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Migrate to Pydantic v2 #180

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Tracked by #180
alyssadai opened this issue Jul 21, 2023 · 5 comments · Fixed by #389
Closed
2 tasks done
Tracked by #180

Migrate to Pydantic v2 #180

alyssadai opened this issue Jul 21, 2023 · 5 comments · Fixed by #389
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dependencies Dependency updates and their version upgrades. released This issue/pull request has been released.

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@alyssadai
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alyssadai commented Jul 21, 2023

The release of Pydantic V2 introduced several breaking changes in the code due to name changes of multiple methods, removed or deprecated types/methods/objects, and broader changes to the logic of fields, validators, + more.

The docs for V2 have not quite caught up to the changes yet, but there is a comprehensive migration guide 🎉

Related are:
#179

TODO:

  • investigate needed refactor for moving to pydantic 2
  • refactor to enable pydantic 2 and migrate
@alyssadai alyssadai added importance:urgent flag:discuss Flag issue that needs to be discussed before it can be implemented. labels Jul 21, 2023
@alyssadai alyssadai added severity:blocker A bug or broken feature with no workaround severity:critical and removed severity:critical severity:blocker A bug or broken feature with no workaround labels Jul 21, 2023
@alyssadai alyssadai moved this to Specify - Active in Neurobagel Jul 21, 2023
@alyssadai
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Any thoughts @surchs?

I've started making some of the necessary changes (based on currently failing tests) in a branch and think the migration shouldn't require any major rewrites on our end, but some of the updates related to deprecated methods would probably benefit from a closer look as they involve a bit of extra code to preserve existing behavior.

@alyssadai alyssadai moved this from Specify - Active to Backlog in Neurobagel Aug 9, 2023
@surchs surchs added importance:medium dependencies Dependency updates and their version upgrades. flag:blocker flag that issue is blocking at least one other issue from being completed. and removed importance:urgent labels Aug 17, 2023
@surchs surchs moved this from Backlog to Implement - Active in Neurobagel Aug 22, 2023
@surchs surchs added severity:blocker A bug or broken feature with no workaround and removed severity:critical labels Aug 22, 2023
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surchs commented Aug 22, 2023

Bumping this up since my ill advised late night commit (1d4cb52) to main has made this an actual blocker.

@surchs surchs moved this from Implement - Active to Specify - Active in Neurobagel Aug 22, 2023
@alyssadai alyssadai removed the status in Neurobagel Aug 22, 2023
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Will pin pydantic version for now. Taking this issue off of backlog in favour of #184.

@alyssadai alyssadai removed flag:blocker flag that issue is blocking at least one other issue from being completed. severity:blocker A bug or broken feature with no workaround labels Aug 22, 2023
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We want to keep our issues up to date and active. This issue hasn't seen any activity in the last 30 days.
We have applied the _flag:stale label to indicate that this issue should be reviewed again.
When you review, please reread the spec and then apply one of these three options:

  • prioritize: apply the flag:schedule label to suggest moving this issue into the backlog now
  • close: if the issue is no longer relevant, explain why (give others a chance to reply) and then close.
  • archive: sometimes an issue has important information or ideas but we won't work on it soon. In this case
    apply the someday label to show that this won't be prioritized. The stalebot will ignore issues with this
    label in the future. Use sparingly!

@github-actions github-actions bot added the _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again label Sep 22, 2023
@alyssadai alyssadai added the flag:schedule Flag issue that should go on the roadmap or backlog. label Oct 8, 2024
@surchs surchs changed the title Migration to pydantic v2 Discuss migration to pydantic v2 Oct 8, 2024
@alyssadai alyssadai removed _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again flag:schedule Flag issue that should go on the roadmap or backlog. labels Oct 8, 2024
@alyssadai alyssadai changed the title Discuss migration to pydantic v2 Migrate to Pydantic v2 Nov 8, 2024
@alyssadai alyssadai removed the flag:discuss Flag issue that needs to be discussed before it can be implemented. label Nov 8, 2024
@alyssadai alyssadai moved this from Specify - Active to Implement - Active in Neurobagel Nov 8, 2024
@alyssadai alyssadai self-assigned this Nov 8, 2024
@alyssadai alyssadai moved this from Implement - Active to Implement - Done in Neurobagel Nov 13, 2024
@github-project-automation github-project-automation bot moved this from Review - Active to Review - Done in Neurobagel Nov 15, 2024
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🚀 Issue was released in v0.3.4 🚀

@neurobagel-bot neurobagel-bot bot added the released This issue/pull request has been released. label Nov 20, 2024
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