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Refactor get_session_path() BIDS util to rely only on BIDS Layout #171

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alyssadai opened this issue Jun 19, 2023 · 3 comments
Open

Refactor get_session_path() BIDS util to rely only on BIDS Layout #171

alyssadai opened this issue Jun 19, 2023 · 3 comments
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_flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again good first issue Good issue for a new contributor. importance:low We are not actively pursuing this item, it may be addressed when there is extra capacity. maint:refactor Simplifying or restructuring existing code or documentation. PR welcome Issue that is not an internal priority, but external PRs to address it are welcome. quick fix Minimal planning and/or implementation work required. type:maintenance Upkeeping efforts & catch-up corrective improvements that are not Features nor Bugs

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@alyssadai
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alyssadai commented Jun 19, 2023

Currently, bids_utils.get_session_path relies on an extra parameter bids_dir to construct the path for no session layer. Given advice in bids-standard/pybids#978, we should simplify the corresponding if block to use layout.root for all cases and just append a session name or empty string depending on whether the session param is None.

Tests may also need updating following this change.

See

bagel-cli/bagel/cli.py

Lines 268 to 273 in 6763e09

session_path = butil.get_session_path(
layout=layout,
bids_dir=bids_dir,
bids_sub_id=bids_sub_id,
session=session,
)

@alyssadai alyssadai added type:maintenance Upkeeping efforts & catch-up corrective improvements that are not Features nor Bugs maint:refactor Simplifying or restructuring existing code or documentation. importance:medium We will address this but will delay for higher priority items. labels Jun 19, 2023
@alyssadai alyssadai added importance:low We are not actively pursuing this item, it may be addressed when there is extra capacity. and removed importance:medium We will address this but will delay for higher priority items. labels Jun 20, 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 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 Jul 21, 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 stale-issue label to indicate that this issue should be reviewed again and then either prioritized or closed.

@alyssadai alyssadai added the quick fix Minimal planning and/or implementation work required. label Aug 26, 2023
@surchs surchs added good first issue Good issue for a new contributor. PR welcome Issue that is not an internal priority, but external PRs to address it are welcome. and removed _flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again labels Dec 5, 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 75 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:

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@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 19, 2024
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Labels
_flag:stale [BOT ONLY] Flag issue that hasn't been updated in a while and needs to be triaged again good first issue Good issue for a new contributor. importance:low We are not actively pursuing this item, it may be addressed when there is extra capacity. maint:refactor Simplifying or restructuring existing code or documentation. PR welcome Issue that is not an internal priority, but external PRs to address it are welcome. quick fix Minimal planning and/or implementation work required. type:maintenance Upkeeping efforts & catch-up corrective improvements that are not Features nor Bugs
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