Merge branch 'main' into papers

MichaelClerx · web-flow · commit 8c040410c2fb · 2026-02-06T14:45:37.000Z
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -18,6 +18,7 @@ All notable changes to this project will be documented in this file.
 - [#1724](https://github.com/pints-team/pints/pull/1724) The classes `PooledLogPDF` and `SumOfIndependentLogPDFs` are deprecated, in favour of `PooledLogLikelihood` and `SumOfIndependentLogLikelihoods` respectively.
 - [#1508](https://github.com/pints-team/pints/pull/1508) The methods `OptimisationController.max_unchanged_iterations` and `set_max_unchanged_iterations` are deprecated, in favour of `function_tolerance` and `set_function_tolerance` respectively.
 ### Removed
+- [#1731](https://github.com/pints-team/pints/pull/1731) The method `ToyLogPDF.suggested_bounds()` and its implementations have been removed.
 ### Fixed
 - [#1713](https://github.com/pints-team/pints/pull/1713) Fixed Numpy 2.4.1 compatibility issues.
 - [#1690](https://github.com/pints-team/pints/pull/1690) Fixed bug in optimisation controller if population size left at `None`.
diff --git a/pints/tests/test_toy_annulus_logpdf.py b/pints/tests/test_toy_annulus_logpdf.py
@@ -68,26 +68,6 @@ def test_bad_constructors(self):
         self.assertRaises(
             ValueError, pints.toy.AnnulusLogPDF, 3, 1, -1)
 
-    def test_suggested_bounds(self):
-        # Tests suggested_bounds() method
-
-        f = pints.toy.AnnulusLogPDF()
-        bounds = f.suggested_bounds()
-        a_val = 55
-        self.assertTrue(np.array_equal([[-a_val, -a_val], [a_val, a_val]],
-                                       bounds))
-        r0 = 25
-        dimensions = 5
-        sigma = 20
-        f = pints.toy.AnnulusLogPDF(dimensions=dimensions,
-                                    r0=r0,
-                                    sigma=sigma)
-        bounds = f.suggested_bounds()
-        r0_magnitude = (r0 + sigma) * (5**(1.0 / (dimensions - 1.0)))
-        self.assertEqual(bounds[0][0], -r0_magnitude)
-        self.assertEqual(bounds[1][0], r0_magnitude)
-        self.assertTrue(np.array_equal(np.array(bounds).shape, [2, 5]))
-
     def test_distance_function(self):
         # Tests distance function
 
diff --git a/pints/tests/test_toy_classes.py b/pints/tests/test_toy_classes.py
@@ -21,8 +21,7 @@ def test_run(self):
         model = pints.toy.Hes1Model()
         vals = [1, 2, 3]
         model.set_initial_conditions(vals)
-        self.assertTrue(np.array_equal(model.initial_conditions(),
-                                       vals))
+        self.assertTrue(np.array_equal(model.initial_conditions(), vals))
 
 
 if __name__ == '__main__':
diff --git a/pints/tests/test_toy_cone_logpdf.py b/pints/tests/test_toy_cone_logpdf.py
@@ -70,22 +70,6 @@ def test_bad_constructors(self):
         self.assertRaises(ValueError, f.__call__, [1, 2, 3])
         self.assertRaises(ValueError, f.__call__, [1, 2, 3, 4, 5])
 
-    def test_bounds(self):
-        # Tests suggested_bounds()
-
-        f = pints.toy.ConeLogPDF()
-        bounds = f.suggested_bounds()
-        self.assertTrue(np.array_equal([[-1000, -1000], [1000, 1000]],
-                                       bounds))
-        beta = 3
-        dimensions = 4
-        f = pints.toy.ConeLogPDF(beta=beta, dimensions=dimensions)
-        magnitude = 1000
-        bounds = np.tile([-magnitude, magnitude], (dimensions, 1))
-        self.assertEqual(bounds[0][0], -magnitude)
-        self.assertEqual(bounds[0][1], magnitude)
-        self.assertTrue(np.array_equal(np.array(bounds).shape, [4, 2]))
-
     def test_sensitivities(self):
         # Tests sensitivities
 
diff --git a/pints/tests/test_toy_eight_schools_logpdf.py b/pints/tests/test_toy_eight_schools_logpdf.py
@@ -21,6 +21,7 @@ def test_basic(self):
 
         # Default settings
         f = pints.toy.EightSchoolsLogPDF()
+        self.assertEqual(f.n_parameters(), 10)
         f1, dp = f.evaluateS1(np.ones(10))
         self.assertEqual(f1, f(np.ones(10)))
         self.assertAlmostEqual(f1, -43.02226038161451)
@@ -83,12 +84,6 @@ def test_negative_sd(self):
         self.assertEqual(logp, -np.inf)
         self.assertTrue(np.array_equal(grad, np.full([1, 10], -np.inf)))
 
-    def test_bounds(self):
-        """ Tests suggested_bounds() """
-        f = pints.toy.EightSchoolsLogPDF()
-        bounds = f.suggested_bounds()
-        self.assertEqual(bounds[0][1], 0)
-
 
 if __name__ == '__main__':
     unittest.main()
diff --git a/pints/tests/test_toy_german_credit_hierarchical_logpdf.py b/pints/tests/test_toy_german_credit_hierarchical_logpdf.py
@@ -71,11 +71,8 @@ def test_sensitivities(self):
         self.assertAlmostEqual(dp[1], -700.8386959844057, places=6)
 
     def test_givens(self):
-        # tests whether boundaries are correct and n_parameters
+        # tests n_parameters
         self.assertEqual(326, self.model.n_parameters())
-        borders = self.model.suggested_bounds()
-        self.assertEqual(borders[0][0], -100)
-        self.assertEqual(borders[1][0], 100)
 
 
 if __name__ == '__main__':
diff --git a/pints/tests/test_toy_german_credit_logpdf.py b/pints/tests/test_toy_german_credit_logpdf.py
@@ -71,11 +71,8 @@ def test_sensitivities(self):
         self.assertAlmostEqual(dp[1], -160.7785147438439, places=6)
 
     def test_givens(self):
-        # tests whether boundaries are correct and n_parameters
+        # tests n_parameters
         self.assertEqual(25, self.model.n_parameters())
-        borders = self.model.suggested_bounds()
-        self.assertEqual(borders[0][0], -100)
-        self.assertEqual(borders[1][0], 100)
 
 
 if __name__ == '__main__':
diff --git a/pints/tests/test_toy_high_dimensional_gaussian_logpdf.py b/pints/tests/test_toy_high_dimensional_gaussian_logpdf.py
@@ -67,18 +67,6 @@ def test_high_dimensional_log_pdf(self):
             f([1, 2]),
             scipy.stats.multivariate_normal.logpdf([1, 2], mean, cov))
 
-        # check suggested bounds
-        f = pints.toy.HighDimensionalGaussianLogPDF(dimension=2)
-        bounds = f.suggested_bounds()
-        magnitude = 3 * np.sqrt(2.0)
-        bounds1 = np.tile([-magnitude, magnitude], (2, 1))
-        bounds1 = np.transpose(bounds1).tolist()
-        self.assertTrue(np.array_equal(bounds, bounds1))
-
-        f = pints.toy.HighDimensionalGaussianLogPDF()
-        bounds = f.suggested_bounds()
-        self.assertTrue(bounds[0][0], np.sqrt(20) * 3.0)
-
         # Test kl_divergence() errors
         n = 1000
         d = f.n_parameters()
diff --git a/pints/tests/test_toy_multimodal_gaussian_logpdf.py b/pints/tests/test_toy_multimodal_gaussian_logpdf.py
@@ -131,33 +131,6 @@ def test_sensitivities(self):
         self.assertAlmostEqual(dl[1], -0.054933536830093638)
         self.assertAlmostEqual(dl[2], -0.39317158556789844)
 
-    def test_suggested_bounds(self):
-        # Tests suggested_bounds().
-
-        f = pints.toy.MultimodalGaussianLogPDF()
-        covariances = [[[5**2, 0.5 * 5 * 3, -0.1 * 5 * 2],
-                        [0.5 * 5 * 3, 3**2, 0.4 * 3 * 2],
-                        [-0.1 * 5 * 2, 0.4 * 3 * 2, 2**2]],
-                       [[5**2, 0.3 * 5 * 6, 0.2 * 5 * 7],
-                        [0.3 * 5 * 6, 6**2, -0.3 * 6 * 7],
-                        [0.2 * 5 * 7, -0.3 * 6 * 7, 7**2]]]
-        bounds = f.suggested_bounds()
-        lower = -10
-        upper = 20
-        bounds1 = np.tile([lower, upper], (2, 1))
-        bounds1 = np.transpose(bounds1).tolist()
-        self.assertTrue(np.array_equal(bounds, bounds1))
-
-        f = pints.toy.MultimodalGaussianLogPDF(
-            modes=[[1, 2, 3], [3, 4, 5]],
-            covariances=covariances)
-        bounds = f.suggested_bounds()
-        lower = 1 - 4
-        upper = 5 + 4
-        bounds1 = np.tile([lower, upper], (3, 1))
-        bounds1 = np.transpose(bounds1).tolist()
-        self.assertTrue(np.array_equal(bounds, bounds1))
-
     def test_distance_function(self):
         # Tests distance function which calls kl_divergence().
 
diff --git a/pints/tests/test_toy_neals_funnel_logpdf.py b/pints/tests/test_toy_neals_funnel_logpdf.py
@@ -93,26 +93,6 @@ def test_bespoke(self):
         x = np.ones((n, d, 2))
         self.assertRaises(ValueError, f.kl_divergence, x)
 
-    def test_suggested_bounds(self):
-        # Tests suggested_bounds().
-        # default
-        f = pints.toy.NealsFunnelLogPDF()
-        bounds = f.suggested_bounds()
-        magnitude = 30
-        bounds1 = np.tile([-magnitude, magnitude],
-                          (f._n_parameters, 1))
-        bounds1 = np.transpose(bounds1).tolist()
-        self.assertTrue(np.array_equal(bounds, bounds1))
-
-        # non-default
-        f = pints.toy.NealsFunnelLogPDF(20)
-        bounds = f.suggested_bounds()
-        magnitude = 30
-        bounds1 = np.tile([-magnitude, magnitude],
-                          (f._n_parameters, 1))
-        bounds1 = np.transpose(bounds1).tolist()
-        self.assertTrue(np.array_equal(bounds, bounds1))
-
 
 if __name__ == '__main__':
     unittest.main()
diff --git a/pints/tests/test_toy_rosenbrock.py b/pints/tests/test_toy_rosenbrock.py
@@ -50,12 +50,7 @@ def test_log_pdf(self):
         self.assertEqual(dl[0], float(-6004.0 / 2505.0))
         self.assertEqual(dl[1], float(200.0 / 501.0))
 
-        # suggested bounds and distance measure
-        bounds = f.suggested_bounds()
-        bounds = [[-2, 4], [-1, 12]]
-        bounds = np.transpose(bounds).tolist()
-        self.assertTrue(np.array_equal(bounds, f.suggested_bounds()))
-
+        # Distance measure
         x = np.ones((100, 3))
         self.assertRaises(ValueError, f.distance, x)
         x = np.ones((100, 3, 2))
diff --git a/pints/tests/test_toy_simple_egg_box_logpdf.py b/pints/tests/test_toy_simple_egg_box_logpdf.py
@@ -70,9 +70,8 @@ def test_sampling_and_divergence(self):
         x = np.ones((n, 2, 2))
         self.assertRaises(ValueError, log_pdf1.kl_divergence, x)
 
-    def test_sensitivity_bounds_distance(self):
+    def test_sensitivity_and_distance(self):
         # Tests :meth:`SimpleEggBoxLogPDF.evaluateS1()`,
-        # :meth:`SimpleEggBoxLogPDF.suggested_bounds()` and
         # :meth:`SimpleEggBoxLogPDF.distance()`
 
         f = pints.toy.SimpleEggBoxLogPDF()
@@ -81,8 +80,6 @@ def test_sensitivity_bounds_distance(self):
         self.assertAlmostEqual(l, -13.781024134434123)
         self.assertAlmostEqual(dl[0], -1.5)
         self.assertAlmostEqual(dl[1], 2.9999991)
-        self.assertTrue(np.array_equal(f.suggested_bounds(),
-                                       [[-16.0, -16.0], [16.0, 16.0]]))
         samples = f.sample(100)
         self.assertTrue(f.kl_divergence(samples) > 0)
         self.assertEqual(f.kl_divergence(samples), f.distance(samples))
@@ -93,8 +90,6 @@ def test_sensitivity_bounds_distance(self):
         self.assertAlmostEqual(l, -46.269777289511559)
         self.assertAlmostEqual(dl[0], -4.6662126879796366)
         self.assertAlmostEqual(dl[1], -2.6666666666666639)
-        self.assertTrue(np.array_equal(f.suggested_bounds(),
-                                       [[-30.0, -30.0], [30.0, 30.0]]))
         samples = f.sample(100)
         self.assertTrue(f.kl_divergence(samples) > 0)
         self.assertEqual(f.kl_divergence(samples), f.distance(samples))
diff --git a/pints/tests/test_toy_twisted_gaussian_logpdf.py b/pints/tests/test_toy_twisted_gaussian_logpdf.py
@@ -84,13 +84,6 @@ def test_sampling_and_kl_divergence(self):
         x = np.ones((n, d, 2))
         self.assertRaises(ValueError, log_pdf1.kl_divergence, x)
 
-        # Test suggested bounds
-        f = pints.toy.TwistedGaussianLogPDF()
-        bounds = f.suggested_bounds()
-        bounds1 = [[-50, 50], [-100, 100]]
-        bounds1 = np.transpose(bounds1).tolist()
-        self.assertTrue(np.array_equal(bounds, bounds1))
-
     def test_values_sensitivity(self):
         # Tests values of log pdf and sensitivities
 
diff --git a/pints/toy/_annulus.py b/pints/toy/_annulus.py
@@ -63,8 +63,7 @@ def __call__(self, x):
     def distance(self, samples):
         """
         Calculates a measure of normed distance of samples from exact mean and
-        covariance matrix assuming uniform prior with bounds given by
-        :meth:`suggested_bounds`.
+        covariance matrix.
 
         See :meth:`ToyLogPDF.distance()`.
         """
@@ -174,16 +173,6 @@ def sigma(self):
         """
         return self._sigma
 
-    def suggested_bounds(self):
-        """ See :meth:`ToyLogPDF.suggested_bounds()`. """
-        # in higher dimensions reduce volume as otherwise gets too wide
-        r0_magnitude = (self._r0 + self._sigma) * (
-            5**(1.0 / (self._n_parameters - 1.0))
-        )
-        bounds = np.tile([-r0_magnitude, r0_magnitude],
-                         (self._n_parameters, 1))
-        return np.transpose(bounds).tolist()
-
     def var_normed(self):
         """
         Returns the variance of the normed distance from the origin.
diff --git a/pints/toy/_cone.py b/pints/toy/_cone.py
@@ -71,8 +71,7 @@ def CDF(self, x):
     def distance(self, samples):
         """
         Calculates a measure of normed distance of samples from exact mean and
-        covariance matrix assuming uniform prior with bounds given by
-        :meth:`suggested_bounds()`.
+        covariance matrix.
 
         See :meth:`pints.toy.ToyLogPDF.distance()`.
         """
@@ -137,12 +136,6 @@ def sample(self, n_samples):
         x_unit = [r[i] * X_norm[i] / y for i, y in enumerate(lambda_x)]
         return np.array(x_unit)
 
-    def suggested_bounds(self):
-        """ See :meth:`ToyLogPDF.suggested_bounds()`. """
-        magnitude = 1000
-        bounds = np.tile([-magnitude, magnitude], (self._n_parameters, 1))
-        return np.transpose(bounds).tolist()
-
     def var_normed(self):
         """
         Returns the variance of the normed distance from the origin.
diff --git a/pints/toy/_eight_schools.py b/pints/toy/_eight_schools.py
@@ -156,9 +156,3 @@ def n_parameters(self):
         """ See :meth:`pints.LogPDF.n_parameters()`. """
         return self._n_parameters
 
-    def suggested_bounds(self):
-        """ See :meth:`pints.toy.ToyLogPDF.suggested_bounds()`. """
-        magnitude = 40
-        bounds = np.tile([-magnitude, magnitude], (self.n_parameters(), 1))
-        bounds[1, 0] = 0
-        return np.transpose(bounds).tolist()
diff --git a/pints/toy/_german_credit.py b/pints/toy/_german_credit.py
@@ -121,8 +121,3 @@ def evaluateS1(self, beta):
     def n_parameters(self):
         return self._n_parameters
 
-    def suggested_bounds(self):
-        """ See :meth:`ToyLogPDF.suggested_bounds()`. """
-        magnitude = 100
-        bounds = np.tile([-magnitude, magnitude], (self._n_parameters, 1))
-        return np.transpose(bounds).tolist()
diff --git a/pints/toy/_german_credit_hierarchical.py b/pints/toy/_german_credit_hierarchical.py
@@ -153,8 +153,3 @@ def evaluateS1(self, theta):
     def n_parameters(self):
         return self._n_parameters
 
-    def suggested_bounds(self):
-        """ See :meth:`ToyLogPDF.suggested_bounds()`. """
-        magnitude = 100
-        bounds = np.tile([-magnitude, magnitude], (self._n_parameters, 1))
-        return np.transpose(bounds).tolist()
diff --git a/pints/toy/_high_dimensional_gaussian.py b/pints/toy/_high_dimensional_gaussian.py
@@ -146,10 +146,3 @@ def sample(self, n_samples):
                 'Number of samples must be greater than or equal to 1.')
         return self._var.rvs(n_samples)
 
-    def suggested_bounds(self):
-        """ See :meth:`pints.toy.ToyLogPDF.suggested_bounds()`. """
-        # maximum variance in one dimension is n_parameters, so use
-        # 3 times sqrt of this as prior bounds
-        magnitude = 3 * np.sqrt(self.n_parameters())
-        bounds = np.tile([-magnitude, magnitude], (self.n_parameters(), 1))
-        return np.transpose(bounds).tolist()
diff --git a/pints/toy/_multimodal_gaussian.py b/pints/toy/_multimodal_gaussian.py
@@ -201,13 +201,3 @@ def sample(self, n_samples):
             samples[i, :] = self._vars[rand_mode].rvs(1)
         return samples
 
-    def suggested_bounds(self):
-        """ See :meth:`pints.toy.ToyLogPDF.suggested_bounds()`. """
-        # make rectangular bounds in each dimension 3X width of range
-        a_max = np.max(self._modes)
-        a_min = np.min(self._modes)
-        a_range = a_max - a_min
-        lower = a_min - a_range
-        upper = a_max + a_range
-        bounds = np.tile([lower, upper], (self._n_parameters, 1))
-        return np.transpose(bounds).tolist()
diff --git a/pints/toy/_neals_funnel.py b/pints/toy/_neals_funnel.py
@@ -126,13 +126,6 @@ def sample(self, n_samples):
             samples[i, n - 1] = nu
         return samples
 
-    def suggested_bounds(self):
-        """ See :meth:`pints.toy.ToyLogPDF.suggested_bounds()`. """
-        magnitude = 30
-        bounds = np.tile([-magnitude, magnitude],
-                         (self._n_parameters, 1))
-        return np.transpose(bounds).tolist()
-
     def var(self):
         """
         Returns the variance of the target distribution in each dimension.
diff --git a/pints/toy/_rosenbrock.py b/pints/toy/_rosenbrock.py
@@ -59,7 +59,6 @@ class RosenbrockLogPDF(ToyLogPDF):
     def __init__(self):
         self._f = RosenbrockError()
 
-        # assumes uniform prior with bounds given by suggested_bounds
         self._true_mean = np.array([0.8693578490590254, 2.599780856590108])
         self._true_cov = np.array([[1.805379677045191, 2.702575590274159],
                                    [2.702575590274159, 8.526583078612177]])
@@ -70,8 +69,7 @@ def __call__(self, x):
     def distance(self, samples):
         """
         Calculates a measure of normed distance of samples from exact mean and
-        covariance matrix assuming uniform prior with bounds given
-        by :meth:`suggested_bounds()`.
+        covariance matrix.
 
         See :meth:`pints.toy.ToyLogPDF.distance()`.
         """
@@ -118,8 +116,3 @@ def optimum(self):
         """
         return self._f.optimum()
 
-    def suggested_bounds(self):
-        """ See :meth:`pints.toy.ToyLogPDF.suggested_bounds()`. """
-        # think the following hard bounds are ok
-        bounds = [[-2, 4], [-1, 12]]
-        return np.transpose(bounds).tolist()
diff --git a/pints/toy/_simple_egg_box.py b/pints/toy/_simple_egg_box.py
diff --git a/pints/toy/_toy_classes.py b/pints/toy/_toy_classes.py
diff --git a/pints/toy/_twisted_gaussian_banana.py b/pints/toy/_twisted_gaussian_banana.py
