Merge pull request #15 from MetExplore/development

Minor pre-release fixes for 0.9.0-beta.2

README.md

@@ -1,5 +1,5 @@
 <div align="center">
-    <a href="https://metexplore.github.io/miom"><img align="center" src="https://github.com/MetExplore/miom/raw/development/docs/assets/img/miom_v1.png" alt="MIOM" width="545" title="MIOM: Mixed Integer Optimization for Metabolism"/>
+    <a href="https://metexplore.github.io/miom"><img align="center" src="https://github.com/MetExplore/miom/raw/development/docs/assets/img/miom_v1.png" alt="MIOM" title="MIOM: Mixed Integer Optimization for Metabolism"/>
     </a>
 </div>
 
@@ -11,9 +11,11 @@
 
 </div>
 
----
+<h4 align="center">
+<a href="https://metexplore.github.io/miom">https://metexplore.github.io/miom</a>
+</h4>
 
-https://metexplore.github.io/miom
+---
 
 __MIOM__ (Mixed Integer Optimization for Metabolism) is a python library for creating and solving complex optimization problems using genome-scale metabolic networks, in just a few lines. 
 

docs/stylesheets/extra.css

@@ -0,0 +1,14 @@
+:root {
+  --md-primary-fg-color: #132a4b;
+  --md-primary-fg-color--light: #2f5a96;
+  --md-primary-fg-color--dark: #0b1b31;
+  --md-primary-bg-color: hsla(0, 0%, 100%, 1);
+  --md-primary-bg-color--light: hsla(0, 0%, 100%, 0.7);
+  --md-text-link-color: #386eb9;
+
+  /* Accent color shades */
+  --md-accent-fg-color: #6896d6;
+  --md-accent-fg-color--transparent: hsla(189, 100%, 37%, 0.1);
+  --md-accent-bg-color: hsla(0, 0%, 100%, 1);
+  --md-accent-bg-color--light: hsla(0, 0%, 100%, 0.7);
+}

miom/miom.py

@@ -502,7 +502,7 @@ def keep(self, reactions):
         return dict(idxs=idxs, valid_rxn_idx=valid_rxn_idx)
 
     @_partial
-    def subset_selection(self, rxn_weights, eps=1e-2):
+    def subset_selection(self, rxn_weights, direction='max', eps=1e-2):
         """Transform the current model into a subset selection problem.
 
         The subset selection problem consists of selecting the positive weighted
@@ -556,7 +556,7 @@ def subset_selection(self, rxn_weights, eps=1e-2):
         rxnw = _weighted_rxns(self.network.R, rxn_weights)
         if self.variables.indicators is None:
             self.variables._assigned_reactions = rxnw
-            return dict(eps=eps)
+            return dict(eps=eps, direction=direction)
         else:
             warnings.warn("Indicator variables were already assigned")
             return False
@@ -867,7 +867,7 @@ def _subset_selection(self, *args, **kwargs):
                 P.add_constraint((1 - X[i]) * rd.lb - V[rd.index] <= 0)
             else:
                 raise ValueError("Unknown type of reaction")
-        P.set_objective('max', C.T * X)
+        P.set_objective(kwargs['direction'], C.T * X)
         self.variables._indicator_vars = X
         return True
 
@@ -982,6 +982,7 @@ def _set_flux_bounds(self, *args, **kwargs):
 
     def _subset_selection(self, *args, **kwargs):
         eps = kwargs["eps"]
+        direction = kwargs["direction"]
         weighted_rxns = self.variables.assigned_reactions
         P = self.problem
         V = self.variables.fluxvars
@@ -998,7 +999,12 @@ def _subset_selection(self, *args, **kwargs):
             else:
                 raise ValueError("Unknown type of reaction")
         P.objective = mip.xsum((c * X[i] for i, c in enumerate(C)))
-        P.sense = mip.MAXIMIZE
+        if direction == "max" or direction == "maximize":
+            P.sense = mip.MAXIMIZE
+        elif direction == "min" or direction == "minimize":
+            P.sense = mip.MINIMIZE
+        else:
+            raise ValueError("Unknown optimization sense")
         self.variables._indicator_vars = X
         return True
 

mkdocs.yml

@@ -7,6 +7,8 @@ repo_url: https://www.github.com/metexplore/miom
 copyright: Copyright © 2021 INRAE Toxalim
 theme:
     name: material
+    palette:
+      primary: '#2e5c87'
     custom_dir: docs/overrides
 plugins:
 - search
@@ -38,6 +40,8 @@ extra:
     property: G-5SV6WE1KMZ
   version:
     provider: mike
+extra_css:
+  - stylesheets/extra.css
 extra_javascript:
   - https://polyfill.io/v3/polyfill.min.js?features=es6
   - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js