Merge branch 'main' into doc/remove-mutabledata

Author: williambdean

.github/workflows/mypy.yml

@@ -19,7 +19,7 @@ jobs:
         with:
           environment-file: conda-envs/environment-test.yml
           create-args: >-
-            python=3.10
+            python=3.11
           environment-name: pymc-test
           init-shell: bash
           cache-environment: true

.github/workflows/tests.yml

@@ -146,7 +146,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     env:
       TEST_SUBSET: ${{ matrix.test-subset }}
-      PYTENSOR_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=native'
+      PYTENSOR_FLAGS: floatX=${{ matrix.floatx }}
     defaults:
       run:
         shell: bash -leo pipefail {0}
@@ -185,7 +185,7 @@ jobs:
       matrix:
         os: [windows-latest]
         floatx: [float64]
-        python-version: ["3.10"]
+        python-version: ["3.11"]
         test-subset:
           - tests/variational/test_approximations.py tests/variational/test_callbacks.py tests/variational/test_inference.py tests/variational/test_opvi.py tests/test_initial_point.py
           - tests/model/test_core.py tests/sampling/test_mcmc.py
@@ -196,7 +196,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     env:
       TEST_SUBSET: ${{ matrix.test-subset }}
-      PYTENSOR_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=core2'
+      PYTENSOR_FLAGS: floatX=${{ matrix.floatx }}
     defaults:
       run:
         shell: cmd /C call {0}
@@ -256,7 +256,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     env:
       TEST_SUBSET: ${{ matrix.test-subset }}
-      PYTENSOR_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=native'
+      PYTENSOR_FLAGS: floatX=${{ matrix.floatx }}
     defaults:
       run:
         shell: bash -leo pipefail {0}
@@ -306,7 +306,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     env:
       TEST_SUBSET: ${{ matrix.test-subset }}
-      PYTENSOR_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=native'
+      PYTENSOR_FLAGS: floatX=${{ matrix.floatx }}
     defaults:
       run:
         shell: bash -leo pipefail {0}
@@ -352,7 +352,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     env:
       TEST_SUBSET: ${{ matrix.test-subset }}
-      PYTENSOR_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=core2'
+      PYTENSOR_FLAGS: floatX=${{ matrix.floatx }}
     defaults:
       run:
         shell: cmd /C call {0}

conda-envs/environment-alternative-backends.yml

@@ -22,7 +22,7 @@ dependencies:
 - numpyro>=0.8.0
 - pandas>=0.24.0
 - pip
-- pytensor>=2.32.0,<2.33
+- pytensor>=2.35.0,<2.36
 - python-graphviz
 - networkx
 - rich>=13.7.1

conda-envs/environment-dev.yml

@@ -12,7 +12,7 @@ dependencies:
 - numpy>=1.25.0
 - pandas>=0.24.0
 - pip
-- pytensor>=2.32.0,<2.33
+- pytensor>=2.35.0,<2.36
 - python-graphviz
 - networkx
 - scipy>=1.4.1

conda-envs/environment-docs.yml

@@ -11,7 +11,7 @@ dependencies:
 - numpy>=1.25.0
 - pandas>=0.24.0
 - pip
-- pytensor>=2.32.0,<2.33
+- pytensor>=2.35.0,<2.36
 - python-graphviz
 - rich>=13.7.1
 - scipy>=1.4.1

conda-envs/environment-test.yml

@@ -14,7 +14,7 @@ dependencies:
 - pandas>=0.24.0
 - pip
 - polyagamma
-- pytensor>=2.32.0,<2.33
+- pytensor>=2.35.0,<2.36
 - python-graphviz
 - networkx
 - rich>=13.7.1

conda-envs/windows-environment-dev.yml

@@ -12,7 +12,7 @@ dependencies:
 - numpy>=1.25.0
 - pandas>=0.24.0
 - pip
-- pytensor>=2.32.0,<2.33
+- pytensor>=2.35.0,<2.36
 - python-graphviz
 - networkx
 - rich>=13.7.1

conda-envs/windows-environment-test.yml

@@ -15,7 +15,7 @@ dependencies:
 - pandas>=0.24.0
 - pip
 - polyagamma
-- pytensor>=2.32.0,<2.33
+- pytensor>=2.35.0,<2.36
 - python-graphviz
 - networkx
 - rich>=13.7.1

pymc/distributions/custom.py

@@ -18,9 +18,9 @@
 
 from pytensor import Variable, clone_replace
 from pytensor import tensor as pt
-from pytensor.graph.basic import io_toposort
 from pytensor.graph.features import ReplaceValidate
 from pytensor.graph.rewriting.basic import GraphRewriter
+from pytensor.graph.traversal import io_toposort
 from pytensor.scan.op import Scan
 from pytensor.tensor import TensorVariable, as_tensor_variable
 from pytensor.tensor.random.op import RandomVariable

pymc/distributions/shape_utils.py

@@ -230,17 +230,17 @@ def rv_size_is_none(size: TensorVariable | Constant | None) -> bool:
 
 
 @singledispatch
-def _change_dist_size(op: Op, dist: TensorVariable, new_size, expand):
+def _change_dist_size(op: Op, dist: Variable, new_size, expand):
     raise NotImplementedError(
         f"Variable {dist} of type {op} has no _change_dist_size implementation."
     )
 
 
 def change_dist_size(
-    dist: TensorVariable,
+    dist: Variable,
     new_size: PotentialShapeType,
     expand: bool = False,
-) -> TensorVariable:
+) -> Variable:
     """Change or expand the size of a Distribution.
 
     Parameters