cleanup

Author: pauleve

merrin/LPModel.py

@@ -7,6 +7,7 @@
 
 from pulp import (
     COIN_CMD,
+    PULP_CBC_CMD,
     LpStatus,
     LpMaximize,
     LpProblem,
@@ -17,6 +18,8 @@
 
 #AUXILIARY#FUNCTIONS##MODELS####################################################
 
+LP_SOLVER = COIN_CMD if COIN_CMD().available() else PULP_CBC_CMD
+
 
 def get_base_fba_lp_model(time, internal_metabolites, reactions, bounds, stoichiometry, obj, removeObj=False):
     # ------------------------------------------------------------------------ #
@@ -113,7 +116,7 @@ def add_maximised_forced_state(fba, f, reactions, reactions_states, bounds, epsi
 
 def solve_rfba(fba_lp_model, lp_variables, obj_reaction):
     # Coin Branch and Cut solver is used to solve the instanced model
-    solver = COIN_CMD(msg=0, timeLimit=5)
+    solver = LP_SOLVER(msg=0, timeLimit=5)
 
     fba_lp_model.solve(solver)
 
@@ -131,7 +134,7 @@ def solve_rfba(fba_lp_model, lp_variables, obj_reaction):
 
 def solve_lp_model(lp_model, lp_variables):
     # Coin Branch and Cut solver is used to solve the instanced model
-    solver = COIN_CMD(msg=0)
+    solver = LP_SOLVER(msg=0)
 
     lp_model.solve(solver)
 

merrin/Loader.py

@@ -1,26 +1,11 @@
-#! /usr/bin/env python3
-# -*- coding: utf-8 -*-
-__author__ = "Kerian Thuillier"
-__email__ = "[email protected]"
-
-#IMPORT#########################################################################
-
 import bonesis
 import pandas as pd
 import networkx as nx
 from libsbml import SBMLReader
 from .Parameters import DATA_TYPE_COLUMN
 from .MetabolicNetworks import MetabolicNetwork
 
-#CODE###########################################################################
-
-
 def load_sbml(sbml_file: str):
-    """
-    Function: 
-    Params: 
-    Return: 
-    """
     sbmld = SBMLReader().readSBML(sbml_file)
     sbmlm = sbmld.getModel()
 
@@ -31,12 +16,6 @@ def load_sbml(sbml_file: str):
 
 
 def load_pkn(pkn_file: str, inputs):
-    """
-    Function: 
-    Params: 
-    Return: 
-    """
-
     pkn = nx.DiGraph()
     with open(pkn_file) as fp:
         for line in fp:
@@ -93,16 +72,3 @@ def load_simulations(files_path: str, k: int = 0, tag: str = None) -> pd.DataFra
             sim[DATA_TYPE_COLUMN] = tag
 
     return simulations
-
-
-def main():
-    """
-    Function: main function executing the project
-    Params: None
-    Return: None
-    """
-
-
-#RUN############################################################################
-if __name__ == '__main__':
-    main()

setup.py

@@ -7,6 +7,7 @@
     author = "Kerian Thuillier",
     author_email = "[email protected]",
     install_requires = [
+        "bonesis",
         "clingo",
         "ginsim",
         "pandas",