refactor: change scope of room_model and room_solution to module; mov…

…e geometric_fba_model to respective module
opencobra · Aug 20, 2018 · 8ee8eaa · 8ee8eaa
1 parent b6c09cd
commit 8ee8eaa
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Showing 2 changed files with 49 additions and 47 deletions.
diff --git a/cobra/test/test_flux_analysis/conftest.py b/cobra/test/test_flux_analysis/conftest.py
@@ -5,10 +5,10 @@
 
 from __future__ import absolute_import
 
+import pytest
 from pandas import Series
 
 import cobra.util.solver as sutil
-import pytest
 from cobra.core import Metabolite, Model, Reaction, Solution
 
 # The scipy interface is currently unstable and may yield errors or infeasible
@@ -31,7 +31,7 @@ def qp_solvers(request):
     return request.param
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(scope="module")
 def room_model():
     """
     Generate ROOM model as described in [1]_
@@ -72,7 +72,7 @@ def room_model():
     return test_model
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(scope="module")
 def room_solution():
     """
     Generate ROOM solution as described in [1]_
@@ -97,47 +97,3 @@ def room_solution():
                    reduced_costs=reduced_costs,
                    shadow_prices=shadow_prices)
     return sol
-
-
-@pytest.fixture(scope="session")
-def geometric_fba_model():
-    """
-    Generate geometric FBA model as described in [1]_
-
-    References
-    ----------
-    .. [1] Smallbone, Kieran & Simeonidis, Vangelis. (2009).
-           Flux balance analysis: A geometric perspective.
-           Journal of theoretical biology.258. 311-5.
-           10.1016/j.jtbi.2009.01.027.
-
-    """
-    test_model = Model('geometric_fba_paper_model')
-
-    test_model.add_metabolites(Metabolite('A'))
-    test_model.add_metabolites(Metabolite('B'))
-
-    v_1 = Reaction('v1', upper_bound=1.0)
-    v_1.add_metabolites({test_model.metabolites.A: 1.0})
-
-    v_2 = Reaction('v2', lower_bound=-1000.0)
-    v_2.add_metabolites({test_model.metabolites.A: -1.0,
-                         test_model.metabolites.B: 1.0})
-
-    v_3 = Reaction('v3', lower_bound=-1000.0)
-    v_3.add_metabolites({test_model.metabolites.A: -1.0,
-                         test_model.metabolites.B: 1.0})
-
-    v_4 = Reaction('v4', lower_bound=-1000.0)
-    v_4.add_metabolites({test_model.metabolites.A: -1.0,
-                         test_model.metabolites.B: 1.0})
-
-    v_5 = Reaction('v5')
-    v_5.add_metabolites({test_model.metabolites.A: 0.0,
-                         test_model.metabolites.B: -1.0})
-
-    test_model.add_reactions([v_1, v_2, v_3, v_4, v_5])
-
-    test_model.objective = 'v5'
-
-    return test_model
diff --git a/cobra/test/test_flux_analysis/test_geometric.py b/cobra/test/test_flux_analysis/test_geometric.py
@@ -7,9 +7,55 @@
 import numpy as np
 from pandas import Series
 
+import pytest
+from cobra.core import Metabolite, Model, Reaction, Solution
 from cobra.flux_analysis import geometric_fba
 
 
+@pytest.fixture(scope="module")
+def geometric_fba_model():
+    """
+    Generate geometric FBA model as described in [1]_
+
+    References
+    ----------
+    .. [1] Smallbone, Kieran & Simeonidis, Vangelis. (2009).
+           Flux balance analysis: A geometric perspective.
+           Journal of theoretical biology.258. 311-5.
+           10.1016/j.jtbi.2009.01.027.
+
+    """
+    test_model = Model('geometric_fba_paper_model')
+
+    test_model.add_metabolites(Metabolite('A'))
+    test_model.add_metabolites(Metabolite('B'))
+
+    v_1 = Reaction('v1', upper_bound=1.0)
+    v_1.add_metabolites({test_model.metabolites.A: 1.0})
+
+    v_2 = Reaction('v2', lower_bound=-1000.0)
+    v_2.add_metabolites({test_model.metabolites.A: -1.0,
+                         test_model.metabolites.B: 1.0})
+
+    v_3 = Reaction('v3', lower_bound=-1000.0)
+    v_3.add_metabolites({test_model.metabolites.A: -1.0,
+                         test_model.metabolites.B: 1.0})
+
+    v_4 = Reaction('v4', lower_bound=-1000.0)
+    v_4.add_metabolites({test_model.metabolites.A: -1.0,
+                         test_model.metabolites.B: 1.0})
+
+    v_5 = Reaction('v5')
+    v_5.add_metabolites({test_model.metabolites.A: 0.0,
+                         test_model.metabolites.B: -1.0})
+
+    test_model.add_reactions([v_1, v_2, v_3, v_4, v_5])
+
+    test_model.objective = 'v5'
+
+    return test_model
+
+
 def test_geometric_fba_benchmark(model, benchmark, all_solvers):
     """Benchmark geometric_fba."""
     model.solver = all_solvers