Merge pull request #23 from MetExplore/development

Prepare v0.9.0-beta.6

README.md

@@ -6,8 +6,9 @@
 <div align="center">
 
 [![Try It Online](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1JAOEHLlRCW8GziIpBqkFwJL2ha3OEOWJ?usp=sharing)
-[![PyPI](https://img.shields.io/pypi/v/miom?style=flat-square&label=PyPI&logo=pypi&logoColor=white)](https://pypi.org/project/miom/)
+[![PyPI](https://img.shields.io/pypi/v/miom?label=PyPI&logo=pypi&logoColor=lightgrey)](https://pypi.org/project/miom/)
 ![Tests](https://github.com/metexplore/miom/actions/workflows/unit-tests.yml/badge.svg)
+[![Downloads](https://pepy.tech/badge/miom)](https://pepy.tech/project/miom)
 
 </div>
 

docs/index.md

@@ -1,8 +1,9 @@
 <a href="https://metexplore.github.io/miom"><img src="assets/img/miom_v1_fit.png" alt="MIOM" title="MIOM: Mixed Integer Optimization for Metabolism"/></a>
 
 [![Try It Online](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1JAOEHLlRCW8GziIpBqkFwJL2ha3OEOWJ?usp=sharing)
-[![PyPI](https://img.shields.io/pypi/v/miom?style=flat-square&label=PyPI&logo=pypi&logoColor=white)](https://pypi.org/project/miom/)
+[![PyPI](https://img.shields.io/pypi/v/miom?label=PyPI)](https://pypi.org/project/miom/)
 ![Tests](https://github.com/metexplore/miom/actions/workflows/unit-tests.yml/badge.svg)
+[![Downloads](https://pepy.tech/badge/miom)](https://pepy.tech/project/miom)
 
 # Introduction
 

miom/__init__.py

@@ -8,4 +8,4 @@
 from miom.mio import load_gem
 
 __all__ = ["load", "load_gem", "Solvers", "Comparator", "ExtractionMode"]
-__version__ = "0.9.0-beta.5"
+__version__ = "0.9.0-beta.6"

miom/miom.py

@@ -148,14 +148,25 @@ class Comparator(str, Enum):
         ("type", _ReactionType)
     ])
 
-def _get_reversible_vars(weighted_rxn):
+def _get_reversible_vars(weighted_rxns):
     d = defaultdict(list)
-    for i, rxn in enumerate(weighted_rxn):
+    for i, rxn in enumerate(weighted_rxns):
         if rxn.type == _ReactionType.RH_POS or rxn.type == _ReactionType.RH_NEG:
             d[rxn.index].append(i)
     return [l for l in d.values() if len(l) > 1]
 
 
+def _get_rxn_var_data(weighted_rxns, rxn_type):
+    idx = [
+        (i, rd.index, rd.lb, rd.ub) 
+        for i, rd in enumerate(weighted_rxns) 
+        if rd.type is rxn_type
+    ]
+    if len(idx) > 0:
+        return [np.array(x) for x in list(zip(*idx))]
+    return None
+
+
 def load(network, solver=Solvers.COIN_OR_CBC):
     """
     Create a MIOM optimization model for a given solver.
@@ -857,20 +868,38 @@ def _subset_selection(self, *args, **kwargs):
         P = self.problem
         # Build the MIP problem
         V = self.variables.fluxvars
-        X = pc.BinaryVariable("X", shape=(len(weighted_rxns), 1))
+        X = pc.BinaryVariable("X", shape=(len(weighted_rxns),))
         C = pc.Constant("C", value=np.array([abs(rxn.cost) for rxn in weighted_rxns]))
-        for i, rd in enumerate(weighted_rxns):
-            if rd.type is _ReactionType.RH_POS:
-                P.add_constraint(V[rd.index] >= X[i] * (eps - rd.lb) + rd.lb)
-            elif rd.type is _ReactionType.RH_NEG:
-                P.add_constraint(V[rd.index] <= rd.ub - X[i] * (rd.ub + eps))
-            elif rd.type is _ReactionType.RL:
-                P.add_constraint((1 - X[i]) * rd.ub - V[rd.index] >= 0)
-                P.add_constraint((1 - X[i]) * rd.lb - V[rd.index] <= 0)
-            else:
-                raise ValueError("Unknown type of reaction")
-        for i, j in _get_reversible_vars(weighted_rxns):
-            self.add_constraint(X[i] + X[j] <= 1)
+        # NOTE: For some reason, PICOS have issues parsing the priority operators, so constraints
+        # are split into many parts, otherwise it does not work. The matrix notation is more
+        # efficient and takes less time and memory than using the add_list_of_constraints method in a loop.
+        var_data = _get_rxn_var_data(weighted_rxns, _ReactionType.RH_POS)
+        if var_data is not None:
+            I, J, LB, UB = var_data
+            EA = eps - LB
+            EB = X[I]^EA
+            expr = V[J] >= EB + LB
+            P.add_constraint(expr)
+        var_data = _get_rxn_var_data(weighted_rxns, _ReactionType.RH_NEG)
+        if var_data is not None:
+            I, J, LB, UB = var_data
+            EA = eps + UB
+            EB = X[I]^EA
+            expr = V[J] <= UB - EB
+            P.add_constraint(expr)
+        var_data = _get_rxn_var_data(weighted_rxns, _ReactionType.RL)
+        if var_data is not None:
+            I, J, LB, UB = var_data
+            EA = 1 - X[I]
+            EB = EA^UB
+            EC = EA^LB
+            P.add_constraint(EB - V[J] >= 0)
+            P.add_constraint(EC - V[J] <= 0)
+        # Strengthen the formulation
+        idx = [np.array(x) for x in list(zip(*_get_reversible_vars(weighted_rxns)))]
+        if len(idx) > 0:
+            I, J = idx
+            P.add_constraint(X[I] + X[J] <= 1)
         P.set_objective(kwargs['direction'], C.T * X)
         self.variables._indicator_vars = X
         return True

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "miom"
-version = "0.9.0-beta.5"
+version = "0.9.0-beta.6"
 description = "Mixed Integer Optimization for Metabolism"
 authors = ["Pablo R. Mier <[email protected]>"]
 keywords = ["optimization", "LP", "MIP", "metabolism", "metabolic-networks"]