Require crowsetta >=5.0.0 in pyproject.toml

NickleDave committed May 21, 2023

Use crowsetta.format.as_list() to make VALID_ANNOT_FORMATS in vak.c… …

…onstants

NickleDave committed May 21, 2023

Fix how files.find_fname and files.from_dir handle extensions tha… …

…t start with a period (by removing it)

NickleDave committed May 21, 2023

Rewrite vak/annotation.py to use crowsetta >= 5.0 …

- Call to_annot on instances returned by Transcriber.from_file
- Use crowsetta.formats.by_name to get format class,
  so we can get its extension (instead of using getattr
  on a module)
- Use `notated_path` attribute instead of `audio_path`

NickleDave committed May 21, 2023

Call to_annot on instances returned by Transcriber.from_file in `io.d… …

…ataframe.from_file` function

NickleDave committed May 21, 2023

Upper bound torch and lightning below 2.0 for now

NickleDave committed May 21, 2023

Fix fixtures/annot.py to use crowsetta>=5.0

NickleDave committed May 21, 2023

Rename function in tests/scripts/generate_data_for_tests.py, main -> … …

…generate_test_data to avoid lightning crash

NickleDave committed May 21, 2023

Fix test in tests/test_transforms/test_labeled_timebins/test_function… …

…al.py to use crowsetta>=5.0 attribute name, notated_path

NickleDave committed May 21, 2023

Add to pytest filterwarnings in pyproject.toml

NickleDave committed May 21, 2023

WIP: Rewrite vak.annotation.map_annotated_to_annot to have 3 ways o… …

…f mapping

NickleDave committed May 22, 2023

WIP: Fix/add tests in tests/test_annotation after rewriting `vak.anno… …

…tation.map_annotated_to_annot`

NickleDave committed May 22, 2023

WIP: More changes to vak/annotation.py

NickleDave committed May 23, 2023

WIP: More changes to tests/test_annotation.py

NickleDave committed May 23, 2023

Make mores fixes to src/vak/annotation.py

NickleDave committed May 23, 2023

Rename audio_stem_from_path -> audio_filename_from_path in vak/an… …

…notation.py

NickleDave committed May 23, 2023

Rename audio_stem_from_path -> audio_filename_from_path in tests/… …

…test_annotation.py

NickleDave committed May 23, 2023

WIP: Further fixes to vak/annotation.py

NickleDave committed May 23, 2023

Fix a reference to a function in a docstring in src/vak/annotation.py

NickleDave committed May 24, 2023

Add more type hints, revise docstring in src/vak/annotation.py

NickleDave committed May 24, 2023

Fix bug in src/vak/annotation.py: 'annot_class.name' -> 'annot.annot_… …

…path.name'

NickleDave committed May 25, 2023

Revise docstring, add type hints to vak.files.from_dir

NickleDave committed May 25, 2023

Modify vak.io.audio.to_spect to take annot_format arg and pass it… …

… to `map_annotated_to_annot`

NickleDave committed May 25, 2023

Modify vak.io.spect.to_dataframe to pass annot_format to `map_ann… …

…otated_to_annot`

NickleDave committed May 25, 2023

Add type hints, rename vak_df -> dataset_df to `vak.io.dataframe.… …

…from_files`

NickleDave committed May 25, 2023

Make fixes in vak.annotation: pass annot_format inside from_df, add a… …

…nnotated_ext parameter to map_annotated_to_annot and _map_using_ext

NickleDave committed May 25, 2023

Add spect_ext parameter to spect.to_dataframe, pass into map_annotate… …

…d_to_annot as annotated_ext

NickleDave committed May 25, 2023

Inside dataframe.to_files, set spect_ext to '.spect.npz' when we make… …

… spectrograms, then pass into spect.to_dataframe

NickleDave committed May 25, 2023

Cast audio_file to path inside vak.io.audio.to_spect to avoid error w… …

…hen loading npz with unpickle_array=False

NickleDave committed May 25, 2023

Rename vak_df -> dataset_df in labels.from_df

NickleDave committed May 25, 2023

Fix functions that map annotated files to annotations so they return … …

…a dict with string paths as keys, since that's what we get out of the dataset dataframe

NickleDave committed May 25, 2023

Fix window_dataset helper function to get annot_format and determine … …

…annotated_ext before it calls map_annotated_to_annot

NickleDave committed May 25, 2023

Fix Annotation kwarg name 'audio_path' -> 'notated_path' in core/pred… …

…ict.py

NickleDave committed May 25, 2023

Fix unit tests in tests/test_annotation.py

NickleDave committed May 25, 2023

Fix how we save annotations to csv in vak/core/predict.py

NickleDave committed May 25, 2023

Add missing argument 'annot_format' in test_io/test_audio.py

NickleDave committed May 25, 2023

Fix attribute name 'audio_path' -> 'annotated_path' in tests/fixtures… …

…/audio.py

NickleDave committed May 25, 2023

Fix attribute name 'audio_path' -> 'annotated_path' in tests/fixtures… …

…/spect.py

NickleDave committed May 26, 2023

Fix unit tests in tests/test_io/test_spect.py

NickleDave committed May 27, 2023

WIP: Fixing unit tests in tests/test_transforms/test_labeled_timebins… …

…/test_functional.py

NickleDave committed May 27, 2023

Fix tests in test_labeled_timebins/test_functional.py -- xfail on .wa… …

…v.mat files that break tests

NickleDave committed May 27, 2023

Fix SPECT_FILES_TO_SKIP -> XFAIL_SPECT_FILES in test_labeled_timebins… …

…/test_transforms.py

NickleDave committed May 27, 2023