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Datajoint pipeline PR into main branch #351

Merged
merged 689 commits into from
Jun 12, 2024
Merged

Datajoint pipeline PR into main branch #351

merged 689 commits into from
Jun 12, 2024
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Oct 27, 2023

  1. Merge pull request #264 from ttngu207/datajoint_pipeline_pyrat 

    modify `subject` schema to align with pyrat - added pyrat sync routine
    @JaerongA
    JaerongA authored Oct 27, 2023
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Commits on Oct 31, 2023

  1. Merge branch 'datajoint_pipeline' of github.com:SainsburyWellcomeCent… 

    …re/aeon_mecha into datajoint_pipeline
    @JaerongA
    JaerongA committed Oct 31, 2023
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  2. hard-code sciviz host name

    @JaerongA
    JaerongA committed Oct 31, 2023
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  3. update docstring to add sciviz url

    @JaerongA
    JaerongA committed Oct 31, 2023
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  4. feat: ✨ add pyrat_worker to docker-compose

    @JaerongA
    JaerongA committed Oct 31, 2023
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  5. Merge pull request #268 from JaerongA/datajoint_pipeline 

    Minor sciviz fix & add pyrat worker to docker-compose
    Thinh Nguyen authored Oct 31, 2023
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  6. fix: 🐛 re-configure pyrat worker

    @JaerongA
    JaerongA committed Oct 31, 2023
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  7. Merge branch 'SainsburyWellcomeCentre:datajoint_pipeline' into datajo… 

    …int_pipeline
    @JaerongA
    JaerongA authored Oct 31, 2023
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  8. Merge pull request #270 from JaerongA/datajoint_pipeline

    @ttngu207
    ttngu207 authored Oct 31, 2023
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Commits on Nov 1, 2023

  1. added lab_id and available

    Thinh Nguyen committed Nov 1, 2023
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  2. Merge remote-tracking branch 'upstream/datajoint_pipeline' into dataj… 

    …oint_pipeline_pyrat
    Thinh Nguyen committed Nov 1, 2023
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  3. added manual table ExperimentSubject

    Thinh Nguyen committed Nov 1, 2023
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  4. deprecate colony.csv ingestion

    Thinh Nguyen committed Nov 1, 2023
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  5. minor bugfix

    Thinh Nguyen committed Nov 1, 2023
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  6. check and update subject's "available" periodically

    Thinh Nguyen committed Nov 1, 2023
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  7. minor bugfix

    Thinh Nguyen committed Nov 1, 2023
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  8. Update aeon/dj_pipeline/subject.py 

    Co-authored-by: JaerongA <[email protected]>
    @ttngu207 @JaerongA
    ttngu207 and JaerongA authored Nov 1, 2023
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Commits on Nov 2, 2023

  1. Use acquisition.Experiment to register new aeon experiments

    Thinh Nguyen committed Nov 2, 2023
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  2. Merge branch 'datajoint_pipeline_pyrat' of https://github.com/ttngu20… 

    …7/aeon_mecha into datajoint_pipeline_pyrat
    Thinh Nguyen committed Nov 2, 2023
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  3. Merge pull request #271 from ttngu207/datajoint_pipeline_pyrat 

    Added `lab_id` and `available` to pyrat subjects
    @JaerongA
    JaerongA authored Nov 2, 2023
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Commits on Nov 3, 2023

  1. feat: ✨ update specsheet.yaml with pyrat tables

    @JaerongA
    JaerongA committed Nov 3, 2023
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  2. fix: 🐛 ignore type annotations

    @JaerongA
    JaerongA committed Nov 3, 2023
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  3. fix: 🐛 add --ignore-requires-python to avoid python versioning error … 

    …in pharus
    @JaerongA
    JaerongA committed Nov 3, 2023
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  4. Merge pull request #273 from JaerongA/dev

    @ttngu207
    ttngu207 authored Nov 3, 2023
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Commits on Nov 6, 2023

  1. minor improvement

    Thinh Nguyen committed Nov 6, 2023
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  2. added SubjectReferenceWeight

    Thinh Nguyen committed Nov 6, 2023
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  3. Merge remote-tracking branch 'upstream/datajoint_pipeline' into dataj… 

    …oint_pipeline_pyrat
    Thinh Nguyen committed Nov 6, 2023
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  4. Update specsheet.yaml

    Thinh Nguyen committed Nov 6, 2023
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  5. pyrat schedule to every 12hours

    Thinh Nguyen committed Nov 6, 2023
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  6. fix: 🐛 add pyrat api as env

    @JaerongA
    JaerongA committed Nov 6, 2023
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  7. chore: 🥅 raise pyrat api error

    @JaerongA
    JaerongA committed Nov 6, 2023
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  8. Merge pull request #274 from ttngu207/datajoint_pipeline_pyrat 

    minor improvement
    @JaerongA
    JaerongA authored Nov 6, 2023
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  9. Merge pull request #275 from JaerongA/dev 

    Fix PyRat worker
    Thinh Nguyen authored Nov 6, 2023
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  10. handles http errors

    Thinh Nguyen committed Nov 6, 2023
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  11. Merge pull request #276 from ttngu207/datajoint_pipeline_pyrat 

    handles http errors
    @JaerongA
    JaerongA authored Nov 6, 2023
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  12. update sciviz

    Thinh Nguyen committed Nov 6, 2023
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  13. Merge remote-tracking branch 'upstream/datajoint_pipeline' into dataj… 

    …oint_pipeline_pyrat
    Thinh Nguyen committed Nov 6, 2023
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  14. Merge pull request #277 from ttngu207/datajoint_pipeline_pyrat 

    update sciviz
    @JaerongA
    JaerongA authored Nov 6, 2023
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Commits on Nov 9, 2023

  1. update food restriction procedure name

    Thinh Nguyen committed Nov 9, 2023
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  2. Merge pull request #279 from ttngu207/datajoint_pipeline_pyrat 

    update food restriction procedure name
    @JaerongA
    JaerongA authored Nov 9, 2023
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Commits on Nov 28, 2023

  1. fix: 🐛 fix file path error

    @JaerongA
    JaerongA committed Nov 28, 2023
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  2. add notebook for directory insertion

    @JaerongA
    JaerongA committed Nov 28, 2023
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  3. Merge pull request #284 from JaerongA/dev 

    Fix epoch ingestion error
    Thinh Nguyen authored Nov 28, 2023
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  4. Merge branch 'main' of https://github.com/SainsburyWellcomeCentre/aeo… 

    …n_mecha into dev
    @JaerongA
    JaerongA committed Nov 28, 2023
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  5. build: ➕ add pillow in pyproject.toml

    @JaerongA
    JaerongA committed Nov 28, 2023
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  6. Merge pull request #286 from JaerongA/datajoint_pipeline 

    build: ➕ add pillow in pyproject.toml
    Thinh Nguyen authored Nov 28, 2023
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Commits on Nov 29, 2023

  1. build: ➕ add libtiff5 to apt_requirements.txt

    @JaerongA
    JaerongA committed Nov 29, 2023
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  2. Merge branch 'SainsburyWellcomeCentre:datajoint_pipeline' into datajo… 

    …int_pipeline
    @JaerongA
    JaerongA authored Nov 29, 2023
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  3. Merge pull request #287 from JaerongA/datajoint_pipeline 

    build: ➕ add libtiff5 to apt_requirements.txt
    @JaerongA
    JaerongA authored Nov 29, 2023
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  4. add experiment devices & schema

    @JaerongA
    JaerongA committed Nov 29, 2023
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  5. fix device_type_mapper.json path

    @JaerongA
    JaerongA committed Nov 29, 2023
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  6. Merge branch 'SainsburyWellcomeCentre:datajoint_pipeline' into datajo… 

    …int_pipeline
    @JaerongA
    JaerongA authored Nov 29, 2023
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  7. Merge pull request #289 from JaerongA/datajoint_pipeline 

    Add experiment devices & schema
    Thinh Nguyen authored Nov 29, 2023
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Commits on Nov 30, 2023

  1. update ingestion for new social experiments

    Thinh Nguyen committed Nov 30, 2023
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Commits on Dec 1, 2023

  1. Ensure data filtered by bitmask

    @jkbhagatio
    jkbhagatio committed Dec 1, 2023
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  2. Fix for #290

    @jkbhagatio
    jkbhagatio committed Dec 1, 2023
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Commits on Dec 4, 2023

  1. Changed 'dataset' name to 'schemas' and refactored

    @jkbhagatio
    jkbhagatio committed Dec 4, 2023
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  2. Added notebook showing finding harp event bitmasks

    @jkbhagatio
    jkbhagatio committed Dec 4, 2023
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  3. Refactored according to #293

    @jkbhagatio
    jkbhagatio committed Dec 4, 2023
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Commits on Dec 5, 2023

  1. Fixed #294

    @jkbhagatio
    jkbhagatio committed Dec 5, 2023
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Commits on Dec 6, 2023

  1. WIP schema-from-scratch tutorial

    @jkbhagatio
    jkbhagatio committed Dec 6, 2023
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  2. Started 'device' section

    @jkbhagatio
    jkbhagatio committed Dec 6, 2023
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Commits on Dec 13, 2023

  1. Updated device terminology

    @jkbhagatio
    jkbhagatio committed Dec 13, 2023
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  2. Finished 'device' and 'schema' explanation

    @jkbhagatio
    jkbhagatio committed Dec 13, 2023
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  3. reintroduce aeon.schema

    @jkbhagatio
    jkbhagatio committed Dec 13, 2023
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Commits on Dec 14, 2023

  1. Refactored to use 'register'

    @jkbhagatio
    jkbhagatio committed Dec 14, 2023
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  2. Social schema WIP

    @jkbhagatio
    jkbhagatio committed Dec 14, 2023
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  3. Refactored for consistent snake_case

    @jkbhagatio
    jkbhagatio committed Dec 14, 2023
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Commits on Dec 15, 2023

  1. Removed device name from path

    @jkbhagatio
    jkbhagatio committed Dec 15, 2023
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Commits on Dec 16, 2023

  1. Finished and tested social schema for data between 2023-12-01 -- 2023… 

    …-12-08
    @jkbhagatio
    jkbhagatio committed Dec 16, 2023
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Commits on Jan 8, 2024

  1. Merge remote-tracking branch 'upstream/social_schema' into datajoint_… 

    …pipeline
    Thinh Nguyen committed Jan 8, 2024
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  2. fix(load_metadata): resolve pull conflicts (removed dataset.py)

    Thinh Nguyen committed Jan 8, 2024
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Commits on Jan 9, 2024

  1. feat(social01): add new aeon schema for social 01

    Thinh Nguyen committed Jan 9, 2024
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  2. rearrange(device_type_mapper)

    Thinh Nguyen committed Jan 9, 2024
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  3. feat(streams): incorporate social 0.1 experiments for ingestion

    Thinh Nguyen committed Jan 9, 2024
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  4. update(sciviz)

    Thinh Nguyen committed Jan 9, 2024
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  5. fix(streams): sanitize column names (remove parenthesis)

    Thinh Nguyen committed Jan 9, 2024
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  6. update(streams)

    Thinh Nguyen committed Jan 9, 2024
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Commits on Jan 10, 2024

  1. Merge branch 'SainsburyWellcomeCentre:social_schema' into social_schema

    @ttngu207
    ttngu207 authored Jan 10, 2024
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  2. feat(schemas): add schema for social 01 experiment

    Thinh Nguyen committed Jan 10, 2024
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  3. Merge branch 'social_schema' into datajoint_pipeline

    Thinh Nguyen committed Jan 10, 2024
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  4. rearrange(social01): moved content to social.py

    Thinh Nguyen committed Jan 10, 2024
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Commits on Jan 11, 2024

  1. refactor(social): refactor binder functions to be more consistent wit… 

    …h other schema
    Thinh Nguyen committed Jan 11, 2024
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  2. Merge branch 'social_schema' into datajoint_pipeline

    Thinh Nguyen committed Jan 11, 2024
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  3. fix(acquisition): missing imports

    Thinh Nguyen committed Jan 11, 2024
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  4. chore(load_metadata): remove obsolete "ingest_subject" mechanism from… 

    … colony.csv file
    Thinh Nguyen committed Jan 11, 2024
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  5. feat(acquisition): specify devices schema for each experiment in a ta… 

    …ble instead of hard-coding
    Thinh Nguyen committed Jan 11, 2024
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  6. fix(social): bugfix Rfid binder function

    Thinh Nguyen committed Jan 11, 2024
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  7. Merge branch 'social_schema' into datajoint_social01

    Thinh Nguyen committed Jan 11, 2024
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Commits on Jan 12, 2024

  1. fix(acquisition): skip Pose reader (this should be manual)

    Thinh Nguyen committed Jan 12, 2024
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  2. chore(streams)

    Thinh Nguyen committed Jan 12, 2024
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  3. fix(social): typo

    Thinh Nguyen committed Jan 12, 2024
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  4. Merge branch 'social_schema' into datajoint_social01

    Thinh Nguyen committed Jan 12, 2024
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  5. fix(social): bugfix setting up RFID binder function

    Thinh Nguyen committed Jan 12, 2024
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  6. Merge branch 'social_schema' into datajoint_social01

    Thinh Nguyen committed Jan 12, 2024
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  7. fix(schemas): remove duplicated device in social01

    Thinh Nguyen committed Jan 12, 2024
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  8. Merge branch 'social_schema' into datajoint_social01

    Thinh Nguyen committed Jan 12, 2024
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  9. feat(streams_maker): simplify, improve robustness

    Thinh Nguyen committed Jan 12, 2024
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Commits on Jan 17, 2024

  1. added SLEAPTracking table

    Thinh Nguyen committed Jan 17, 2024
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  2. feat(reader): update Pose reader

    Thinh Nguyen committed Jan 17, 2024
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  3. Merge branch 'social_schema' into datajoint_social01

    Thinh Nguyen committed Jan 17, 2024
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Commits on Jan 19, 2024

  1. fix(social): bugfix for "Environment" readers

    Thinh Nguyen committed Jan 19, 2024
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  2. Merge branch 'social_schema' into datajoint_social01

    Thinh Nguyen committed Jan 19, 2024
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  3. Merge pull request #306 from ttngu207/datajoint_social01 

    Datajoint social01
    @JaerongA
    JaerongA authored Jan 19, 2024
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Commits on Jan 23, 2024

  1. feat(acquisition): add Environment table to store data from Environ… 

    …ment's streams
    Thinh Nguyen committed Jan 23, 2024
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  2. chore(tracking): cleanup make call for SLEAP ingestion

    Thinh Nguyen committed Jan 23, 2024
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  3. feat(analysis): add Block-level analysis

    Thinh Nguyen committed Jan 23, 2024
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  4. fix(social01): bugfix in setting up the readers

    Thinh Nguyen committed Jan 23, 2024
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  5. Merge branch 'social_schema' into datajoint_social01

    Thinh Nguyen committed Jan 23, 2024
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  6. feat(block_analysis): add analysis and plots for Block

    Thinh Nguyen committed Jan 23, 2024
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Commits on Jan 29, 2024

  1. feat(analysis): add logic for BlockDetection and BlockAnalysis

    Thinh Nguyen committed Jan 29, 2024
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  2. feat(get_maintenance_periods): update logic, cleaner & more robust

    Thinh Nguyen committed Jan 29, 2024
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Commits on Jan 30, 2024

  1. fix(block_analysis): minor bugfix

    Thinh Nguyen committed Jan 30, 2024
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  2. feat(block_analysis): add example notebook

    Thinh Nguyen committed Jan 30, 2024
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  3. update(notebook)

    Thinh Nguyen committed Jan 30, 2024
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  4. Create clone_and_freeze_exp02.py

    Thinh Nguyen committed Jan 30, 2024
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  5. Merge pull request #309 from ttngu207/datajoint_social01 

    Block-level analysis and plots - draft 1
    @JaerongA
    JaerongA authored Jan 30, 2024
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  6. fix(foraging): bugfix, duplicated code in resolving merge conflict

    Thinh Nguyen committed Jan 30, 2024
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  7. update(dj_pipeline): remove obsolete tables

    Thinh Nguyen committed Jan 30, 2024
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  8. update(report): disable report schema for now

    Thinh Nguyen committed Jan 30, 2024
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  9. update(worker): update worker

    Thinh Nguyen committed Jan 30, 2024
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Commits on Jan 31, 2024

  1. fix: 🐛 fix type annotation error with __future__

    @JaerongA
    JaerongA committed Jan 31, 2024
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  2. chore(dj_pipeline): remove obsolete tables, helper functions

    Thinh Nguyen committed Jan 31, 2024
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  3. refactor(reader): minor tweak in PoseReader

    Thinh Nguyen committed Jan 31, 2024
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  4. Update specsheet.yaml

    Thinh Nguyen committed Jan 31, 2024
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  5. fix: 🐛 fix naming error & streamline BlockPlots make function

    @JaerongA
    JaerongA committed Jan 31, 2024
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  6. feat: ✨ add patch_rate_plot and cumulative_pellet_plot to BlockPlots

    @JaerongA
    JaerongA committed Jan 31, 2024
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  7. Merge pull request #313 from JaerongA/datajoint_pipeline 

    Bug fix & add block analysis plots
    Thinh Nguyen authored Jan 31, 2024
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  8. fix: 🐛 fix type hinting issue using 'from future import annotations

    @JaerongA
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  9. Merge pull request #315 from JaerongA/datajoint_pipeline 

    fix: 🐛 fix type hinting issue using 'from future import annotations
    Thinh Nguyen authored Jan 31, 2024
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  10. feat(acqusition): add tables to store Experiment Notes and to extract… 

    … ActiveRegions
    Thinh Nguyen committed Jan 31, 2024
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  11. feat(social): update binder function for social0.2

    Thinh Nguyen committed Jan 31, 2024
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  12. Merge branch 'social_schema' into datajoint_social01

    Thinh Nguyen committed Jan 31, 2024
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  13. Merge remote-tracking branch 'upstream/datajoint_pipeline' into dataj… 

    …oint_social01
    Thinh Nguyen committed Jan 31, 2024
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  14. Update block_analysis.py

    Thinh Nguyen committed Jan 31, 2024
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  15. fix(subject): set ref_weight to -1 if not available

    Thinh Nguyen committed Jan 31, 2024
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  16. build: 📌 bump sciviz

    @JaerongA
    JaerongA committed Jan 31, 2024
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Commits on Feb 1, 2024

  1. refactor: 🚚 modify specsheet to point to archived db

    @JaerongA
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  2. feat: ✨ add BlockAnalysis page to sciviz

    @JaerongA
    JaerongA committed Feb 1, 2024
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  3. Merge pull request #316 from ttngu207/datajoint_social01 

    Major cleanup - removing obsolete tables and previous analysis routines - update worker
    @JaerongA
    JaerongA authored Feb 1, 2024
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  4. Merge branch 'SainsburyWellcomeCentre:datajoint_pipeline' into datajo… 

    …int_pipeline
    @JaerongA
    JaerongA authored Feb 1, 2024
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  5. fix: 🐛 bugfix exp_note_form in sciviz

    @JaerongA
    JaerongA committed Feb 1, 2024
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  6. Merge pull request #317 from JaerongA/datajoint_pipeline 

    Add block analysis to sciviz
    Thinh Nguyen authored Feb 1, 2024
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  7. docs: 📝 update sciviz README.md

    @JaerongA
    JaerongA committed Feb 1, 2024
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  8. Merge pull request #318 from JaerongA/datajoint_pipeline 

    docs: 📝 update sciviz README.md
    Thinh Nguyen authored Feb 1, 2024
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  9. fix(block_analysis): SubjectState is not a reliable indication of sub… 

    …jects in the block, use identities from SLEAP data
    Thinh Nguyen committed Feb 1, 2024
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  10. Update social.py

    Thinh Nguyen committed Feb 1, 2024
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Commits on Feb 2, 2024

  1. Merge pull request #319 from ttngu207/datajoint_social01 

    SubjectState is not a reliable indication of subjects in the block, use identities from SLEAP data
    @jkbhagatio
    jkbhagatio authored Feb 2, 2024
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  2. Update worker.py

    Thinh Nguyen committed Feb 2, 2024
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  3. Merge remote-tracking branch 'upstream/datajoint_pipeline' into dataj… 

    …oint_pipeline
    Thinh Nguyen committed Feb 2, 2024
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  4. feat(worker): update worker for social01 and social02

    Thinh Nguyen committed Feb 2, 2024
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  5. feat(block_analysis): Ensure the relevant streams ingestion are caugh… 

    …t up before each block analysis
    Thinh Nguyen committed Feb 2, 2024
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  6. chore(worker): minor worker tuning

    Thinh Nguyen committed Feb 2, 2024
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  7. feat: ✨ add a cronjob script for dj workers

    @JaerongA
    JaerongA committed Feb 2, 2024
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  8. Merge branch 'SainsburyWellcomeCentre:datajoint_pipeline' into datajo… 

    …int_pipeline
    @JaerongA
    JaerongA authored Feb 2, 2024
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  9. update(worker): fine tune workers

    Thinh Nguyen committed Feb 2, 2024
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  10. Update specsheet.yaml

    Thinh Nguyen committed Feb 2, 2024
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  11. Merge pull request #321 from ttngu207/datajoint_pipeline 

    social0.2 ingestion and worker setup for automation
    @JaerongA
    JaerongA authored Feb 2, 2024
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  12. Merge pull request #322 from JaerongA/datajoint_pipeline 

    feat: ✨ add a cronjob script for dj workers
    Thinh Nguyen authored Feb 2, 2024
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  13. fix: bugfix in specsheet and tune worker

    Thinh Nguyen committed Feb 2, 2024
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  14. Merge pull request #323 from ttngu207/datajoint_pipeline 

    fix: bugfix in specsheet and tune worker
    Thinh Nguyen authored Feb 2, 2024
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  15. fix: 🐛 compose down workers first before removing images

    @JaerongA
    JaerongA committed Feb 2, 2024
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  16. Merge branch 'SainsburyWellcomeCentre:datajoint_pipeline' into datajo… 

    …int_pipeline
    @JaerongA
    JaerongA authored Feb 2, 2024
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  17. Merge pull request #324 from JaerongA/datajoint_pipeline

    @ttngu207
    ttngu207 authored Feb 2, 2024
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Commits on Feb 5, 2024

  1. chore: 🔊 Create a logger for a cron job

    @JaerongA
    JaerongA committed Feb 5, 2024
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  2. Merge branch 'datajoint_pipeline' of https://github.com/JaerongA/aeon… 

    …_mecha into datajoint_pipeline
    @JaerongA
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  3. Merge branch 'SainsburyWellcomeCentre:datajoint_pipeline' into datajo… 

    …int_pipeline
    @JaerongA
    JaerongA authored Feb 5, 2024
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  4. Merge pull request #325 from JaerongA/datajoint_pipeline 

    chore: 🔊 Create a logger for a cron job
    Thinh Nguyen authored Feb 5, 2024
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Commits on Feb 6, 2024

  1. fix: 🐛 specify docker path 

    cron job runs a different version of docker-compose which yields version incompatibility issue
    @JaerongA
    JaerongA committed Feb 6, 2024
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  2. fix cron logger

    @JaerongA
    JaerongA committed Feb 6, 2024
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  3. Merge pull request #326 from JaerongA/datajoint_pipeline 

    fix: 🐛 specify docker path
    Thinh Nguyen authored Feb 6, 2024
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  4. fix(social02): bugfix social schema reader

    Thinh Nguyen committed Feb 6, 2024
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  5. update: more robust check for subjects in a given block

    Thinh Nguyen committed Feb 6, 2024
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  6. Merge remote-tracking branch 'upstream/datajoint_pipeline' into dataj… 

    …oint_pipeline
    Thinh Nguyen committed Feb 6, 2024
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Commits on Feb 7, 2024

  1. Update social_experiments_block_analysis.ipynb

    Thinh Nguyen committed Feb 7, 2024
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  2. fix(sciviz): fix typo

    Thinh Nguyen committed Feb 7, 2024
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  3. Merge pull request #329 from ttngu207/datajoint_pipeline 

    update: more robust check for subjects in a given block
    @JaerongA
    JaerongA authored Feb 7, 2024
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Commits on Feb 15, 2024

  1. fix(reader): bugfix csv reader dropping column when the csv file is e… 

    …mpty
    Thinh Nguyen committed Feb 15, 2024
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  2. feat(block_analysis): add BlockSubject analysis based on Jai's initia… 

    …l work
    Thinh Nguyen committed Feb 15, 2024
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  3. feat(metadata): explicitly extract and store frame rate for video source

    Thinh Nguyen committed Feb 15, 2024
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  4. fix(block_analysis): minor bugfix

    Thinh Nguyen committed Feb 15, 2024
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Commits on Feb 16, 2024

  1. Merge pull request #336 from ttngu207/datajoint_pipeline 

    add BlockSubjectPatch analysis & other minor fixes
    @JaerongA
    JaerongA authored Feb 16, 2024
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Commits on Mar 1, 2024

  1. Update license.md

    @lochhh
    lochhh authored Mar 1, 2024
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Commits on Mar 8, 2024

  1. feat: ✨ add SocialExperiment page in sciviz

    @JaerongA
    JaerongA committed Mar 8, 2024
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  2. fix: 🐛 add return statement

    @JaerongA
    JaerongA committed Mar 8, 2024
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Commits on Mar 11, 2024

  1. feat: ✨ simplify with GROUP CONCAT

    @JaerongA
    JaerongA committed Mar 11, 2024
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  2. Merge pull request #339 from JaerongA/datajoint_pipeline 

    feat: ✨ add SocialExperiment page in sciviz
    Thinh Nguyen authored Mar 11, 2024
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Commits on Mar 12, 2024

  1. Update license.md year range

    @lochhh
    lochhh authored Mar 12, 2024
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Commits on Mar 19, 2024

  1. fix: 🐛 fix KeyError in BlockDetection

    @JaerongA
    JaerongA committed Mar 19, 2024
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Commits on Mar 20, 2024

  1. apply .sort_index() inside BlockDetection make function

    @JaerongA
    JaerongA committed Mar 20, 2024
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  2. Add object model for new stream io infrastructure

    @glopesdev
    glopesdev committed Mar 20, 2024
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  3. Support legacy stream group classes

    @glopesdev
    glopesdev committed Mar 20, 2024
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  4. Ensure deprecation message

    @glopesdev
    glopesdev committed Mar 20, 2024
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  5. Merge pull request #341 from JaerongA/datajoint_pipeline 

    fix: 🐛 fix KeyError in BlockDetection
    Thinh Nguyen authored Mar 20, 2024
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  6. Refactor stream classes for clarity

    @glopesdev
    glopesdev committed Mar 20, 2024
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  7. Ensure name is not None

    @glopesdev
    glopesdev committed Mar 20, 2024
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  8. Remove unused conditional

    @glopesdev
    glopesdev committed Mar 20, 2024
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  9. Improve deprecation warnings

    @glopesdev
    glopesdev committed Mar 20, 2024
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  10. Avoid exception handling on deprecated code path

    @glopesdev
    glopesdev committed Mar 20, 2024
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  11. Avoid clashing with built-in function names

    @glopesdev
    glopesdev committed Mar 20, 2024
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  12. Move stream schema classes to the schema module

    @glopesdev
    glopesdev committed Mar 20, 2024
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  13. Fix check for auto-generated initializer

    @glopesdev
    glopesdev committed Mar 20, 2024
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  14. Allow automatic import of nested stream schemas

    @glopesdev
    glopesdev committed Mar 20, 2024
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  15. Black formatting

    @glopesdev
    glopesdev committed Mar 20, 2024
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  16. Refactor dataset module to use stream schemas

    @glopesdev
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Commits on Mar 27, 2024

  1. Merge pull request #342 from SainsburyWellcomeCentre/io-reorg 

    Introduce explicit object model for device streams
    @jkbhagatio
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  2. Merge pull request #338 from SainsburyWellcomeCentre/add-license 

    Add BSD-3 license to project
    @jkbhagatio
    jkbhagatio authored Mar 27, 2024
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  3. Add sciviz local specsheet

    @lochhh
    lochhh committed Mar 27, 2024
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  4. Update docker-compose-local.yaml

    @lochhh
    lochhh committed Mar 27, 2024
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  5. Update sciviz local setup readme

    @lochhh
    lochhh committed Mar 27, 2024
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Commits on Apr 3, 2024

  1. Merge pull request #346 from SainsburyWellcomeCentre/sciviz-local-setup 

    Update SciViz local setup
    @ttngu207
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  2. Merge remote-tracking branch 'upstream/main' into datajoint_pipeline

    @ttngu207
    ttngu207 committed Apr 3, 2024
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Commits on Apr 4, 2024

  1. update(schemas): update social schemas to use the refactored Stream, … 

    …StreamGroup and Device
    @ttngu207
    ttngu207 committed Apr 4, 2024
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  2. Merge remote-tracking branch 'upstream/datajoint_pipeline' into dataj… 

    …oint_pipeline
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    ttngu207 committed Apr 4, 2024
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  3. chore: code cleanup

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    ttngu207 committed Apr 4, 2024
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  4. Merge pull request #347 from ttngu207/datajoint_pipeline 

    Update ingestion - using new Stream/Device io
    @ttngu207
    ttngu207 authored Apr 4, 2024
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  5. feat(dj): ingest data by searching multiple directories in specified … 

    …order
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    ttngu207 committed Apr 4, 2024
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  6. feat(sciviz): add load_order in Directory input page

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    ttngu207 committed Apr 4, 2024
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  7. Merge pull request #348 from ttngu207/datajoint_pipeline 

    feat(dj): ingest data by searching multiple directories in specified order
    @ttngu207
    ttngu207 authored Apr 4, 2024
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Commits on Apr 9, 2024

  1. feat(acquisition): refactor Epoch & Metadata ingestion

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    ttngu207 committed Apr 9, 2024
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  2. Merge pull request #349 from ttngu207/datajoint_pipeline 

    feat(acquisition): refactor Epoch & Metadata ingestion
    @ttngu207
    ttngu207 authored Apr 9, 2024
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  3. fix(tracking): bugfix searching for SLEAP model config file for multi… 

    …-dir
    @ttngu207
    ttngu207 committed Apr 9, 2024
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  4. Merge pull request #350 from ttngu207/datajoint_pipeline 

    fix(tracking): bugfix searching for SLEAP model config file for multi-dir
    @ttngu207
    ttngu207 authored Apr 9, 2024
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Commits on Apr 10, 2024

  1. fix(acquisition): remove debugging codeblock

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    ttngu207 committed Apr 10, 2024
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  2. Merge pull request #352 from ttngu207/datajoint_pipeline 

    fix(acquisition): remove debugging codeblock
    @ttngu207
    ttngu207 authored Apr 10, 2024
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Commits on Apr 11, 2024

  1. feat(block_analysis): retrieve patch offset

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    ttngu207 committed Apr 11, 2024
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  2. Merge pull request #353 from ttngu207/datajoint_pipeline 

    feat(block_analysis): retrieve patch offset
    @ttngu207
    ttngu207 authored Apr 11, 2024
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Commits on Apr 19, 2024

  1. update(tracking): raise error if no SLEAP data found

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    ttngu207 committed Apr 19, 2024
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  2. chore: update error message

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    ttngu207 committed Apr 19, 2024
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  3. Merge pull request #355 from ttngu207/datajoint_pipeline 

    update(tracking): raise error if no SLEAP data found
    @ttngu207
    ttngu207 authored Apr 19, 2024
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Commits on Apr 25, 2024

  1. fix: add .sort_index() on the streams dataframe

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    ttngu207 committed Apr 25, 2024
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  2. fix: more robust automated analysis - skip BlockAnalysis that are n… 

    …ot ready
    @ttngu207
    ttngu207 committed Apr 25, 2024
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  3. fix(chunk): fix first chunk starting before epoch start

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    ttngu207 committed Apr 25, 2024
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  4. disable automatic BlockDetection

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    ttngu207 committed Apr 25, 2024
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  5. Merge pull request #360 from ttngu207/datajoint_pipeline 

    fix first chunk starting before epoch start & disable automatic BlockDetection
    @ttngu207
    ttngu207 authored Apr 25, 2024
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Commits on May 2, 2024

  1. feat(block_analysis): skip subjects with no position data, select fir… 

    …st patch rate
    @ttngu207
    ttngu207 committed May 2, 2024
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  2. fix(test): remove blank return

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    ttngu207 committed May 2, 2024
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  3. fix(block_analysis): bugfix missing experiment_name in query

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    ttngu207 committed May 2, 2024
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  4. Update worker.py

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    ttngu207 committed May 2, 2024
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  5. Merge pull request #361 from ttngu207/datajoint_pipeline 

    Improve block analysis - skip subjects with no position data, bugfix Block detection
    @ttngu207
    ttngu207 authored May 2, 2024
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Commits on May 23, 2024

  1. feat: add patch preference calculation and block-patch-subject plots

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    ttngu207 committed May 23, 2024
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  2. chore: more robust code + black formatting

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    ttngu207 committed May 23, 2024
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Commits on May 24, 2024

  1. feat(block_analysis): add pref plots

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    ttngu207 committed May 24, 2024
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Commits on Jun 4, 2024

  1. Update block_analysis.py

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    ttngu207 committed Jun 4, 2024
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  2. black format

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    ttngu207 committed Jun 4, 2024
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  3. Update specsheet.yaml

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    ttngu207 committed Jun 4, 2024
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  4. feat: update comment, add to worker

    @ttngu207
    ttngu207 committed Jun 4, 2024
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  5. fix: skip over 0 pellet patch

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    ttngu207 committed Jun 4, 2024
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Commits on Jun 5, 2024

  1. update sciviz plots layout

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    ttngu207 committed Jun 5, 2024
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Commits on Jun 12, 2024

  1. Merge pull request #363 from ttngu207/datajoint_pipeline 

    BlockSubjectPatch analysis, patch preference plot and SciViz update
    @jkbhagatio
    jkbhagatio authored Jun 12, 2024
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