Restore numpy compatibility

.vscode/launch.json

@@ -0,0 +1,17 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Test: Parameterized Tests",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "parameterized_tests.py",
+            "console": "integratedTerminal",
+            "cwd": "${workspaceFolder}/paramz/tests",
+            "justMyCode": false
+        }
+    ]
+}

paramz/core/indexable.py

@@ -158,7 +158,7 @@ def _raveled_index_for(self, param):
         """
         from ..param import ParamConcatenation
         if isinstance(param, ParamConcatenation):
-            return np.hstack((self._raveled_index_for(p) for p in param.params))
+            return np.hstack([self._raveled_index_for(p) for p in param.params])
         return param._raveled_index() + self._offset_for(param)
 
     def _raveled_index_for_transformed(self, param):

paramz/core/parameter_core.py

@@ -38,6 +38,8 @@
 import re
 import logging
 
+from paramz.util import _set_mem_addr
+
 from ..transformations import __fixed__, FIXED
 from .constrainable import Constrainable
 from .nameable import adjust_name_for_printing
@@ -287,8 +289,8 @@ def _propagate_param_grad(self, parray, garray):
             self.param_array[pislice] = pi.param_array.flat  # , requirements=['C', 'W']).flat
             self.gradient_full[pislice] = pi.gradient_full.flat  # , requirements=['C', 'W']).flat
 
-            pi.param_array.data = parray[pislice].data
-            pi.gradient_full.data = garray[pislice].data
+            _set_mem_addr(pi.param_array, parray[pislice])
+            _set_mem_addr(pi.gradient_full, garray[pislice])
 
             pi._propagate_param_grad(parray[pislice], garray[pislice])
             pi_old_size += pi.size

paramz/model.py

@@ -370,9 +370,9 @@ def _checkgrad(self, target_param=None, verbose=False, step=1e-6, tolerance=1e-3
             for xind in zip(transformed_index):
                 xx = x.copy()
                 xx[xind] += step
-                f1 = float(self._objective(xx))
+                f1 = self._objective(xx)
                 xx[xind] -= 2.*step
-                f2 = float(self._objective(xx))
+                f2 = self._objective(xx)
                 #Avoid divide by zero, if any of the values are above 1e-15, otherwise both values are essentiall
                 #the same
                 if f1 > 1e-15 or f1 < -1e-15 or f2 > 1e-15 or f2 < -1e-15:
@@ -396,11 +396,11 @@ def _checkgrad(self, target_param=None, verbose=False, step=1e-6, tolerance=1e-3
                 if df_unstable:  # pragma: no cover
                     formatted_name = "\033[94m {0} \033[0m".format(names[xind])
 
-                r = '%.6f' % float(ratio)
-                d = '%.6f' % float(difference)
+                r = '%.6f' % ratio
+                d = '%.6f' % difference
                 g = '%.6f' % gradient[xind]
-                ng = '%.6f' % float(numerical_gradient)
-                df = '%1.e' % float(df_ratio)
+                ng = '%.6f' % numerical_gradient
+                df = '%1.e' % df_ratio
                 grad_string = "{0:<{c0}}|{1:^{c1}}|{2:^{c2}}|{3:^{c3}}|{4:^{c4}}|{5:^{c5}}".format(formatted_name, r, d, g, ng, df, c0=cols[0] + 9, c1=cols[1], c2=cols[2], c3=cols[3], c4=cols[4], c5=cols[5])
                 print(grad_string)
 

paramz/parameterized.py

@@ -28,7 +28,10 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #===============================================================================
 
-import numpy; np = numpy
+import ctypes
+import numpy
+
+from paramz.util import _set_mem_addr; np = numpy
 from re import compile
 try:
     from re import _pattern_type
@@ -268,8 +271,8 @@ def _connect_parameters(self, ignore_added_names=False):
             self.param_array[pslice] = p.param_array.flat  # , requirements=['C', 'W']).ravel(order='C')
             self.gradient_full[pslice] = p.gradient_full.flat  # , requirements=['C', 'W']).ravel(order='C')
 
-            p.param_array.data = self.param_array[pslice].data
-            p.gradient_full.data = self.gradient_full[pslice].data
+            _set_mem_addr(p.param_array, self.param_array[pslice])
+            _set_mem_addr(p.gradient_full, self.gradient_full[pslice])
 
             self._param_slices_.append(pslice)
 

paramz/tests/model_tests.py

@@ -268,7 +268,7 @@ def test_constraints_set_direct(self):
         #self.assertSequenceEqual(cache_str, str(self.testmodel), None, str)
 
     def test_updates(self):
-        val = float(self.testmodel.objective_function())
+        val = self.testmodel.objective_function()
         self.testmodel.update_toggle()
         self.testmodel.kern.randomize(np.random.normal, loc=1, scale=.2)
         self.testmodel.likelihood.randomize()
@@ -284,7 +284,7 @@ def test_set_gradients(self):
 
     def test_fixing_optimize(self):
         self.testmodel.kern.lengthscale.fix()
-        val = float(self.testmodel.kern.lengthscale)
+        val = self.testmodel.kern.lengthscale
         self.testmodel.randomize()
         self.assertEqual(val, self.testmodel.kern.lengthscale)
         self.testmodel.optimize(max_iters=2)
@@ -299,7 +299,7 @@ def test_regular_expression_misc(self):
         np.testing.assert_((self.testmodel[''][:2] == [10,10]).all())
 
         self.testmodel.kern.lengthscale.fix()
-        val = float(self.testmodel.kern.lengthscale)
+        val = self.testmodel.kern.lengthscale
         self.testmodel.randomize()
         self.assertEqual(val, self.testmodel.kern.lengthscale)
 
@@ -354,7 +354,7 @@ def test_fix_unfix_constraints(self):
 
 
         # Assert fixing works and does not randomize the - say - lengthscale:
-        val = float(self.testmodel.kern.lengthscale)
+        val = self.testmodel.kern.lengthscale
         self.testmodel.randomize()
         self.assertEqual(val, self.testmodel.kern.lengthscale)
 

paramz/tests/parameterized_tests.py

@@ -131,8 +131,8 @@ def test_num_params(self):
         self.assertEqual(self.test1.add.rbf.num_params, 2)
 
     def test_index_operations(self):
-        self.assertRaisesRegexp(AttributeError, "An index operation with the name constraints was already taken", self.test1.add_index_operation, 'constraints', None)
-        self.assertRaisesRegexp(AttributeError, "No index operation with the name", self.test1.remove_index_operation, 'not_an_index_operation')
+        self.assertRaisesRegex(AttributeError, "An index operation with the name constraints was already taken", self.test1.add_index_operation, 'constraints', None)
+        self.assertRaisesRegex(AttributeError, "No index operation with the name", self.test1.remove_index_operation, 'not_an_index_operation')
 
     def test_names(self):
         self.assertSequenceEqual(self.test1.parameter_names(adjust_for_printing=True), self.test1.parameter_names(adjust_for_printing=False))
@@ -182,7 +182,7 @@ def max_recursion():
             from builtins import RecursionError as RE
         except:
             RE = RuntimeError
-        self.assertRaisesRegexp(RE, "aximum recursion depth", max_recursion)
+        self.assertRaisesRegex(RE, "aximum recursion depth", max_recursion)
         # Recursion limit not reached if kernels are named individually:
         sys.setrecursionlimit(1000)
         p = Parameterized('add')
@@ -239,7 +239,7 @@ def test_remove_parameter_param_array_grad_array(self):
         self.assertListEqual(self.test1.kern.param_array.tolist(), val[:2].tolist())
 
     def test_add_parameter_already_in_hirarchy(self):
-        self.assertRaisesRegexp(HierarchyError, "You cannot add a parameter twice into the hierarchy", self.test1.link_parameter, self.white.parameters[0])
+        self.assertRaisesRegex(HierarchyError, "You cannot add a parameter twice into the hierarchy", self.test1.link_parameter, self.white.parameters[0])
 
     def test_default_constraints(self):
         self.assertIs(self.rbf.variance.constraints._param_index_ops, self.rbf.constraints._param_index_ops)
@@ -274,7 +274,7 @@ def test_constraints_views(self):
 
     def test_fixing_randomize(self):
         self.white.fix(warning=True)
-        val = float(self.white.variance)
+        val = self.white.variance
         self.test1.randomize()
         self.assertEqual(val, self.white.variance)
 
@@ -286,7 +286,7 @@ def test_randomize(self):
 
     def test_fixing_randomize_parameter_handling(self):
         self.rbf.fix(0.1, warning=True)
-        val = float(self.rbf.variance)
+        val = self.rbf.variance
         self.test1.kern.randomize()
         self.assertEqual(val, self.rbf.variance)
 
@@ -309,4 +309,7 @@ def test_printing(self):
 
 if __name__ == "__main__":
     #import sys;sys.argv = ['', 'Test.test_add_parameter']
-    unittest.main()
+    # unittest.main()
+    obj = ParameterizedTest()
+    obj.setUp()
+    obj.test_unfixed_param_array()

paramz/util.py

@@ -27,6 +27,7 @@
 # OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #===============================================================================
+import warnings
 
 def _inherit_doc(fromclass, done_classes = None):
     inherited = ''
@@ -44,4 +45,23 @@ def _inherit_doc(fromclass, done_classes = None):
                 pass
         inherited += _inherit_doc(c, done_classes=done_classes)        
 
-    return inherited
+    return inherited
+
+
+def _set_mem_addr(dest, src) -> None:
+    """
+    This function serves to replace the `.data` getter/setter that existed in
+    `numpy<2` and got removed in `numpy>=2`.
+    The original behavior was setting the memory address of dest to that of src.
+    However, directly setting the memory address of a numpy array to the data of
+    another one seems to be unwanted in `numpy>=2`, which is causing some major 
+    problems here.
+    """
+    # with warnings.catch_warnings():
+    #     warnings.simplefilter("ignore", DeprecationWarning)
+
+    # original
+    # dest.data = src.data
+
+    # take 1
+    dest.data = memoryview(src)

pyproject.toml

@@ -0,0 +1,55 @@
+[project]
+name = "paramz"
+dynamic = ["version", "readme"]
+authors = [
+    {name = "Max Zwiessele", email = "ibinbei@gmail.com"},
+]
+description = "The Parameterization Framework"
+license = {text = "BSD 3-clause"}
+keywords = ["machine-learning", "gaussian-processes", "kernels"]
+classifiers = [
+    "License :: OSI Approved :: BSD License",
+    "Natural Language :: English",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Python :: 2.7",
+    "Programming Language :: Python :: 3.5",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+]
+
+dependencies = [
+    "numpy>=1.7",
+    "scipy",
+    "six",
+    "decorator>=4.0.10",
+]
+
+[project.optional-dependencies]
+docs = ["sphinx"]
+notebook = [
+    "jupyter_client >= 4.0.6",
+    "ipywidgets >= 4.0.3",
+    "ipykernel >= 4.1.0",
+    "notebook >= 4.0.5",
+]
+optimization = ["climin"]
+
+[project.urls]
+Homepage = "https://github.com/sods/paramz"
+
+[tool.setuptools]
+packages = ["paramz", "paramz.core", "paramz.optimization", "paramz.examples", "paramz.tests"]
+
+[tool.setuptools.dynamic]
+version = {attr = "paramz.__version__.__version__"}
+readme = {file = ["README.rst"]}
+
+[build-system]
+requires = ["setuptools>=42", "wheel"]
+build-backend = "setuptools.build_meta"

pytest.ini

@@ -0,0 +1,3 @@
+[pytest]
+testpaths = paramz/tests
+python_files = *_tests.py