CLN run isort on source code files (#4239)

.pre-commit-config.yaml

@@ -13,6 +13,12 @@ repos:
       additional_dependencies: [isort==5.6.4]
     - id: nbqa-pyupgrade
       additional_dependencies: [pyupgrade==2.7.4]
+
+- repo: https://github.com/PyCQA/isort
+  rev: 5.6.4
+  hooks:
+    - id: isort
+      name: isort (python)
 - repo: https://github.com/asottile/pyupgrade
   rev: v2.7.4
   hooks:

benchmarks/benchmarks/benchmarks.py

@@ -17,10 +17,11 @@
 
 import numpy as np
 import pandas as pd
-import pymc3 as pm
 import theano
 import theano.tensor as tt
 
+import pymc3 as pm
+
 
 def glm_hierarchical_model(random_seed=123):
     """Sample glm hierarchical model to use in benchmarks"""

docs/source/conf.py

@@ -12,8 +12,8 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
 import os
+import sys
 
 import pymc3
 

docs/source/sphinxext/gallery_generator.py

@@ -4,11 +4,11 @@
 Modified from the seaborn project, which modified the mpld3 project.
 """
 import base64
+import glob
 import json
 import os
-import glob
-import shutil
 import runpy
+import shutil
 
 import matplotlib
 

pymc3/__init__.py

@@ -38,38 +38,33 @@ def __set_compiler_flags():
 
 __set_compiler_flags()
 
+from . import gp, ode, sampling
+from .backends import load_trace, save_trace
+from .backends.tracetab import *
 from .blocking import *
+from .data import *
 from .distributions import *
 from .distributions import transforms
+from .exceptions import *
 from .glm import *
-from . import gp
 from .math import (
+    expand_packed_triangular,
+    invlogit,
+    invprobit,
     logaddexp,
-    logsumexp,
     logit,
-    invlogit,
-    expand_packed_triangular,
+    logsumexp,
     probit,
-    invprobit,
 )
 from .model import *
 from .model_graph import model_to_graphviz
-from . import ode
-from .stats import *
+from .plots import *
 from .sampling import *
-from .step_methods import *
 from .smc import *
+from .stats import *
+from .step_methods import *
+from .tests import test
 from .theanof import *
 from .tuning import *
 from .variational import *
 from .vartypes import *
-from .exceptions import *
-from . import sampling
-
-from .backends.tracetab import *
-from .backends import save_trace, load_trace
-
-from .plots import *
-from .tests import test
-
-from .data import *

pymc3/backends/__init__.py

@@ -60,4 +60,4 @@
 Saved backends can be loaded using `arviz.from_netcdf`
 
 """
-from ..backends.ndarray import NDArray, save_trace, load_trace, point_list_to_multitrace
+from ..backends.ndarray import NDArray, load_trace, point_list_to_multitrace, save_trace

pymc3/backends/base.py

@@ -18,16 +18,17 @@
 """
 import itertools as itl
 import logging
-from typing import List
+import warnings
+
 from abc import ABC
+from typing import List
 
 import numpy as np
-import warnings
 import theano.tensor as tt
 
 from ..model import modelcontext
-from .report import SamplerReport, merge_reports
 from ..util import get_var_name
+from .report import SamplerReport, merge_reports
 
 logger = logging.getLogger("pymc3")
 

pymc3/backends/ndarray.py

@@ -20,14 +20,16 @@
 import json
 import os
 import shutil
-from typing import Optional, Dict, Any, List
 import warnings
 
+from typing import Any, Dict, List, Optional
+
 import numpy as np
+
 from pymc3.backends import base
 from pymc3.backends.base import MultiTrace
-from pymc3.model import Model, modelcontext
 from pymc3.exceptions import TraceDirectoryError
+from pymc3.model import Model, modelcontext
 
 
 def save_trace(trace: MultiTrace, directory: Optional[str] = None, overwrite=False) -> str:

pymc3/backends/report.py

@@ -12,15 +12,16 @@
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 
-import logging
-import enum
-from typing import Any, Optional
 import dataclasses
+import enum
+import logging
 
-from ..util import is_transformed_name, get_untransformed_name
+from typing import Any, Optional
 
 import arviz
 
+from ..util import get_untransformed_name, is_transformed_name
+
 logger = logging.getLogger("pymc3")
 
 

pymc3/backends/tracetab.py

@@ -15,9 +15,10 @@
 """Functions for converting traces into a table-like format
 """
 
+import warnings
+
 import numpy as np
 import pandas as pd
-import warnings
 
 from ..util import get_default_varnames
 

pymc3/blocking.py

@@ -17,9 +17,10 @@
 
 Classes for working with subsets of parameters.
 """
+import collections
 import copy
+
 import numpy as np
-import collections
 
 from .util import get_var_name
 

pymc3/data.py

@@ -13,17 +13,19 @@
 #   limitations under the License.
 
 import collections
-from copy import copy
 import io
 import os
 import pkgutil
-from typing import Dict, List, Any
+
+from copy import copy
+from typing import Any, Dict, List
 
 import numpy as np
 import pandas as pd
-import pymc3 as pm
-import theano.tensor as tt
 import theano
+import theano.tensor as tt
+
+import pymc3 as pm
 
 __all__ = [
     "get_data",