Merge branch 'tox-qsoptex' into develop

.travis.yml

@@ -3,6 +3,8 @@ install: pip install tox
 script: tox -v
 env:
     - TOXENV=py27-nosolver
+    - TOXENV=py27-qsoptex
     - TOXENV=py34-nosolver
+    - TOXENV=py34-qsoptex
     - TOXENV=docs
     - TOXENV=flake

psamm/tests/test_fastcore.py

@@ -77,7 +77,8 @@ def test_lp7(self):
 
         result = fastcore.lp7(self.model, {'rxn_5'}, 0.001, solver=self.solver)
         supp = set(fastcore.support_positive(result, 0.001*0.999))
-        self.assertEqual(supp, { 'rxn_1', 'rxn_4', 'rxn_5', 'rxn_6' })
+        # Test that the support contains at least the given reactions
+        self.assertLessEqual({'rxn_4', 'rxn_5', 'rxn_6'}, supp)
 
     def test_find_sparse_mode_singleton(self):
         core = { 'rxn_1' }
@@ -168,9 +169,9 @@ class TestFastcoreTinyBiomassModel(unittest.TestCase):
     fastcore.
 
     In this particular model, rxn_2 can take a maximum flux of 1000. At the
-    same time rxn_1 will have to take a flux of 1e-4. This is the maximum
+    same time rxn_1 will have to take a flux of 1e-3. This is the maximum
     possible flux for rxn_1 so running fastcore with an epsilon larger than
-    1e-4 will indicate that the model is not consistent.
+    1e-3 will indicate that the model is not consistent.
     """
 
     def setUp(self):
@@ -189,18 +190,21 @@ def setUp(self):
 
     def test_fastcc_is_consistent(self):
         self.assertTrue(fastcore.fastcc_is_consistent(
-            self.model, 0.001, solver=self.solver))
+            self.model, 0.0001, solver=self.solver))
+
+    def test_fastcc_is_consistent_high_epsilon(self):
+        self.assertFalse(fastcore.fastcc_is_consistent(
+            self.model, 0.1, solver=self.solver))
 
     def test_fastcore_induced_model(self):
-        core = { 'rxn_2' }
-        self.assertEquals(set(fastcore.fastcore(
-            self.model, core, 0.001, solver=self.solver)),
-            { 'rxn_1', 'rxn_2' })
+        core = {'rxn_2'}
+        self.assertEqual(set(fastcore.fastcore(
+            self.model, core, 0.0001, solver=self.solver)), {'rxn_1', 'rxn_2'})
 
     def test_fastcore_induced_model_high_epsilon(self):
-        core = { 'rxn_2' }
-        self.assertEquals(set(fastcore.fastcore(
-            self.model, core, 0.1, solver=self.solver)), { 'rxn_1', 'rxn_2' })
+        core = {'rxn_2'}
+        self.assertEqual(set(fastcore.fastcore(
+            self.model, core, 0.1, solver=self.solver)), {'rxn_1', 'rxn_2'})
 
 
 class TestFlippingModel(unittest.TestCase):

tox.ini

@@ -1,7 +1,7 @@
 [tox]
 envlist =
-    py27-{nosolver,cplex},
-    py34-{nosolver},
+    py27-{nosolver,cplex,qsoptex},
+    py34-{nosolver,qsoptex},
     coverage,
     flake,
     docs
@@ -14,9 +14,11 @@ exclude = psamm/tests
 setenv =
     nosolver: PSAMM_SOLVER=nosolver
     cplex: PSAMM_SOLVER=cplex
+    qsoptex: PSAMM_SOLVER=qsoptex
 deps =
     coverage
     cplex: {env:CPLEX_PYTHON_PACKAGE}
+    qsoptex: python-qsoptex
 commands =
     coverage run -p --branch --omit={envdir},psamm/tests \
         ./setup.py test