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Add Codespaces + update tutorial notebook #53

Merged
merged 39 commits into from
Jan 9, 2024
Merged

Add Codespaces + update tutorial notebook #53

merged 39 commits into from
Jan 9, 2024

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kushalbakshi
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@kushalbakshi kushalbakshi commented Nov 22, 2023 •
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This PR adds DevContainers configured to run Codespaces for tutorials and workshops. The proposed changes will include the following:

  • DevContainer configuration that builds a Codespace on the GitHub repository with S3-mounted sample data
  • Tutorial pipeline
  • 60 min tutorial notebook
  • Updated setup.py
  • Updated version.py and CHANGELOG

kushalbakshi and others added 30 commits October 31, 2023 13:36
@kushalbakshi
Add DevContainer for codespaces
5fdbe82
@kushalbakshi
Add tutorial notebook
c6e2ff7
@kushalbakshi
Update tutorial pipeline + notebook
69073fb
@kushalbakshi
Update devcontainer docker-compose
0d9c58a
@kushalbakshi
Merge branch 'codespace' of https://github.com/kushalbakshi/element-m…
eea7efe 
…iniscope into codespace
@kushalbakshi
Black formatting + minor fixes
0c4a09e
@kushalbakshi
Add vscode settings
5b787bd
@kushalbakshi
Debug s3fs mounting
c0e7c29
@kushalbakshi
Revert PUBLIC_S3_LOCATION
1b62bbc
@kushalbakshi
Update tutorial notebook for miniscope pipeline
e43a059
@kushalbakshi
Fix errors in notebook
6665e13
@kushalbakshi
Update Black formatting package name
3aeb5b9
@kushalbakshi
Black formatting
99b120a
@kushalbakshi
Add caiman import
c006271
@kushalbakshi
Add caiman requirement
c89bd7a
@kushalbakshi
Update caiman requirements and devcontainer build
a574088
@kushalbakshi
Debug caiman devcontainer
ad313a3
@kushalbakshi
Change order of caiman install
2d12fa2
@kushalbakshi
Remove caiman install from Dockerfile
9fc5d99
@kushalbakshi
Update setup.py and Dockerfile
8146105
@kushalbakshi
Fixes to package caiman into devcontainer
373a2f3
@kushalbakshi
Install elements in DevContainer
8a9f06d
@kushalbakshi
Revert paramset_idx to paramset_id
e203726
@kushalbakshi
Update tutorial to new structure
ebc7608
@kushalbakshi
Merge branch 'codespace' of https://github.com/kushalbakshi/element-m…
d73adce 
…iniscope into codespace
@kushalbakshi
Continue updating the tutorial notebook
9f321ee
@kushalbakshi
Update tutorial, README, license
ce9a185
@kushalbakshi
Update CHANGELOG
7afe5d2
@kushalbakshi
Move tutorial config to tutorial_pipeline.py
62fffab
@kushalbakshi
Remove db_prefix import
0551f33
@kushalbakshi kushalbakshi marked this pull request as ready for review November 29, 2023 17:37
ttngu207
ttngu207 reviewed Jan 4, 2024
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.vscode/launch.json
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We don't need anything in the .vscode right? Should be in the gitignore

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I was under the impression that Codespaces was using those settings when it sets up the vscode in the browser. I'm not sure if that was an accidental commit that has propagated through all the Elements. Let me know if you think it should be removed.

@ttngu207 ttngu207 merged commit 09b736e into datajoint:main Jan 9, 2024
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@kushalbakshi kushalbakshi deleted the codespace branch January 29, 2024 19:55
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@ttngu207 ttngu207 ttngu207 approved these changes

@MilagrosMarin MilagrosMarin Awaiting requested review from MilagrosMarin

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2 participants
@kushalbakshi @ttngu207