Apply pre-commit

Author: pymc-devs

benchmarks/benchmarks/benchmarks.py

@@ -14,11 +14,11 @@
 import time
 import timeit
 
-import pytensor
-import pytensor.tensor as at
 import arviz as az
 import numpy as np
 import pandas as pd
+import pytensor
+import pytensor.tensor as at
 
 import pymc as pm
 

pymc/__init__.py

@@ -47,7 +47,6 @@ def __set_compiler_flags():
 __set_compiler_flags()
 
 from pymc import _version, gp, ode, sampling
-from pymc.pytensorf import *
 from pymc.backends import *
 from pymc.blocking import *
 from pymc.data import *
@@ -68,6 +67,7 @@ def __set_compiler_flags():
 from pymc.model_graph import model_to_graphviz, model_to_networkx
 from pymc.plots import *
 from pymc.printing import *
+from pymc.pytensorf import *
 from pymc.sampling import *
 from pymc.smc import *
 from pymc.stats import *

pymc/backends/arviz.py

@@ -17,16 +17,16 @@
 
 import numpy as np
 
+from arviz import InferenceData, concat, rcParams
+from arviz.data.base import CoordSpec, DimSpec, dict_to_dataset, requires
 from pytensor.graph.basic import Constant
 from pytensor.tensor.sharedvar import SharedVariable
 from pytensor.tensor.subtensor import AdvancedIncSubtensor, AdvancedIncSubtensor1
-from arviz import InferenceData, concat, rcParams
-from arviz.data.base import CoordSpec, DimSpec, dict_to_dataset, requires
 
 import pymc
 
-from pymc.pytensorf import extract_obs_data
 from pymc.model import Model, modelcontext
+from pymc.pytensorf import extract_obs_data
 from pymc.util import get_default_varnames
 
 if TYPE_CHECKING:

pymc/backends/base.py

@@ -23,8 +23,8 @@
 from abc import ABC
 from typing import List, Sequence, Tuple, cast
 
-import pytensor.tensor as at
 import numpy as np
+import pytensor.tensor as at
 
 from pymc.backends.report import SamplerReport
 from pymc.model import modelcontext

pymc/data.py

@@ -22,9 +22,9 @@
 from copy import copy
 from typing import Any, Dict, List, Optional, Sequence, Tuple, Union, cast
 
+import numpy as np
 import pytensor
 import pytensor.tensor as at
-import numpy as np
 
 from pytensor.compile.sharedvalue import SharedVariable
 from pytensor.graph.basic import Apply

pymc/distributions/bound.py

@@ -13,21 +13,21 @@
 #   limitations under the License.
 import warnings
 
-import pytensor.tensor as at
 import numpy as np
+import pytensor.tensor as at
 
 from pytensor.tensor import as_tensor_variable
 from pytensor.tensor.random.op import RandomVariable
 from pytensor.tensor.var import TensorVariable
 
-from pymc.pytensorf import floatX, intX
 from pymc.distributions.continuous import BoundedContinuous, bounded_cont_transform
 from pymc.distributions.dist_math import check_parameters
 from pymc.distributions.distribution import Continuous, Discrete
 from pymc.distributions.logprob import ignore_logprob, logp
 from pymc.distributions.shape_utils import to_tuple
 from pymc.distributions.transforms import _default_transform
 from pymc.model import modelcontext
+from pymc.pytensorf import floatX, intX
 from pymc.util import check_dist_not_registered
 
 __all__ = ["Bound"]

pymc/distributions/censored.py

@@ -11,8 +11,8 @@
 #   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
-import pytensor.tensor as at
 import numpy as np
+import pytensor.tensor as at
 
 from pytensor.tensor import TensorVariable
 from pytensor.tensor.random.op import RandomVariable

pymc/distributions/continuous.py

@@ -24,9 +24,9 @@
 
 from typing import List, Optional, Union
 
+import numpy as np
 import pytensor
 import pytensor.tensor as at
-import numpy as np
 
 from pytensor.graph.basic import Apply, Variable
 from pytensor.graph.op import Op
@@ -76,7 +76,6 @@ def polyagamma_cdf(*args, **kwargs):
 from scipy.interpolate import InterpolatedUnivariateSpline
 from scipy.special import expit
 
-from pymc.pytensorf import floatX
 from pymc.distributions import transforms
 from pymc.distributions.dist_math import (
     SplineWrapper,
@@ -93,6 +92,7 @@ def polyagamma_cdf(*args, **kwargs):
 from pymc.distributions.shape_utils import rv_size_is_none
 from pymc.distributions.transforms import _default_transform
 from pymc.math import invlogit, logdiffexp, logit
+from pymc.pytensorf import floatX
 
 __all__ = [
     "Uniform",

pymc/distributions/discrete.py

@@ -13,8 +13,8 @@
 #   limitations under the License.
 import warnings
 
-import pytensor.tensor as at
 import numpy as np
+import pytensor.tensor as at
 
 from pytensor.tensor import TensorConstant
 from pytensor.tensor.random.basic import (
@@ -33,7 +33,6 @@
 
 import pymc as pm
 
-from pymc.pytensorf import floatX, intX
 from pymc.distributions.dist_math import (
     betaln,
     binomln,
@@ -49,6 +48,7 @@
 from pymc.distributions.mixture import Mixture
 from pymc.distributions.shape_utils import rv_size_is_none
 from pymc.math import sigmoid
+from pymc.pytensorf import floatX, intX
 from pymc.vartypes import continuous_types
 
 __all__ = [

pymc/distributions/dist_math.py

@@ -21,9 +21,9 @@
 
 from typing import Iterable
 
+import numpy as np
 import pytensor
 import pytensor.tensor as at
-import numpy as np
 import scipy.linalg
 import scipy.stats
 
@@ -35,9 +35,9 @@
 from pytensor.tensor.elemwise import Elemwise
 from pytensor.tensor.slinalg import Cholesky, SolveTriangular
 
-from pymc.pytensorf import floatX
 from pymc.distributions.shape_utils import to_tuple
 from pymc.logprob.utils import CheckParameterValue
+from pymc.pytensorf import floatX
 
 solve_lower = SolveTriangular(lower=True)
 solve_upper = SolveTriangular(lower=False)

pymc/distributions/distribution.py

@@ -35,7 +35,6 @@
 from pytensor.tensor.var import TensorVariable
 from typing_extensions import TypeAlias
 
-from pymc.pytensorf import convert_observed_data
 from pymc.distributions.shape_utils import (
     Dims,
     Shape,
@@ -54,6 +53,7 @@
 )
 from pymc.logprob.rewriting import logprob_rewrites_db
 from pymc.printing import str_for_dist
+from pymc.pytensorf import convert_observed_data
 from pymc.util import UNSET, _add_future_warning_tag
 from pymc.vartypes import string_types
 

pymc/distributions/logprob.py

@@ -15,19 +15,19 @@
 
 from typing import Dict, List, Sequence, Union
 
-import pytensor
 import numpy as np
+import pytensor
 
 from pytensor import tensor as at
 from pytensor.tensor.random.op import RandomVariable
 from pytensor.tensor.var import TensorVariable
 
-from pymc.pytensorf import floatX
 from pymc.logprob.abstract import assign_custom_measurable_outputs
 from pymc.logprob.abstract import logcdf as logcdf_logprob
 from pymc.logprob.abstract import logprob as logp_logprob
 from pymc.logprob.joint_logprob import factorized_joint_logprob
 from pymc.logprob.transforms import RVTransform, TransformValuesRewrite
+from pymc.pytensorf import floatX
 
 TOTAL_SIZE = Union[int, Sequence[int], None]
 

pymc/distributions/mixture.py

@@ -13,9 +13,9 @@
 #   limitations under the License.
 import warnings
 
+import numpy as np
 import pytensor
 import pytensor.tensor as at
-import numpy as np
 
 from pytensor.graph.basic import Node, equal_computations
 from pytensor.tensor import TensorVariable

pymc/distributions/multivariate.py

@@ -20,9 +20,9 @@
 from functools import reduce
 from typing import Optional
 
+import numpy as np
 import pytensor
 import pytensor.tensor as at
-import numpy as np
 import scipy
 
 from pytensor.graph.basic import Apply, Constant, Variable
@@ -40,7 +40,6 @@
 
 import pymc as pm
 
-from pymc.pytensorf import floatX, intX
 from pymc.distributions import transforms
 from pymc.distributions.continuous import BoundedContinuous, ChiSquared, Normal
 from pymc.distributions.dist_math import (
@@ -70,6 +69,7 @@
 from pymc.distributions.transforms import Interval, ZeroSumTransform, _default_transform
 from pymc.logprob.abstract import _logprob
 from pymc.math import kron_diag, kron_dot
+from pymc.pytensorf import floatX, intX
 from pymc.util import check_dist_not_registered
 
 __all__ = [

pymc/distributions/shape_utils.py

@@ -34,8 +34,8 @@
 from pytensor.tensor.var import TensorVariable
 from typing_extensions import TypeAlias
 
-from pymc.pytensorf import convert_observed_data
 from pymc.model import modelcontext
+from pymc.pytensorf import convert_observed_data
 
 __all__ = [
     "to_tuple",
@@ -48,8 +48,8 @@
     "change_dist_size",
 ]
 
-from pymc.pytensorf import PotentialShapeType
 from pymc.exceptions import ShapeError
+from pymc.pytensorf import PotentialShapeType
 from pymc.util import _add_future_warning_tag
 
 

pymc/distributions/simulator.py

@@ -14,18 +14,18 @@
 
 import logging
 
+import numpy as np
 import pytensor
 import pytensor.tensor as at
-import numpy as np
 
 from pytensor.graph.op import Apply, Op
 from pytensor.tensor.random.op import RandomVariable
 from pytensor.tensor.var import TensorVariable
 from scipy.spatial import cKDTree
 
-from pymc.pytensorf import floatX
 from pymc.distributions.distribution import Distribution, _moment
 from pymc.logprob.abstract import _logprob
+from pymc.pytensorf import floatX
 
 __all__ = ["Simulator"]
 
@@ -366,6 +366,8 @@ def make_node(self, epsilon, obs_data, sim_data):
 
         def perform(self, node, inputs, outputs):
             eps, obs_data, sim_data = inputs
-            outputs[0][0] = np.atleast_1d(fn(eps, obs_data, sim_data)).astype(pytensor.config.floatX)
+            outputs[0][0] = np.atleast_1d(fn(eps, obs_data, sim_data)).astype(
+                pytensor.config.floatX
+            )
 
     return Distance()

pymc/distributions/timeseries.py

@@ -17,15 +17,14 @@
 from abc import ABCMeta
 from typing import Callable, Optional
 
+import numpy as np
 import pytensor
 import pytensor.tensor as at
-import numpy as np
 
 from pytensor.graph.basic import Node, clone_replace
 from pytensor.tensor import TensorVariable
 from pytensor.tensor.random.op import RandomVariable
 
-from pymc.pytensorf import constant_fold, floatX, intX
 from pymc.distributions.continuous import Normal, get_tau_sigma
 from pymc.distributions.distribution import (
     Distribution,
@@ -43,6 +42,7 @@
 )
 from pymc.exceptions import NotConstantValueError
 from pymc.logprob.abstract import _logprob
+from pymc.pytensorf import constant_fold, floatX, intX
 from pymc.util import check_dist_not_registered
 
 __all__ = [

pymc/distributions/transforms.py

@@ -13,15 +13,14 @@
 #   limitations under the License.
 from functools import singledispatch
 
-import pytensor.tensor as at
 import numpy as np
-
-from pytensor.graph import Op
-from pytensor.tensor import TensorVariable
+import pytensor.tensor as at
 
 # ignore mypy error because it somehow considers that
 # "numpy.core.numeric has no attribute normalize_axis_tuple"
 from numpy.core.numeric import normalize_axis_tuple  # type: ignore
+from pytensor.graph import Op
+from pytensor.tensor import TensorVariable
 
 from pymc.logprob.transforms import (
     CircularTransform,

pymc/distributions/truncated.py

@@ -1,8 +1,8 @@
 from functools import singledispatch
 
+import numpy as np
 import pytensor
 import pytensor.tensor as at
-import numpy as np
 
 from pytensor import scan
 from pytensor.graph import Op

pymc/func_utils.py

@@ -13,8 +13,8 @@
 #   limitations under the License.
 from typing import Callable, Dict, Optional, Union
 
-import pytensor.tensor as aet
 import numpy as np
+import pytensor.tensor as aet
 
 from pytensor.gradient import NullTypeGradError
 from scipy import optimize

pymc/gp/cov.py

@@ -18,9 +18,9 @@
 from numbers import Number
 from operator import add, mul
 
+import numpy as np
 import pytensor
 import pytensor.tensor as at
-import numpy as np
 
 from pytensor.graph.basic import Variable
 from pytensor.tensor.sharedvar import TensorSharedVariable

pymc/gp/gp.py

@@ -14,8 +14,8 @@
 
 import warnings
 
-import pytensor.tensor as at
 import numpy as np
+import pytensor.tensor as at
 
 from pytensor.tensor.nlinalg import eigh