Add isort as a dev dependency and use it to keep imports tidy. (#16)

ci/check.sh

@@ -45,6 +45,7 @@ fi
 
 banner "Executing in conda environment ${CONDA_DEFAULT_ENV} in directory ${root}"
 run "Unit Tests"     "python -m pytest -vv -r sx fgpyo"
+run "Import Sorting" "isort --force-single-line-imports --profile black fgpyo"
 run "Style Checking" "black --line-length 99 $black_extra_args fgpyo"
 run "Linting"        "flake8 --config=$parent/flake8.cfg fgpyo"
 run "Type Checking"  "mypy -p fgpyo --config $parent/mypy.ini"

fgpyo/collections/__init__.py

@@ -68,7 +68,6 @@
 from typing import TypeVar
 from typing import Union
 
-
 IterType = TypeVar("IterType")
 
 

fgpyo/read_structure.py

@@ -62,10 +62,10 @@
         correspond to the given read segment
 """
 import enum
-from typing import Optional
 from typing import Iterable
 from typing import Iterator
 from typing import List
+from typing import Optional
 from typing import Tuple
 
 import attr

fgpyo/sam/__init__.py

@@ -156,19 +156,19 @@
 import enum
 import io
 from pathlib import Path
+from typing import IO
 from typing import Any
 from typing import Dict
-from typing import IO
 from typing import List
 from typing import Optional
 from typing import Tuple
 from typing import Union
 
 import attr
 import pysam
+from pysam import AlignedSegment
 from pysam import AlignmentFile as SamFile
 from pysam import AlignmentHeader as SamHeader
-from pysam import AlignedSegment
 
 """The valid base classes for opening a SAM/BAM/CRAM file."""
 SamPath = Union[IO[Any], Path, str]

fgpyo/sam/builder.py

@@ -22,7 +22,8 @@
 from typing import Tuple
 
 import pysam
-from pysam import AlignmentHeader, AlignedSegment
+from pysam import AlignedSegment
+from pysam import AlignmentHeader
 
 from fgpyo import sam
 

fgpyo/sam/tests/test_supplementary_alignments.py

@@ -1,6 +1,6 @@
 import pytest
-from fgpyo.sam import Cigar
 
+from fgpyo.sam import Cigar
 from fgpyo.sam import SupplementaryAlignment
 
 

fgpyo/tests/test_read_structure.py

@@ -1,7 +1,9 @@
-import pytest
 from typing import Tuple
-from fgpyo.read_structure import ReadStructure
+
+import pytest
+
 from fgpyo.read_structure import ReadSegment
+from fgpyo.read_structure import ReadStructure
 from fgpyo.read_structure import SegmentType
 
 

fgpyo/util/inspect.py

@@ -9,14 +9,16 @@
     from typing import Literal
 except ImportError:  # py<38
     from typing_extensions import Literal
-import attr
-from typing import Callable
+
 import functools
-from functools import partial
 from enum import Enum
+from functools import partial
 from pathlib import PurePath
+from typing import Callable
 from typing import Optional
 
+import attr
+
 import fgpyo.util.types as types
 
 

fgpyo/util/tests/test_metric.py

@@ -1,9 +1,10 @@
 import enum
 from pathlib import Path
-from typing import Any, Optional
+from typing import Any
 from typing import Callable
 from typing import Dict
 from typing import List
+from typing import Optional
 from typing import Set
 from typing import Tuple
 

fgpyo/util/types.py

@@ -1,13 +1,13 @@
-from enum import Enum
-import typing
 import collections
-from typing import Union
-from typing import TypeVar
-from typing import Iterable
-from typing import Type
-from typing import Callable
 import inspect
+import typing
+from enum import Enum
 from functools import partial
+from typing import Callable
+from typing import Iterable
+from typing import Type
+from typing import TypeVar
+from typing import Union
 
 try:
     from typing import Literal

pyproject.toml

@@ -25,7 +25,7 @@ include = [
 ]
 
 [tool.poetry.dependencies]
-python = ">=3.6.0"
+python = ">=3.6.1,<4.0"
 attrs = ">=19.3.0"
 typing_extensions = { version = ">=3.7.4", python = "<3.8" }  # Literal support
 typing_inspect = { version = ">=0.3.1", python = "<3.8" }  # inspecting types
@@ -41,6 +41,7 @@ mypy = ">=0.770"
 flake8 = ">=3.8.1"
 black = ">=19.10b0"
 pytest-cov = ">=2.8.1"
+isort = ">=5.10.1"
 
 [build-system]
 requires = ["poetry>=0.12"]