Upgrade Aesara and Aeppl dependencies

Author: michaelosthege

.pre-commit-config.yaml

@@ -26,8 +26,8 @@ repos:
       - types-filelock
       - types-setuptools
       - arviz
-      - aesara==2.5.1
-      - aeppl==0.0.27
+      - aesara==2.6.2
+      - aeppl==0.0.28
       always_run: true
       require_serial: true
       pass_filenames: false

conda-envs/environment-dev-py37.yml

@@ -4,8 +4,8 @@ channels:
 - conda-forge
 - defaults
 dependencies:
-- aeppl=0.0.27
-- aesara=2.5.1
+- aeppl=0.0.28
+- aesara=2.6.2
 - arviz>=0.12.0
 - blas
 - cachetools>=4.2.1

conda-envs/environment-dev-py38.yml

@@ -4,8 +4,8 @@ channels:
 - conda-forge
 - defaults
 dependencies:
-- aeppl=0.0.27
-- aesara=2.5.1
+- aeppl=0.0.28
+- aesara=2.6.2
 - arviz>=0.12.0
 - blas
 - cachetools>=4.2.1

conda-envs/environment-dev-py39.yml

@@ -4,8 +4,8 @@ channels:
 - conda-forge
 - defaults
 dependencies:
-- aeppl=0.0.27
-- aesara=2.5.1
+- aeppl=0.0.28
+- aesara=2.6.2
 - arviz>=0.12.0
 - blas
 - cachetools>=4.2.1

conda-envs/environment-test-py37.yml

@@ -4,8 +4,8 @@ channels:
 - conda-forge
 - defaults
 dependencies:
-- aeppl=0.0.27
-- aesara=2.5.1
+- aeppl=0.0.28
+- aesara=2.6.2
 - arviz>=0.12.0
 - blas
 - cachetools>=4.2.1

conda-envs/environment-test-py38.yml

@@ -4,8 +4,8 @@ channels:
 - conda-forge
 - defaults
 dependencies:
-- aeppl=0.0.27
-- aesara=2.5.1
+- aeppl=0.0.28
+- aesara=2.6.2
 - arviz>=0.12.0
 - blas
 - cachetools>=4.2.1

conda-envs/environment-test-py39.yml

@@ -4,8 +4,8 @@ channels:
 - conda-forge
 - defaults
 dependencies:
-- aeppl=0.0.27
-- aesara=2.5.1
+- aeppl=0.0.28
+- aesara=2.6.2
 - arviz>=0.12.0
 - blas
 - cachetools>=4.2.1

conda-envs/windows-environment-dev-py38.yml

@@ -4,8 +4,8 @@ channels:
 - defaults
 dependencies:
  # base dependencies (see install guide for Windows)
-- aeppl=0.0.27
-- aesara=2.5.1
+- aeppl=0.0.28
+- aesara=2.6.2
 - arviz>=0.12.0
 - blas
 - cachetools>=4.2.1

conda-envs/windows-environment-test-py38.yml

@@ -4,8 +4,8 @@ channels:
 - defaults
 dependencies:
  # base dependencies (see install guide for Windows)
-- aeppl=0.0.27
-- aesara=2.5.1
+- aeppl=0.0.28
+- aesara=2.6.2
 - arviz>=0.12.0
 - blas
 - cachetools>=4.2.1

pymc/distributions/mixture.py

@@ -274,10 +274,7 @@ def rv_op(cls, weights, *components, size=None, rngs=None):
 
         # Index components and squeeze mixture dimension
         mix_out_ = at.take_along_axis(stacked_components_, mix_indexes_padded_, axis=mix_axis)
-        # There is a Aesara bug in squeeze with negative axis
-        # https://github.com/aesara-devs/aesara/issues/830
-        # this is equivalent to np.squeeze(mix_out_, axis=mix_axis)
-        mix_out_ = at.squeeze(mix_out_, axis=mix_out_.ndim + mix_axis)
+        mix_out_ = at.squeeze(mix_out_, axis=mix_axis)
 
         # Output mix_indexes rng update so that it can be updated in place
         mix_indexes_rng_next_ = mix_indexes_.owner.outputs[0]
@@ -458,7 +455,7 @@ def marginal_mixture_moment(op, rv, rng, weights, *components):
     transforms.LogExpM1,
     transforms.LogOddsTransform,
     transforms.Ordered,
-    transforms.Simplex,
+    transforms.SimplexTransform,
     transforms.SumTo1,
 )
 

pymc/distributions/transforms.py

@@ -22,7 +22,7 @@
     LogOddsTransform,
     LogTransform,
     RVTransform,
-    Simplex,
+    SimplexTransform,
 )
 from aesara.graph import Op
 from aesara.tensor import TensorVariable
@@ -174,9 +174,9 @@ def log_jac_det(self, value, *inputs):
         return det
 
 
-simplex = Simplex()
+simplex = SimplexTransform()
 simplex.__doc__ = """
-Instantiation of :class:`aeppl.transforms.Simplex`
+Instantiation of :class:`aeppl.transforms.SimplexTransform`
 for use in the ``transform`` argument of a random variable."""
 
 logodds = LogOddsTransform()

pymc/tests/test_mixture.py

@@ -19,8 +19,7 @@
 import pytest
 import scipy.stats as st
 
-from aeppl.transforms import IntervalTransform, LogTransform
-from aeppl.transforms import Simplex as SimplexTransform
+from aeppl.transforms import IntervalTransform, LogTransform, SimplexTransform
 from aesara import tensor as at
 from aesara.tensor import TensorVariable
 from aesara.tensor.random.op import RandomVariable

requirements-dev.txt

@@ -1,8 +1,8 @@
 # This file is auto-generated by scripts/generate_pip_deps_from_conda.py, do not modify.
 # See that file for comments about the need/usage of each dependency.
 
-aeppl==0.0.27
-aesara==2.5.1
+aeppl==0.0.28
+aesara==2.6.2
 arviz>=0.12.0
 cachetools>=4.2.1
 cloudpickle

requirements.txt

@@ -1,5 +1,5 @@
-aeppl==0.0.27
-aesara==2.5.1
+aeppl==0.0.28
+aesara==2.6.2
 arviz>=0.12.0
 cachetools>=4.2.1
 cloudpickle