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[ENH] Remove co-located warnings by moving forceps into separate bd, update default_18 to default#138

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36000 merged 5 commits into
tractometry:mainfrom
36000:colocated
Jan 8, 2026
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[ENH] Remove co-located warnings by moving forceps into separate bd, update default_18 to default#138
36000 merged 5 commits into
tractometry:mainfrom
36000:colocated

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@36000 36000 commented Jan 7, 2026

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Copilot AI review requested due to automatic review settings January 7, 2026 23:09

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Pull request overview

This pull request renames default18_bd() to default_bd() and extracts the Forceps Major and Forceps Minor bundles into a separate forceps_bd() function to resolve co-located warnings. Additionally, it includes several spelling corrections across documentation and comments.

Key Changes

  • Renamed default18_bd() to default_bd() throughout the codebase
  • Extracted Forceps Major and Forceps Minor bundles from default_bd() into a new forceps_bd() function
  • Fixed multiple spelling errors in comments, documentation, and examples

Reviewed changes

Copilot reviewed 16 out of 16 changed files in this pull request and generated 5 comments.

Show a summary per file
File Description
AFQ/api/bundle_dict.py Renamed function from default18_bd to default_bd and created separate forceps_bd() function
AFQ/tasks/data.py Updated default bundle reference from default18_bd() to default_bd()
AFQ/tests/test_bundle_dict.py Updated test references from default18_bd() to default_bd()
AFQ/tests/test_api.py Updated test references from default18_bd() to default_bd()
examples/tutorial_examples/plot_007_rois.py Updated function call from default18_bd() to default_bd()
examples/tutorial_examples/plot_006_bids_layout.py Updated function call from default18_bd() to default_bd()
examples/howto_examples/vof_example.py Updated function call from default18_bd() to default_bd()
examples/howto_examples/pyafq_2.py Updated function call and fixed spelling errors in comments
examples/howto_examples/plot_stages_of_tractometry.py Fixed spelling errors in comments
examples/howto_examples/optic_radiations.py Updated function reference in comment and modified citation
examples/howto_examples/afq_fwdti.py Updated function call from default18_bd() to default_bd()
examples/howto_examples/afq_callosal.py Updated function reference in comment
examples/howto_examples/add_custom_bundle.py Updated function reference in comment and fixed spelling error
examples/howto_examples/use_subject_space_rois_from_freesurfer.py Fixed spelling error in comment
docs/source/reference/bundledict.rst Updated function references and fixed spelling errors
.codespellrc Added "abd" to ignore-words-list
Comments suppressed due to low confidence (1)

AFQ/api/bundle_dict.py:23

  • The newly created forceps_bd function is not exported in the __all__ list. This function should be added to the exports so it can be imported and used by users who want to include the forceps bundles in their analysis.
__all__ = [
    "BundleDict",
    "default_bd",
    "reco_bd",
    "callosal_bd",
    "cerebellar_bd",
    "baby_bd",
]

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Comment thread AFQ/tests/test_bundle_dict.py Outdated
Comment thread AFQ/tasks/data.py
Comment thread examples/howto_examples/optic_radiations.py Outdated
Comment thread AFQ/tests/test_bundle_dict.py Outdated
Comment thread AFQ/tests/test_bundle_dict.py Outdated

@arokem arokem left a comment

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LGTM! I think that copilot did catch some tests that need to be fixed? But also some of those comments are not correct, I believe.

Comment thread AFQ/tasks/data.py
@36000
36000 merged commit dde4a02 into tractometry:main Jan 8, 2026
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3 participants