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Single subject anatomical workflow#6

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kaitj wants to merge 21 commits into
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enh/anatomical
Closed

Single subject anatomical workflow#6
kaitj wants to merge 21 commits into
mainfrom
enh/anatomical

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@kaitj
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@kaitj kaitj commented Jan 30, 2026

First implementation of workflow with modular pieces of RBC anatomical / structural.

nx10 and others added 15 commits January 28, 2026 14:15
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5 to 6.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v5...v6)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 5.5.1 to 5.5.2.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](codecov/codecov-action@5a10915...671740a)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-version: 5.5.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Bumps [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) from 5.4.2 to 7.2.0.
- [Release notes](https://github.com/astral-sh/setup-uv/releases)
- [Commits](astral-sh/setup-uv@d4b2f3b...61cb8a9)

---
updated-dependencies:
- dependency-name: astral-sh/setup-uv
  dependency-version: 7.2.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
…s/astral-sh/setup-uv-7.2.0

Bump astral-sh/setup-uv from 5.4.2 to 7.2.0
…s/codecov/codecov-action-5.5.2

Bump codecov/codecov-action from 5.5.1 to 5.5.2
…s/actions/setup-python-6

Bump actions/setup-python from 5 to 6
Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 6.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v4...v6)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
…s/actions/checkout-6

Bump actions/checkout from 4 to 6
* Update project description

- Removed mention of "derivative" as this is implied.
- Similarly mention of longitudinal is not strictly necessary.

* Remove structural modules

* Add functional module
@kaitj
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kaitj commented Jan 30, 2026

cc @jpillai00

Comment thread src/rbc/core/anatomical/registration.py Outdated
Comment thread src/rbc/core/resources/__init__.py
Comment thread src/rbc/core/common.py Outdated
Comment thread src/rbc/core/utils.py Outdated
Comment thread src/rbc/core/utils.py Outdated
Comment thread src/rbc/workflows/anatomical.py Outdated
Comment thread src/rbc/core/utils.py
@nx10
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nx10 commented Feb 2, 2026

See also #14

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codecov Bot commented Feb 2, 2026

Codecov Report

❌ Patch coverage is 0% with 56 lines in your changes missing coverage. Please review.
✅ Project coverage is 0.00%. Comparing base (ac7b2bb) to head (8b15e1c).
⚠️ Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
src/rbc/core/utils.py 0.00% 21 Missing ⚠️
src/rbc/core/anatomical/registration.py 0.00% 10 Missing ⚠️
src/rbc/core/common.py 0.00% 8 Missing ⚠️
src/rbc/core/resources/__init__.py 0.00% 8 Missing ⚠️
src/rbc/core/anatomical/skull_stripping.py 0.00% 5 Missing ⚠️
src/rbc/core/anatomical/__init__.py 0.00% 3 Missing ⚠️
src/rbc/core/__init__.py 0.00% 1 Missing ⚠️

❌ Your project check has failed because the head coverage (0.00%) is below the target coverage (80.00%). You can increase the head coverage or adjust the target coverage.

Additional details and impacted files
@@         Coverage Diff          @@
##           main      #6   +/-   ##
====================================
  Coverage      0   0.00%           
====================================
  Files         0       7    +7     
  Lines         0      56   +56     
====================================
- Misses        0      56   +56     

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@kaitj kaitj closed this Feb 2, 2026
nx10 added a commit that referenced this pull request Apr 6, 2026
- Resolve merge conflicts (keep orchestration layer, discard old inline logic)
- Fix docstring paths in generate_bids_tools.py (#1)
- Remove redundant extension=Extension.NII_GZ in longitudinal export (#5)
- Clarify verbose docstring in RunnerConfig (#6)
gkiar pushed a commit that referenced this pull request May 23, 2026
Renames tests/data/cpac_rbc_divergences.md to docs/cpac_comparison.md
and splits findings into Bugs (#4, #5) and Divergences (#1, #2, #3, #6)
to distinguish unambiguous numerical errors from defensible design
choices. Adds a new divergence about CPAC's duplicate motion correction.
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