CUQIpy 1.3.0.post0.dev58__tar.gz → 1.3.0.post0.dev86__tar.gz

{cuqipy-1.3.0.post0.dev58 → cuqipy-1.3.0.post0.dev86}/CUQIpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: CUQIpy
-Version: 1.3.0.post0.dev58
+Version: 1.3.0.post0.dev86
 Summary: Computational Uncertainty Quantification for Inverse problems in Python
 Maintainer-email: "Nicolai A. B. Riis" <nabr@dtu.dk>, "Jakob S. Jørgensen" <jakj@dtu.dk>, "Amal M. Alghamdi" <amaal@dtu.dk>, Chao Zhang <chaz@dtu.dk>
 License:                                  Apache License
@@ -202,9 +202,11 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: matplotlib
 Requires-Dist: numpy>=1.17.0
-Requires-Dist: scipy<1.13
+Requires-Dist: scipy==1.12.0; python_version <= "3.9"
+Requires-Dist: scipy; python_version > "3.9"
 Requires-Dist: arviz
 Requires-Dist: tqdm
+Dynamic: license-file
 
 <div align="center">
 <img src="https://cuqi-dtu.github.io/CUQIpy/_static/logo.png" alt="CUQIpy logo" width="250"/>

cuqipy-1.3.0.post0.dev86/CUQIpy.egg-info/requires.txt

@@ -0,0 +1,10 @@
+matplotlib
+numpy>=1.17.0
+arviz
+tqdm
+
+[:python_version <= "3.9"]
+scipy==1.12.0
+
+[:python_version > "3.9"]
+scipy

{cuqipy-1.3.0.post0.dev58 → cuqipy-1.3.0.post0.dev86}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: CUQIpy
-Version: 1.3.0.post0.dev58
+Version: 1.3.0.post0.dev86
 Summary: Computational Uncertainty Quantification for Inverse problems in Python
 Maintainer-email: "Nicolai A. B. Riis" <nabr@dtu.dk>, "Jakob S. Jørgensen" <jakj@dtu.dk>, "Amal M. Alghamdi" <amaal@dtu.dk>, Chao Zhang <chaz@dtu.dk>
 License:                                  Apache License
@@ -202,9 +202,11 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: matplotlib
 Requires-Dist: numpy>=1.17.0
-Requires-Dist: scipy<1.13
+Requires-Dist: scipy==1.12.0; python_version <= "3.9"
+Requires-Dist: scipy; python_version > "3.9"
 Requires-Dist: arviz
 Requires-Dist: tqdm
+Dynamic: license-file
 
 <div align="center">
 <img src="https://cuqi-dtu.github.io/CUQIpy/_static/logo.png" alt="CUQIpy logo" width="250"/>

{cuqipy-1.3.0.post0.dev58 → cuqipy-1.3.0.post0.dev86}/cuqi/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-03-19T09:20:29+0100",
+ "date": "2025-04-10T10:50:04+0200",
  "dirty": false,
  "error": null,
- "full-revisionid": "0b4dcbc57fa9d6e7e9844b42d0434f9e335c572a",
- "version": "1.3.0.post0.dev58"
+ "full-revisionid": "fe056d15f6ff918511cf7ee579dc8e7689c1dbc4",
+ "version": "1.3.0.post0.dev86"
 }
 '''  # END VERSION_JSON
 

{cuqipy-1.3.0.post0.dev58 → cuqipy-1.3.0.post0.dev86}/cuqi/distribution/__init__.py

@@ -14,6 +14,6 @@ from ._lognormal import Lognormal
 from ._normal import Normal
 from ._truncated_normal import TruncatedNormal
 from ._posterior import Posterior
-from ._uniform import Uniform
+from ._uniform import Uniform, UnboundedUniform
 from ._custom import UserDefinedDistribution, DistributionGallery
 from ._joint_distribution import JointDistribution, _StackedJointDistribution, MultipleLikelihoodPosterior

{cuqipy-1.3.0.post0.dev58 → cuqipy-1.3.0.post0.dev86}/cuqi/distribution/_truncated_normal.py

@@ -107,7 +107,7 @@ class TruncatedNormal(Distribution):
         """
         # check if x falls in the range between np.array a and b
         if np.any(x < self.low) or np.any(x > self.high):
-            return np.NaN*np.ones_like(x)
+            return np.nan*np.ones_like(x)
         else:
             return self._normal.gradient(x, *args, **kwargs)
 

{cuqipy-1.3.0.post0.dev58 → cuqipy-1.3.0.post0.dev86}/cuqi/distribution/_uniform.py

@@ -1,5 +1,6 @@
 import numpy as np
 from cuqi.distribution import Distribution
+from cuqi.geometry import Geometry
 
 class Uniform(Distribution):
 
@@ -46,7 +47,7 @@ class Uniform(Distribution):
         Computes the gradient of logpdf at the given values of x.
         """
         if np.any(x < self.low) or np.any(x > self.high):
-            return np.NaN*np.ones_like(x)
+            return np.nan*np.ones_like(x)
         else:
             return np.zeros_like(x)
 
@@ -57,4 +58,37 @@ class Uniform(Distribution):
         else:
             s = np.random.uniform(self.low, self.high, (N,self.dim)).T
 
-        return s
+        return s
+
+class UnboundedUniform(Distribution):
+    """
+    Unbounded uniform distribution. This is a special case of the
+    Uniform distribution, where the lower and upper bounds are set to
+    -inf and inf, respectively. This distribution is not normalizable,
+    and therefore cannot be sampled from. It is mainly used for
+    initializing non-informative priors.
+    Parameters
+    ----------
+    geometry : int or Geometry
+        The geometry of the distribution. If an integer is given, it is
+        interpreted as the dimension of the distribution. If a
+        Geometry object is given, its par_dim attribute is used.
+    """
+    def __init__(self, geometry, is_symmetric=True, **kwargs):
+        super().__init__(geometry=geometry, is_symmetric=is_symmetric, **kwargs) 
+
+    def logpdf(self, x):
+        """
+        Evaluate the logarithm of the unnormalized PDF at the given values of x.
+        """
+        # Always return 1.0 (the unnormalized log PDF)
+        return 1.0
+
+    def gradient(self, x):
+        """
+        Computes the gradient of logpdf at the given values of x.
+        """
+        return np.zeros_like(x)
+
+    def _sample(self, N=1, rng=None):
+        raise NotImplementedError("Cannot sample from UnboundedUniform distribution")

{cuqipy-1.3.0.post0.dev58 → cuqipy-1.3.0.post0.dev86}/cuqi/implicitprior/_regularizedGaussian.py

@@ -189,12 +189,18 @@ class RegularizedGaussian(Distribution):
             elif c_lower == "increasing":
                 if not isinstance(self.geometry, Continuous1D):
                     raise ValueError("Geometry not supported for " + c_lower)
-                self._constraint_prox = lambda z, _: spoptimize.isotonic_regression(z, increasing=True).x
+                if hasattr(spoptimize, 'isotonic_regression'):
+                    self._constraint_prox = lambda z, _: spoptimize.isotonic_regression(z, increasing=True).x
+                else:
+                    raise AttributeError(f"The function 'isotonic_regression' does not exist in scipy.optimize. Installed scipy version: {spoptimize.__version__}. You need to install a scipy >= 1.12.0")
                 self._preset["constraint"] = "increasing"
             elif c_lower == "decreasing":
                 if not isinstance(self.geometry, Continuous1D):
                     raise ValueError("Geometry not supported for " + c_lower)
-                self._constraint_prox = lambda z, _: spoptimize.isotonic_regression(z, increasing=False).x
+                if hasattr(spoptimize, 'isotonic_regression'):
+                    self._constraint_prox = lambda z, _: spoptimize.isotonic_regression(z, increasing=False).x
+                else:
+                    raise AttributeError(f"The function 'isotonic_regression' does not exist in scipy.optimize. Installed scipy version: {spoptimize.__version__}. You need to install a scipy >= 1.12.0")
                 self._preset["constraint"] = "decreasing"
             elif c_lower == "convex":
                 if not isinstance(self.geometry, Continuous1D):

{cuqipy-1.3.0.post0.dev58 → cuqipy-1.3.0.post0.dev86}/cuqi/utilities/_utilities.py

@@ -188,7 +188,7 @@ def approx_derivative(func, wrt, direction=None, epsilon=np.sqrt(np.finfo(float)
     # We compute the Jacobian matrix of func using forward differences.
     # If the function is scalar-valued, we compute the gradient instead.
     # If the direction is provided, we compute the direction-Jacobian product.
-    wrt = np.asfarray(wrt)
+    wrt = np.asarray(wrt)
     f0 = func(wrt)
     Matr = np.zeros([infer_len(wrt), infer_len(f0)])
     dx = np.zeros(len(wrt))

cuqipy-1.3.0.post0.dev86/requirements.txt

@@ -0,0 +1,6 @@
+matplotlib
+numpy>=1.17.0
+scipy==1.12.0; python_version <= '3.9'
+scipy; python_version > '3.9'
+arviz
+tqdm

{cuqipy-1.3.0.post0.dev58 → cuqipy-1.3.0.post0.dev86}/tests/test_bayesian_inversion.py

@@ -2,7 +2,9 @@ from typing import Dict
 
 import pytest
 import numpy as np
+import scipy
 import sys
+from packaging import version
 
 from cuqi.testproblem import Deconvolution1D
 from cuqi.distribution import Gaussian, GMRF, CMRF, LMRF, Gamma
@@ -25,6 +27,14 @@ def test_TP_BayesianProblem_sample(copy_reference, TP_type, phantom, prior, Ns,
     # SKIP NUTS test if not windows (for now)
     if isinstance(prior, CMRF) and not sys.platform.startswith('win'):
         pytest.skip("NUTS(CMRF) regression test is not implemented for this platform")
+    elif (
+        isinstance(prior, RegularizedGaussian) 
+        or isinstance(prior, RegularizedGMRF)
+    ) and version.parse(scipy.__version__) >= version.parse('1.13.0'):
+        pytest.skip(
+            "Saved reference data is not consistent with scipy>=1.13.0 "
+            "(due to different default behaviour of scipy.optimize)"
+        )
 
     np.random.seed(19937)
 

{cuqipy-1.3.0.post0.dev58 → cuqipy-1.3.0.post0.dev86}/tests/test_distribution.py

@@ -203,7 +203,6 @@ def test_Uniform_logpdf(low, high, toeval, expected):
     UD = cuqi.distribution.Uniform(low, high)
     assert np.allclose(UD.logpdf(toeval), expected) 
 
-
 @pytest.mark.parametrize("low,high,expected",[(np.array([1, .5]), 
                                                np.array([2, 2.5]),
                                                np.array([[1.5507979 , 1.29090474, 1.89294695],
@@ -217,6 +216,19 @@ def test_Uniform_sample(low, high, expected):
     print(cuqi_samples)
     assert np.allclose(cuqi_samples.samples, expected) 
 
+def test_UnboundedUniform_logpdf_and_gradient():
+    x1 = cuqi.distribution.UnboundedUniform(geometry=1)
+    assert np.allclose(x1.logpdf(np.array([1])), 1.0)
+    assert np.allclose(x1.gradient(np.array([0])), np.array([0]))
+    x2 = cuqi.distribution.UnboundedUniform(geometry=cuqi.geometry.Discrete(2))
+    assert np.allclose(x2.logpdf(np.array([1, 2])), 1.0)
+    assert np.allclose(x2.gradient(np.array([0, 0])), np.array([0, 0]))
+
+def test_UnboundedUniform_sample():
+    x = cuqi.distribution.UnboundedUniform(geometry=2)
+    with pytest.raises(NotImplementedError, match="Cannot sample from UnboundedUniform distribution"):
+        x.sample()
+
 @pytest.mark.parametrize("distribution, kwargs",
                          [(cuqi.distribution.Uniform, 
                           {'low':np.array([2, 2.5, 3,5]),

{cuqipy-1.3.0.post0.dev58 → cuqipy-1.3.0.post0.dev86}/tests/test_distributions_shape.py

@@ -13,6 +13,7 @@ ignore_list = [
     "Posterior",
     "Distribution",
     "JointGaussianSqrtPrec",
+    "UnboundedUniform",
 ]
 
 # Define cases to skip (these are TODO)

{cuqipy-1.3.0.post0.dev58 → cuqipy-1.3.0.post0.dev86}/tests/test_implicit_priors.py

@@ -1,6 +1,8 @@
 import cuqi
 import numpy as np
+import scipy
 import pytest
+from packaging import version
 
 def test_RegularizedGaussian_default_init():
     """ Test that the implicit regularized Gaussian requires at least 1 regularization argument """
@@ -186,6 +188,7 @@ def test_RegularizedGaussian_double_preset():
     assert len(x.proximal[0]) == 2
     assert len(x.proximal[1]) == 2
 
+@pytest.mark.skipif(version.parse(scipy.__version__) < version.parse('1.12.0'), reason="isotonic_regression in not available in scipy < 1.12.0")
 def test_regression_increasing():
     """ Regression test for the increasing constraints in RegularizedGaussian"""
 

{cuqipy-1.3.0.post0.dev58 → cuqipy-1.3.0.post0.dev86}/tests/test_model.py

@@ -19,7 +19,7 @@ def test_LinearModel_getMatrix(seed):
     mat1 = model1.get_matrix() #Normal matrix
     mat2 = model2.get_matrix() #Sparse matrix (generated from functions)
 
-    assert np.allclose(mat1,mat2.A)
+    assert np.allclose(mat1,mat2.toarray())
 
 def test_initialize_model_dim():
     model1 = cuqi.model.Model(lambda x:x, range_geometry=4, domain_geometry=4)

cuqipy-1.3.0.post0.dev58/CUQIpy.egg-info/requires.txt

@@ -1,5 +0,0 @@
-matplotlib
-numpy>=1.17.0
-scipy<1.13
-arviz
-tqdm

cuqipy-1.3.0.post0.dev58/requirements.txt

@@ -1,5 +0,0 @@
-matplotlib
-numpy>=1.17.0
-scipy<1.13
-arviz
-tqdm