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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

5.1.0

Added

  • Make crowsetta.SimpleSeq.from_file work with an "empty" csv file, one that has no annotated segments (e.g. because no audio was above threshold for segmenting) #280. Fixes #264.
  • Add default_label argument to crowsetta.SimpleSeq.from_file that will add labels to segments in a csv file if there are none #280. Fixes #271.
  • Add example csv file from Jourjine et al. 2023 dataset #280. Fixes #274.
  • Add how-to showing how to work with unannotated segmentation in a csv file, using the csv from the Jourjine et al. 2023 dataset #280. Fixes #275.

Changed

  • Rename crowsetta.data to crowsetta.examples, simplify how crowsetta.example works (to be more like vocalpy.example) and give all the example annotation files more specific names so that we can have multiple examples per annotation format #280. Fixes #278.
  • Import format classes at package level, so we can just type e.g. crowsetta.SimpleSeq instead of crowsetta.formats.seq.SimpleSeq ("flat is better than nested") #280. Fixes #273.

Fixed

  • Make crowsetta.SimpleSeq.from_file use columns_map arg to rename only columns whose names are keys in the supplied dict, and ignore other columns in the csv file #280. Fixes #272.

5.0.3

Fixed

  • Replace deprecated pandera.SchemaModel with DataFrameModel, fixes AttributeError on import after new install #266. Fixes #265.
  • Change range of Python version supported from 3.9-3.11 to 3.10-3.12 #268. Fixes #267.

5.0.2 -- 2024-01-01

Fixed

  • Vendor code from evfuncs and birdsong-recognition-dataset packages, to reduce the number of dependencies and make sure the code is maintained #263. Fixes #262.

5.0.1 -- 2023-05-27

Fixed

  • Fix bug in "generic-seq" format; use validated dataframe returned by pandera schema, so that "label" column is coerced to strings #258. Fixes #257.

5.0.0 -- 2023-03-29

Added

  • Add information on contributing and setting up a development environment #212. Fixes #30.
  • Add method to convert generic sequence format to a pandas DataFrame #216.
  • Add additional vignettes to docs: on removing "silent" labels from TextGrid annotations, on converting to the simple sequence and generic sequence formats #216. Fixes #152 and #197.
  • Add format class for Audacity extended label track format #226. Fixes #222 and #213.
  • Add the ability for a crowsetta.Annotation to have multiple sequences #243. Fixes #42.
  • Rewrite TextGrid class to better handle file formats: parse both "short" and default format in either UTF-8 or UTF-16 encoding; remove empty intervals from interval tiers by default; can convert multiple interval tiers to a single crowsetta.Annotation with multiple crowsetta.Sequences #243. Fixes #241

Removed

  • Remove Segment.from_row method, no longer used #232. Fixes #231

Fixed

  • Revise landing page of docs, and some vignettes. Make other changes to clean up the docs build process #216.
  • Coerce path-like attributes of GenericSeq dataframe schema to be strings. This helps ensure these columns are always native Pandas types #237.
  • Fix how the crowsetta.Segment class converts onset sample and offset sample to int; correctly handle multiple numpy integer subtypes #238.

4.0.0.post2 -- 2022-06-25

Changed

  • c6ba100 Fix description and uri in pyproject.toml and crowsetta/about.py
  • f70828f Make README images link to raw GitHub files so they render on PyPI

4.0.0.post1 -- 2022-06-25

Changed

  • clean up README and make other doc fixes #201. Fixes #199.

4.0.0 -- 2022-06-25

Added

  • add Raven format #164. Fixes #84.
  • add example data #180. Fixes #90.
  • add examples to docstrings, using example data #180. Fixes #158.
  • import register_format at top level of package, to be able to just write @crowsetta.register_format #181. Fixes #177.
  • add 'aud-txt' format, for Audacity standard LabelTracks exported to .txt files #183. Fixes #96.
  • add ability to extract example data to local file system; avoids need to use context manager returned by importlib.resources to access the example data files. #185. Fixes #184.
  • add logo #198. Fixes #17.

Changed

  • change Annotation class to represent both sequence-like annotation formats and bounding box-like annotation formats #164. Resolves #149 and #150.
  • re-design API, and rewrite annotation formats as classes #161.
    • Re-writing as classes fixes #99.
    • API re-design fixes #120.
    • Adds an interface sub-package that specifies an interface for two types of annotations: sequence-like and bounding-box like. Fixes #105
    • All existing annotation formats were sequence-like, and they now adhere to that interface; the classes are registered as sub-classes.
      • Some classes were additionally re-factored; e.g.
        • 'generic-seq' now uses pandas (fixes #63)
        • 'simple-seq' can parse multiple formats (fixes #134)
    • Formats themselves are now in a formats sub-package, fixes #109
    • Add better functions to list the formats in this sub-package (fixes #92); can call crowsetta.formats.as_list to get a list of shorthand string names, and crowsetta.formats.by_name with the shorthand string name to get back to the corresponding class.
    • Transcriber.from_file now returns an instance of an annotation format classes. Methods like to_annot can be called on this instance. This refactor greatly simplifies the Transcriber class while maintaining mostly the same API (now need to chain calls like Transcriber.from_file().to_annot(), or capture the returned annotation instance in a variable and use it instead). Fixes #144.
  • convert docs to markdown and use myst-parser #153. Fixes #151.
  • require Python >= 3.8 to adhere to NEP-29 #168. Fixes #166.
  • rename Annotation.audio_path attribute to notated_path to be more general, e.g., because annotations can also annotate a spectrogram #169. Fixes #148.
  • rename onset_ind and offset_ind to onset_sample and offset_sample for clarity #174. Fixes #156.
  • rename first parameter of from_file method for all format classes to annot_path for consistency. #182. Fixes #178.
  • Revise documentation #191. Fixes #152 as well as #21, #35, #138, and #157.
  • have formats.as_list return list sorted (i.e., alphabetically) #194. Fixes #187.

Fixed

  • fix crowsetta.formats.register_format function added in #161 and rewrite example custom annotation formats to use it #176. Fixes #119.

Removed

  • remove Stack class -- was not being used #172. Fixes #170.
  • remove deprecated 'csv' format that was replaced by 'generic-seq' #173. Fixes #171.
  • remove Meta class -- no longer used #193. Fixes #190.

3.4.0 -- 2022-03-26

Added

  • add a __repr__ to the Transcriber class #145. Fixes #142.

Changed

  • change format names 'simple-csv' and 'csv' to 'simple-seq' and 'generic-seq'. With goal of eventually having 'simple-seq' work on other file formats, e.g. .txt, and for 'csv' to be the "generic" sequence format that allow for converting between others. #140. Fixes #133.

  • deprecate the name 'csv' for the 'generic-seq' format; a FutureWarning is raised when creating a Transcriber with format='csv'. #143. Fixes #141.

  • switch to using nox for development, instead of make #137. Fixes [#132](#132.

3.3.0 -- 2022-01-02

Added

  • add 'simple-csv' format #130. Fixes #97.

Changed

  • change dependency / format name koumura to birdsong-recognition-dataset because package was renamed #126. Fixes #124.
  • switch to using flit to build / publish. Remove poetry. #127. Fixes #125.
  • move textgrid package into sub-package _vendor, since flit only works with a single top-level package. #127. This is the approach pip takes, as discussed on pypa/flit#497.
  • rename attributes / variables onsets_Hz and offsets_Hz to onset_inds and offset_inds #128. Fixes #87.
  • rename function crowsetta.validation._parse_file to validate_ext #129. Fixes #123.

3.2.0 -- 2021-12-19

Added

Changed

Fixed

  • Fix .TextGrid and .phn docstrings that referred to ".not.mat files" #118.

Removed

  • remove data module #110 that downloaded data from other sources. Fixes #93.

3.1.1.post1 -- 2021-03-04

fixed

  • add missing packages to pyproject.toml so that textgrid is included in build 857ba09
  • add metadata to pyproject.toml so that README is used as "long description" and appears on PyPI e8b8209

3.1.1 -- 2021-03-04

changed

  • switch to using poetry for development #79
  • raise minimum version of evfuncs to 0.3.1 #79
  • raise minimum version of koumura to 0.2.0 #79
  • change to using GitHub Actions for continuous integration #83

fixed

  • fix dependencies and Python so they are not pinned to major version #83

3.1.0

changed

  • switch to using soundfile library to parse .wav files #75 see discussion on issue #67.

fixed

  • fix phn2annot function so it works with .PHN and .WAV files found in some versions of TIMIT dataset #75
    • needed to make extension checking case-insensitive, see issue #68
    • and also switch to soundfile library to be able to parse the specific NIST format of .WAV files

3.0.1

fixed

  • add missing comma in ENTRY_POINTS in setup.py so that built-in formats are properly installed 599149f

3.0.0

added

  • make csv a format #60; See discussion on #55.

changed

  • change name of Transcriber parameter annot_format to just format #64
  • change name of Annotation attributes annot_file and audio_file to annot_path and audio_path, for clarity and to match what's used in the vak library #65

2.3.0

added

  • add phn module that parses .phn files from TIMIT dataset #59

2.2.0

changed

  • change types of Annotation attributes annot_file and audio_path from str (string) to pathlib.Path, to fix errors raised when passing in Path objects (because the attribute validator requires a string), and because it's preferable to work with Path objects over strings #52
  • change default value for koumura2annot parameter wavpath so that the function will work regardless of current working directory for user, instead of requiring them to be in the parent directory of the .wav files that wavpath refers to #53

fixed

  • fixed error that koumura2annot function threw when annot_file was a pathlib.Path and not a string #53

2.1.0

changed

  • modify functions for .not.mat annotation files (created by evsonganaly GUI) so they do not require other files such as .rec files (created by evTAF data acquisition program)
    • notmat.notmat2annot no longer looks for .rec files, which it used to get the sampling rate and convert onsets and offsets from seconds to Hz
  • the make_notmat for creating .not.mat files from Annotations also now expects onsets and offsets in seconds, not Hz.
    • the idea being that one can go from .not.mat to Annotation and back without doing any extra conversion. If user needs conversion to Hz for some other reason they can do this using the Annotation

2.0.0

added

  • add Annotation class
    • which has 'audio_file' and 'annot_file' attributes, along with 'seq' attribute

changed

  • rewrite everything centered around Annotation class
    • meaning Sequence and Segment lose their redundant 'file' attributes and all format modules convert to and from Annotations and so does the csv module
  • single-source version
    • now found in an __about__.py file in src/crowsetta that is used by setup.py.

1.1.1

changed

  • segments property of a Sequence is a tuple, not a list, so that class is immutable + hashable

fixed

  • __hash__ implementation for Sequence class
    • convert attributes that are numpy.ndarrays into tuples before hashing
  • tests for Sequence
    • no longer assert that calling __hash__ raises NotImplementedError
    • test that segments attribute is a tuple not a list

1.1.0

added

  • implement hashing and equality for Sequence class
    • this makes it possible to use with concurrency, e.g. with the Dask library

1.0.0

added

  • entry point group crowsetta.format to make it possible to 'install' formats
    • removes special casing for built-in formats, they just get added via entry point
    • instead of parsing a config.json file built into the package
  • module for working with Praat Textgrid format
  • Meta class which represents metadata about a format
    • such as file extension associated with it
    • and the module / functions that a Transcriber instance should use to work with this format

changed

  • Each instance of Transcriber has only one vocal annotation format that it handles
    • because it's annoying to type file_format every time you call a method like to_seq
    • instead you just make an instance of Transcriber for each format you want
    • This also works better with crowsetta.format entry points and Meta class; when you instantiate a Transcriber for a given voc_format, the __init__ uses the Meta for that format to figure out which function to use for to_seq, to_csv, etc.
    • For this reason bumping to 1.0.0, new Transcriber not backwards compatible
      • although this will be inconvenient for millions of people

0.2.0a5

added

  • Sequence instances have attributes: labels, onsets_s, offsets_s, onset_inds, offset_inds, and file.
  • Explanation of default to_csv function for user formats in howto-user-config.

changed

  • Sequence class totally re-written
    • no longer attrs-based
    • because of somewhat complicated logic for validating arguments that was necessary in init (to prevent user from creating a 'bad' instance.)
  • Sequences are immutable. Idea is they are just connectors between annotation and whatever user needs to do with it so you shouldn't need to change any attribute values after loading annotation
  • Segment also immutable (by setting frozen=True in call to attr.s decorator)
  • Transcriber.init uses config.json instead of config.ini to read defaults
    • this makes init logic more readable since we don't have to convert user_config dict to strings and then back again; default config just loads as a dict from the .json file and we add the user_config dicts to it

0.2.0a4

added

  • data module that downloads small example datasets for each annotation format
    • includes formats function that is imported at package level and prints formats built in to crowsetta
  • to_seq_func_to_csv that takes a yourformat2seq function and returns a function that will convert the same format to csv files (just a wrapper around your function and seq2csv)
  • for docs, Makefile that generates ./notebooks folder from ./doc/notebooks

changed

  • major revamp of docs
  • config_dicts for user_config arg of Transcriber.init only require module and to_seq keys; to_csv and to_format are optional, can be specified Python None or a string 'None'

fixed

  • Transcriber raises NotImplemented error when to_csv or to_format are None for a specified format (instead of crashing mysteriously)
  • seq2csv and csv2seq can deal with None values for one pair of onsets and offsets

0.2.0a3

changed

  • fix failing tests

0.2.0a2

added

  • Segment class, attrs-based
    • has asdict method (wrapper around attrs function)
    • has class variable _FIELDS which is used in any place where we need to know how to go from Segment attributes to rows of a csv file, e.g. in src/crowsetta/csv.py and in tests

changed

  • Sequence class is now attrs-based, has factory functions, is itself just a list of Segments
    • now has to_dict method
  • Crowsetta class is now called Transcriber

0.2.0a1

added

  • add Crowsetta class with simple interface for converting any annotation to
  • add ability to work with user-defined functions
    • user passes an extra_config dict when instantiating Crowsetta
  • add docs

changed

  • change package name to Crowsetta
  • change function names so they are all 'format2seq' or 'format2csv' or 'toformat' for consistency

0.1.0

changed

  • Convert tests to Python unittest format (instead of using PyTest library)

added

  • Write README.md with usage