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See if we can speed things up with ancpBIDS #8

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surchs opened this issue Sep 6, 2022 · 8 comments
Closed
3 tasks

See if we can speed things up with ancpBIDS #8

surchs opened this issue Sep 6, 2022 · 8 comments
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flag:discuss Flag issue that needs to be discussed before it can be implemented. _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again importance:medium We will address this but will delay for higher priority items. maint:usability General improvements to product usability that are unrelated to feature prioritization. type:maintenance Upkeeping efforts & catch-up corrective improvements that are not Features nor Bugs

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@surchs
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surchs commented Sep 6, 2022

Right now, parsing a large dataset takes an annoyingly long time. ancpBIDS is known to be faster. It should also support the core queries that we are interested in. So maybe we can remove the pyBIDS dependency, use ancpBIDS instead, and speed things up

  • take a look to see if we could use ancpBIDS instead of pyBIDS
  • migrate to ancpBIDS
  • make a speed comparison for a large dataset and then decide what to keep
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stale bot commented Nov 29, 2022

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

@stale stale bot added the _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again label Nov 29, 2022
@stale stale bot closed this as completed Dec 6, 2022
@surchs surchs reopened this Dec 6, 2022
@stale stale bot removed the _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again label Dec 6, 2022
@surchs surchs added feat:improve Incremental, user facing improvements of an existing feature. flag:discuss Flag issue that needs to be discussed before it can be implemented. type:maintenance Upkeeping efforts & catch-up corrective improvements that are not Features nor Bugs maint:usability General improvements to product usability that are unrelated to feature prioritization. importance:medium We will address this but will delay for higher priority items. and removed feat:improve Incremental, user facing improvements of an existing feature. labels Jan 3, 2023
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github-actions bot commented Feb 3, 2023

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 stale-issue label to indicate that this issue should be reviewed again and then either prioritized or closed.

@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 Feb 3, 2023
@surchs
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surchs commented Mar 21, 2023

I would close this issue. It makes sense, but I don't think we'll get to it anytime soon. What do you think @alyssadai? If you agree, feel free to just close

@alyssadai
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@surchs I'm not super familiar with ancpBIDS, but I wonder if it'd be worth leaving this issue open at least until we've attempted to run the CLI on the PPMI and QPN datasets (which I think are a couple hundred subjects each)? I just did a quick search of "ancpBIDS" in the PyBIDS issues and based on this post/comment I suspect the long runtime might become an issue sooner than we think - it looks like it can take almost 6 min to validate a dataset of ~500 subjects. We can always just wait it out if that's the case, but I think at that point this issue might be worth revisiting, if only to figure out a game plan for the migration. Thoughts?

@github-actions github-actions bot removed the _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again label Mar 22, 2023
@surchs
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surchs commented Mar 22, 2023

I put it on the roadmap for "Next", we can move it up if it becomes a more pressing problem

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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 stale-issue label to indicate that this issue should be reviewed again and then either prioritized or closed.

@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 Apr 22, 2023
@surchs
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surchs commented Jun 6, 2023

I'm closing this. It's stale, we may eventually do it, but right now it does not seem to be the priority.

@surchs surchs closed this as completed Jun 6, 2023
@alyssadai
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@surchs minor - but should we close as "not planned" instead?

@alyssadai alyssadai mentioned this issue Mar 18, 2024
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flag:discuss Flag issue that needs to be discussed before it can be implemented. _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again importance:medium We will address this but will delay for higher priority items. maint:usability General improvements to product usability that are unrelated to feature prioritization. type:maintenance Upkeeping efforts & catch-up corrective improvements that are not Features nor Bugs
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