Merge pull request #590 from opencobra/fix-matrix

fix: remove redundant test case

HISTORY.rst

@@ -3,6 +3,8 @@ History
 
 Next Release
 ------------
+* Remove 'Steady-state flux solution vectors' test case.
+* Improve the descriptions of stoichiometric matrix test cases.
 * Fix the discovery or orphan and dead-end metabolites.
 * Improve detection of metabolites that are not consumed or not produced by 
   only opening exchange reactions not other boundary reactions.

memote/suite/templates/test_config.yml

@@ -114,7 +114,6 @@ cards:
     cases:
     - test_absolute_extreme_coefficient_ratio
     - test_number_independent_conservation_relations
-    - test_number_steady_state_flux_solutions
     - test_matrix_rank
     - test_degrees_of_freedom
   experimental:

memote/suite/tests/test_matrix.py

@@ -27,12 +27,12 @@
           format_type="percent")
 def test_absolute_extreme_coefficient_ratio(model, threshold=1e9):
     """
-    Show ratio of the absolute largest and smallest non-zero coefficients.
+    Show the ratio of the absolute largest and smallest non-zero coefficients.
 
     This test will return the absolute largest and smallest, non-zero
-    coefficients from the S-Matrix. A large ratio of these values may point to
-    potential numerical issues when trying to solve the underlying system of
-    equations.
+    coefficients of the stoichiometric matrix. A large ratio of these values
+    may point to potential numerical issues when trying to solve different
+    mathematical optimization problems such as flux-balance analysis.
 
     To pass this test the ratio should not exceed 10^9. This threshold has
     been selected based on experience, and is likely to be adapted when more
@@ -55,13 +55,12 @@ def test_absolute_extreme_coefficient_ratio(model, threshold=1e9):
           format_type="raw")
 def test_number_independent_conservation_relations(model):
     """
-    Show number of independent conservation relations in the model.
+    Show the number of independent conservation relations in the model.
 
-    This test will return the number of conservation relations, i.e.
-    conservation pools through the left null space of the S-Matrix.
-
-    This test is not scored, as the dimension of the left null space
-    depends on the S-Matrix constructed, which is system-specific.
+    This test will return the number of conservation relations, i.e.,
+    conservation pools through the left null space of the stoichiometric
+    matrix. This test is not scored, as the dimension of the left null space
+    is system-specific.
 
     """
     ann = test_number_independent_conservation_relations.annotation
@@ -71,35 +70,13 @@ def test_number_independent_conservation_relations(model):
             ann["data"]))
 
 
-@annotate(title="Steady-state Flux Solution Vectors",
-          format_type="raw")
-def test_number_steady_state_flux_solutions(model):
-    """
-    Show number of independent steady-state flux solution vectors for model.
-
-    This test will return the number of independent steady-state flux solution
-    vector through the null space of the S-Matrix.
-
-    This test is not scored, as the dimension of the null space depends on the
-    S-Matrix constructed, which is system-specific.
-
-    """
-    ann = test_number_steady_state_flux_solutions.annotation
-    ann["data"] = matrix.number_steady_state_flux_solutions(model)
-    ann["message"] = wrapper.fill(
-        """The number of independent steady-state flux solution vectors is {}.
-        """.format(ann["data"]))
-
-
 @annotate(title="Rank", format_type="raw")
 def test_matrix_rank(model):
     """
-    Show rank of the S-Matrix.
-
-    This test will return the rank of the S-Matrix of the model.
+    Show the rank of the stoichiometric matrix.
 
-    This test is not scored, as the rank depends on the S-Matrix constructed,
-    which is system-specific.
+    The rank of the stoichiometric matrix is system specific. It is
+    calculated using singular value decomposition (SVD).
 
     """
     ann = test_matrix_rank.annotation
@@ -111,13 +88,11 @@ def test_matrix_rank(model):
 @annotate(title="Degrees Of Freedom", format_type="raw")
 def test_degrees_of_freedom(model):
     """
-    Show degrees of freedom of the S-Matrix.
-
-    This test will return the degrees of freedom, i.e. "free variables" of the
-    S-Matrix.
+    Show the degrees of freedom of the stoichiometric matrix.
 
-    This test is not scored, as the degrees of freedom depends on S-Matrix
-    constructed, which is system-specific.
+    The degrees of freedom of the stoichiometric matrix, i.e., the number
+    of 'free variables' is system specific and corresponds to the dimension
+    of the right nullspace of the matrix.
 
     """
     ann = test_degrees_of_freedom.annotation

memote/support/consistency_helpers.py

@@ -99,7 +99,7 @@ def stoichiometry_matrix(metabolites, reactions):
 
 def rank(matrix, atol=1e-13, rtol=0):
     """
-    Estimate the rank, i.e. the dimension of the column space, of a matrix.
+    Estimate the rank, i.e., the dimension of the column space, of a matrix.
 
     The algorithm used by this function is based on the singular value
     decomposition of `stoichiometry_matrix`.

memote/support/matrix.py

@@ -28,29 +28,24 @@
 
 def absolute_extreme_coefficient_ratio(model):
     """
-    Return the absolute max and absolute non-zero min coefficients.
+    Return the maximum and minimum absolute, non-zero coefficients.
 
     Parameters
     ----------
     model : cobra.Model
         The metabolic model under investigation.
 
     """
-    # S-Matrix with absolute values:
     s_matrix, _, _ = con_helpers.stoichiometry_matrix(
         model.metabolites, model.reactions
     )
-    abs_matrix = np.absolute(s_matrix)
-
-    absolute_max_coef = np.amax(abs_matrix)
-    absolute_non_zero_min_coef = abs_matrix[abs_matrix > 0].min()
-
-    return (absolute_max_coef, absolute_non_zero_min_coef)
+    abs_matrix = np.abs(s_matrix)
+    return abs_matrix.max(), abs_matrix[abs_matrix > 0].min()
 
 
 def number_independent_conservation_relations(model):
     """
-    Return the amount of conserved metabolic pools.
+    Return the number of conserved metabolite pools.
 
     Parameters
     ----------
@@ -100,22 +95,22 @@ def matrix_rank(model):
 
 def degrees_of_freedom(model):
     """
-    Return the degrees of freedom, i.e. number of "free variables".
+    Return the degrees of freedom, i.e., number of "free variables".
 
     Parameters
     ----------
     model : cobra.Model
         The metabolic model under investigation.
 
-    Notes:
-    ------
+    Notes
+    -----
     This specifically refers to the dimensionality of the right nullspace
-    of the S matrix, as dim(Null(S)) corresponds directly to the number of
-    free variables in the system [1]_. The forumla used calculates this using
-    the rank-nullity theorem [2]_.
+    of the stoichiometric matrix, as dim(Null(S)) corresponds directly to the
+    number of free variables in the system [1]_. The formula used calculates
+    this using the rank-nullity theorem [2]_.
 
-    References:
-    -----------
+    References
+    ----------
     .. [1] Fukuda, K. & Terlaky, T. Criss-cross methods: A fresh view on
        pivot algorithms. Mathematical Programming 79, 369-395 (1997).
 

tests/test_for_support/test_for_matrix.py

@@ -118,16 +118,6 @@ def test_number_independent_conservation_relations(model, num):
     assert matrix.number_independent_conservation_relations(model) == num
 
 
-@pytest.mark.parametrize("model, num", [
-    ("three_components_closed", 0),
-    ("three_components_open", 1),
-    ("x2_cycle_closed", 0),
-    ("x2_cycle_open", 1),
-], indirect=["model"])
-def test_number_steady_state_flux_solutions(model, num):
-    assert matrix.number_steady_state_flux_solutions(model) == num
-
-
 @pytest.mark.parametrize("model, num", [
     ("three_components_closed", 2),
     ("three_components_open", 3),