Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

ENH: Use crowsetta 5.0, fixes #526 #657

Merged
merged 42 commits into from
May 27, 2023
Merged

ENH: Use crowsetta 5.0, fixes #526 #657

merged 42 commits into from
May 27, 2023

Conversation

NickleDave
Copy link
Collaborator

@NickleDave NickleDave commented May 27, 2023 •
edited
Loading

Fixes #526

@NickleDave
Require crowsetta >=5.0.0 in pyproject.toml
b2e952c
@NickleDave
Use crowsetta.format.as_list() to make VALID_ANNOT_FORMATS in vak.c…
b4b2e17 
…onstants
@NickleDave
Fix how files.find_fname and files.from_dir handle extensions tha…
f26e637 
…t start with a period (by removing it)
@NickleDave
Rewrite vak/annotation.py to use crowsetta >= 5.0
6a3622d 
- 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
Call to_annot on instances returned by Transcriber.from_file in `io.d…
75a9ea8 
…ataframe.from_file` function
@NickleDave
Upper bound torch and lightning below 2.0 for now
a568d5f
@NickleDave
Fix fixtures/annot.py to use crowsetta>=5.0
af6c16b
@NickleDave
Rename function in tests/scripts/generate_data_for_tests.py, main -> …
750b741 
…generate_test_data to avoid lightning crash
@NickleDave
Fix test in tests/test_transforms/test_labeled_timebins/test_function…
86c038b 
…al.py to use crowsetta>=5.0 attribute name, notated_path
@NickleDave
Add to pytest filterwarnings in pyproject.toml
331beb3
@NickleDave
WIP: Rewrite vak.annotation.map_annotated_to_annot to have 3 ways o…
c10c038 
…f mapping
@NickleDave
WIP: Fix/add tests in tests/test_annotation after rewriting `vak.anno…
ebfb352 
…tation.map_annotated_to_annot`
@NickleDave
WIP: More changes to vak/annotation.py
e66bb32
@NickleDave
WIP: More changes to tests/test_annotation.py
014a242
@NickleDave
Make mores fixes to src/vak/annotation.py
8d6a8c0
@NickleDave
Rename audio_stem_from_path -> audio_filename_from_path in vak/an…
cabcb43 
…notation.py
@NickleDave
Rename audio_stem_from_path -> audio_filename_from_path in tests/…
44bb198 
…test_annotation.py
@NickleDave
WIP: Further fixes to vak/annotation.py
ae5e7af
@NickleDave
Fix a reference to a function in a docstring in src/vak/annotation.py
d765f4f
@NickleDave
Add more type hints, revise docstring in src/vak/annotation.py
e13cc36
@NickleDave
Fix bug in src/vak/annotation.py: 'annot_class.name' -> 'annot.annot_…
6eca315 
…path.name'
@NickleDave
Revise docstring, add type hints to vak.files.from_dir
21c8fda
@NickleDave
Modify vak.io.audio.to_spect to take annot_format arg and pass it…
fcb7fc2 
… to `map_annotated_to_annot`
@NickleDave
Modify vak.io.spect.to_dataframe to pass annot_format to `map_ann…
eb123e6 
…otated_to_annot`
@NickleDave
Add type hints, rename vak_df -> dataset_df to `vak.io.dataframe.…
a544358 
…from_files`
@NickleDave
Make fixes in vak.annotation: pass annot_format inside from_df, add a…
ffb3797 
…nnotated_ext parameter to map_annotated_to_annot and _map_using_ext
@NickleDave
Add spect_ext parameter to spect.to_dataframe, pass into map_annotate…
e26bd92 
…d_to_annot as annotated_ext
@NickleDave
Inside dataframe.to_files, set spect_ext to '.spect.npz' when we make…
91ddae3 
… spectrograms, then pass into spect.to_dataframe
@NickleDave
Cast audio_file to path inside vak.io.audio.to_spect to avoid error w…
23a68fa 
…hen loading npz with unpickle_array=False
@NickleDave
Rename vak_df -> dataset_df in labels.from_df
fef01b4
@NickleDave
Fix functions that map annotated files to annotations so they return …
039bc2e 
…a dict with string paths as keys, since that's what we get out of the dataset dataframe
@NickleDave
Fix window_dataset helper function to get annot_format and determine …
7a2640a 
…annotated_ext before it calls map_annotated_to_annot
@NickleDave
Fix Annotation kwarg name 'audio_path' -> 'notated_path' in core/pred…
15517a7 
…ict.py
@NickleDave
Fix unit tests in tests/test_annotation.py
8338e26
@NickleDave
Fix how we save annotations to csv in vak/core/predict.py
6b83c60
@NickleDave
Add missing argument 'annot_format' in test_io/test_audio.py
717a48c
@NickleDave
Fix attribute name 'audio_path' -> 'annotated_path' in tests/fixtures…
331dff1 
…/audio.py
@NickleDave
Fix attribute name 'audio_path' -> 'annotated_path' in tests/fixtures…
2dcbfe0 
…/spect.py
@NickleDave
Fix unit tests in tests/test_io/test_spect.py
979ddf4
@NickleDave
WIP: Fixing unit tests in tests/test_transforms/test_labeled_timebins…
259a1fa 
…/test_functional.py
@NickleDave
Fix tests in test_labeled_timebins/test_functional.py -- xfail on .wa…
7cd123c 
…v.mat files that break tests
@NickleDave
Fix SPECT_FILES_TO_SKIP -> XFAIL_SPECT_FILES in test_labeled_timebins…
7a2b54c 
…/test_transforms.py
@NickleDave
Copy link
Collaborator Author

I know CI will fail, need to make other fixes in other branches I'm about to rebase after merging this, so will just ignore for now

@NickleDave NickleDave merged commit 27f09bd into main May 27, 2023
@NickleDave NickleDave deleted the use-crowsetta-5.0 branch May 27, 2023 15:45
@NickleDave NickleDave mentioned this pull request May 27, 2023
Closed
@NickleDave NickleDave changed the title ENH: Use crowsetta 5.0, fix #256 ENH: Use crowsetta 5.0, fix #526 May 27, 2023
@NickleDave NickleDave mentioned this pull request May 27, 2023
Closed
4 tasks
@NickleDave NickleDave changed the title ENH: Use crowsetta 5.0, fix #526 ENH: Use crowsetta 5.0, fixes #526 May 27, 2023
@NickleDave NickleDave mentioned this pull request Jun 4, 2023
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

DEP: use crowsetta 5.0.0 (post pyOpenSci review)
1 participant
@NickleDave