chore: Switch to ruff (#140)

* chore: Update pyproject.toml

* chore: formatting

* chore: update lockfile

* chore: update GHA

* fix: rm deprecated bits from check.sh

* chore: reorder checks

.github/workflows/pythonpackage.yml

@@ -55,31 +55,26 @@ jobs:
       run: |
         poetry install --extras docs 
 
-    - name: Run pytest
-      shell: bash
-      run: |
-        poetry run python -m pytest --cov=fgpyo --cov-report=xml --cov-branch 
-
-    - name: Run isort
-      shell: bash
-      run: |
-        poetry run isort --force-single-line-imports --profile black fgpyo
-
     - name: Style checking
       shell: bash
       run: |
-        poetry run black --line-length 99 --check fgpyo
+        poetry run ruff format --check fgpyo
 
     - name: Run lint
       shell: bash
       run: |
-        poetry run flake8 --config=ci/flake8.cfg fgpyo
+        poetry run ruff check fgpyo
 
     - name: Run mypy
       shell: bash
       run: |
         poetry run mypy -p fgpyo --config=ci/mypy.ini
 
+    - name: Run pytest
+      shell: bash
+      run: |
+        poetry run python -m pytest --cov=fgpyo --cov-report=xml --cov-branch 
+
     - name: Run docs
       shell: bash
       run: |

ci/check.sh

@@ -37,18 +37,11 @@ function run() {
 
 parent=$(cd $(dirname $0) && pwd -P)
 
-# If the script is invoked with --check only have black check, otherwise have it fix!
-black_extra_args=""
-if [[ "$1" == "--check" ]]; then
-    black_extra_args="--check"
-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"
+banner "Executing in conda environment ${CONDA_DEFAULT_ENV} in directory fgpyo"
+run "Style Checking" "ruff format fgpyo"
+run "Linting"        "ruff check --fix fgpyo"
 run "Type Checking"  "mypy -p fgpyo --config $parent/mypy.ini"
+run "Unit Tests"     "python -m pytest -vv -r sx fgpyo"
 
 if [ -z "$failures" ]; then
     banner "Checks Passed"

fgpyo/read_structure.py

@@ -231,9 +231,7 @@ def fixed_length(self) -> int:
         """The fixed length if there is one. Throws an exception on segments without fixed
         lengths!"""
         if not self.has_fixed_length:
-            raise AttributeError(
-                f"fixed_length called on a variable length read structure: {self}"
-            )
+            raise AttributeError(f"fixed_length called on a variable length read structure: {self}")
         return self._min_length
 
     @property
@@ -307,9 +305,9 @@ def from_segments(
                 segs.append(seg)
             segments = tuple(segs)
 
-        assert all(
-            s.length is None or s.length > 0 for s in segments
-        ), "Read structure contained zero length segments" + "".join(str(s) for s in segments)
+        assert all(s.length is None or s.length > 0 for s in segments), (
+            "Read structure contained zero length segments" + "".join(str(s) for s in segments)
+        )
 
         return ReadStructure(segments=segments)
 

fgpyo/sam/tests/test_builder.py

@@ -254,9 +254,7 @@ def test_sorting() -> None:
 
 def make_sort_order_builder(tmp_path: Path, sort_order: SamOrder) -> Path:
     builder = SamBuilder(sort_order=sort_order)
-    builder.add_pair(
-        name="test3", chrom="chr1", start1=5000, start2=4700, strand1="-", strand2="+"
-    )
+    builder.add_pair(name="test3", chrom="chr1", start1=5000, start2=4700, strand1="-", strand2="+")
     builder.add_pair(name="test2", chrom="chr1", start1=4000, start2=4300)
     builder.add_pair(name="test1", chrom="chr5", start1=4000, start2=4300)
     builder.add_pair(name="test4", chrom="chr2", start1=4000, start2=4300)

fgpyo/sam/tests/test_sam.py

@@ -146,7 +146,10 @@ def test_sam_file_open_writing(
     with NamedTemp(suffix=file_type.extension, dir=tmp_path, mode="w", delete=False) as fp:
         kwargs = {"header": header_dict}
         with sam._pysam_open(
-            path=fp.file, open_for_reading=False, file_type=file_type, **kwargs  # type: ignore
+            path=fp.file,
+            open_for_reading=False,
+            file_type=file_type,
+            **kwargs,  # type: ignore
         ) as sam_writer:
             for r in expected_records:
                 sam_writer.write(r)

fgpyo/util/inspect.py

@@ -210,8 +210,7 @@ def set_parser(
             set({})
             if s == "{}"
             else [
-                subtype_parser(item)
-                for item in set(split_at_given_level(s[1:-1], split_delim=","))
+                subtype_parser(item) for item in set(split_at_given_level(s[1:-1], split_delim=","))
             ]
         )
     )
@@ -392,7 +391,7 @@ def get_parser() -> partial:
 
 
 def get_fields_dict(
-    cls: Union[_DataclassesOrAttrClass, Type[_DataclassesOrAttrClass]]
+    cls: Union[_DataclassesOrAttrClass, Type[_DataclassesOrAttrClass]],
 ) -> Mapping[str, FieldType]:
     """Get the fields dict from either a dataclasses or attr dataclass (or instance)"""
     if is_dataclasses_class(cls):
@@ -404,7 +403,7 @@ def get_fields_dict(
 
 
 def get_fields(
-    cls: Union[_DataclassesOrAttrClass, Type[_DataclassesOrAttrClass]]
+    cls: Union[_DataclassesOrAttrClass, Type[_DataclassesOrAttrClass]],
 ) -> Tuple[FieldType, ...]:
     """Get the fields tuple from either a dataclasses or attr dataclass (or instance)"""
     if is_dataclasses_class(cls):

fgpyo/vcf/tests/test_builder.py

@@ -200,7 +200,7 @@ def test_sort_order(random_generator: random.Random) -> None:
 
 
 def test_zero_sample_records_match_inputs(
-    zero_sample_record_inputs: Tuple[Mapping[str, Any]]
+    zero_sample_record_inputs: Tuple[Mapping[str, Any]],
 ) -> None:
     """Test if zero-sample VCF (no genotypes) records produced match the requested inputs."""
     variant_builder = VariantBuilder()