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LtBio V.2 #69

Merged
merged 128 commits into from
Mar 11, 2024
Merged

LtBio V.2 #69

merged 128 commits into from
Mar 11, 2024

Commits on Mar 30, 2023

  1. Make to_array public

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  2. Fix Timeseries.to_array

    @jomy-kk
    jomy-kk committed Mar 30, 2023
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  3. Fix Biosignal.to_array and add to_dataframe

    @jomy-kk
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  4. Minor fix in Timeseries to_array

    @jomy-kk
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  5. Minor fix in Biosignal.to_array

    @jomy-kk
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Commits on Apr 11, 2023

  1. Disregard patient match in MultimodalBiosignal

    @jomy-kk
    jomy-kk committed Apr 11, 2023
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Commits on Apr 28, 2023

  1. Add derived biosignals: ACCMAG, IBI, RRI, HR

    @jomy-kk
    jomy-kk authored and João Saraiva committed Apr 28, 2023
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  2. Fix bug in Segment._partition 

    When called during Segmenter.apply, the _partition method did not consider the last complete fragment of the Segment, and so this would be lost. This was an issue when the no. samples was divisible by the given fragment's length.
    @jomy-kk
    jomy-kk authored and João Saraiva committed Apr 28, 2023
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  3. Add some quality indexes for EDA

    @jomy-kk
    jomy-kk authored and João Saraiva committed Apr 28, 2023
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  4. Add some quality indexes for HR

    @jomy-kk
    jomy-kk authored and João Saraiva committed Apr 28, 2023
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  5. Add some quality indexes for PPG

    @jomy-kk
    jomy-kk authored and João Saraiva committed Apr 28, 2023
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  6. Add some quality indexes for TEMP

    @jomy-kk
    jomy-kk authored and João Saraiva committed Apr 28, 2023
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  7. Add Timeline

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    jomy-kk authored and João Saraiva committed Apr 28, 2023
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  8. Remove segment copies on making new Segment and Timeseries

    @jomy-kk
    jomy-kk authored and João Saraiva committed Apr 28, 2023
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  9. Fix tests regarding previous commit 1a58476

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    jomy-kk authored and João Saraiva committed Apr 28, 2023
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  10. Fix visibility of 'aux_date' from E4

    @jomy-kk
    jomy-kk authored and João Saraiva committed Apr 28, 2023
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  11. Add Biosignal.when and shortcuts for binary logical operations

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    jomy-kk authored and João Saraiva committed Apr 28, 2023
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  12. Add Biosignal indexing with Timeline

    @jomy-kk
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  13. Fix Biosignal indexing with tuple

    @jomy-kk
    jomy-kk authored and João Saraiva committed Apr 28, 2023
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  14. Fix Biosignal.doamin_timeline (temporarly) 

    This feature is to be refactored to Biosignal.domain
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  15. Fix 'source' in binary Biosignal operations

    @jomy-kk
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  16. Add Biosignal.acquisition_scores and onbody score example for E4

    @jomy-kk
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  17. Add DateTimeRange operability to Timeseries._indices_to_timepoints

    @jomy-kk
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  18. Remove compression on saving Biosignals (v. 2023.0)

    @jomy-kk
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  19. Add union and intersection methods to Timeline

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    jomy-kk authored and João Saraiva committed Apr 28, 2023
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  20. Fix semantic bug in E4.onbody

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Commits on May 3, 2023

  1. Allow different channel names when adding 2 Biosignals with just one … 

    …channel each
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  2. Add ECG.acceptable_quality based on BioSPPy

    @jomy-kk
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  3. Add Timeseries.sliding_window iterator

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  4. Add empty ACC.acceptable_quality

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  5. First commit of research journal

    @jomy-kk
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  6. Wednesday research

    @jomy-kk
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  7. New logic for ECG.flatrate

    @jomy-kk
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  8. Allow hierarchy of BodyLocations

    @jomy-kk
    jomy-kk committed May 3, 2023
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Commits on May 4, 2023

  1. Add Rafael's Sense configuration

    @jomy-kk
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  2. Fix minor bug

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  3. Fix minor bug on propagating Events when copying

    @jomy-kk
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  4. Change path config.ini to new computers

    @jomy-kk
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  5. Be verbose about subject's code

    @jomy-kk
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  6. Refactor Sense.onbody for ECG 

    está muito mau
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Commits on May 5, 2023

  1. Add 2 scripts to rapidly retest ECG correctness assessment

    @jomy-kk
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  2. Changed how CSVs are saved and more verbose

    @jomy-kk
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  3. Fix flatline and discrepency thresholds on Sense.onbody for ECG

    @jomy-kk
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  4. Fix minor bug on Timeline initial and final datetimes

    @jomy-kk
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  5. Add Timeline has_intervals, has_points, is_empty, group_names, and __… 

    …getitem__
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  6. Fix textual representation of Timeline

    @jomy-kk
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  7. Fix major bug in Timeline.plot (when there are no intervals)

    @jomy-kk
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  8. Fix major bug in Timeline.intersection (when there are no intervals)

    @jomy-kk
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  9. Add try-except blocks when computing R peaks with BioSPPy

    @jomy-kk
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  10. Add plotting options when getting Biosignal scores

    @jomy-kk
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Commits on May 8, 2023

  1. Research: PPG Correctness score first trials

    @jomy-kk
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  2. Add PPG onbody on E4 and Sense

    @jomy-kk
    jomy-kk committed May 8, 2023
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Commits on May 9, 2023

  1. Research Tuesday

    @jomy-kk
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  2. Fix minor bugs in passing Event objects

    @jomy-kk
    jomy-kk committed May 9, 2023
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  3. Add Biosignal.timeshift

    @jomy-kk
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  4. Remove sorting intervals of Timeline, when indexing a Biosignal with … 

    …Timeline

This assumes they already come ordered from Timeline._as_index, which I am not sure if that's guaranteed. But for the current use cases, they come sorted.
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  5. First commit of EMG quality methods

    @jomy-kk
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  6. Fixing yesterday research scripts

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Commits on May 10, 2023

  1. Add Timeline to import shortcuts

    @jomy-kk
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  2. Implement Biosignal.apply_operation_and_return

    @jomy-kk
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  3. Wednesday Research on EMG

    @jomy-kk
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  4. Add ARM as an anatomical group

    @jomy-kk
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  5. Second commit of EMG quality methods 

    Validated today
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  6. Separates EMG and ECG logic in Sense.onbody

    @jomy-kk
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  7. Add - operation to Timeline 

    In proper mathematical terms, this computes A\B, i.e. A except B, where A and B are two Timelines with intervals.
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Commits on May 12, 2023

  1. Add centi as Unit Multiplier

    @jomy-kk
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  2. Add Meter and Percentage to Unit

    @jomy-kk
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  3. Thursday research

    @jomy-kk
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  4. Fix minor bug in Timeline.intersection 

    Intersection with empty single Group would not be returned. There's probably the same issue in Timeline.union
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  5. Add / operator to Biosignal

    @jomy-kk
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  6. Fix minor bug in Biosignal.quality_score 

    Exception was raised when denominator (onbody duration) was zero. In this case, quality is 0. But shouldn't it be None or something else, to pass the idea of n.a.?
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  7. Add RESOLUTION to Sense

    @jomy-kk
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  8. Add Sense.onbody for EDA

    @jomy-kk
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  9. Add transfer function for Bitalino RESP sensor inside Sense 

    Should we not refactor BiosignalSources, in order to have hierarchy of sensors, devices, institutions, etc.?
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Commits on May 13, 2023

  1. Friday research

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  2. Add Sense.onbody for chest ACC

    @jomy-kk
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  3. Add ACC.acceptable_quality

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  4. Saturday research

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Commits on May 15, 2023

  1. Fix major bug in Biosignal.duration

    @jomy-kk
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  2. Fix major bug in Biosignal.timeshift

    @jomy-kk
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  3. Add Event.timeshift

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Commits on May 16, 2023

  1. Monday and Tuesday Research (Dataset preparation)

    @jomy-kk
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  2. Minor fix in Biosignal.duration

    @jomy-kk
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  3. Minor fix in Biosignal.__repr__

    @jomy-kk
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  4. Add convert(units) method to Biosignal and Timeseries

    @jomy-kk
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  5. Major fix in Biosignal.to_array memory allocation

    @jomy-kk
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  6. Minor fix in Biosignal.__contains__ when looking if channel is in Bio… 

    …signal using its name
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  7. Major fix in Biosignal.timeshift, Add Patient.timeshift 

    Dates of surgical procedures wer not being shifted
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  8. Add Event.domain_timeline

    @jomy-kk
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  9. Add Timeseries.domain_timeline

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  10. Minor (temporary) fix in Segment._memory_map 

    Case where Segment is empty
    @jomy-kk
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  11. Make G unit's SHORT lowercase

    @jomy-kk
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  12. Refactor Sense._transfer for the most common modalities and units

    @jomy-kk
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  13. EDA previews of 30 seconds

    @jomy-kk
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Commits on May 17, 2023

  1. Last Friday research

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  2. Fix typo in ACC.acceptable_quality stringdocs

    @jomy-kk
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Commits on May 22, 2023

  1. Weekend research

    @jomy-kk
    jomy-kk committed May 22, 2023
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  2. Minor fix on IndexError message

    @jomy-kk
    jomy-kk committed May 22, 2023
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  3. Refactor _onbody parameter of Biosignal.quality_score

    @jomy-kk
    jomy-kk committed May 22, 2023
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  4. Fix ECG.acceptable quality when segment is too short

    @jomy-kk
    jomy-kk committed May 22, 2023
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  5. Fix EMG.acceptable quality when no rest periods are found

    @jomy-kk
    jomy-kk committed May 22, 2023
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  6. Fix Sense.onbody to match units of Biosignal

    @jomy-kk
    jomy-kk committed May 22, 2023
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  7. Add Timeline.agglomerate

    @jomy-kk
    jomy-kk committed May 22, 2023
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  8. Monday's research

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Commits on May 23, 2023

  1. Tuesday's research

    @jomy-kk
    jomy-kk committed May 23, 2023
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Commits on May 25, 2023

  1. Add COVID.__repr__

    @jomy-kk
    jomy-kk committed May 25, 2023
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  2. Thursday's research

    @jomy-kk
    jomy-kk committed May 25, 2023
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Commits on May 26, 2023

  1. Friday's research

    @jomy-kk
    jomy-kk committed May 26, 2023
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Commits on Jun 21, 2023

  1. To EDF (1)

    @jomy-kk
    jomy-kk committed Jun 21, 2023
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Commits on Jul 14, 2023

  1. Dataset Article fixes

    @jomy-kk
    jomy-kk committed Jul 14, 2023
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  2. Minor fixes

    @jomy-kk
    jomy-kk committed Jul 14, 2023
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  3. EDF and Numpy core

    @jomy-kk
    jomy-kk committed Jul 14, 2023
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  4. Add exceptions module

    @jomy-kk
    jomy-kk committed Jul 14, 2023
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  5. Add operations module

    @jomy-kk
    jomy-kk committed Jul 14, 2023
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  6. IT research update

    @jomy-kk
    jomy-kk committed Jul 14, 2023
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  7. Minor fixes in biosignal package and Patient

    @jomy-kk
    jomy-kk committed Jul 14, 2023
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Commits on Oct 11, 2023

  1. Research

    @jomy-kk
    jomy-kk committed Oct 11, 2023
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  2. Fix patient_code method

    @jomy-kk
    jomy-kk committed Oct 11, 2023
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  3. Fix union of Events when instantiating a MultimodalBiosignal from mul… 

    …tiple Biosignals
    @jomy-kk
    jomy-kk committed Oct 11, 2023
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  4. Delete .readthedocs.yaml

    @jomy-kk
    jomy-kk committed Oct 11, 2023
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  5. Add new .readthedocs.yaml

    @jomy-kk
    jomy-kk committed Oct 11, 2023
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Commits on Oct 24, 2023

  1. Re-submition to Physionet

    @jomy-kk
    jomy-kk committed Oct 24, 2023
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Commits on Mar 10, 2024

  1. Delete research folders

    @jomy-kk
    jomy-kk committed Mar 10, 2024
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  2. Update requirements.txt

    @jomy-kk
    jomy-kk committed Mar 10, 2024
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  3. Merge branch 'main' into ltbio_v2

    @jomy-kk
    jomy-kk committed Mar 10, 2024
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  4. Relax PyQt5 versions

    @jomy-kk
    jomy-kk committed Mar 10, 2024
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  5. Relax MNE versions

    @jomy-kk
    jomy-kk committed Mar 10, 2024
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Commits on Mar 11, 2024

  1. Fix tests for v2

    @jomy-kk
    jomy-kk committed Mar 11, 2024
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