Merge pull request #647 from FZJ-INM1-BDA/maint_pep8_import_order

Maint pep8 import order

Author: AhmetNSimsek

siibra/__init__.py

@@ -13,16 +13,18 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import os as _os
+
 from .commons import (
     logger,
     QUIET,
     VERBOSE,
     MapType,
-    MapIndex,
     set_log_level,
     __version__
 )
-
+from . import configuration, features, livequeries
+from .configuration import factory
 from .core import (
     atlas as _atlas,
     parcellation as _parcellation,
@@ -31,13 +33,9 @@
 from .volumes import parcellationmap as _parcellationmap
 from .retrieval.requests import CACHE as cache
 from .retrieval.cache import Warmup, WarmupLevel
+from .locations import Point, PointCloud, Plane, BoundingBox
 
-from . import configuration
-from .configuration import factory
-from . import features, livequeries
-from siibra.locations import Point, PointCloud, Plane, BoundingBox
 
-import os as _os
 logger.info(f"Version: {__version__}")
 logger.warning("This is a development release. Use at your own risk.")
 logger.info(

siibra/commons.py

@@ -17,24 +17,26 @@
 import os
 import re
 from enum import Enum
-from nibabel import Nifti1Image
-from nilearn.image import resample_to_img
 import logging
-from tqdm import tqdm
-import numpy as np
-import pandas as pd
-from typing import Generic, Iterable, Iterator, List, TypeVar, Union, Dict, Generator, Tuple
-from skimage.filters import gaussian
 from dataclasses import dataclass
 from hashlib import md5
 from uuid import UUID
 import math
+from typing import Generic, Iterable, Iterator, List, TypeVar, Union, Dict, Generator, Tuple
 try:
     from typing import TypedDict
 except ImportError:
     # support python 3.7
     from typing_extensions import TypedDict
 
+from tqdm import tqdm
+import numpy as np
+import pandas as pd
+from nibabel import Nifti1Image
+from nilearn.image import resample_to_img
+from skimage.filters import gaussian
+
+
 logging.addLevelName(21, "INFO_WO_PROGRESS_BARS")
 logger = logging.getLogger(__name__.split(os.path.extsep)[0])
 ch = logging.StreamHandler()

siibra/configuration/configuration.py

@@ -13,16 +13,16 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from ..commons import logger, __version__, SIIBRA_USE_CONFIGURATION, siibra_tqdm
-from ..retrieval.repositories import GitlabConnector, RepositoryConnector, GithubConnector
-from ..retrieval.exceptions import NoSiibraConfigMirrorsAvailableException
-from ..retrieval.requests import SiibraHttpRequestError
-
 from typing import Union, List
 from collections import defaultdict
 from requests.exceptions import ConnectionError
 from os import path
 
+from ..commons import logger, __version__, SIIBRA_USE_CONFIGURATION, siibra_tqdm
+from ..retrieval.repositories import GitlabConnector, RepositoryConnector, GithubConnector
+from ..retrieval.exceptions import NoSiibraConfigMirrorsAvailableException
+from ..retrieval.requests import SiibraHttpRequestError
+
 
 class Configuration:
     """

siibra/configuration/factory.py

@@ -13,6 +13,15 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from os import path
+import json
+from typing import List, Dict, Callable
+from io import BytesIO
+from functools import wraps
+
+import numpy as np
+import pandas as pd
+
 from ..commons import logger, Species
 from ..features import anchor, connectivity
 from ..features.tabular import (
@@ -29,14 +38,6 @@
 from ..volumes import volume, sparsemap, parcellationmap
 from ..volumes.providers.provider import VolumeProvider
 
-from os import path
-import json
-import numpy as np
-from typing import List, Dict, Callable
-import pandas as pd
-from io import BytesIO
-from functools import wraps
-
 
 _registered_build_fns: Dict[str, Callable] = {}
 

siibra/core/assignment.py

@@ -17,6 +17,7 @@
 from enum import Enum
 from dataclasses import dataclass
 from typing import Dict, Generic, TypeVar, TYPE_CHECKING
+
 if TYPE_CHECKING:
     from .structure import BrainStructure
 

siibra/core/atlas.py

@@ -13,12 +13,12 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """Provides reference systems for brains."""
-from . import concept, space as _space, parcellation as _parcellation
-
-from ..commons import MapType, logger, InstanceTable, Species
 
 from typing import List
 
+from . import concept, space as _space, parcellation as _parcellation
+from ..commons import MapType, logger, InstanceTable, Species
+
 
 VERSION_BLACKLIST_WORDS = ["beta", "rc", "alpha"]
 

siibra/core/concept.py

@@ -13,6 +13,10 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """Parent class to siibra main concepts."""
+
+import re
+from typing import TypeVar, Type, Union, List, TYPE_CHECKING, Dict
+
 from ..commons import (
     create_key,
     clear_name,
@@ -23,8 +27,6 @@
 )
 from ..retrieval import cache
 
-import re
-from typing import TypeVar, Type, Union, List, TYPE_CHECKING, Dict
 
 T = TypeVar("T", bound="AtlasConcept")
 _REGISTRIES: Dict[Type[T], InstanceTable[T]] = {}

siibra/core/parcellation.py

@@ -13,11 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """Hierarchal brain regions and metadata."""
-from . import region
-
-from ..commons import logger, MapType, Species
-from ..volumes import parcellationmap
-from ..exceptions import MapNotFound
 
 from functools import lru_cache
 import re
@@ -28,6 +23,11 @@
     # support python 3.7
     from typing_extensions import Literal
 
+from . import region
+from ..commons import logger, MapType, Species
+from ..volumes import parcellationmap
+from ..exceptions import MapNotFound
+
 
 if TYPE_CHECKING:
     from .space import Space

siibra/core/region.py

@@ -14,6 +14,17 @@
 # limitations under the License.
 """Representation of a brain region."""
 
+import re
+from typing import List, Union, Iterable, Dict, Callable, Tuple, Set
+from difflib import SequenceMatcher
+import json
+from functools import wraps, reduce
+from concurrent.futures import ThreadPoolExecutor
+from functools import lru_cache
+
+import anytree
+from ebrains_drive import BucketApiClient
+
 from . import concept, structure, space as _space, parcellation as _parcellation, assignment
 from ..retrieval.cache import cache_user_fn
 from ..locations import location, pointcloud, boundingbox as _boundingbox
@@ -27,16 +38,6 @@
 )
 from ..exceptions import NoMapAvailableError, SpaceWarpingFailedError
 
-import re
-import anytree
-from typing import List, Union, Iterable, Dict, Callable, Tuple, Set
-from difflib import SequenceMatcher
-from ebrains_drive import BucketApiClient
-import json
-from functools import wraps, reduce
-from concurrent.futures import ThreadPoolExecutor
-from functools import lru_cache
-
 
 REGEX_TYPE = type(re.compile("test"))
 

siibra/core/space.py

@@ -14,12 +14,11 @@
 # limitations under the License.
 """A particular brain reference space."""
 
+from typing import List, TYPE_CHECKING, Union
 
 from . import concept
 from ..commons import logger, Species
 
-from typing import List, TYPE_CHECKING, Union
-
 if TYPE_CHECKING:
     from ..volumes import volume
 

siibra/core/structure.py

@@ -21,11 +21,11 @@
 bounding box in MNI space is a structure, but not an AtlasConcept.
 """
 
-from . import assignment, region as _region
-
 from abc import ABC, abstractmethod
 from typing import Tuple, Dict
 
+from . import assignment, region as _region
+
 
 class BrainStructure(ABC):
     """Abstract base class for types who can act as a location filter."""

siibra/features/anchor.py

@@ -14,20 +14,18 @@
 # limitations under the License.
 """Handles the relation between study targets and BrainStructures."""
 
-from ..commons import Species, logger
+from typing import Union, List, Dict, Iterable
 
+from ..commons import Species, logger
 from ..core.structure import BrainStructure
 from ..core.assignment import AnatomicalAssignment, Qualification
 from ..locations.location import Location
 from ..core.parcellation import Parcellation, find_regions
 from ..core.region import Region
 from ..core.space import Space
 from ..exceptions import SpaceWarpingFailedError
-
 from ..vocabularies import REGION_ALIASES
 
-from typing import Union, List, Dict, Iterable
-
 
 class AnatomicalAnchor:
     """

siibra/features/connectivity/regional_connectivity.py

@@ -14,28 +14,25 @@
 # limitations under the License.
 
 from zipfile import ZipFile
-from ..feature import Feature, Compoundable
-from ..tabular.tabular import Tabular
+from typing import Callable, Union, List, Tuple, Iterator
+try:
+    from typing import Literal
+except ImportError:  # support python 3.7
+    from typing_extensions import Literal
 
-from .. import anchor as _anchor
+import numpy as np
+import pandas as pd
 
+from .. import anchor as _anchor
+from ..feature import Feature, Compoundable
+from ..tabular.tabular import Tabular
 from ...commons import logger, QUIET, siibra_tqdm
 from ...core import region as _region
 from ...locations import pointcloud
 from ...retrieval.repositories import RepositoryConnector
 from ...retrieval.requests import HttpRequest
 
 
-import pandas as pd
-import numpy as np
-from typing import Callable, Union, List, Tuple, Iterator
-
-try:
-    from typing import Literal
-except ImportError:  # support python 3.7
-    from typing_extensions import Literal
-
-
 class RegionalConnectivity(Feature, Compoundable):
     """
     Parcellation-averaged connectivity, providing one or more matrices of a

siibra/features/dataset/ebrains.py

@@ -15,9 +15,9 @@
 """Non-preconfigured data features hosted at EBRAINS."""
 
 from zipfile import ZipFile
+
 from .. import anchor as _anchor
 from .. import feature
-
 from ...retrieval import datasets
 
 

siibra/features/feature.py

@@ -14,12 +14,6 @@
 # limitations under the License.
 """Handles multimodal data features and related queries."""
 
-from . import anchor as _anchor
-
-from ..commons import logger, InstanceTable, siibra_tqdm, __version__
-from ..core import concept, space, region, parcellation, structure
-from ..volumes import volume
-
 from typing import Union, TYPE_CHECKING, List, Dict, Type, Tuple, BinaryIO, Any, Iterator
 from hashlib import md5
 from collections import defaultdict
@@ -28,6 +22,11 @@
 from re import sub
 from textwrap import wrap
 
+from . import anchor as _anchor
+from ..commons import logger, InstanceTable, siibra_tqdm, __version__
+from ..core import concept, space, region, parcellation, structure
+from ..volumes import volume
+
 if TYPE_CHECKING:
     from ..retrieval.datasets import EbrainsDataset
     TypeDataset = EbrainsDataset

siibra/features/image/image.py

@@ -14,15 +14,13 @@
 # limitations under the License.
 """Base type of features in volume format and related anatomical anchor."""
 
+from typing import List, TYPE_CHECKING
 from zipfile import ZipFile
-from .. import feature
 
+from .. import feature
 from .. import anchor as _anchor
-
 from ...volumes import volume as _volume
 
-from typing import List, TYPE_CHECKING
-
 if TYPE_CHECKING:
     from ...locations.boundingbox import BoundingBox
     from ...volumes.providers import provider

siibra/features/image/sections.py

@@ -14,9 +14,10 @@
 # limitations under the License.
 """Multimodal data features in 2D section."""
 
-from . import image
 from typing import TYPE_CHECKING
 
+from . import image
+
 if TYPE_CHECKING:
     from ...locations import AxisAlignedPatch, Contour
     from ...features.anchor import AnatomicalAnchor

siibra/features/tabular/bigbrain_intensity_profile.py

@@ -13,9 +13,10 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from typing import List, TYPE_CHECKING
+
 from . import cortical_profile
 
-from typing import List, TYPE_CHECKING
 if TYPE_CHECKING:
     from ...features.anchor import AnatomicalAnchor