fix warnings

Author: RomanBoegli

.claude/settings.local.json

@@ -0,0 +1,7 @@
+{
+  "permissions": {
+    "allow": [
+      "Bash(python -m pytest symplex/test.py -W error::DeprecationWarning)"
+    ]
+  }
+}

branch_and_bound.py

@@ -118,7 +118,7 @@ def __str__(self):
                 out.append("global update")  #: {z_lb}")
             out = "\n".join(out) + "\n"
             # \l is graphviz' new line and left align escape sequence
-            return out.replace("\n", "\l")
+            return out.replace("\n", "\\l")
 
     step = 0
     r_global = 0

cspell.json

@@ -0,0 +1,10 @@
+{
+  "version": "0.2",
+  "words": [
+    "symplex",
+    "lexmin",
+    "lexmax",
+    "lexcmp",
+    "lexfeasible"
+  ]
+}

pytest.ini

@@ -1,2 +1,7 @@
 [pytest]
 pythonpath = .
+filterwarnings =
+    ignore::DeprecationWarning:mpmath
+    ignore::DeprecationWarning:networkx
+    ignore:::matplotlib
+    ignore:::pyparsing

symplex/perturb.py

@@ -2,9 +2,9 @@
 from symplex.utils import *
 
 
-def pertubation_vector(perm: Iterable[int], eps):
-    """
-    Provided a sufficiently small epsilon returns a pertubation vector
+def perturbation_vector(perm: Iterable[int], eps):
+    r"""
+    Provided a sufficiently small epsilon returns a perturbation vector
     s.t. (A, b+e(\epsilon)) is in general position
     :param: permutation of m constraints, usually `range(m)`
     :param eps:
@@ -15,7 +15,7 @@ def pertubation_vector(perm: Iterable[int], eps):
 
 def perturbed_polygon(A: Matrix, b: Matrix, eps=Rational(1, 128)):
     m = A.shape[0]
-    return A, b + pertubation_vector(range(m), eps)
+    return A, b + perturbation_vector(range(m), eps)
 
 
 def v_star_from_perturbed_polygon(A: Matrix, b: Matrix, b_pert: Matrix, v_pert: Matrix):

symplex/test.py

@@ -101,24 +101,24 @@ def test_example3428():
     r1 = range(m)
     r2 = [5, 4, 3, 1, 0, 7, 6, 2]
 
-    # once with explicit pertubation
-    e = pertubation_vector(r1, Rational(1, 64))
+    # once with explicit perturbation
+    e = perturbation_vector(r1, Rational(1, 64))
     v_3_e = v_3 + (sub_matrix(A, B) ** -1 * sub_matrix(e, B))
     b_e = b + e
-    res, v_r1_star_expl_pert, _, _ = simplex(A, b_e, c, v_3_e, B, pivot_rule_i=PivotRule.MINIMAL())
-    v_r1_star_expl = v_star_from_perturbed_polygon(A, b, b_e, v_r1_star_expl_pert)
+    res, v_r1_star_explicit_pert, _, _ = simplex(A, b_e, c, v_3_e, B, pivot_rule_i=PivotRule.MINIMAL())
+    v_r1_star_explicit = v_star_from_perturbed_polygon(A, b, b_e, v_r1_star_explicit_pert)
 
-    e = pertubation_vector(r2, Rational(1, 64))
+    e = perturbation_vector(r2, Rational(1, 64))
     v_3_e = v_3 + (sub_matrix(A, B) ** -1 * sub_matrix(e, B))
     b_e = b + e
-    res, v_r2_star_expl_pert, _, _ = simplex(A, b_e, c, v_3_e, B, pivot_rule_i=PivotRule.MINIMAL())
-    v_r2_star_expl = v_star_from_perturbed_polygon(A, b, b_e, v_r2_star_expl_pert)
+    res, v_r2_star_explicit_pert, _, _ = simplex(A, b_e, c, v_3_e, B, pivot_rule_i=PivotRule.MINIMAL())
+    v_r2_star_explicit = v_star_from_perturbed_polygon(A, b, b_e, v_r2_star_explicit_pert)
 
     # and once with our fancy lexmin rule
     res, v_r1_star_lexmin, _, _ = simplex(A, b, c, v_3, B, pivot_rule_i=PivotRule.LEXMIN(r1))
     res, v_r2_star_lexmin, _, _ = simplex(A, b, c, v_3, B, pivot_rule_i=PivotRule.LEXMIN(r2))
-    assert v_r1_star_expl == v_r1_star_lexmin
-    assert v_r2_star_expl == v_r2_star_lexmin
+    assert v_r1_star_explicit == v_r1_star_lexmin
+    assert v_r2_star_explicit == v_r2_star_lexmin
 
 
 def test_ex93():

toolbox.py

@@ -92,7 +92,7 @@ def __get_graph_from_adjacency_matrix(csvfile, filling_values=None, isDirected=F
 
 
 def __get_graph_from_edge_list(csvfile, directed=True):
-    xs = np.genfromtxt(csvfile, delimiter=",", dtype=None, names=True)
+    xs = np.genfromtxt(csvfile, delimiter=",", dtype=None, names=True, encoding=None)
     edges = []
     for x in xs:
         fnode = x[0]