Ruff lint fixes (scikit-bio#1922)

* fixed linting errors in sequence directory

* fixed linting errors in io directory

* removed repeated dictionary key in diversity directory

* fixed type comparison in alignment directory

* fixed second repeated key literal in diversity directory

skbio/alignment/tests/test_ssw.py

@@ -86,7 +86,7 @@ def _check_bit_flag_sets_properties_falsy_or_negative(
         kwarg = {}
 
         def falsy_or_negative(alignment, prop):
-            if type(alignment[prop]) is int:
+            if isinstance(alignment[prop], int):
                 return alignment[prop] < 0
             else:
                 return not alignment[prop]

skbio/diversity/alpha/_lladser.py

@@ -426,8 +426,6 @@ def _ul_confidence_bounds(f, r, alpha):
     (6, 6, 0.95): (1.8207383, 2.58658608),
     (5, 7, 0.95): (2.48303930, 3.22806682),
     (3, 14, 0.95): (7.17185045, 8.27008349),
-    (2.5, 19, 0.95): (11.26109001, 11.96814857),
-    (1.5, 94, 0.95): (75.9077267, 76.5492088),
     (1.25, 309, 0.95): (275.661191, 275.949782)
 }
 

skbio/io/format/gff3.py

@@ -359,9 +359,9 @@ def _interval_metadata_to_gff3(obj, fh, seq_id, skip_subregion=True):
 
 def _construct_seq(fh, constructor=DNA, seq_num=1):
     lines = []
-    for i, (data_type, seq_id, l) in enumerate(_yield_record(fh), 1):
+    for i, (data_type, seq_id, L) in enumerate(_yield_record(fh), 1):
         if data_type == 'data' and seq_num == i:
-            lines = l
+            lines = L
     seq = _get_nth_sequence(_fasta_to_generator(fh, constructor=constructor),
                             seq_num=seq_num)
     seq.interval_metadata = _parse_record(lines, len(seq))

skbio/io/registry.py

@@ -887,7 +887,7 @@ def sniffer(self, override=False):
         (False, {})
 
         """
-        if not type(override) is bool:
+        if isinstance(override, bool) is not True:
             raise InvalidRegistrationError("`override` must be a bool not %r"
                                            % override)
 

skbio/sequence/_sequence.py

@@ -648,7 +648,7 @@ def __init__(self, sequence, metadata=None, positional_metadata=None,
             self._convert_to_uppercase(lowercase_mask)
 
             # If it isn't True, it must be a string_type
-            if not (lowercase is True):
+            if lowercase is not True:
                 self.positional_metadata[lowercase] = lowercase_mask
         else:
             raise TypeError("lowercase keyword argument expected a bool or "
@@ -1414,7 +1414,7 @@ def replace(self, where, character):
         True
 
         """
-        if type(character) is not bytes:
+        if isinstance(character, bytes) is not True:
             character = character.encode('ascii')
         character = ord(character)
         index = self._munge_to_index_array(where)
@@ -2179,7 +2179,7 @@ def _munge_to_sequence(self, other, method):
         return Sequence(other)
 
     def _munge_to_bytestring(self, other, method):
-        if type(other) is bytes:
+        if isinstance(other, bytes):
             return other
         elif isinstance(other, str):
             return other.encode('ascii')