refactor(eyepy): Use isort with google style for imports and yapf for…

… code formating

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ repos:
   rev: v4.3.0
 - hooks:
   - id: isort
-    args: ["--profile", "black"]
+    args: ["--profile", "google"]
     name: isort (python)
   repo: https://github.com/pycqa/isort
   rev: 5.10.1

src/eyepy/__init__.py

@@ -5,22 +5,18 @@
 __email__ = "oli4morelle@gmail.com"
 __version__ = "0.6.8"
 
-from eyepy.core import (
-    EyeBscan,
-    EyeBscanLayerAnnotation,
-    EyeBscanMeta,
-    EyeEnface,
-    EyeEnfaceAreaAnnotation,
-    EyeEnfaceMeta,
-    EyeVolume,
-    EyeVolumeLayerAnnotation,
-    EyeVolumeMeta,
-    EyeVolumeVoxelAnnotation,
-)
-from eyepy.io import (
-    import_bscan_folder,
-    import_duke_mat,
-    import_heyex_vol,
-    import_heyex_xml,
-    import_retouch,
-)
+from eyepy.core import EyeBscan
+from eyepy.core import EyeBscanLayerAnnotation
+from eyepy.core import EyeBscanMeta
+from eyepy.core import EyeEnface
+from eyepy.core import EyeEnfaceAreaAnnotation
+from eyepy.core import EyeEnfaceMeta
+from eyepy.core import EyeVolume
+from eyepy.core import EyeVolumeLayerAnnotation
+from eyepy.core import EyeVolumeMeta
+from eyepy.core import EyeVolumeVoxelAnnotation
+from eyepy.io import import_bscan_folder
+from eyepy.io import import_duke_mat
+from eyepy.io import import_heyex_vol
+from eyepy.io import import_heyex_xml
+from eyepy.io import import_retouch

src/eyepy/core/__init__.py

@@ -1,5 +1,10 @@
-from .annotations import EyeVolumeLayerAnnotation, EyeVolumeVoxelAnnotation
-from .eyebscan import EyeBscan, EyeBscanLayerAnnotation
-from .eyeenface import EyeEnface, EyeEnfaceAreaAnnotation
-from .eyemeta import EyeBscanMeta, EyeEnfaceMeta, EyeVolumeMeta
+from .annotations import EyeVolumeLayerAnnotation
+from .annotations import EyeVolumeVoxelAnnotation
+from .eyebscan import EyeBscan
+from .eyebscan import EyeBscanLayerAnnotation
+from .eyeenface import EyeEnface
+from .eyeenface import EyeEnfaceAreaAnnotation
+from .eyemeta import EyeBscanMeta
+from .eyemeta import EyeEnfaceMeta
+from .eyemeta import EyeVolumeMeta
 from .eyevolume import EyeVolume

src/eyepy/core/annotations.py

@@ -1,21 +1,24 @@
 from __future__ import annotations
 
-import logging
 from collections import defaultdict
-from typing import TYPE_CHECKING, List, Optional
+import logging
+from typing import List, Optional, TYPE_CHECKING
 
+from matplotlib import cm
+from matplotlib import colors
+from matplotlib import patches
 import matplotlib.pyplot as plt
+from mpl_toolkits.axes_grid1 import make_axes_locatable
 import numpy as np
 import numpy.typing as npt
-from matplotlib import cm, colors, patches
-from mpl_toolkits.axes_grid1 import make_axes_locatable
 from skimage import transform
 from skimage.transform._geometric import GeometricTransform
 
 from eyepy import config
 
 if TYPE_CHECKING:
-    from eyepy import EyeEnface, EyeVolume
+    from eyepy import EyeEnface
+    from eyepy import EyeVolume
 
 logger = logging.getLogger("eyepy.core.annotations")
 

src/eyepy/core/eyebscan.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, List
+from typing import List, TYPE_CHECKING
 
 import matplotlib.colors as mcolors
 import matplotlib.patches as mpatches

src/eyepy/core/eyeenface.py

@@ -1,8 +1,8 @@
 from typing import Optional
 
 import matplotlib.pyplot as plt
-import numpy as np
 from numpy import typing as npt
+import numpy as np
 
 from eyepy.core.annotations import EyeEnfaceAreaAnnotation
 

src/eyepy/core/eyevolume.py

@@ -1,35 +1,30 @@
+from collections import defaultdict
 import json
 import logging
+from pathlib import Path
 import shutil
 import tempfile
+from typing import (Callable, List, Optional, overload, SupportsIndex, Tuple,
+                    TypedDict, Union)
 import warnings
 import zipfile
-from collections import defaultdict
-from pathlib import Path
-from typing import (
-    Callable,
-    List,
-    Optional,
-    SupportsIndex,
-    Tuple,
-    TypedDict,
-    Union,
-    overload,
-)
 
-import matplotlib.pyplot as plt
-import numpy as np
 from matplotlib import patches
+import matplotlib.pyplot as plt
 from mpl_toolkits.axes_grid1 import make_axes_locatable
 from numpy import typing as npt
+import numpy as np
 from skimage import transform
 from skimage.transform._geometric import GeometricTransform
 
 from eyepy import config
-from eyepy.core.annotations import EyeVolumeLayerAnnotation, EyeVolumeVoxelAnnotation
+from eyepy.core.annotations import EyeVolumeLayerAnnotation
+from eyepy.core.annotations import EyeVolumeVoxelAnnotation
 from eyepy.core.eyebscan import EyeBscan
 from eyepy.core.eyeenface import EyeEnface
-from eyepy.core.eyemeta import EyeBscanMeta, EyeEnfaceMeta, EyeVolumeMeta
+from eyepy.core.eyemeta import EyeBscanMeta
+from eyepy.core.eyemeta import EyeEnfaceMeta
+from eyepy.core.eyemeta import EyeVolumeMeta
 from eyepy.core.utils import intensity_transforms
 
 logger = logging.getLogger("eyepy.core.eyevolume")

src/eyepy/data/__init__.py

@@ -1,8 +1,8 @@
 # -*- coding: utf-8 -*-
 import logging
+from pathlib import Path
 import urllib.request
 import zipfile
-from pathlib import Path
 
 import eyepy as ep
 

src/eyepy/io/__init__.py

@@ -4,7 +4,9 @@
 import imageio
 import numpy as np
 
-from eyepy import EyeBscanMeta, EyeVolume, EyeVolumeMeta
+from eyepy import EyeBscanMeta
+from eyepy import EyeVolume
+from eyepy import EyeVolumeMeta
 from eyepy.io.he_vol_reader import HeVolReader
 from eyepy.io.he_xml_reader import HeXmlReader
 

src/eyepy/io/base.py

@@ -2,7 +2,8 @@
 from pathlib import Path
 from typing import Any, Dict, List, Tuple, Union
 
-from nptyping import NDArray, Shape
+from nptyping import NDArray
+from nptyping import Shape
 
 
 class BaseLayerAnnotation(metaclass=abc.ABCMeta):

src/eyepy/io/he_e2e_reader.py

@@ -5,7 +5,9 @@
 import numpy as np
 
 from eyepy.core.eyeenface import EyeEnface
-from eyepy.core.eyemeta import EyeBscanMeta, EyeEnfaceMeta, EyeVolumeMeta
+from eyepy.core.eyemeta import EyeBscanMeta
+from eyepy.core.eyemeta import EyeEnfaceMeta
+from eyepy.core.eyemeta import EyeVolumeMeta
 from eyepy.core.eyevolume import EyeVolume
 from eyepy.io.he_vol_reader import SEG_MAPPING
 from eyepy.io.utils import _compute_localizer_oct_transform

src/eyepy/io/he_vol_reader.py

@@ -11,15 +11,17 @@
 import numpy as np
 from skimage import transform
 
-from eyepy import EyeBscanMeta, EyeEnface, EyeEnfaceMeta, EyeVolume, EyeVolumeMeta
-from eyepy.io.utils import (
-    Bscan,
-    FloatDate,
-    IntDate,
-    Localizer,
-    Segmentations,
-    _compute_localizer_oct_transform,
-)
+from eyepy import EyeBscanMeta
+from eyepy import EyeEnface
+from eyepy import EyeEnfaceMeta
+from eyepy import EyeVolume
+from eyepy import EyeVolumeMeta
+from eyepy.io.utils import _compute_localizer_oct_transform
+from eyepy.io.utils import Bscan
+from eyepy.io.utils import FloatDate
+from eyepy.io.utils import IntDate
+from eyepy.io.utils import Localizer
+from eyepy.io.utils import Segmentations
 
 logger = logging.getLogger("eyepy.io.HeVolReader")
 

src/eyepy/io/he_xml_reader.py

@@ -1,25 +1,25 @@
 # -*- coding: utf-8 -*-
 import functools
 import logging
-import xml.etree.ElementTree as ElementTree
 from pathlib import Path
 from typing import List
+import xml.etree.ElementTree as ElementTree
 
 import imageio
 import numpy as np
 from skimage import img_as_ubyte
 
 from eyepy.core.eyeenface import EyeEnface
-from eyepy.core.eyemeta import EyeBscanMeta, EyeEnfaceMeta, EyeVolumeMeta
+from eyepy.core.eyemeta import EyeBscanMeta
+from eyepy.core.eyemeta import EyeEnfaceMeta
+from eyepy.core.eyemeta import EyeVolumeMeta
 from eyepy.core.eyevolume import EyeVolume
-from eyepy.io.utils import (
-    _compute_localizer_oct_transform,
-    _get_date_from_xml,
-    _get_datetime_from_xml,
-    _get_first_as_float,
-    _get_first_as_int,
-    _get_first_as_str,
-)
+from eyepy.io.utils import _compute_localizer_oct_transform
+from eyepy.io.utils import _get_date_from_xml
+from eyepy.io.utils import _get_datetime_from_xml
+from eyepy.io.utils import _get_first_as_float
+from eyepy.io.utils import _get_first_as_int
+from eyepy.io.utils import _get_first_as_str
 
 logger = logging.getLogger(__name__)
 

src/eyepy/io/utils.py

@@ -1,6 +1,8 @@
 # -*- coding: utf-8 -*-
+from datetime import datetime
+from datetime import timedelta
+from datetime import timezone
 import logging
-from datetime import datetime, timedelta, timezone
 from typing import MutableMapping, Tuple, Union
 
 import construct as cs