rever reformatting

fgpyo/fasta/builder.py

@@ -49,6 +49,7 @@ def samtools_dict(*args: Any) -> None:
     def samtools_faidx(*args: Any) -> None:
         pass
 
+
 else:
     from pysam import dict as samtools_dict
     from pysam import faidx as samtools_faidx
@@ -91,10 +92,7 @@ class ContigBuilder:
     """
 
     def __init__(
-        self,
-        name: str,
-        assembly: str,
-        species: str,
+        self, name: str, assembly: str, species: str,
     ):
         self.name = name
         self.assembly = assembly
@@ -146,10 +144,7 @@ class FastaBuilder:
     """
 
     def __init__(
-        self,
-        assembly: str = "testassembly",
-        species: str = "testspecies",
-        line_length: int = 80,
+        self, assembly: str = "testassembly", species: str = "testspecies", line_length: int = 80,
     ):
         self.assembly: str = assembly
         self.species: str = species
@@ -161,10 +156,7 @@ def __getitem__(self, key: str) -> ContigBuilder:
         return self.__contig_builders[key]
 
     def add(
-        self,
-        name: str,
-        assembly: Optional[str] = None,
-        species: Optional[str] = None,
+        self, name: str, assembly: Optional[str] = None, species: Optional[str] = None,
     ) -> ContigBuilder:
         """
         Creates and returns a new ContigBuilder for a contig with the provided name.
@@ -189,10 +181,7 @@ def add(
         self.__contig_builders[name] = builder
         return builder
 
-    def to_file(
-        self,
-        path: Path,
-    ) -> None:
+    def to_file(self, path: Path,) -> None:
         """
         Writes out the set of accumulated contigs to a FASTA file at the `path` given.
         Also generates the accompanying fasta index file (`.fa.fai`) and sequence

fgpyo/fasta/tests/test_builder.py

@@ -25,17 +25,10 @@ def test_bases_length_from_ContigBuilder_add_default() -> None:
 
 
 @pytest.mark.parametrize(
-    "name, bases, times, length_bases",
-    [
-        ("chr1", "AAA", 3, 9),
-        ("chr2", "TTT", 10, 30),
-    ],
+    "name, bases, times, length_bases", [("chr1", "AAA", 3, 9), ("chr2", "TTT", 10, 30),],
 )
 def test_bases_length_from_ContigBuilder_add(
-    name: str,
-    bases: str,
-    times: int,
-    length_bases: int,
+    name: str, bases: str, times: int, length_bases: int,
 ) -> None:
     """Checks that the number of bases in each contig is correct"""
     builder = FastaBuilder()
@@ -60,17 +53,10 @@ def test_contig_dict_is_not_accessable() -> None:
 
 @pytest.mark.parametrize(
     "name, bases, times, expected",
-    [
-        ("chr3", "AAA a", 3, ("AAAA" * 3)),
-        ("chr2", "TT T gT", 10, ("TTTGT" * 10)),
-    ],
+    [("chr3", "AAA a", 3, ("AAAA" * 3)), ("chr2", "TT T gT", 10, ("TTTGT" * 10)),],
 )
 def test_bases_string_from_ContigBuilder_add(
-    name: str,
-    bases: str,
-    times: int,
-    expected: str,
-    tmp_path: Path,
+    name: str, bases: str, times: int, expected: str, tmp_path: Path,
 ) -> None:
     """
     Reads bases back from fasta and checks that extra spaces are removed and bases are uppercase

fgpyo/io/tests/test_io.py

@@ -84,33 +84,19 @@ def test_assert_path_is_writeable_pass() -> None:
 
 
 @pytest.mark.parametrize(
-    "suffix, expected",
-    [
-        (".gz", io.TextIOWrapper),
-        (".fa", io.TextIOWrapper),
-    ],
+    "suffix, expected", [(".gz", io.TextIOWrapper), (".fa", io.TextIOWrapper),],
 )
-def test_reader(
-    suffix: str,
-    expected: Any,
-) -> None:
+def test_reader(suffix: str, expected: Any,) -> None:
     """Tests fgpyo.io.to_reader"""
     with NamedTemp(suffix=suffix, mode="r", delete=True) as read_file:
         with fio.to_reader(path=Path(read_file.name)) as reader:
             assert isinstance(reader, expected)
 
 
 @pytest.mark.parametrize(
-    "suffix, expected",
-    [
-        (".gz", io.TextIOWrapper),
-        (".fa", io.TextIOWrapper),
-    ],
+    "suffix, expected", [(".gz", io.TextIOWrapper), (".fa", io.TextIOWrapper),],
 )
-def test_writer(
-    suffix: str,
-    expected: Any,
-) -> None:
+def test_writer(suffix: str, expected: Any,) -> None:
     """Tests fgpyo.io.to_writer()"""
     with NamedTemp(suffix=suffix, mode="w", delete=True) as write_file:
         with fio.to_writer(path=Path(write_file.name)) as writer:
@@ -121,10 +107,7 @@ def test_writer(
     "suffix, list_to_write",
     [(".txt", ["Test with a flat file", 10]), (".gz", ["Test with a gzip file", 10])],
 )
-def test_read_and_write_lines(
-    suffix: str,
-    list_to_write: List[Any],
-) -> None:
+def test_read_and_write_lines(suffix: str, list_to_write: List[Any],) -> None:
     """Test fgpyo.fio.read_lines and write_lines"""
     with NamedTemp(suffix=suffix, mode="w", delete=True) as read_file:
         fio.write_lines(path=Path(read_file.name), lines_to_write=list_to_write)

fgpyo/sam/__init__.py

@@ -863,11 +863,7 @@ def all_recs(self) -> Iterator[AlignedSegment]:
             for rec in recs:
                 yield rec
 
-    def write_to(
-        self,
-        writer: SamFile,
-        primary_only: bool = False,
-    ) -> None:
+    def write_to(self, writer: SamFile, primary_only: bool = False,) -> None:
         """Write the records associated with the template to file.
 
         Args:
@@ -883,11 +879,7 @@ def write_to(
         for rec in rec_iter:
             writer.write(rec)
 
-    def set_tag(
-        self,
-        tag: str,
-        value: Union[str, int, float, None],
-    ) -> None:
+    def set_tag(self, tag: str, value: Union[str, int, float, None],) -> None:
         """Add a tag to all records associated with the template.
 
         Setting a tag to `None` will remove the tag.

fgpyo/sam/tests/test_sam.py

@@ -154,9 +154,7 @@ def test_sam_file_open_writing(
 
 
 def test_sam_file_open_writing_header_keyword(
-    expected_records: List[pysam.AlignedSegment],
-    header_dict: AlignmentHeader,
-    tmp_path: Path,
+    expected_records: List[pysam.AlignedSegment], header_dict: AlignmentHeader, tmp_path: Path,
 ) -> None:
     # Use SamWriter
     # use header as a keyword argument

fgpyo/sam/tests/test_template_iterator.py

@@ -73,9 +73,7 @@ def test_to_templates() -> None:
     assert len(list(template2.all_recs())) == 2
 
 
-def test_write_template(
-    tmp_path: Path,
-) -> None:
+def test_write_template(tmp_path: Path,) -> None:
     builder = SamBuilder()
     template = Template.build(
         [

fgpyo/tests/test_read_structure.py

@@ -31,24 +31,9 @@ def _S(off: int, len: int) -> ReadSegment:
         ("1M", (_M(0, 1),)),
         ("1S", (_S(0, 1),)),
         ("101T", (_T(0, 101),)),
-        (
-            "5B101T",
-            (
-                _B(0, 5),
-                _T(5, 101),
-            ),
-        ),
+        ("5B101T", (_B(0, 5), _T(5, 101),),),
         ("123456789T", (_T(0, 123456789),)),
-        (
-            "10T10B10B10S10M",
-            (
-                _T(0, 10),
-                _B(10, 10),
-                _B(20, 10),
-                _S(30, 10),
-                _M(40, 10),
-            ),
-        ),
+        ("10T10B10B10S10M", (_T(0, 10), _B(10, 10), _B(20, 10), _S(30, 10), _M(40, 10),),),
     ],
 )
 def test_read_structure_from_string(string: str, segments: Tuple[ReadSegment, ...]) -> None:
@@ -58,24 +43,8 @@ def test_read_structure_from_string(string: str, segments: Tuple[ReadSegment, ..
 @pytest.mark.parametrize(
     "string,segments",
     [
-        (
-            "75T 8B 8B 75T",
-            (
-                _T(0, 75),
-                _B(75, 8),
-                _B(83, 8),
-                _T(91, 75),
-            ),
-        ),
-        (
-            " 75T  8B   8B     75T  ",
-            (
-                _T(0, 75),
-                _B(75, 8),
-                _B(83, 8),
-                _T(91, 75),
-            ),
-        ),
+        ("75T 8B 8B 75T", (_T(0, 75), _B(75, 8), _B(83, 8), _T(91, 75),),),
+        (" 75T  8B   8B     75T  ", (_T(0, 75), _B(75, 8), _B(83, 8), _T(91, 75),),),
     ],
 )
 def test_read_structure_from_string_with_whitespace(
@@ -98,8 +67,7 @@ def test_read_structure_variable_once_and_only_once_last_segment_ok(
 
 
 @pytest.mark.parametrize(
-    "string",
-    ["++M", "5M++T", "5M70+T", "+M+T", "+M70T"],
+    "string", ["++M", "5M++T", "5M70+T", "+M+T", "+M70T"],
 )
 def test_read_structure_variable_once_and_only_once_last_segment_exception(string: str) -> None:
     with pytest.raises(Exception):

fgpyo/util/inspect.py

@@ -68,9 +68,7 @@ def split_at_given_level(
 
 
 def _get_parser(
-    cls: Type,
-    type_: TypeAlias,
-    parsers: Optional[Dict[type, Callable[[str], Any]]] = None,
+    cls: Type, type_: TypeAlias, parsers: Optional[Dict[type, Callable[[str], Any]]] = None,
 ) -> partial:
     """Attempts to find a parser for a provided type.
 
@@ -114,11 +112,7 @@ def get_parser() -> partial:
                 assert (
                     len(subtypes) == 1
                 ), "Lists are allowed only one subtype per PEP specification!"
-                subtype_parser = _get_parser(
-                    cls,
-                    subtypes[0],
-                    parsers,
-                )
+                subtype_parser = _get_parser(cls, subtypes[0], parsers,)
                 return functools.partial(
                     lambda s: list(
                         []
@@ -134,11 +128,7 @@ def get_parser() -> partial:
                 assert (
                     len(subtypes) == 1
                 ), "Sets are allowed only one subtype per PEP specification!"
-                subtype_parser = _get_parser(
-                    cls,
-                    subtypes[0],
-                    parsers,
-                )
+                subtype_parser = _get_parser(cls, subtypes[0], parsers,)
                 return functools.partial(
                     lambda s: set(
                         set({})
@@ -151,12 +141,7 @@ def get_parser() -> partial:
                 )
             elif typing.get_origin(type_) == tuple:
                 subtype_parsers = [
-                    _get_parser(
-                        cls,
-                        subtype,
-                        parsers,
-                    )
-                    for subtype in typing.get_args(type_)
+                    _get_parser(cls, subtype, parsers,) for subtype in typing.get_args(type_)
                 ]
 
                 def tuple_parse(tuple_string: str) -> Tuple[Any, ...]:
@@ -185,16 +170,8 @@ def tuple_parse(tuple_string: str) -> Tuple[Any, ...]:
                     len(subtypes) == 2
                 ), "Dict object must have exactly 2 subtypes per PEP specification!"
                 (key_parser, val_parser) = (
-                    _get_parser(
-                        cls,
-                        subtypes[0],
-                        parsers,
-                    ),
-                    _get_parser(
-                        cls,
-                        subtypes[1],
-                        parsers,
-                    ),
+                    _get_parser(cls, subtypes[0], parsers,),
+                    _get_parser(cls, subtypes[1], parsers,),
                 )
 
                 def dict_parse(dict_string: str) -> Dict[Any, Any]:
@@ -254,9 +231,7 @@ def dict_parse(dict_string: str) -> Dict[Any, Any]:
 
 
 def attr_from(
-    cls: Type,
-    kwargs: Dict[str, str],
-    parsers: Optional[Dict[type, Callable[[str], Any]]] = None,
+    cls: Type, kwargs: Dict[str, str], parsers: Optional[Dict[type, Callable[[str], Any]]] = None,
 ) -> Any:
     """Builds an attr class from key-word arguments
 

fgpyo/util/logging.py

@@ -125,9 +125,7 @@ def __exit__(
         return False
 
     def record(
-        self,
-        reference_name: Optional[str] = None,
-        position: Optional[int] = None,
+        self, reference_name: Optional[str] = None, position: Optional[int] = None,
     ) -> bool:
         """Record an item at a given genomic coordinate.
         Args:
@@ -147,10 +145,7 @@ def record(
         else:
             return False
 
-    def record_alignment(
-        self,
-        rec: AlignedSegment,
-    ) -> bool:
+    def record_alignment(self, rec: AlignedSegment,) -> bool:
         """Correctly record pysam.AlignedSegments (zero-based coordinates).
 
         Args:
@@ -164,11 +159,7 @@ def record_alignment(
         else:
             return self.record(rec.reference_name, rec.reference_start + 1)
 
-    def _log(
-        self,
-        refname: Optional[str] = None,
-        position: Optional[int] = None,
-    ) -> None:
+    def _log(self, refname: Optional[str] = None, position: Optional[int] = None,) -> None:
         """Helper method to print the log message.
 
         Args:
@@ -187,9 +178,7 @@ def _log(
 
         self.printer(f"{self.verb} {self.count:,d} {self.noun}: {coordinate}")
 
-    def log_last(
-        self,
-    ) -> bool:
+    def log_last(self,) -> bool:
         """Force logging the last record, for example when progress has completed."""
         if self._count_mod_unit != 0:
             self._log(refname=self._last_reference_name, position=self._last_position)

fgpyo/util/tests/test_logging.py

@@ -43,12 +43,7 @@ def test_progress_logger_as_context_manager() -> None:
 
 
 @pytest.mark.parametrize(
-    "record",
-    [
-        (r1_mapped_named),
-        (r2_unmapped_named),
-        (r2_unmapped_un_named),
-    ],
+    "record", [(r1_mapped_named), (r2_unmapped_named), (r2_unmapped_un_named),],
 )
 def test_record_alignment_mapped_record(record: pysam.AlignedSegment) -> None:
     # Define instance of ProgressLogger