Add isort to pre commit hooks and CI (#780)

* isort config

* isort

* set black profile

* black isort

* removed double set of black profile

* hike required python to 3.9

* fix isort MPI

* fix circular import

* fix imports after merge

* revert merge trigger

* fix isort

.github/workflows/isort.yml

@@ -0,0 +1,19 @@
+name: Run isort
+on:
+  - push
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - name: Install apt dependencies
+        run: |
+          sudo apt update
+          # Install `libopenmpi` for MPI
+          sudo apt install openmpi-bin libopenmpi-dev
+      - run: pip install -e .[parallel]
+      - uses: isort/isort-action@master

.pre-commit-config.yaml

@@ -1,6 +1,11 @@
 repos:
-  - repo: https://github.com/psf/black
+  - repo: https://github.com/psf/black-pre-commit-mirror
     rev: 23.11.0
     hooks:
       - id: black
-        language_version: python3
+        language_version: python3.11
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort (python)

bsb/_encoding.py

@@ -1,5 +1,7 @@
-import numpy as np
 import itertools
+
+import numpy as np
+
 from ._util import obj_str_insert
 
 

bsb/_util.py

@@ -1,13 +1,12 @@
+import contextlib as _ctxlib
+import functools
 import itertools as _it
 import os as _os
 import sys as _sys
-import contextlib as _ctxlib
 import typing
 
 import numpy as np
-
 import numpy as _np
-import functools
 
 ichain = _it.chain.from_iterable
 

bsb/cell_types.py

@@ -4,9 +4,9 @@
 import typing
 
 from . import config
+from ._util import obj_str_insert
 from .config import types
 from .placement.indicator import PlacementIndications
-from ._util import obj_str_insert
 
 if typing.TYPE_CHECKING:
     from .core import Scaffold

bsb/cli/__init__.py

@@ -1,9 +1,10 @@
+import builtins
+import inspect
+import sys
+
 from .._contexts import get_cli_context, reset_cli_context
-from .commands import load_root_command
 from ..exceptions import *
-import sys
-import inspect
-import builtins
+from .commands import load_root_command
 
 
 def handle_cli():

bsb/cli/commands/__init__.py

@@ -7,6 +7,7 @@
 BSB.
 """
 import argparse
+
 from ...exceptions import CommandError
 from ...reporting import report
 

bsb/cli/commands/_commands.py

@@ -1,17 +1,18 @@
 """
 Contains builtin commands.
 """
+import itertools
 from uuid import uuid4
 
-from . import BaseCommand
-from ...option import BsbOption
+import errr
+
 from ..._options import ConfigOption
-from ...core import from_storage, Scaffold
-from ...storage import open_storage
 from ...config import from_file
+from ...core import Scaffold, from_storage
 from ...exceptions import NodeNotFoundError
-import itertools
-import errr
+from ...option import BsbOption
+from ...storage import open_storage
+from . import BaseCommand
 
 
 class XScale(BsbOption, name="x", cli=("x",), env=("BSB_CONFIG_NETWORK_X",)):
@@ -227,6 +228,7 @@ class CacheCommand(BaseCommand, name="cache"):  # pragma: nocover
     def handler(self, context):
         import shutil
         from datetime import datetime
+
         from ...storage._util import _cache_path
 
         if context.clear:

bsb/cli/commands/_projects.py

@@ -1,9 +1,11 @@
-from . import BaseCommand
-from ...reporting import report
-from ... import config
 import pathlib
+
 import toml
 
+from ... import config
+from ...reporting import report
+from . import BaseCommand
+
 
 class ProjectNewCommand(BaseCommand, name="new"):
     def get_options(self):

bsb/config/__init__.py

@@ -6,42 +6,46 @@
 config.attr/dict/list/ref/reflist`` to populate your classes with powerful attributes.
 """
 
-import os
-import sys
+import builtins
 import glob
 import itertools
+import os
+import sys
+import traceback
 import typing
 from importlib.machinery import ModuleSpec
 from shutil import copy2 as copy_file
-import builtins
-import traceback
 
+from .. import plugins
+from .._util import ichain
+from ..exceptions import ConfigTemplateNotFoundError, ParserError, PluginError
+from . import parsers
 from ._attrs import (
+    ConfigurationAttribute,
     attr,
-    list,
+    catch_all,
     dict,
+    dynamic,
     file,
+    list,
     node,
-    root,
-    dynamic,
+    pluggable,
+    property,
+    provide,
     ref,
     reflist,
+    root,
     slot,
-    property,
-    provide,
     unset,
-    pluggable,
-    catch_all,
-    ConfigurationAttribute,
 )
-from .._util import ichain
-from ._make import walk_node_attributes, walk_nodes, compose_nodes, get_config_attributes
-from ._hooks import on, before, after, run_hook, has_hook
 from ._distributions import Distribution
-from .. import plugins
-from ..exceptions import ConfigTemplateNotFoundError, ParserError, PluginError
-from . import parsers
-
+from ._hooks import after, before, has_hook, on, run_hook
+from ._make import (
+    compose_nodes,
+    get_config_attributes,
+    walk_node_attributes,
+    walk_nodes,
+)
 
 _path = __path__
 ConfigurationAttribute.__module__ = __name__
@@ -56,7 +60,7 @@
 # ConfigurationModule should not inherit from `ModuleType`, otherwise Sphinx doesn't
 # document all the properties.
 class ConfigurationModule:
-    from . import types, refs
+    from . import refs, types
 
     def __init__(self, name):
         self.__name__ = name

bsb/config/_attrs.py

@@ -1,34 +1,34 @@
 """
     An attrs-inspired class annotation system, but my A stands for amateuristic.
 """
+import builtins
 import traceback
 
 import errr
 
+from ..exceptions import (
+    BootError,
+    CastError,
+    CfgReferenceError,
+    NoReferenceAttributeSignal,
+    RequirementError,
+)
+from ..services import MPI
+from ._compile import _wrap_reserved
 from ._hooks import run_hook
 from ._make import (
     MISSING,
+    _resolve_references,
     compile_class,
-    compile_postnew,
-    compile_new,
     compile_isc,
-    make_get_node_name,
+    compile_new,
+    compile_postnew,
     make_dictable,
+    make_get_node_name,
     make_tree,
-    wrap_root_postnew,
     walk_nodes,
-    _resolve_references,
-)
-from ._compile import _wrap_reserved
-from ..exceptions import (
-    RequirementError,
-    NoReferenceAttributeSignal,
-    CastError,
-    CfgReferenceError,
-    BootError,
+    wrap_root_postnew,
 )
-from ..services import MPI
-import builtins
 
 
 def root(root_cls):

bsb/config/_compile.py

@@ -1,7 +1,6 @@
 import functools
 from inspect import signature as _inspect_signature
 
-
 _reserved_keywords = ["_parent", "_key"]
 
 

bsb/config/_config.py

@@ -1,24 +1,19 @@
 import typing
 
+import numpy as np
+
 from .. import config
-from . import types
+from .._util import merge_dicts
 from ..cell_types import CellType
-from ._attrs import _boot_nodes, cfgdict, cfglist
+from ..connectivity import ConnectionStrategy
 from ..placement import PlacementStrategy
+from ..postprocessing import PostProcessingHook
+from ..simulation.simulation import Simulation
 from ..storage._files import CodeDependencyNode, MorphologyDependencyNode
 from ..storage.interfaces import StorageNode
-from ..connectivity import ConnectionStrategy
-from ..simulation.simulation import Simulation
-from ..postprocessing import PostProcessingHook
-from .._util import merge_dicts
-from ..topology import (
-    get_partitions,
-    create_topology,
-    RegionGroup,
-    Region,
-    Partition,
-)
-import numpy as np
+from ..topology import Partition, Region, RegionGroup, create_topology, get_partitions
+from . import types
+from ._attrs import _boot_nodes, cfgdict, cfglist
 
 if typing.TYPE_CHECKING:
     from ..core import Scaffold

bsb/config/_distributions.py

@@ -1,9 +1,12 @@
 import typing
 
+import errr
+import numpy as np
+import scipy.stats.distributions as _distributions
+
 from .. import config
-from . import types
 from ..exceptions import DistributionCastError
-import scipy.stats.distributions as _distributions, errr, numpy as np
+from . import types
 
 if typing.TYPE_CHECKING:
     from ..core import Scaffold

bsb/config/_make.py

@@ -1,24 +1,26 @@
+import importlib
+import inspect
+import os
+import sys
+import types
+import warnings
+from re import sub
+
+import errr
+
 from ..exceptions import (
     CastError,
-    RequirementError,
     ConfigurationWarning,
+    DynamicClassError,
     DynamicClassInheritanceError,
+    DynamicObjectNotFoundError,
+    PluginError,
+    RequirementError,
     UnfitClassCastError,
-    DynamicClassError,
     UnresolvedClassCastError,
-    PluginError,
-    DynamicObjectNotFoundError,
 )
 from ..reporting import warn
 from ._hooks import overrides
-from re import sub
-import warnings
-import errr
-import importlib
-import inspect
-import sys
-import os
-import types
 
 
 def _has_own_init(meta_subject, kwargs):

bsb/config/refs.py

@@ -74,7 +74,7 @@ def __call__(self, root, here):
         return merged
 
     def is_ref(self, value):
-        from ..topology import Region, Partition
+        from ..topology import Partition, Region
 
         return isinstance(value, Region) or isinstance(value, Partition)
 

bsb/config/types.py

@@ -2,18 +2,20 @@
 import builtins
 import inspect
 import math
-import numpy as np
 from weakref import WeakKeyDictionary
-from ._compile import _reserved_kw_passes, _wrap_reserved
-from ._make import _load_object
+
+import numpy as np
+
 from ..exceptions import (
-    ClassMapMissingError,
     CastError,
-    NoneReferenceError,
+    ClassMapMissingError,
     InvalidReferenceError,
-    TypeHandlingError,
+    NoneReferenceError,
     RequirementError,
+    TypeHandlingError,
 )
+from ._compile import _reserved_kw_passes, _wrap_reserved
+from ._make import _load_object
 
 
 class TypeHandler(abc.ABC):