[49m
+[1;32m 557[0m [43m [49m[43mwarm_start[49m[38;5;241;43m=[39;49m[43mwarm_start[49m[43m,[49m
+[1;32m 558[0m [43m [49m[43mverbosity[49m[38;5;241;43m=[39;49m[43mverbosity[49m[43m,[49m
+[1;32m 559[0m [43m [49m[38;5;241;43m*[39;49m[38;5;241;43m*[39;49m[43moptions[49m[43m,[49m
+[1;32m 560[0m [43m[49m[43m)[49m
-File [0;32m~/work/corneto/corneto/corneto/backend/_base.py:751[0m, in [0;36mBackend.solve[0;34m(self, p, solver, max_seconds, warm_start, verbosity, **options)[0m
-[1;32m 745[0m [38;5;28;01melse[39;00m:
-[1;32m 746[0m o [38;5;241m=[39m (
-[1;32m 747[0m p[38;5;241m.[39mweights[[38;5;241m0[39m] [38;5;241m*[39m p[38;5;241m.[39mobjectives[[38;5;241m0[39m]
-[1;32m 748[0m [38;5;28;01mif[39;00m p[38;5;241m.[39mobjectives [38;5;129;01mand[39;00m p[38;5;241m.[39mweights[[38;5;241m0[39m] [38;5;241m!=[39m [38;5;241m0[39m
-[1;32m 749[0m [38;5;28;01melse[39;00m [38;5;28;01mNone[39;00m
-[1;32m 750[0m )
-[0;32m--> 751[0m [38;5;28;01mreturn[39;00m [38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43m_solve[49m[43m([49m
-[1;32m 752[0m [43m [49m[43mp[49m[43m,[49m
-[1;32m 753[0m [43m [49m[43mobjective[49m[38;5;241;43m=[39;49m[43mo[49m[43m,[49m
-[1;32m 754[0m [43m [49m[43msolver[49m[38;5;241;43m=[39;49m[43msolver[49m[43m,[49m
-[1;32m 755[0m [43m [49m[43mmax_seconds[49m[38;5;241;43m=[39;49m[43mmax_seconds[49m[43m,[49m
-[1;32m 756[0m [43m [49m[43mwarm_start[49m[38;5;241;43m=[39;49m[43mwarm_start[49m[43m,[49m
-[1;32m 757[0m [43m [49m[43mverbosity[49m[38;5;241;43m=[39;49m[43mverbosity[49m[43m,[49m
-[1;32m 758[0m [43m [49m[38;5;241;43m*[39;49m[38;5;241;43m*[39;49m[43moptions[49m[43m,[49m
-[1;32m 759[0m [43m[49m[43m)[49m
+File [0;32m~/work/corneto/corneto/corneto/backend/_base.py:810[0m, in [0;36mBackend.solve[0;34m(self, p, solver, max_seconds, warm_start, verbosity, **options)[0m
+[1;32m 804[0m [38;5;28;01melse[39;00m:
+[1;32m 805[0m o [38;5;241m=[39m (
+[1;32m 806[0m p[38;5;241m.[39mweights[[38;5;241m0[39m] [38;5;241m*[39m p[38;5;241m.[39mobjectives[[38;5;241m0[39m]
+[1;32m 807[0m [38;5;28;01mif[39;00m p[38;5;241m.[39mobjectives [38;5;129;01mand[39;00m p[38;5;241m.[39mweights[[38;5;241m0[39m] [38;5;241m!=[39m [38;5;241m0[39m
+[1;32m 808[0m [38;5;28;01melse[39;00m [38;5;28;01mNone[39;00m
+[1;32m 809[0m )
+[0;32m--> 810[0m [38;5;28;01mreturn[39;00m [38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43m_solve[49m[43m([49m
+[1;32m 811[0m [43m [49m[43mp[49m[43m,[49m
+[1;32m 812[0m [43m [49m[43mobjective[49m[38;5;241;43m=[39;49m[43mo[49m[43m,[49m
+[1;32m 813[0m [43m [49m[43msolver[49m[38;5;241;43m=[39;49m[43msolver[49m[43m,[49m
+[1;32m 814[0m [43m [49m[43mmax_seconds[49m[38;5;241;43m=[39;49m[43mmax_seconds[49m[43m,[49m
+[1;32m 815[0m [43m [49m[43mwarm_start[49m[38;5;241;43m=[39;49m[43mwarm_start[49m[43m,[49m
+[1;32m 816[0m [43m [49m[43mverbosity[49m[38;5;241;43m=[39;49m[43mverbosity[49m[43m,[49m
+[1;32m 817[0m [43m [49m[38;5;241;43m*[39;49m[38;5;241;43m*[39;49m[43moptions[49m[43m,[49m
+[1;32m 818[0m [43m[49m[43m)[49m
-File [0;32m~/work/corneto/corneto/corneto/backend/_cvxpy_backend.py:152[0m, in [0;36mCvxpyBackend._solve[0;34m(self, p, objective, solver, max_seconds, warm_start, verbosity, **options)[0m
-[1;32m 150[0m solvers [38;5;241m=[39m cp[38;5;241m.[39minstalled_solvers()
-[1;32m 151[0m [38;5;28;01mif[39;00m s [38;5;129;01mis[39;00m [38;5;129;01mnot[39;00m [38;5;28;01mNone[39;00m [38;5;129;01mand[39;00m s [38;5;129;01mnot[39;00m [38;5;129;01min[39;00m solvers:
-[0;32m--> 152[0m [38;5;28;01mraise[39;00m [38;5;167;01mValueError[39;00m(
-[1;32m 153[0m [38;5;124mf[39m[38;5;124m"[39m[38;5;124mSolver [39m[38;5;132;01m{[39;00ms[38;5;132;01m}[39;00m[38;5;124m is not installed/supported, supported solvers are: [39m[38;5;132;01m{[39;00msolvers[38;5;132;01m}[39;00m[38;5;124m"[39m
-[1;32m 154[0m )
-[1;32m 155[0m [38;5;66;03m# TODO: Implement parameter mapping for solvers and backends[39;00m
-[1;32m 156[0m [38;5;28;01mif[39;00m max_seconds [38;5;129;01mis[39;00m [38;5;129;01mnot[39;00m [38;5;28;01mNone[39;00m:
+File [0;32m~/work/corneto/corneto/corneto/backend/_cvxpy_backend.py:169[0m, in [0;36mCvxpyBackend._solve[0;34m(self, p, objective, solver, max_seconds, warm_start, verbosity, **options)[0m
+[1;32m 167[0m solvers [38;5;241m=[39m cp[38;5;241m.[39minstalled_solvers()
+[1;32m 168[0m [38;5;28;01mif[39;00m s [38;5;129;01mis[39;00m [38;5;129;01mnot[39;00m [38;5;28;01mNone[39;00m [38;5;129;01mand[39;00m s [38;5;129;01mnot[39;00m [38;5;129;01min[39;00m solvers:
+[0;32m--> 169[0m [38;5;28;01mraise[39;00m [38;5;167;01mValueError[39;00m(
+[1;32m 170[0m [38;5;124mf[39m[38;5;124m"[39m[38;5;124mSolver [39m[38;5;132;01m{[39;00ms[38;5;132;01m}[39;00m[38;5;124m is not installed/supported, supported solvers are: [39m[38;5;132;01m{[39;00msolvers[38;5;132;01m}[39;00m[38;5;124m"[39m
+[1;32m 171[0m )
+[1;32m 172[0m [38;5;66;03m# TODO: Implement parameter mapping for solvers and backends[39;00m
+[1;32m 173[0m [38;5;28;01mif[39;00m max_seconds [38;5;129;01mis[39;00m [38;5;129;01mnot[39;00m [38;5;28;01mNone[39;00m:
[0;31mValueError[0m: Solver GUROBI is not installed/supported, supported solvers are: ['CLARABEL', 'CVXOPT', 'ECOS', 'ECOS_BB', 'GLPK', 'GLPK_MI', 'OSQP', 'SCIP', 'SCIPY', 'SCS']
diff --git a/dev/searchindex.js b/dev/searchindex.js
index fbbe1d7..5497055 100644
--- a/dev/searchindex.js
+++ b/dev/searchindex.js
@@ -1 +1 @@
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transcriptomics data": [[36, "context-specific-metabolic-model-from-transcriptomics-data"]], "Context-specific models (iMAT)": [[23, "context-specific-models-imat"]], "Creating a weighted graph": [[30, "creating-a-weighted-graph"]], "Decoupler: Ensemble of methods to infer biological activities": [[11, "decoupler-ensemble-of-methods-to-infer-biological-activities"]], "Edge attributes": [[21, "edge-attributes"]], "Exact Steiner Trees with CORNETO": [[31, "exact-steiner-trees-with-corneto"]], "FBA with CORNETO": [[22, "fba-with-corneto"]], "Flux Balance Analysis (FBA)": [[22, "flux-balance-analysis-fba"]], "Getting started": [[19, "getting-started"]], "Heuristic steiner tree from NetworkX": [[31, "heuristic-steiner-tree-from-networkx"]], "Hypergraphs": [[21, "hypergraphs"]], "Importing graphs": [[21, "importing-graphs"]], "Interactomics": [[8, "interactomics"]], "Interoperability": [[12, "interoperability"]], "LIANA+: An all-in-one cell-cell communication framework": [[13, 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\ No newline at end of file
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\ No newline at end of file
- Parameters:
-
diff --git a/dev/guide/interoperability/cvxpy.html b/dev/guide/interoperability/cvxpy.html
index d04795f..24d4355 100644
--- a/dev/guide/interoperability/cvxpy.html
+++ b/dev/guide/interoperability/cvxpy.html
@@ -503,25 +503,25 @@
CVXPY: Convex optimization, for everyone diff --git a/dev/guide/intro/acyclic-flows.html b/dev/guide/intro/acyclic-flows.html index a79ae85..c0bb6b4 100644 --- a/dev/guide/intro/acyclic-flows.html +++ b/dev/guide/intro/acyclic-flows.html @@ -539,8 +539,8 @@
Largest DAG from a given source and sink vertex
+{'_flow': Variable((14,), _flow), - '_flow_ineg': Variable((14,), _flow_ineg, boolean=True), '_flow_ipos': Variable((14,), _flow_ipos, boolean=True), + '_flow_ineg': Variable((14,), _flow_ineg, boolean=True), '_dag_layer_pos': Variable((7,), _dag_layer_pos), 'positive_flow': Variable((14,), _flow_ipos, boolean=True), 'negative_flow': Variable((14,), _flow_ineg, boolean=True), diff --git a/dev/guide/intro/constrained-optimization.html b/dev/guide/intro/constrained-optimization.html index 7b44743..04eafbe 100644 --- a/dev/guide/intro/constrained-optimization.html +++ b/dev/guide/intro/constrained-optimization.html @@ -505,7 +505,7 @@The Knapsack Problem
-@@ -543,7 +543,7 @@<corneto.DeprecatedBackend at 0x7fced04c68d0> +
<corneto.DeprecatedBackend at 0x7fb898e1ab10>
The Knapsack Problem
-@@ -723,26 +723,26 @@@@ -557,9 +557,9 @@<corneto.backend._base.ProblemDef at 0x7fce80114fd0> +
<corneto.backend._base.ProblemDef at 0x7fb84dd2eed0>
The Knapsack Problem
{'obj5': Variable((1,), obj5, boolean=True), 'obj4': Variable((1,), obj4, boolean=True), - 'obj3': Variable((1,), obj3, boolean=True), 'obj2': Variable((1,), obj2, boolean=True), - 'obj1': Variable((1,), obj1, boolean=True)} + 'obj1': Variable((1,), obj1, boolean=True), + 'obj3': Variable((1,), obj3, boolean=True)}A more complex knapsackA more complex knapsack
Problem(Maximize(Expression(AFFINE, NONNEGATIVE, ())), [Inequality(Expression(AFFINE, NONNEGATIVE, ()))]) diff --git a/dev/guide/intro/multi-commodity-network-flows.html b/dev/guide/intro/multi-commodity-network-flows.html index 6acdb58..3b21c0d 100644 --- a/dev/guide/intro/multi-commodity-network-flows.html +++ b/dev/guide/intro/multi-commodity-network-flows.html @@ -572,25 +572,25 @@
Multi-commodity Network Flows
+Problem(Minimize(Expression(AFFINE, UNKNOWN, ())), [Inequality(Constant(CONSTANT, ZERO, (10, 2))), Inequality(Variable((10, 2), _flow)), Equality(Expression(AFFINE, UNKNOWN, (5, 2)), Constant(CONSTANT, ZERO, ())), Inequality(Expression(AFFINE, UNKNOWN, (10,))), Inequality(Constant(CONSTANT, ZERO, (10,)))]) diff --git a/dev/guide/intro/prior-knowledge.html b/dev/guide/intro/prior-knowledge.html index 2cb8473..b7d3fc3 100644 --- a/dev/guide/intro/prior-knowledge.html +++ b/dev/guide/intro/prior-knowledge.html @@ -736,7 +736,7 @@
Hypergraphs -
diff --git a/dev/guide/metabolism/imat.html b/dev/guide/metabolism/imat.html index 060b734..e300bed 100644 --- a/dev/guide/metabolism/imat.html +++ b/dev/guide/metabolism/imat.html @@ -512,7 +512,7 @@@@ -745,7 +745,7 @@Hypergraphs -
diff --git a/dev/guide/metabolism/flux-balance-analysis.html b/dev/guide/metabolism/flux-balance-analysis.html index 44edf28..07f7c54 100644 --- a/dev/guide/metabolism/flux-balance-analysis.html +++ b/dev/guide/metabolism/flux-balance-analysis.html @@ -511,7 +511,7 @@('B', 'A', 'C', 'D', 'F', 'E') +('B', 'A', 'C', 'D', 'E', 'F')Using COBRApy -
+@@ -624,7 +624,7 @@<Solution 0.874 at 0x7fa457ba20d0> +
<Solution 0.874 at 0x7f7408cf1a90>
Using COBRApy -
@@ -651,7 +651,7 @@+Using COBRApy -
Context-specific models (iMAT) -
@@ -551,7 +551,7 @@+Context-specific models (iMAT) -
We can make the plot to look more like the image from the original paper by drawing the reactions with fluxes above a certain threshold with a wider line:
@@ -563,7 +563,7 @@+Context-specific models (iMAT) -
diff --git a/dev/guide/metabolism/sparse-fba.html b/dev/guide/metabolism/sparse-fba.html
index 955acb0..50363e6 100644
--- a/dev/guide/metabolism/sparse-fba.html
+++ b/dev/guide/metabolism/sparse-fba.html
@@ -545,7 +545,7 @@ Manual implementation of sparse FBA -
+
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 -
+
diff --git a/dev/guide/networks/pcst.html b/dev/guide/networks/pcst.html index d256694..72f343e 100644 --- a/dev/guide/networks/pcst.html +++ b/dev/guide/networks/pcst.html @@ -554,7 +554,7 @@ diff --git a/dev/guide/networks/shortest-paths.html b/dev/guide/networks/shortest-paths.html index e69dd8a..8a00092 100644 --- a/dev/guide/networks/shortest-paths.html +++ b/dev/guide/networks/shortest-paths.html @@ -560,7 +560,7 @@Prize-Collecting Steiner Trees (PCSTs) -
+
Random graphs -
diff --git a/dev/guide/networks/steiner-trees.html b/dev/guide/networks/steiner-trees.html index 2b6651c..465ceab 100644 --- a/dev/guide/networks/steiner-trees.html +++ b/dev/guide/networks/steiner-trees.html @@ -605,25 +605,25 @@@@ -572,7 +572,7 @@[2125, 3529, 71, 3705, 1596, 464, 1388] +
[4963, 361, 9, 38, 76, 285]
Random graphs -
@@ -592,7 +592,7 @@14.367935129555612 +
12.929288678466708
Random graphs -
+@@ -604,7 +604,7 @@14.367935129555613 +
12.929288678466705
Random graphs -
Exact Steiner Trees with CORNETO @@ -835,37 +835,37 @@
Exact Steiner Trees with CORNETO +
diff --git a/dev/guide/signaling/carnival.html b/dev/guide/signaling/carnival.html
index 91f0775..9fa8fba 100644
--- a/dev/guide/signaling/carnival.html
+++ b/dev/guide/signaling/carnival.html
@@ -531,48 +531,48 @@ A toy example -
(CORNETO) May 15 07:51:41 AM - INFO : 2/2 inputs mapped to the graph -(CORNETO) May 15 07:51:41 AM - INFO : 2/2 outputs mapped to the graph -(CORNETO) May 15 07:51:41 AM - INFO : Pruning the graph with size: V x E = (6, 6)... -(CORNETO) May 15 07:51:41 AM - INFO : Finished. Final size: V x E = (6, 6). -(CORNETO) May 15 07:51:41 AM - INFO : 2/2 inputs after pruning. -(CORNETO) May 15 07:51:41 AM - INFO : 2/2 outputs after pruning. -(CORNETO) May 15 07:51:41 AM - INFO : Converting into a flow graph... -(CORNETO) May 15 07:51:41 AM - INFO : Creating a network flow problem... -(CORNETO) May 15 07:51:41 AM - INFO : Preprocess completed. +
+(CORNETO) May 21 03:51:04 PM - INFO : 2/2 inputs mapped to the graph +(CORNETO) May 21 03:51:04 PM - INFO : 2/2 outputs mapped to the graph +(CORNETO) May 21 03:51:04 PM - INFO : Pruning the graph with size: V x E = (6, 6)... +(CORNETO) May 21 03:51:04 PM - INFO : Finished. Final size: V x E = (6, 6). +(CORNETO) May 21 03:51:04 PM - INFO : 2/2 inputs after pruning. +(CORNETO) May 21 03:51:04 PM - INFO : 2/2 outputs after pruning. +(CORNETO) May 21 03:51:04 PM - INFO : Converting into a flow graph... +(CORNETO) May 21 03:51:04 PM - INFO : Creating a network flow problem... +(CORNETO) May 21 03:51:04 PM - INFO : Preprocess completed. =============================================================================== CVXPY v1.5.1 =============================================================================== -(CVXPY) May 15 07:51:41 AM: Your problem has 86 variables, 197 constraints, and 0 parameters. -(CVXPY) May 15 07:51:41 AM: It is compliant with the following grammars: DCP, DQCP -(CVXPY) May 15 07:51:41 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.) -(CVXPY) May 15 07:51:41 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution. -(CVXPY) May 15 07:51:41 AM: Your problem is compiled with the CPP canonicalization backend. +(CVXPY) May 21 03:51:04 PM: Your problem has 86 variables, 197 constraints, and 0 parameters. +(CVXPY) May 21 03:51:04 PM: It is compliant with the following grammars: DCP, DQCP +(CVXPY) May 21 03:51:04 PM: (If you need to solve this problem multiple times, but with different data, consider using parameters.) +(CVXPY) May 21 03:51:04 PM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution. +(CVXPY) May 21 03:51:04 PM: Your problem is compiled with the CPP canonicalization backend. ------------------------------------------------------------------------------- Compilation ------------------------------------------------------------------------------- -(CVXPY) May 15 07:51:41 AM: Compiling problem (target solver=SCIP). -(CVXPY) May 15 07:51:41 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP -(CVXPY) May 15 07:51:41 AM: Applying reduction Dcp2Cone -(CVXPY) May 15 07:51:41 AM: Applying reduction CvxAttr2Constr -(CVXPY) May 15 07:51:41 AM: Applying reduction ConeMatrixStuffing -(CVXPY) May 15 07:51:41 AM: Applying reduction SCIP -(CVXPY) May 15 07:51:41 AM: Finished problem compilation (took 2.971e-02 seconds). +(CVXPY) May 21 03:51:04 PM: Compiling problem (target solver=SCIP). +(CVXPY) May 21 03:51:04 PM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP +(CVXPY) May 21 03:51:04 PM: Applying reduction Dcp2Cone +(CVXPY) May 21 03:51:04 PM: Applying reduction CvxAttr2Constr +(CVXPY) May 21 03:51:04 PM: Applying reduction ConeMatrixStuffing +(CVXPY) May 21 03:51:04 PM: Applying reduction SCIP +(CVXPY) May 21 03:51:04 PM: Finished problem compilation (took 2.959e-02 seconds). ------------------------------------------------------------------------------- Numerical solver ------------------------------------------------------------------------------- -(CVXPY) May 15 07:51:41 AM: Invoking solver SCIP to obtain a solution. +(CVXPY) May 21 03:51:04 PM: Invoking solver SCIP to obtain a solution. 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 -(round 4, fast) 65 del vars, 147 del conss, 0 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 0 upgd conss, 0 impls, 18 clqs -(round 5, fast) 67 del vars, 151 del conss, 0 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 0 upgd conss, 0 impls, 18 clqs -(round 6, exhaustive) 67 del vars, 151 del conss, 0 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 40 upgd conss, 0 impls, 18 clqs +(round 2, fast) 54 del vars, 131 del conss, 0 add conss, 53 chg bounds, 10 chg sides, 32 chg coeffs, 0 upgd conss, 0 impls, 20 clqs +(round 3, fast) 62 del vars, 145 del conss, 0 add conss, 53 chg bounds, 12 chg sides, 34 chg coeffs, 0 upgd conss, 0 impls, 18 clqs +(round 4, fast) 64 del vars, 147 del conss, 0 add conss, 53 chg bounds, 16 chg sides, 38 chg coeffs, 0 upgd conss, 0 impls, 18 clqs +(round 5, fast) 66 del vars, 151 del conss, 0 add conss, 53 chg bounds, 16 chg sides, 38 chg coeffs, 0 upgd conss, 0 impls, 18 clqs +(round 6, exhaustive) 66 del vars, 151 del conss, 0 add conss, 53 chg bounds, 16 chg sides, 38 chg coeffs, 40 upgd conss, 0 impls, 18 clqs (0.0s) probing cycle finished: starting next cycle -(round 7, exhaustive) 69 del vars, 151 del conss, 0 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 40 upgd conss, 28 impls, 46 clqs -(round 8, medium) 69 del vars, 155 del conss, 0 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 40 upgd conss, 28 impls, 46 clqs +(round 7, exhaustive) 68 del vars, 151 del conss, 0 add conss, 53 chg bounds, 16 chg sides, 38 chg coeffs, 40 upgd conss, 28 impls, 46 clqs +(round 8, medium) 68 del vars, 155 del conss, 0 add conss, 53 chg bounds, 16 chg sides, 38 chg coeffs, 40 upgd conss, 28 impls, 46 clqs (0.0s) probing cycle finished: starting next cycle (0.0s) symmetry computation started: requiring (bin +, int +, cont +), (fixed: bin -, int -, cont -) (0.0s) symmetry computation finished: 2 generators found (max: 1500, log10 of symmetry group size: 0.6) (symcode time: 0.00) @@ -581,9 +581,9 @@A toy example -
diff --git a/dev/reports/guide/signaling/carnival.err.log b/dev/reports/guide/signaling/carnival.err.log index ed94aa4..cd650b6 100644 --- a/dev/reports/guide/signaling/carnival.err.log +++ b/dev/reports/guide/signaling/carnival.err.log @@ -34,49 +34,49 @@ Cell [0;32mIn[11], line 5[0m [1;32m 4[0m [38;5;66;03m# to the old R function https://saezlab.github.io/CARNIVAL/reference/runVanillaCarnival.html[39;00m [0;32m----> 5[0m P [38;5;241m=[39m [43mrunCARNIVAL_AcyclicFlow[49m[43m([49m[43mG2[49m[43m,[49m[43m [49m[43mexp_list[49m[43m,[49m[43m [49m[43msolver[49m[38;5;241;43m=[39;49m[38;5;124;43m"[39;49m[38;5;124;43mGUROBI[39;49m[38;5;124;43m"[39;49m[43m)[49m -File [0;32m~/work/corneto/corneto/corneto/methods/carnival.py:553[0m, in [0;36mrunCARNIVAL_AcyclicFlow[0;34m(G, exp_list, betaWeight, solver, verbosity)[0m -[1;32m 550[0m P[38;5;241m.[39madd_objectives([38;5;28msum[39m(Z[m_nodes_positions, iexp][38;5;241m.[39mmultiply([38;5;28mabs[39m(m_values)))) -[1;32m 551[0m P[38;5;241m.[39madd_objectives(betaWeight [38;5;241m*[39m [38;5;28msum[39m([38;5;28msum[39m(Eact [38;5;241m+[39m Einh))) -[0;32m--> 553[0m [43mP[49m[38;5;241;43m.[39;49m[43msolve[49m[43m([49m[43msolver[49m[38;5;241;43m=[39;49m[43msolver[49m[43m,[49m[43m [49m[43mverbosity[49m[38;5;241;43m=[39;49m[43mverbosity[49m[43m)[49m -[1;32m 554[0m [38;5;28;01mreturn[39;00m P +File [0;32m~/work/corneto/corneto/corneto/methods/carnival.py:546[0m, in [0;36mrunCARNIVAL_AcyclicFlow[0;34m(G, exp_list, betaWeight, solver, verbosity)[0m +[1;32m 543[0m P[38;5;241m.[39madd_objectives([38;5;28msum[39m(Z[m_nodes_positions, iexp][38;5;241m.[39mmultiply([38;5;28mabs[39m(m_values)))) +[1;32m 544[0m P[38;5;241m.[39madd_objectives(betaWeight [38;5;241m*[39m [38;5;28msum[39m([38;5;28msum[39m(Eact [38;5;241m+[39m Einh))) +[0;32m--> 546[0m [43mP[49m[38;5;241;43m.[39;49m[43msolve[49m[43m([49m[43msolver[49m[38;5;241;43m=[39;49m[43msolver[49m[43m,[49m[43m [49m[43mverbosity[49m[38;5;241;43m=[39;49m[43mverbosity[49m[43m)[49m +[1;32m 547[0m [38;5;28;01mreturn[39;00m P -File [0;32m~/work/corneto/corneto/corneto/backend/_base.py:494[0m, in [0;36mProblemDef.solve[0;34m(self, solver, max_seconds, warm_start, verbosity, **options)[0m -[1;32m 492[0m [38;5;28;01mif[39;00m [38;5;28mself[39m[38;5;241m.[39m_backend [38;5;129;01mis[39;00m [38;5;28;01mNone[39;00m: -[1;32m 493[0m [38;5;28;01mraise[39;00m [38;5;167;01mValueError[39;00m([38;5;124m"[39m[38;5;124mNo backend assigned.[39m[38;5;124m"[39m) -[0;32m--> 494[0m [38;5;28;01mreturn[39;00m [38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43m_backend[49m[38;5;241;43m.[39;49m[43msolve[49m[43m([49m -[1;32m 495[0m [43m [49m[38;5;28;43mself[39;49m[43m,[49m -[1;32m 496[0m [43m [49m[43msolver[49m[38;5;241;43m=[39;49m[43msolver[49m[43m,[49m -[1;32m 497[0m [43m [49m[43mmax_seconds[49m[38;5;241;43m=[39;49m[43mmax_seconds[49m[43m,[49m -[1;32m 498[0m [43m [49m[43mwarm_start[49m[38;5;241;43m=[39;49m[43mwarm_start[49m[43m,[49m -[1;32m 499[0m [43m [49m[43mverbosity[49m[38;5;241;43m=[39;49m[43mverbosity[49m[43m,[49m -[1;32m 500[0m [43m [49m[38;5;241;43m*[39;49m[38;5;241;43m*[39;49m[43moptions[49m[43m,[49m -[1;32m 501[0m [43m[49m[43m)[49m +File [0;32m~/work/corneto/corneto/corneto/backend/_base.py:553[0m, in [0;36mProblemDef.solve[0;34m(self, solver, max_seconds, warm_start, verbosity, **options)[0m +[1;32m 551[0m [38;5;28;01mif[39;00m [38;5;28mself[39m[38;5;241m.[39m_backend [38;5;129;01mis[39;00m [38;5;28;01mNone[39;00m: +[1;32m 552[0m [38;5;28;01mraise[39;00m [38;5;167;01mValueError[39;00m([38;5;124m"[39m[38;5;124mNo backend assigned.[39m[38;5;124m"[39m) +[0;32m--> 553[0m [38;5;28;01mreturn[39;00m [38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43m_backend[49m[38;5;241;43m.[39;49m[43msolve[49m[43m([49m +[1;32m 554[0m [43m [49m[38;5;28;43mself[39;49m[43m,[49m +[1;32m 555[0m [43m [49m[43msolver[49m[38;5;241;43m=[39;49m[43msolver[49m[43m,[49m +[1;32m 556[0m [43m [49m[43mmax_seconds[49m[38;5;241;43m=[39;49m[43mmax_seconds[49m[43m,[49m +[1;32m 557[0m [43m [49m[43mwarm_start[49m[38;5;241;43m=[39;49m[43mwarm_start[49m[43m,[49m +[1;32m 558[0m [43m [49m[43mverbosity[49m[38;5;241;43m=[39;49m[43mverbosity[49m[43m,[49m +[1;32m 559[0m [43m [49m[38;5;241;43m*[39;49m[38;5;241;43m*[39;49m[43moptions[49m[43m,[49m +[1;32m 560[0m [43m[49m[43m)[49m -File [0;32m~/work/corneto/corneto/corneto/backend/_base.py:751[0m, in [0;36mBackend.solve[0;34m(self, p, solver, max_seconds, warm_start, verbosity, **options)[0m -[1;32m 745[0m [38;5;28;01melse[39;00m: -[1;32m 746[0m o [38;5;241m=[39m ( -[1;32m 747[0m p[38;5;241m.[39mweights[[38;5;241m0[39m] [38;5;241m*[39m p[38;5;241m.[39mobjectives[[38;5;241m0[39m] -[1;32m 748[0m [38;5;28;01mif[39;00m p[38;5;241m.[39mobjectives [38;5;129;01mand[39;00m p[38;5;241m.[39mweights[[38;5;241m0[39m] [38;5;241m!=[39m [38;5;241m0[39m -[1;32m 749[0m [38;5;28;01melse[39;00m [38;5;28;01mNone[39;00m -[1;32m 750[0m ) -[0;32m--> 751[0m [38;5;28;01mreturn[39;00m [38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43m_solve[49m[43m([49m -[1;32m 752[0m [43m [49m[43mp[49m[43m,[49m -[1;32m 753[0m [43m [49m[43mobjective[49m[38;5;241;43m=[39;49m[43mo[49m[43m,[49m -[1;32m 754[0m [43m [49m[43msolver[49m[38;5;241;43m=[39;49m[43msolver[49m[43m,[49m -[1;32m 755[0m [43m [49m[43mmax_seconds[49m[38;5;241;43m=[39;49m[43mmax_seconds[49m[43m,[49m -[1;32m 756[0m [43m [49m[43mwarm_start[49m[38;5;241;43m=[39;49m[43mwarm_start[49m[43m,[49m -[1;32m 757[0m [43m [49m[43mverbosity[49m[38;5;241;43m=[39;49m[43mverbosity[49m[43m,[49m -[1;32m 758[0m [43m [49m[38;5;241;43m*[39;49m[38;5;241;43m*[39;49m[43moptions[49m[43m,[49m -[1;32m 759[0m [43m[49m[43m)[49m +File [0;32m~/work/corneto/corneto/corneto/backend/_base.py:810[0m, in [0;36mBackend.solve[0;34m(self, p, solver, max_seconds, warm_start, verbosity, **options)[0m +[1;32m 804[0m [38;5;28;01melse[39;00m: +[1;32m 805[0m o [38;5;241m=[39m ( +[1;32m 806[0m p[38;5;241m.[39mweights[[38;5;241m0[39m] [38;5;241m*[39m p[38;5;241m.[39mobjectives[[38;5;241m0[39m] +[1;32m 807[0m [38;5;28;01mif[39;00m p[38;5;241m.[39mobjectives [38;5;129;01mand[39;00m p[38;5;241m.[39mweights[[38;5;241m0[39m] [38;5;241m!=[39m [38;5;241m0[39m +[1;32m 808[0m [38;5;28;01melse[39;00m [38;5;28;01mNone[39;00m +[1;32m 809[0m ) +[0;32m--> 810[0m [38;5;28;01mreturn[39;00m [38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43m_solve[49m[43m([49m +[1;32m 811[0m [43m [49m[43mp[49m[43m,[49m +[1;32m 812[0m [43m [49m[43mobjective[49m[38;5;241;43m=[39;49m[43mo[49m[43m,[49m +[1;32m 813[0m [43m [49m[43msolver[49m[38;5;241;43m=[39;49m[43msolver[49m[43m,[49m +[1;32m 814[0m [43m [49m[43mmax_seconds[49m[38;5;241;43m=[39;49m[43mmax_seconds[49m[43m,[49m +[1;32m 815[0m [43m [49m[43mwarm_start[49m[38;5;241;43m=[39;49m[43mwarm_start[49m[43m,[49m +[1;32m 816[0m [43m [49m[43mverbosity[49m[38;5;241;43m=[39;49m[43mverbosity[49m[43m,[49m +[1;32m 817[0m [43m [49m[38;5;241;43m*[39;49m[38;5;241;43m*[39;49m[43moptions[49m[43m,[49m +[1;32m 818[0m [43m[49m[43m)[49m -File [0;32m~/work/corneto/corneto/corneto/backend/_cvxpy_backend.py:152[0m, in [0;36mCvxpyBackend._solve[0;34m(self, p, objective, solver, max_seconds, warm_start, verbosity, **options)[0m -[1;32m 150[0m solvers [38;5;241m=[39m cp[38;5;241m.[39minstalled_solvers() -[1;32m 151[0m [38;5;28;01mif[39;00m s [38;5;129;01mis[39;00m [38;5;129;01mnot[39;00m [38;5;28;01mNone[39;00m [38;5;129;01mand[39;00m s [38;5;129;01mnot[39;00m [38;5;129;01min[39;00m solvers: -[0;32m--> 152[0m [38;5;28;01mraise[39;00m [38;5;167;01mValueError[39;00m( -[1;32m 153[0m [38;5;124mf[39m[38;5;124m"[39m[38;5;124mSolver [39m[38;5;132;01m{[39;00ms[38;5;132;01m}[39;00m[38;5;124m is not installed/supported, supported solvers are: [39m[38;5;132;01m{[39;00msolvers[38;5;132;01m}[39;00m[38;5;124m"[39m -[1;32m 154[0m ) -[1;32m 155[0m [38;5;66;03m# TODO: Implement parameter mapping for solvers and backends[39;00m -[1;32m 156[0m [38;5;28;01mif[39;00m max_seconds [38;5;129;01mis[39;00m [38;5;129;01mnot[39;00m [38;5;28;01mNone[39;00m: +File [0;32m~/work/corneto/corneto/corneto/backend/_cvxpy_backend.py:169[0m, in [0;36mCvxpyBackend._solve[0;34m(self, p, objective, solver, max_seconds, warm_start, verbosity, **options)[0m +[1;32m 167[0m solvers [38;5;241m=[39m cp[38;5;241m.[39minstalled_solvers() +[1;32m 168[0m [38;5;28;01mif[39;00m s [38;5;129;01mis[39;00m [38;5;129;01mnot[39;00m [38;5;28;01mNone[39;00m [38;5;129;01mand[39;00m s [38;5;129;01mnot[39;00m [38;5;129;01min[39;00m solvers: +[0;32m--> 169[0m [38;5;28;01mraise[39;00m [38;5;167;01mValueError[39;00m( +[1;32m 170[0m [38;5;124mf[39m[38;5;124m"[39m[38;5;124mSolver [39m[38;5;132;01m{[39;00ms[38;5;132;01m}[39;00m[38;5;124m is not installed/supported, supported solvers are: [39m[38;5;132;01m{[39;00msolvers[38;5;132;01m}[39;00m[38;5;124m"[39m +[1;32m 171[0m ) +[1;32m 172[0m [38;5;66;03m# TODO: Implement parameter mapping for solvers and backends[39;00m +[1;32m 173[0m [38;5;28;01mif[39;00m max_seconds [38;5;129;01mis[39;00m [38;5;129;01mnot[39;00m [38;5;28;01mNone[39;00m: [0;31mValueError[0m: Solver GUROBI is not installed/supported, supported solvers are: ['CLARABEL', 'CVXOPT', 'ECOS', 'ECOS_BB', 'GLPK', 'GLPK_MI', 'OSQP', 'SCIP', 'SCIPY', 'SCS'] diff --git a/dev/searchindex.js b/dev/searchindex.js index fbbe1d7..5497055 100644 --- a/dev/searchindex.js +++ b/dev/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"A more complex knapsack": [[18, "a-more-complex-knapsack"]], "A toy example": [[32, "a-toy-example"]], "API Reference": [[5, "api-reference"]], "Acknowledgements": [[35, "acknowledgements"]], "Acyclic Flows": [[17, "acyclic-flows"]], "CARNIVAL": [[32, "carnival"]], "CARNIVAL with Acyclic signaling": [[32, "carnival-with-acyclic-signaling"]], "CARNIVAL with acyclic flow - single condition": [[32, "carnival-with-acyclic-flow-single-condition"]], "CARNIVAL with acyclic flow - two conditions": [[32, "carnival-with-acyclic-flow-two-conditions"]], "COBRApy: Constraint-based metabolic modeling in Python": [[9, "cobrapy-constraint-based-metabolic-modeling-in-python"]], "CORNETO": [[5, "corneto"]], "CORNETO ": [[35, "corneto"]], "CVXPY: Convex optimization, for everyone": [[10, "cvxpy-convex-optimization-for-everyone"]], "Constrained Optimization": [[18, "constrained-optimization"]], "Contents:": [[5, null]], "Context-specific metabolic model from transcriptomics data": [[36, "context-specific-metabolic-model-from-transcriptomics-data"]], "Context-specific models (iMAT)": [[23, "context-specific-models-imat"]], "Creating a weighted graph": [[30, "creating-a-weighted-graph"]], "Decoupler: Ensemble of methods to infer biological activities": [[11, "decoupler-ensemble-of-methods-to-infer-biological-activities"]], "Edge attributes": [[21, "edge-attributes"]], "Exact Steiner Trees with CORNETO": [[31, "exact-steiner-trees-with-corneto"]], "FBA with CORNETO": [[22, "fba-with-corneto"]], 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