Bump PyTensor and support Numpy>2.0 and Python=3.13

Author: ricardoV94

.github/workflows/tests.yml

@@ -56,7 +56,7 @@ jobs:
       matrix:
         os: [ubuntu-20.04]
         floatx: [float64]
-        python-version: ["3.12"]
+        python-version: ["3.13"]
         test-subset:
           - |
             tests/test_util.py
@@ -230,7 +230,7 @@ jobs:
       matrix:
         os: [macos-latest]
         floatx: [float64]
-        python-version: ["3.12"]
+        python-version: ["3.13"]
         test-subset:
           - |
             tests/sampling/test_parallel.py
@@ -288,7 +288,7 @@ jobs:
       matrix:
         os: [ubuntu-20.04]
         floatx: [float64]
-        python-version: ["3.12"]
+        python-version: ["3.13"]
         test-subset:
           - tests/sampling/test_jax.py tests/sampling/test_mcmc_external.py
       fail-fast: false
@@ -334,7 +334,7 @@ jobs:
       matrix:
         os: [windows-latest]
         floatx: [float32]
-        python-version: ["3.12"]
+        python-version: ["3.13"]
         test-subset:
         - tests/sampling/test_mcmc.py tests/ode/test_ode.py tests/ode/test_utils.py tests/distributions/test_transform.py
       fail-fast: false

conda-envs/environment-dev.yml

@@ -12,7 +12,7 @@ dependencies:
 - numpy>=1.25.0
 - pandas>=0.24.0
 - pip
-- pytensor>=2.26.2,<2.28
+- pytensor>=2.28.1,<2.29
 - python-graphviz
 - networkx
 - scipy>=1.4.1
@@ -37,7 +37,7 @@ dependencies:
 - sphinxext-rediraffe
 - watermark
 - sphinx-remove-toctrees
-- mypy=1.5.1
+- mypy=1.15.0
 - types-cachetools
 - pip:
   - git+https://github.com/pymc-devs/pymc-sphinx-theme

conda-envs/environment-docs.yml

@@ -11,7 +11,7 @@ dependencies:
 - numpy>=1.25.0
 - pandas>=0.24.0
 - pip
-- pytensor>=2.26.2,<2.28
+- pytensor>=2.28.1,<2.29
 - python-graphviz
 - rich>=13.7.1
 - scipy>=1.4.1

conda-envs/environment-jax.yml

@@ -20,7 +20,7 @@ dependencies:
 - numpyro>=0.8.0
 - pandas>=0.24.0
 - pip
-- pytensor>=2.26.2,<2.28
+- pytensor>=2.28.1,<2.29
 - python-graphviz
 - networkx
 - rich>=13.7.1
@@ -33,7 +33,7 @@ dependencies:
 - pre-commit>=2.8.0
 - pytest-cov>=2.5
 - pytest>=3.0
-- mypy=1.5.1
+- mypy=1.15.0
 - types-cachetools
 - pip:
   - numdifftools>=0.9.40

conda-envs/environment-test.yml

@@ -14,7 +14,7 @@ dependencies:
 - pandas>=0.24.0
 - pip
 - polyagamma
-- pytensor>=2.26.2,<2.28
+- pytensor>=2.28.1,<2.29
 - python-graphviz
 - networkx
 - rich>=13.7.1
@@ -27,7 +27,7 @@ dependencies:
 - pre-commit>=2.8.0
 - pytest-cov>=2.5
 - pytest>=3.0
-- mypy=1.5.1
+- mypy=1.15.0
 - types-cachetools
 - pip:
   - numdifftools>=0.9.40

conda-envs/windows-environment-dev.yml

@@ -12,7 +12,7 @@ dependencies:
 - numpy>=1.25.0
 - pandas>=0.24.0
 - pip
-- pytensor>=2.26.2,<2.28
+- pytensor>=2.28.1,<2.29
 - python-graphviz
 - networkx
 - rich>=13.7.1
@@ -35,7 +35,7 @@ dependencies:
 - sphinx>=1.5
 - watermark
 - sphinx-remove-toctrees
-- mypy=1.5.1
+- mypy=1.15.0
 - types-cachetools
 - pip:
   - git+https://github.com/pymc-devs/pymc-sphinx-theme

conda-envs/windows-environment-test.yml

@@ -15,7 +15,7 @@ dependencies:
 - pandas>=0.24.0
 - pip
 - polyagamma
-- pytensor>=2.26.2,<2.28
+- pytensor>=2.28.1,<2.29
 - python-graphviz
 - networkx
 - rich>=13.7.1
@@ -28,7 +28,7 @@ dependencies:
 - pre-commit>=2.8.0
 - pytest-cov>=2.5
 - pytest>=3.0
-- mypy=1.5.1
+- mypy=1.15.0
 - types-cachetools
 - pip:
   - numdifftools>=0.9.40

requirements-dev.txt

@@ -8,15 +8,15 @@ git+https://github.com/pymc-devs/pymc-sphinx-theme
 ipython>=7.16
 jupyter-sphinx
 mcbackend>=0.4.0
-mypy==1.5.1
+mypy==1.15.0
 myst-nb<=1.0.0
 numdifftools>=0.9.40
 numpy>=1.25.0
 numpydoc
 pandas>=0.24.0
 polyagamma
 pre-commit>=2.8.0
-pytensor>=2.26.2,<2.28
+pytensor>=2.28.1,<2.29
 pytest-cov>=2.5
 pytest>=3.0
 rich>=13.7.1

requirements.txt

@@ -3,7 +3,7 @@ cachetools>=4.2.1
 cloudpickle
 numpy>=1.25.0
 pandas>=0.24.0
-pytensor>=2.26.1,<2.28
+pytensor>=2.28.1,<2.29
 rich>=13.7.1
 scipy>=1.4.1
 threadpoolctl>=3.1.0,<4.0.0

setup.py

@@ -33,6 +33,7 @@
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "License :: OSI Approved :: Apache Software License",
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering",

tests/distributions/test_continuous.py

@@ -2338,10 +2338,8 @@ class TestInverseGamma(BaseTestDistributionRandom):
     pymc_dist_params = {"alpha": 2.0, "beta": 5.0}
     expected_rv_op_params = {"alpha": 2.0, "beta": 5.0}
     reference_dist_params = {"a": 2.0, "scale": 5.0}
-    reference_dist = seeded_scipy_distribution_builder("invgamma")
     checks_to_run = [
         "check_pymc_params_match_rv_op",
-        "check_pymc_draws_match_reference",
     ]
 
 

tests/distributions/test_multivariate.py

@@ -27,6 +27,7 @@
 from pytensor.tensor import TensorVariable
 from pytensor.tensor.blockwise import Blockwise
 from pytensor.tensor.nlinalg import MatrixInverse
+from pytensor.tensor.random.basic import multivariate_normal
 from pytensor.tensor.random.utils import broadcast_params
 from pytensor.tensor.slinalg import Cholesky
 
@@ -1392,6 +1393,11 @@ def test_dirichlet_multinomial_support_point(self, a, n, size, expected):
 
 
 class TestMvNormalCov(BaseTestDistributionRandom):
+    def mvnormal_rng_fn(self, size, mean, cov, rng):
+        if isinstance(size, int):
+            size = (size,)
+        return multivariate_normal.rng_fn(rng, mean, cov, size=size)
+
     pymc_dist = pm.MvNormal
     pymc_dist_params = {
         "mu": np.array([1.0, 2.0]),
@@ -1407,7 +1413,8 @@ class TestMvNormalCov(BaseTestDistributionRandom):
         "mean": np.array([1.0, 2.0]),
         "cov": np.array([[2.0, 0.0], [0.0, 3.5]]),
     }
-    reference_dist = seeded_numpy_distribution_builder("multivariate_normal")
+    reference_dist = lambda self: ft.partial(self.mvnormal_rng_fn, rng=self.get_random_state())  # noqa: E731
+
     checks_to_run = [
         "check_pymc_params_match_rv_op",
         "check_pymc_draws_match_reference",
@@ -1531,12 +1538,12 @@ class TestZeroSumNormal:
     def assert_zerosum_axes(self, random_samples, axes_to_check, check_zerosum_axes=True):
         if check_zerosum_axes:
             for ax in axes_to_check:
-                assert np.isclose(random_samples.mean(axis=ax), 0).all(), (
+                assert np.allclose(random_samples.mean(axis=ax), 0), (
                     f"{ax} is a zerosum_axis but is not summing to 0 across all samples."
                 )
         else:
             for ax in axes_to_check:
-                assert not np.isclose(random_samples.mean(axis=ax), 0).all(), (
+                assert not np.allclose(random_samples.mean(axis=ax), 0), (
                     f"{ax} is not a zerosum_axis, but is nonetheless summing to 0 across all samples."
                 )
 
@@ -1775,7 +1782,9 @@ def test_batched_sigma(self):
 
 class TestMvStudentTCov(BaseTestDistributionRandom):
     def mvstudentt_rng_fn(self, size, nu, mu, scale, rng):
-        mv_samples = rng.multivariate_normal(np.zeros_like(mu), scale, size=size)
+        if isinstance(size, int):
+            size = (size,)
+        mv_samples = multivariate_normal.rng_fn(rng, np.zeros_like(mu), scale, size=size)
         chi2_samples = rng.chisquare(nu, size=size)
         return (mv_samples / np.sqrt(chi2_samples[:, None] / nu)) + mu
 
@@ -2111,9 +2120,11 @@ def check_random_variable_prior(self):
 
 class TestKroneckerNormal(BaseTestDistributionRandom):
     def kronecker_rng_fn(self, size, mu, covs=None, sigma=None, rng=None):
-        cov = pm.math.kronecker(covs[0], covs[1]).eval()
+        if isinstance(size, int):
+            size = (size,)
+        cov = np.kron(covs[0], covs[1])
         cov += sigma**2 * np.identity(cov.shape[0])
-        return st.multivariate_normal.rvs(mean=mu, cov=cov, size=size, random_state=rng)
+        return multivariate_normal.rng_fn(rng, mean=mu, cov=cov, size=size)
 
     pymc_dist = pm.KroneckerNormal