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Update the BIDS-like saving to align with template directory #77

Merged
merged 56 commits into from
Sep 16, 2024
Merged

Update the BIDS-like saving to align with template directory #77

merged 56 commits into from
Sep 16, 2024

Commits on Jul 1, 2024

  1. Update features to save in individual files

    @ibevers
    ibevers committed Jul 1, 2024
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  2. Fix dir doesn't exist bug

    @ibevers
    ibevers committed Jul 1, 2024
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Commits on Jul 7, 2024

  1. Update feature saving to conform to BIDS and use pathlib

    @ibevers
    ibevers committed Jul 7, 2024
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Commits on Aug 21, 2024

  1. Add to-do and automated style fixes

    @ibevers
    ibevers committed Aug 21, 2024
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  2. Move data to src/b2aiprep

    @ibevers
    ibevers committed Aug 21, 2024
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  3. Add workflow for automatically updating bids-like template CHANGES.md

    @ibevers
    ibevers committed Aug 21, 2024
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Commits on Aug 22, 2024

  1. Change summer_school to bids_like

    @ibevers
    ibevers committed Aug 22, 2024
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  2. Add copying of README.md and CHANGES.md from template

    @ibevers
    ibevers committed Aug 22, 2024
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  3. Move directory initialization to separ 

    ate function
    @ibevers
    ibevers committed Aug 22, 2024
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Commits on Aug 23, 2024

  1. Update dataset_description.json

    @ibevers
    ibevers committed Aug 23, 2024
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  2. Add dataset_description.json to the data saving

    @ibevers
    ibevers committed Aug 23, 2024
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  3. Add RedCap column names file to the data dir

    @ibevers
    ibevers committed Aug 23, 2024
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  4. Add first iteration of participants.json

    @ibevers
    ibevers committed Aug 23, 2024
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  5. Reorganize files

    @ibevers
    ibevers committed Aug 23, 2024
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  6. Remove redundancy in import

    @ibevers
    ibevers committed Aug 23, 2024
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Commits on Aug 26, 2024

  1. Add create participants.tsv functionality

    @ibevers
    ibevers committed Aug 26, 2024
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  2. Add template phenotype JSON files

    @ibevers
    ibevers committed Aug 26, 2024
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  3. Add phenotype tsv files to template

    @ibevers
    ibevers committed Aug 26, 2024
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  4. Replace flake8 with ruff

    @ibevers
    ibevers committed Aug 26, 2024
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  5. Add utils and util tests

    @ibevers
    ibevers committed Aug 26, 2024
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  6. Move bids-like template to resources and add phenotype files to template

    @ibevers
    ibevers committed Aug 26, 2024
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  7. Add ruff fixes to notebooks

    @ibevers
    ibevers committed Aug 26, 2024
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  8. Add construct all tsvs from jsons function to utils with test

    @ibevers
    ibevers committed Aug 26, 2024
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  9. Add phenotype tsv file generation

    @ibevers
    ibevers committed Aug 26, 2024
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Commits on Aug 27, 2024

  1. Remove duplicated template directory

    @ibevers
    ibevers committed Aug 27, 2024
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Commits on Aug 28, 2024

  1. Clean up and clarify comment

    @ibevers
    ibevers committed Aug 28, 2024
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  2. Move recording tasks and acoustic tasks to audio dir

    @ibevers
    ibevers committed Aug 28, 2024
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  3. Remove beh directory and redundant per-participant files

    @ibevers
    ibevers committed Aug 28, 2024
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  4. Replace task with recording name where applicable

    @ibevers
    ibevers committed Aug 28, 2024
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  5. Remove redundant information from audio file names

    @ibevers
    ibevers committed Aug 28, 2024
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  6. Update JSON suffix to include 'metadata'

    @ibevers
    ibevers committed Aug 28, 2024
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  7. Add sessions.tsv and remove session jsons

    @ibevers
    ibevers committed Aug 28, 2024
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Commits on Aug 29, 2024

  1. Merge in bids-like-updates

    @ibevers
    ibevers committed Aug 29, 2024
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  2. Add separate feature saving changes manually

    @ibevers
    ibevers committed Aug 29, 2024
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  3. Fix senselab integration bugs

    @ibevers
    ibevers committed Aug 29, 2024
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  4. Fix incorrect import

    @ibevers
    ibevers committed Aug 29, 2024
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  5. Fix out of date path in test

    @ibevers
    ibevers committed Aug 29, 2024
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  6. Fix transcript saving

    @ibevers
    ibevers committed Aug 29, 2024
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  7. Make default transcription whisper tiny

    @ibevers
    ibevers committed Aug 29, 2024
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Commits on Aug 30, 2024

  1. Add parameter for transcription model size

    @ibevers
    ibevers committed Aug 30, 2024
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  2. Add n_cores as parameter for feature extraction

    @ibevers
    ibevers committed Aug 30, 2024
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  3. Add batching for feature extraction

    @ibevers
    ibevers committed Aug 30, 2024
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  4. Remove argument parsing from prepare.py

    @ibevers
    ibevers committed Aug 30, 2024
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Commits on Sep 11, 2024

  1. Remove TODO comment

    @ibevers
    ibevers committed Sep 11, 2024
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Commits on Sep 12, 2024

  1. Add 1000 row synthetic data

    @ibevers
    ibevers committed Sep 12, 2024
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  2. Add test for each bids_like_data function

    @ibevers
    ibevers committed Sep 12, 2024
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Commits on Sep 13, 2024

  1. Add CLI test

    @ibevers
    ibevers committed Sep 13, 2024
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  2. Add descriptions to participants.json

    @ibevers
    ibevers committed Sep 13, 2024
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Commits on Sep 16, 2024

  1. Sort participants.json

    @ibevers
    ibevers committed Sep 16, 2024
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  2. Update test_prepare.py

    @ibevers
    ibevers committed Sep 16, 2024
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  3. Update phenotype descriptions

    @ibevers
    ibevers committed Sep 16, 2024
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  4. Require senselab>=0.12.0

    @ibevers
    ibevers committed Sep 16, 2024
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  5. Add flag to exclude sensitive data: .wav and transcripts

    @ibevers
    ibevers committed Sep 16, 2024
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  6. Add license and update dataset_description.json

    @ibevers
    ibevers committed Sep 16, 2024
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  7. Update test to use with_sensitive parameter

    @ibevers
    ibevers committed Sep 16, 2024
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  8. Move data directory out of src

    @ibevers
    ibevers committed Sep 16, 2024
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