From d95ab0f4ae2bf728442859b1534c1291a4d47540 Mon Sep 17 00:00:00 2001 From: James <12661555+jmsmkn@users.noreply.github.com> Date: Fri, 25 Feb 2022 10:06:55 +0100 Subject: [PATCH] Adds isort (#68) --- .pre-commit-config.yaml | 7 ++++--- panimg/contrib/oct_converter/image_types/__init__.py | 2 +- panimg/contrib/oct_converter/readers/__init__.py | 2 +- panimg/contrib/oct_converter/readers/e2e.py | 7 ++++--- panimg/contrib/oct_converter/readers/fda.py | 10 ++++++---- panimg/contrib/oct_converter/readers/fds.py | 8 +++++--- panimg/image_builders/dicom.py | 2 +- panimg/image_builders/fallback.py | 2 +- panimg/image_builders/oct.py | 2 +- panimg/models.py | 2 +- pyproject.toml | 5 +++++ setup.cfg | 4 ---- tests/test_mhd.py | 2 +- tests/test_utils.py | 4 ++-- 14 files changed, 33 insertions(+), 26 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8ddcb6b..d678588 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,5 +1,3 @@ -default_language_version: - python: python3.8 repos: - repo: https://github.com/pre-commit/pre-commit-hooks rev: v4.1.0 @@ -15,6 +13,10 @@ repos: - id: pyupgrade language: python args: [--py37-plus] + - repo: https://github.com/pycqa/isort + rev: 5.10.1 + hooks: + - id: isort - repo: https://github.com/ambv/black rev: 22.1.0 hooks: @@ -27,7 +29,6 @@ repos: language: python additional_dependencies: - flake8-bugbear - - flake8-import-order - pep8-naming - flake8-docstrings - mccabe diff --git a/panimg/contrib/oct_converter/image_types/__init__.py b/panimg/contrib/oct_converter/image_types/__init__.py index dee77d5..5369359 100644 --- a/panimg/contrib/oct_converter/image_types/__init__.py +++ b/panimg/contrib/oct_converter/image_types/__init__.py @@ -1,4 +1,4 @@ -from .oct import OCTVolumeWithMetaData from .fundus import FundusImageWithMetaData +from .oct import OCTVolumeWithMetaData __all__ = ["OCTVolumeWithMetaData", "FundusImageWithMetaData"] diff --git a/panimg/contrib/oct_converter/readers/__init__.py b/panimg/contrib/oct_converter/readers/__init__.py index 1459e5e..5af67e4 100644 --- a/panimg/contrib/oct_converter/readers/__init__.py +++ b/panimg/contrib/oct_converter/readers/__init__.py @@ -1,5 +1,5 @@ -from .fds import FDS from .e2e import E2E from .fda import FDA +from .fds import FDS __all__ = ["FDS", "E2E", "FDA"] diff --git a/panimg/contrib/oct_converter/readers/e2e.py b/panimg/contrib/oct_converter/readers/e2e.py index 6e23e38..3c471a1 100644 --- a/panimg/contrib/oct_converter/readers/e2e.py +++ b/panimg/contrib/oct_converter/readers/e2e.py @@ -1,13 +1,14 @@ import re import struct +from pathlib import Path import numpy as np -from construct import PaddedString, Int16un, Struct, Int32sn, Int32un, Int8un +from construct import Int8un, Int16un, Int32sn, Int32un, PaddedString, Struct + from panimg.contrib.oct_converter.image_types import ( - OCTVolumeWithMetaData, FundusImageWithMetaData, + OCTVolumeWithMetaData, ) -from pathlib import Path class E2E: diff --git a/panimg/contrib/oct_converter/readers/fda.py b/panimg/contrib/oct_converter/readers/fda.py index 09c34e0..04f51bc 100644 --- a/panimg/contrib/oct_converter/readers/fda.py +++ b/panimg/contrib/oct_converter/readers/fda.py @@ -1,11 +1,13 @@ -from construct import PaddedString, Struct, Int32un +from pathlib import Path + import numpy as np +from construct import Int32un, PaddedString, Struct +from pylibjpeg import decode + from panimg.contrib.oct_converter.image_types import ( - OCTVolumeWithMetaData, FundusImageWithMetaData, + OCTVolumeWithMetaData, ) -from pylibjpeg import decode -from pathlib import Path class FDA: diff --git a/panimg/contrib/oct_converter/readers/fds.py b/panimg/contrib/oct_converter/readers/fds.py index b6f26cb..7271a7d 100644 --- a/panimg/contrib/oct_converter/readers/fds.py +++ b/panimg/contrib/oct_converter/readers/fds.py @@ -1,10 +1,12 @@ -from construct import PaddedString, Struct, Int32un +from pathlib import Path + import numpy as np +from construct import Int32un, PaddedString, Struct + from panimg.contrib.oct_converter.image_types import ( - OCTVolumeWithMetaData, FundusImageWithMetaData, + OCTVolumeWithMetaData, ) -from pathlib import Path class FDS: diff --git a/panimg/image_builders/dicom.py b/panimg/image_builders/dicom.py index effc39e..a6d2f15 100644 --- a/panimg/image_builders/dicom.py +++ b/panimg/image_builders/dicom.py @@ -4,9 +4,9 @@ from pathlib import Path from typing import DefaultDict, Iterator, List, Set -import SimpleITK import numpy as np import pydicom +import SimpleITK from panimg.exceptions import UnconsumedFilesException from panimg.models import ( diff --git a/panimg/image_builders/fallback.py b/panimg/image_builders/fallback.py index a69b375..818ad4d 100644 --- a/panimg/image_builders/fallback.py +++ b/panimg/image_builders/fallback.py @@ -2,8 +2,8 @@ from pathlib import Path from typing import DefaultDict, Iterator, List, Set -import SimpleITK import numpy as np +import SimpleITK from PIL import Image from PIL.Image import DecompressionBombError diff --git a/panimg/image_builders/oct.py b/panimg/image_builders/oct.py index 2452273..a9a36d8 100644 --- a/panimg/image_builders/oct.py +++ b/panimg/image_builders/oct.py @@ -11,9 +11,9 @@ Union, ) -import SimpleITK import numpy as np import numpy.typing as npt +import SimpleITK from construct.core import Float64l, Int8ul, PaddedString, StreamError, Struct from pydantic import BaseModel diff --git a/panimg/models.py b/panimg/models.py index 9f6bff6..4003a26 100644 --- a/panimg/models.py +++ b/panimg/models.py @@ -7,9 +7,9 @@ from typing import Any, Dict, List, NamedTuple, Optional, Set, Tuple from uuid import UUID, uuid4 -from SimpleITK import Image, WriteImage from pydantic import BaseModel, validator from pydantic.dataclasses import dataclass +from SimpleITK import Image, WriteImage from panimg.exceptions import ValidationError diff --git a/pyproject.toml b/pyproject.toml index eb0119b..a186ce5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -47,6 +47,11 @@ pytest-cov = "*" requires = ["poetry-core>=1.0.0"] build-backend = "poetry.core.masonry.api" +[tool.isort] +profile = "black" +known_first_party = ["panimg", "tests"] +line_length = 79 + [tool.black] line-length = 79 target-version = ['py37'] diff --git a/setup.cfg b/setup.cfg index 1cfe04a..bd9c177 100644 --- a/setup.cfg +++ b/setup.cfg @@ -24,10 +24,6 @@ warn_untyped_fields = True [flake8] max-line-length = 79 -application-import-names = - tests - panimg -import-order-style = pycharm docstring-convention = numpy max-complexity = 10 select = diff --git a/tests/test_mhd.py b/tests/test_mhd.py index 6bf6e16..97c6874 100644 --- a/tests/test_mhd.py +++ b/tests/test_mhd.py @@ -3,8 +3,8 @@ from pathlib import Path from typing import List, Union -import SimpleITK import pytest +import SimpleITK from panimg.exceptions import ValidationError from panimg.image_builders.metaio_utils import ( diff --git a/tests/test_utils.py b/tests/test_utils.py index b9e40d1..41dd0a0 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -1,11 +1,11 @@ from pathlib import Path -import SimpleITK import pytest +import SimpleITK from pytest import approx from panimg.image_builders.metaio_utils import load_sitk_image -from panimg.models import ColorSpace, EXTRA_METADATA, SimpleITKImage +from panimg.models import EXTRA_METADATA, ColorSpace, SimpleITKImage from tests import RESOURCE_PATH