chore: Add isort to code checks (#32)

* chore: isort

* build: add isort to GHA

* build: add isort to dev dependencies

.github/workflows/pythonpackage.yml

@@ -63,6 +63,11 @@ jobs:
       run: |
         poetry run black --line-length 99 --check pybedlite
 
+    - name: Import sorting
+      shell: bash
+      run: |
+        poetry run isort --force-single-line-imports --profile black --check pybedlite
+
     - name: Run lint
       shell: bash
       run: |

ci/check.sh

@@ -46,6 +46,7 @@ fi
 banner "Executing in conda environment ${CONDA_DEFAULT_ENV} in directory ${root}"
 run "Unit Tests"     "python -m pytest -vv -r sx pybedlite"
 run "Style Checking" "black --line-length 99 $black_extra_args pybedlite"
+run "Import sorting" "isort --force-single-line-imports --profile black pybedlite"
 run "Linting"        "flake8 --config=$parent/flake8.cfg pybedlite"
 run "Type Checking"  "mypy -p pybedlite --config $parent/mypy.ini"
 

pybedlite/__init__.py

@@ -53,11 +53,11 @@
 
 from typing import Optional
 
-from pybedlite.bed_writer import BedWriter
-from pybedlite.bed_source import BedSource
-from pybedlite.bed_source import BedPath
 from pybedlite.bed_record import BedRecord
 from pybedlite.bed_record import BedStrand
+from pybedlite.bed_source import BedPath
+from pybedlite.bed_source import BedSource
+from pybedlite.bed_writer import BedWriter
 
 
 def reader(path: BedPath) -> "BedSource":

pybedlite/bed_record.py

@@ -14,14 +14,15 @@
 
 from __future__ import annotations
 
-import attr
 import enum
+from typing import TYPE_CHECKING
+from typing import ClassVar
+from typing import List
 from typing import Optional
 from typing import Tuple
-from typing import List
-from typing import ClassVar
 from typing import Type
-from typing import TYPE_CHECKING
+
+import attr
 
 if TYPE_CHECKING:
     from pybedlite.overlap_detector import Interval

pybedlite/bed_source.py

@@ -12,24 +12,24 @@
 """
 
 import io
-from typing import IO
-from typing import Optional
-from typing import TypeVar
-from typing import Union
-from typing import Type
-from typing import Tuple
-from typing import List
 from pathlib import Path
 from types import TracebackType
+from typing import IO
+from typing import Any
 from typing import Callable
 from typing import ContextManager
+from typing import Dict
 from typing import Iterable
 from typing import Iterator
-from typing import Dict
-from typing import Any
+from typing import List
+from typing import Optional
+from typing import Tuple
+from typing import Type
+from typing import TypeVar
+from typing import Union
 
-from pybedlite.bed_record import BedStrand
 from pybedlite.bed_record import BedRecord
+from pybedlite.bed_record import BedStrand
 
 """The classes that should be treated as file-like classes"""
 _IOClasses = (io.TextIOBase, io.BufferedIOBase, io.RawIOBase, io.IOBase)

pybedlite/bed_writer.py

@@ -10,19 +10,18 @@
     - :class:`~pybedtools.bed_source.BedWriter` -- Writer class for writing BED files
 """
 
-from typing import IO
-from typing import Optional
-from typing import Type
 from pathlib import Path
 from types import TracebackType
+from typing import IO
 from typing import ContextManager
 from typing import Iterable
+from typing import Optional
+from typing import Type
 
 from pybedlite.bed_record import BedRecord
 from pybedlite.bed_source import BedPath
 from pybedlite.bed_source import _IOClasses
 
-
 """Maximum BED fields that can be present in a well formed BED file written to specification"""
 MAX_BED_FIELDS: int = 12
 

pybedlite/overlap_detector.py

@@ -49,11 +49,11 @@
 from typing import Type
 
 import attr
-import cgranges as cr
 
+import cgranges as cr
+from pybedlite.bed_record import BedRecord
 from pybedlite.bed_record import BedStrand
 from pybedlite.bed_source import BedSource
-from pybedlite.bed_record import BedRecord
 
 
 @attr.s(frozen=True, auto_attribs=True)

pybedlite/tests/conftest.py

@@ -1,5 +1,7 @@
-import pytest
 from typing import List
+
+import pytest
+
 from pybedlite.bed_record import BedRecord
 from pybedlite.bed_record import BedStrand
 

pybedlite/tests/test_overlap_detector.py

@@ -2,10 +2,10 @@
 
 from typing import List
 
+from pybedlite.bed_record import BedRecord
+from pybedlite.bed_record import BedStrand
 from pybedlite.overlap_detector import Interval
 from pybedlite.overlap_detector import OverlapDetector
-from pybedlite.bed_record import BedStrand
-from pybedlite.bed_record import BedRecord
 
 
 def run_test(targets: List[Interval], query: Interval, results: List[Interval]) -> None:

pybedlite/tests/test_pybedlite.py

@@ -1,15 +1,16 @@
 """Tests for :py:mod:`~pybedlite.__init__.py`"""
 
-import pytest
 from pathlib import Path
 from typing import List
+
+import pytest
+
 import pybedlite as pybed
-from pybedlite.bed_writer import MAX_BED_FIELDS
-from pybedlite.bed_writer import BedWriter
-from pybedlite.bed_source import BedSource
 from pybedlite.bed_record import BedRecord
 from pybedlite.bed_record import BedStrand
-
+from pybedlite.bed_source import BedSource
+from pybedlite.bed_writer import MAX_BED_FIELDS
+from pybedlite.bed_writer import BedWriter
 
 SNIPPET_BED = """\
 # Test header, with a line with whitespace below it.

pyproject.toml

@@ -37,6 +37,7 @@ pytest = "^7.0.0"
 mypy = "^1.5.0"
 flake8 = "^5.0.0"
 black = "^23.0.0"
+isort = "^5.13.0"
 pytest-cov = "^4.0.0"
 
 [tool.poetry.extras]