updated version number

conda-recipe/meta.yaml

@@ -1,4 +1,4 @@
-{% set version = '1.12' %}
+{% set version = '1.13' %}
 
 package:
   name: straindesign

docs/source/conf.py

@@ -21,7 +21,7 @@
 author = "Philipp Schneider"
 
 # The full version, including alpha/beta/rc tags
-release = "1.12"
+release = "1.13"
 
 # -- General configuration ---------------------------------------------------
 

setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name="straindesign",
-    version="1.12",
+    version="1.13",
     url="https://github.com/klamt-lab/straindesign.git",
     description="Computational strain design package for the COBRApy framework",
     long_description=

straindesign/efmtool.py

@@ -62,7 +62,7 @@
         _java_executable = ''
 except:
     _java_executable = ''
-    
+
 if _java_executable == '':
     _java_executable = os.path.join(os.environ.get('JAVA_HOME', ''), "bin", "java")
     try:
@@ -73,7 +73,8 @@
         _java_executable = ''
 if _java_executable == '':
     _java_executable = os.path.join(str(jpype.jSystem.getProperty("java.home")), "bin", "java")
-
+
+
 def basic_columns_rat(mx, tolerance=0):  # mx is ch.javasoft.smx.impl.DefaultBigIntegerRationalMatrix
     """efmtool: Translate matrix coefficients to rational numbers"""
     if type(mx) is numpy.ndarray:

straindesign/solver_interface.py

@@ -101,7 +101,7 @@ class MILP_LP(object):
     """
 
     def __init__(self, **kwargs):
-        allowed_keys = { 
+        allowed_keys = {
             'c', 'A_ineq', 'b_ineq', 'A_eq', 'b_eq', 'lb', 'ub', 'vtype', 'indic_constr', 'M', SOLVER, 'skip_checks', 'tlim', SEED
         }
         # set all keys passed in kwargs
@@ -115,14 +115,14 @@ def __init__(self, **kwargs):
             if key not in kwargs.keys():
                 setattr(self, key, None)
         # Select solver (either by choice or automatically cplex > gurobi > glpk)
-        if getattr(self,SOLVER) is None:
+        if getattr(self, SOLVER) is None:
             if len(avail_solvers) > 0:
-                setattr(self,SOLVER,list(avail_solvers)[0])
+                setattr(self, SOLVER, list(avail_solvers)[0])
             else:
                 raise Exception('No solver available. Please ensure that one of the following '\
                     'solvers is avaialable in your Python environment: CPLEX, Gurobi, SCIP, GLPK')
-        elif getattr(self,SOLVER) not in avail_solvers:
-            raise Exception("Selected solver '" + getattr(self,SOLVER) + "' is not installed / set up correctly.")
+        elif getattr(self, SOLVER) not in avail_solvers:
+            raise Exception("Selected solver '" + getattr(self, SOLVER) + "' is not installed / set up correctly.")
         # Copy parameters to object
         if self.A_ineq is not None:
             numvars = self.A_ineq.shape[1]

straindesign/strainDesignProblem.py

@@ -499,13 +499,14 @@ def link_z(self):
 
         logging.info('  Bounding MILP.')
         if processes > 1 and num_Ms > 1000:
-            with SDPool(processes, initializer=worker_init,
-                        initargs=(M_A, M_A_ineq, M_b_ineq, M_A_eq, M_b_eq, M_lb, M_ub, getattr(self,SOLVER), getattr(self,SEED))) as pool:
+            with SDPool(processes,
+                        initializer=worker_init,
+                        initargs=(M_A, M_A_ineq, M_b_ineq, M_A_eq, M_b_eq, M_lb, M_ub, getattr(self, SOLVER), getattr(self, SEED))) as pool:
                 chunk_size = num_Ms // processes
                 for i, value in pool.imap_unordered(worker_compute, range(num_Ms), chunksize=chunk_size):
                     max_Ax[i] = value
         else:
-            worker_init(M_A, M_A_ineq, M_b_ineq, M_A_eq, M_b_eq, M_lb, M_ub, getattr(self,SOLVER), getattr(self,SEED))
+            worker_init(M_A, M_A_ineq, M_b_ineq, M_A_eq, M_b_eq, M_lb, M_ub, getattr(self, SOLVER), getattr(self, SEED))
             for i in range(num_Ms):
                 _, max_Ax[i] = worker_compute(i)
 

tests/test_01_load_models_and_solvers.py

@@ -24,14 +24,17 @@ def model_small_example():
     """Load example model with two substrates."""
     return read_sbml_model(dirname(abspath(__file__)) + "/model_small_example.xml")
 
+
 @pytest.fixture
 def model_core():
     """Load example core model. Large enough to test strain design with multiprocessing"""
     return read_sbml_model(dirname(abspath(__file__)) + "/iMLcore.xml")
 
+
 def test_import_sd():
     import straindesign
 
+
 def test_solver_availability(curr_solver):
     """Test solver availability."""
     assert (curr_solver in sd.avail_solvers)

tests/test_06_multiprocessing.py

@@ -3,22 +3,15 @@
 import straindesign as sd
 import logging
 
+
 @pytest.mark.timeout(600)
-def test_mcs_larger_model(curr_solver,model_core):
+def test_mcs_larger_model(curr_solver, model_core):
     logging.basicConfig(level=logging.INFO)
     modules = [sd.SDModule(model_core, SUPPRESS, constraints=["EX_etoh_e <= 0.5"])]
     modules += [sd.SDModule(model_core, SUPPRESS, constraints=["EX_etoh_e <= 0.5"])]
     modules += [sd.SDModule(model_core, SUPPRESS, constraints=["EX_etoh_e <= 0.5"])]
     # modules += [sd.SDModule(model_core, SUPPRESS, constraints=["EX_etoh_e <= 0.5"])]
     modules += [sd.SDModule(model_core, PROTECT, constraints=["BIOMASS_Ec_iML1515_core_75p37M >= 0.1"])]
-    sd_setup = {
-        MODULES: modules,
-        MAX_COST: 4,
-        MAX_SOLUTIONS: 0,
-        SOLUTION_APPROACH: ANY,
-        SOLVER: curr_solver,
-        'compress': False
-    }
+    sd_setup = {MODULES: modules, MAX_COST: 4, MAX_SOLUTIONS: 0, SOLUTION_APPROACH: ANY, SOLVER: curr_solver, 'compress': False}
     solution = sd.compute_strain_designs(model_core, sd_setup=sd_setup)
     assert (len(solution.get_reaction_sd()) == 0)
-