Apply linting + flake8 fixes

src/crowsetta/annotation.py

@@ -1,8 +1,8 @@
 """A class to represent annotations for a single file."""
 from __future__ import annotations
 
-from pathlib import Path
 import reprlib
+from pathlib import Path
 from typing import Optional
 
 import crowsetta
@@ -89,12 +89,10 @@ def __init__(
 
         if seq:
             if not (
-                    isinstance(seq, crowsetta.Sequence) or
-                    (isinstance(seq, list) and all([isinstance(seq_, crowsetta.Sequence) for seq_ in seq]))
+                isinstance(seq, crowsetta.Sequence)
+                or (isinstance(seq, list) and all([isinstance(seq_, crowsetta.Sequence) for seq_ in seq]))
             ):
-                raise TypeError(
-                    f"``seq`` should be a crowsetta.Sequence or list of Sequences but was: {type(seq)}"
-                )
+                raise TypeError(f"``seq`` should be a crowsetta.Sequence or list of Sequences but was: {type(seq)}")
             self.seq = seq
 
         if bboxes:

src/crowsetta/formats/seq/birdsongrec.py

@@ -8,11 +8,13 @@
 Boundaries in the Birdsong with Variable Sequences. PLoS ONE 11(7): e0159188.
 doi:10.1371/journal.pone.0159188
 """
+from __future__ import annotations
+
 import os
 import pathlib
 import warnings
-from typing import ClassVar, List, Optional
 import xml.etree.ElementTree as ET
+from typing import ClassVar, List, Optional
 
 import attr
 import numpy as np
@@ -36,13 +38,14 @@ class BirdsongRecSyllable:
         text representation of syllable as classified by a human
         or a machine learning algorithm
     """
-    def __init__(self, position, length, label):
+
+    def __init__(self, position: int, length: int, label: str) -> None:
         if not isinstance(position, int):
-            raise TypeError(f'position must be an int, not type {type(position)}')
+            raise TypeError(f"position must be an int, not type {type(position)}")
         if not isinstance(length, int):
-            raise TypeError(f'length must be an int, not type {type(length)}')
+            raise TypeError(f"length must be an int, not type {type(length)}")
         if not isinstance(label, str):
-            raise TypeError(f'label must be a string, not type {type(label)}')
+            raise TypeError(f"label must be a string, not type {type(label)}")
         self.position = position
         self.length = length
         self.label = label
@@ -67,20 +70,19 @@ class BirdsongRecSequence:
         list of syllable objects that make up sequence
     seq_spect : spectrogram object
     """
-    def __init__(self, wav_file, position, length, syl_list):
 
+    def __init__(self, wav_file: PathLike, position: int, length: int, syl_list: list[BirdsongRecSyllable]):
         if not isinstance(wav_file, (str, pathlib.Path)):
-            raise TypeError(f'wav_file must be a string or pathlib.Path, not type {type(wav_file)}')
+            raise TypeError(f"wav_file must be a string or pathlib.Path, not type {type(wav_file)}")
         wav_file = str(wav_file)
         if not isinstance(position, int):
-            raise TypeError(f'position must be an int, not type {type(position)}')
+            raise TypeError(f"position must be an int, not type {type(position)}")
         if not isinstance(length, int):
-            raise TypeError(f'length must be an int, not type {type(length)}')
+            raise TypeError(f"length must be an int, not type {type(length)}")
         if not isinstance(syl_list, list):
-            raise TypeError(f'syl_list must be a list, not type {type(syl_list)}')
+            raise TypeError(f"syl_list must be a list, not type {type(syl_list)}")
         if not all([type(syl) == BirdsongRecSyllable for syl in syl_list]):
-            raise TypeError('not all elements in syl list are of type BirdsongRecSyllable: '
-                            f'{syl_list}')
+            raise TypeError("not all elements in syl list are of type BirdsongRecSyllable: " f"{syl_list}")
         self.wav_file = wav_file
         self.position = position
         self.length = length
@@ -91,9 +93,12 @@ def __repr__(self):
         return f"Sequence(wav_file={self.wav_file}, position={self.position}, length={self.length}, syls={self.syls})"
 
 
-
-def parse_xml(xml_file, concat_seqs_into_songs=False, return_wav_abspath=False,
-              wav_abspath=None):
+def parse_xml(
+    xml_file: PathLike,
+    concat_seqs_into_songs: bool = False,
+    return_wav_abspath: bool = False,
+    wav_abspath: PathLike = None,
+) -> list[BirdsongRecSequence]:
     """parses Annotation.xml files from the BirdsongRecognition dataset:
     Koumura, T. (2016). BirdsongRecognition (Version 1). figshare.
     https://doi.org/10.6084/m9.figshare.3470165.v1
@@ -138,12 +143,11 @@ def parse_xml(xml_file, concat_seqs_into_songs=False, return_wav_abspath=False,
     if return_wav_abspath:
         if wav_abspath:
             if not os.path.isdir(wav_abspath):
-                raise NotADirectoryError(f'return_wav_abspath is True but {wav_abspath} '
-                                         'is not a valid directory.')
+                raise NotADirectoryError(f"return_wav_abspath is True but {wav_abspath} " "is not a valid directory.")
     tree = ET.ElementTree(file=xml_file)
     seq_list = []
-    for seq in tree.iter(tag='Sequence'):
-        wav_file = seq.find('WaveFileName').text
+    for seq in tree.iter(tag="Sequence"):
+        wav_file = seq.find("WaveFileName").text
         if return_wav_abspath:
             if wav_abspath:
                 wav_file = os.path.join(wav_abspath, wav_file)
@@ -152,26 +156,21 @@ def parse_xml(xml_file, concat_seqs_into_songs=False, return_wav_abspath=False,
                 # Annotation.xml file is kept (since this is how the repository is
                 # structured)
                 xml_dirname = os.path.dirname(xml_file)
-                wav_file = os.path.join(xml_dirname, 'Wave', wav_file)
+                wav_file = os.path.join(xml_dirname, "Wave", wav_file)
             if not os.path.isfile(wav_file):
-                raise FileNotFoundError('File {wav_file} is not found')
+                raise FileNotFoundError("File {wav_file} is not found")
 
-        position = int(seq.find('Position').text)
-        length = int(seq.find('Length').text)
+        position = int(seq.find("Position").text)
+        length = int(seq.find("Length").text)
         syl_list = []
-        for syl in seq.iter(tag='Note'):
-            syl_position = int(syl.find('Position').text)
-            syl_length = int(syl.find('Length').text)
-            label = syl.find('Label').text
-
-            syl_obj = BirdsongRecSyllable(position=syl_position,
-                               length=syl_length,
-                               label=label)
+        for syl in seq.iter(tag="Note"):
+            syl_position = int(syl.find("Position").text)
+            syl_length = int(syl.find("Length").text)
+            label = syl.find("Label").text
+
+            syl_obj = BirdsongRecSyllable(position=syl_position, length=syl_length, label=label)
             syl_list.append(syl_obj)
-        seq_obj = BirdsongRecSequence(wav_file=wav_file,
-                           position=position,
-                           length=length,
-                           syl_list=syl_list)
+        seq_obj = BirdsongRecSequence(wav_file=wav_file, position=position, length=length, syl_list=syl_list)
         seq_list.append(seq_obj)
 
     if concat_seqs_into_songs:

src/crowsetta/formats/seq/notmat.py

@@ -1,6 +1,8 @@
 """Module with functions that handle .not.mat annotation files
 produced by evsonganaly GUI.
 """
+from __future__ import annotations
+
 import pathlib
 from typing import ClassVar, Dict, Optional
 
@@ -12,7 +14,7 @@
 from crowsetta.typing import PathLike
 
 
-def load_notmat(filename):
+def load_notmat(filename: PathLike) -> dict:
     """loads .not.mat files created by evsonganaly (Matlab GUI for labeling song)
 
     Parameters
@@ -52,12 +54,10 @@ def load_notmat(filename):
         filename = filename.parent.joinpath(filename.name + ".not.mat")
     else:
         ext = filename.suffix
-        raise ValueError(
-            f"Filename should have extension .cbin.not.mat or .cbin but extension was: {ext}"
-        )
+        raise ValueError(f"Filename should have extension .cbin.not.mat or .cbin but extension was: {ext}")
     notmat_dict = scipy.io.loadmat(filename, squeeze_me=True)
     # ensure that onsets and offsets are always arrays, not scalar
-    for key in ('onsets', 'offsets'):
+    for key in ("onsets", "offsets"):
         if np.isscalar(notmat_dict[key]):  # `squeeze_me` makes them a ``float``, this will be True in that case
             value = np.array(notmat_dict[key])[np.newaxis]  # ``np.newaxis`` ensures 1-d array with shape (1,)
             notmat_dict[key] = value

src/crowsetta/formats/seq/textgrid/parse.py

@@ -173,7 +173,7 @@ def parse_fp(fp: TextIO, keep_empty: bool = False) -> dict:
     }
 
     tiers = []
-    for i in range(n_tier):
+    for _ in range(n_tier):
         if not is_short:
             fp.readline()  # skip item[\d]: (where \d is some number)
         tier_type = get_str_from_next_line(fp)
@@ -182,7 +182,7 @@ def parse_fp(fp: TextIO, keep_empty: bool = False) -> dict:
         xmax_tier = get_float_from_next_line(fp)
 
         entries = []  # intervals or points depending on tier type
-        for i in range(get_int_from_next_line(fp)):
+        for _ in range(get_int_from_next_line(fp)):
             if not is_short:
                 fp.readline()  # skip intervals [\d]
             if tier_type == INTERVAL_TIER:
@@ -246,7 +246,7 @@ def parse(textgrid_path: str | pathlib.Path, keep_empty: bool = False) -> dict:
     try:
         with textgrid_path.open("r", encoding="utf-16") as fp:
             textgrid_raw = parse_fp(fp, keep_empty)
-    except (UnicodeError, UnicodeDecodeError):
+    except UnicodeError:
         with textgrid_path.open("r", encoding="utf-8") as fp:
             textgrid_raw = parse_fp(fp, keep_empty)
     return textgrid_raw

src/crowsetta/formats/seq/textgrid/textgrid.py

@@ -368,7 +368,9 @@ def to_seq(
 
         return seq
 
-    def to_annot(self, tier: int | str | None = None, round_times: bool = True, decimals: int = 3) -> crowsetta.Annotation:
+    def to_annot(
+        self, tier: int | str | None = None, round_times: bool = True, decimals: int = 3
+    ) -> crowsetta.Annotation:
         """Convert interval tier or tiers from this TextGrid annotation
         to a :class:`crowsetta.Annotation` with a :data:`seq` attribute.
 

src/crowsetta/transcriber.py

@@ -121,6 +121,7 @@ def __init__(self, format: "Union[str, crowsetta.interface.SeqLike, crowsetta.in
                     "and the name 'csv' will stop working in the next version. "
                     "Please change any usages of the name 'csv' to 'generic-seq'` now.",
                     FutureWarning,
+                    stacklevel=2,
                 )
             _format_class = formats.by_name(format)
         elif inspect.isclass(format):