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Update pipeline declaration, ingestion script, and notebooks #18

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Merged
merged 32 commits into from
Apr 29, 2022
Merged

Update pipeline declaration, ingestion script, and notebooks #18

merged 32 commits into from
Apr 29, 2022

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@kabilar
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@kabilar kabilar commented Apr 24, 2022 •
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  • Update Docker and Compose files
  • Update diagram
  • Remove previous notebooks
  • Add new notebooks with Jupytext paired python scripts
  • Update automated ingest script
  • Add table definition to pipeline script
  • Also see: Add Miniscope-DAQ-V4 and CaImAn trigger element-miniscope#13
  • In a future pull request, I will add the following:
    • 04-automate and 05-explore Jupyter notebooks
    • pytests

kabilar added 25 commits April 23, 2022 10:20
@kabilar
Fix format
a09e53c
@kabilar
Add requirement
8561af8
@kabilar
Remove tests/user_data
6285d87
@kabilar
Remove previous notebook versions.
9184e65
@kabilar
Add jupytext paired script
13108f7
@kabilar
Update Compose file
c5df6b0
@kabilar
Update data download notebook
0b99792
@kabilar
Update attribute name and import statement
8645c5e
@kabilar
Update workflow structure notebook
0fe7b3c
@kabilar
Update path handling
e5e5170
@kabilar
Update database configuration notebook
781e75d
@kabilar
Update automated ingestion script
c9ffda9
@kabilar
Update package version
acee799
@kabilar
Add acquisition software to sessions csv
849cd94
@kabilar
Pin version number
d05965f
@kabilar
Add CaImAn installation
ae40356
@kabilar
Add specific json file name
d054b16
@kabilar
Update image version
99ceda4
@kabilar
Install CaImAn from flatironinstitute base repo
5e22ce1
@kabilar
Update Dockerfiles
3a53849
@kabilar
Revert import
74ed693
@kabilar
Update Docker files
b8f0c48
@kabilar
Update paths
db78117
@kabilar
Add AnatomicalLocation table
b286063
@kabilar
Add diagram
dcdf9e9
@kabilar kabilar mentioned this pull request Apr 26, 2022
Merged
@kabilar kabilar marked this pull request as ready for review April 26, 2022 17:02
@kabilar
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kabilar commented Apr 26, 2022

Hi @tdincer, this pull request is ready for review. Let's try to merge by Friday, April 29. Thanks!

CBroz1
CBroz1 reviewed Apr 27, 2022
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@CBroz1 CBroz1 mentioned this pull request Apr 27, 2022
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CBroz1
CBroz1 reviewed Apr 28, 2022
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@ttngu207 ttngu207 merged commit 058014a into datajoint:main Apr 29, 2022
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@ttngu207 ttngu207 ttngu207 approved these changes

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@kabilar @CBroz1 @ttngu207 @tdincer