Remove cvxpy for weight minimization, fix test values and refactor tests codes

news/cvxpy.rst

@@ -0,0 +1,25 @@
+**Added:**
+
+* L-BFGS-B method in scipy for weight optimization in def get_weights
+* Support for Python 3.13
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* cvxpy depenedency for linear weight optmization in def get_weights
+* Support for Python 3.10
+
+**Fixed:**
+
+* Absolute tolerance for updated weighted matrix from 0.5 to 1e-05 in test_subroutines.py
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -14,7 +14,7 @@ maintainers = [
 description = "A python package implementing the stretched NMF algorithm."
 keywords = ['diffpy', 'PDF']
 readme = "README.rst"
-requires-python = ">=3.10, <3.13"
+requires-python = ">=3.11, <3.14"
 classifiers = [
         'Development Status :: 4 - Beta',
         'Environment :: Console',

requirements/conda.txt

@@ -1,5 +1,4 @@
 numpy
 scipy
-cvxpy
 diffpy.utils
 numdifftools

requirements/pip.txt

@@ -1,5 +1,4 @@
 numpy
 scipy
-cvxpy
 diffpy.utils
 numdifftools

src/diffpy/snmf/optimizers.py

@@ -1,5 +1,5 @@
-import cvxpy
 import numpy as np
+from scipy.optimize import minimize
 
 
 def get_weights(stretched_component_gram_matrix, linear_coefficient, lower_bound, upper_bound):
@@ -36,20 +36,19 @@ def get_weights(stretched_component_gram_matrix, linear_coefficient, lower_bound
       input set. Has length C
 
     """
+
     stretched_component_gram_matrix = np.asarray(stretched_component_gram_matrix)
     linear_coefficient = np.asarray(linear_coefficient)
     upper_bound = np.asarray(upper_bound)
     lower_bound = np.asarray(lower_bound)
 
-    problem_size = max(linear_coefficient.shape)
-    solution_variable = cvxpy.Variable(problem_size)
-
-    objective = cvxpy.Minimize(
-        linear_coefficient.T @ solution_variable
-        + 0.5 * cvxpy.quad_form(solution_variable, stretched_component_gram_matrix)
-    )
-    constraints = [lower_bound <= solution_variable, solution_variable <= upper_bound]
+    # Set dynamic bounds based on the size of the linear coefficient
+    bounds = [(lower_bound, upper_bound) for _ in range(len(linear_coefficient))]
+    initial_guess = np.zeros_like(linear_coefficient)
 
-    cvxpy.Problem(objective, constraints).solve()
+    # Find optimal weights of linear coefficients
+    def obj_func(y):
+        return linear_coefficient.T @ y + 0.5 * y.T @ stretched_component_gram_matrix @ y
 
-    return solution_variable.value
+    result = minimize(obj_func, initial_guess, method="L-BFGS-B", bounds=bounds)
+    return result.x

tests/test_optimizers.py

@@ -2,8 +2,9 @@
 
 from diffpy.snmf.optimizers import get_weights
 
-tm = [
-    ([[[1, 0], [0, 1]], [1, 1], [0, 0], [1, 1]], [0, 0]),
+test_matrix = [
+    # ([stretched_component_gram_matrix, linear_coefficient, lower_bound, upper_bound], expected)
+    ([[[1, 0], [0, 1]], [1, 1], 0, 0], [0, 0]),
     ([[[1, 0], [0, 1]], [1, 1], -1, 1], [-1, -1]),
     ([[[1.75, 0], [0, 1.5]], [1, 1.2], -1, 1], [-0.571428571428571, -0.8]),
     ([[[0.75, 0.2], [0.2, 0.75]], [-0.1, -0.2], -1, 1], [0.066985645933014, 0.248803827751196]),
@@ -13,8 +14,12 @@
 ]
 
 
-@pytest.mark.parametrize("tm", tm)
+@pytest.mark.parametrize("tm", test_matrix)
 def test_get_weights(tm):
+    stretched_component_gram_matrix = tm[0][0]
+    linear_coefficient = tm[0][1]
+    lower_bound = tm[0][2]
+    upper_bound = tm[0][3]
     expected = tm[1]
-    actual = get_weights(tm[0][0], tm[0][1], tm[0][2], tm[0][3])
+    actual = get_weights(stretched_component_gram_matrix, linear_coefficient, lower_bound, upper_bound)
     assert actual == pytest.approx(expected, rel=1e-4, abs=1e-6)

tests/test_subroutines.py

@@ -125,7 +125,7 @@ def test_get_stretched_component(tgso):
             [[0.78, 0.12], [0.5, 0.5]],
             None,
         ],
-        [[0, 1], [1, 1]],
+        [[0.533333, 0.933333], [0.533333, 0.933333]],
     ),
     (
         [2, 3, [[0.5], [0.5]], [[1, 2.5], [1.5, 3], [2, 3.5]], [[1, 2], [3, 4], [5, 6]], 1, [[0.5], [0.5]], None],
@@ -155,7 +155,7 @@ def test_get_stretched_component(tgso):
             [[0.9, 0.4, 0.5], [1, 0, 0.4], [0, 0, 0.98]],
             None,
         ],
-        [[1, 0.0651, 0], [0.5848, 0.0381, 0.1857], [0, 1, 1]],
+        [[1.0, 0.0900485, 0.0], [0.585632, 0.497497, 0.179719], [0.0, 0.52223655, 1.0]],
     ),
     ([2, 2, [[0.5], [0.5]], [[0, 0], [0, 0]], [[0, 0], [0, 0]], 1, [[0.6], [0.4]], "align"], [[0], [0]]),
     ([1, 3, [[0.5, 0.3]], [[1], [1.1], [1.3]], [[1, 2], [2, 3], [3, 2]], 2, [[0.6, 0.4]], None], [[1, 1]]),
@@ -170,7 +170,7 @@ def test_get_stretched_component(tgso):
             [[0.78, 0.12], [0.5, 0.5]],
             "align",
         ],
-        [[0, 0], [1.0466, 1.46]],
+        [[0, 0], [0.8, 1.4]],
     ),
     (
         [
@@ -196,7 +196,7 @@ def test_get_stretched_component(tgso):
             [[0.9, 0.4, 0.5], [1, 0, 0.4], [0, 0, 0.98]],
             "align",
         ],
-        [[1.2605, 0.0552, 0], [0.2723, 0, 0], [0, 1.0538, 1.1696]],
+        [[1.281265, 0.104355, 0], [0.0, 0.0, 0.0], [0.239578, 0.965215, 1.162571]],
     ),
     ([2, 2, [[0.5], [0.5]], [[0, 0], [0, 0]], [[0, 0], [0, 0]], 1, [[0.6], [0.4]], "align"], [[0], [0]]),
     ([1, 3, [[0.5, 0.3]], [[1], [1.1], [1.3]], [[1, 2], [2, 3], [3, 2]], 2, [[0.6, 0.4]], "align"], [[1.3383, 2]]),
@@ -208,8 +208,11 @@ def test_update_weights_matrix(tuwm):
     actual = update_weights_matrix(
         tuwm[0][0], tuwm[0][1], tuwm[0][2], tuwm[0][3], tuwm[0][4], tuwm[0][5], tuwm[0][6], tuwm[0][7]
     )
+
+    print("Actual test get stretched component", actual)
+    print("Expected test get stretched component", tuwm[1])
     expected = tuwm[1]
-    np.testing.assert_allclose(actual, expected, rtol=1e-03, atol=0.5)
+    np.testing.assert_allclose(actual, expected, rtol=1e-03, atol=1e-05)
 
 
 tgrm = [