Merge pull request #100 from aebrahim/cglpk_module_load

cglpk loaded as module, not class

Author: aebrahim

cobra/solvers/__init__.py

@@ -1,6 +1,6 @@
 # attempt to import all working solvers in this directory
 from __future__ import absolute_import
-from warnings import warn
+from warnings import warn as _warn
 from os import name as __name
 
 solver_dict = {}
@@ -44,10 +44,9 @@ def add_solver(solver_name, use_name=None):
         continue
     if i.startswith("parameters"):
         continue
-    if i.endswith(".py") or i.endswith(".so"):
-        possible_solvers.add(i[:-3])
-    if i.endswith(".pyc") or i.endswith(".pyd"):
-        possible_solvers.add(i[:-4])
+    if i.endswith(".py") or i.endswith(".so") or i.endswith(".pyc") \
+            or i.endswith(".pyd"):
+        possible_solvers.add(i.split(".")[0])
 
 for solver in possible_solvers:
     nicer_name = solver[:-7] if solver.endswith("_solver") else solver
@@ -57,15 +56,12 @@ def add_solver(solver_name, use_name=None):
         pass
     del solver, nicer_name
 
-try:
-    from .cglpk import GLP
-    solver_dict["cglpk"] = GLP
-except:
-    None
-
 del path, listdir
 del i, possible_solvers
 
+if len(solver_dict) == 0:
+    _warn("No LP solvers found")
+
 def get_solver_name(mip=False, qp=False):
     """returns a solver name"""
     if len(solver_dict) == 0:
@@ -86,7 +82,7 @@ def get_solver_name(mip=False, qp=False):
                 return solver_name
         for solver_name in solver_dict:
             if solver_name not in qp_incapable:
-                warn("could not verify if %s supports qp" % solver_name)
+                _warn("could not verify if %s supports qp" % solver_name)
                 return solver_name
         return None  # don't want to return glpk
     else:

cobra/solvers/cglpk.pyx

@@ -325,3 +325,24 @@ cdef class GLP:
         glp_copy_prob(other.glp, self.glp, GLP_ON)
         return other
 
+# wrappers for all the functions at the module level
+create_problem = GLP.create_problem
+def set_objective_sense(lp, objective_sense="maximize"):
+    return lp.set_objective_sense(lp, objective_sense=objective_sense)
+cpdef change_variable_bounds(lp, int index, double lower_bound, double upper_bound):
+    return lp.change_variable_bounds(index, lower_bound, upper_bound)
+cpdef change_variable_objective(lp, int index, double value):
+    return lp.change_variable_objective(index, value)
+cpdef change_coefficient(lp, int met_index, int rxn_index, double value):
+    return lp.change_coefficient(met_index, rxn_index, value)
+cpdef set_parameter(lp, parameter_name, value):
+    return lp.set_parameter(parameter_name, value)
+def solve_problem(lp, **kwargs):
+    return lp.solve_problem(**kwargs)
+cpdef get_status(lp):
+    return lp.get_status()
+cpdef get_objective_value(lp):
+    return lp.get_objective_value()
+cpdef format_solution(lp, cobra_model):
+    return lp.format_solution(cobra_model)
+solve = GLP.solve