Integrate longitudinal template generation (Stage 2 of #301)

[nx10]

Summary

Stage 2 of the longitudinal refactor (tracker: #301). Ports scripts/build_robust_template.py into the rbc package layout, updates xfm naming, and wires up rbc longitudinal template as a nested subcommand. The standalone script is deleted.

What moved / changed

• Workflow split into proper layers
  • core/longitudinal/freesurfer.py -- generate_robust_template + fs_to_itk_xfm via niwrap freesurfer + rbc.core.fsl2itk (replaces c3d_affine_tool).
  • workflows/longitudinal/template.py -- LongitudinalTemplateOutputs + generate_subject_template.
  • bids/longitudinal/template.py -- discover_template_inputs + export_template.
  • orchestration/longitudinal/template.py -- per-subject loop.
• Bug fix Implement BOLD Brain Masking #19 -- per-subject volume count check now lives inside the per-subject loop instead of on the whole df, so multi-subject runs no longer fail when one subject happens to have a single session.
• xfm naming updated (Implement Slice Timing Correction #18) -- writes sub-X_ses-longitudinal_from-Y_to-longitudinal_mode-image_xfm.txt. resolve_longitudinal_{anat,func} now query by extra={"from": ses, "to": "longitudinal"}. The multi-entity-extras spike confirmed Bids.expect() ANDs each predicate, so this Just Works.
• CLI -- cli/longitudinal/ is now a package with nested subparsers and a long alias. New: rbc longitudinal template. Legacy --anatomical/--functional flow lives at rbc longitudinal process until Stage 3 splits it into proper per-stage subcommands. (rbc long template works.)
• No FS license required. Investigated upstream chklc(): if SURFER_SIDEDOOR is set, the check returns 1 immediately. Orchestration sets it on runner.environ, so users don't need --fs-license, FS_LICENSE, or any registration to run mri_robust_template. The original script's license-mounting plumbing is gone.
• noit=True ported as-is with a TODO comment referencing Evaluate noit=True in longitudinal robust template generation #302 (quality spike).
• Deletes scripts/build_robust_template.py.

Test plan

• uv run pytest -m unit (750 passed, 1 skipped)
• uv run ruff check src/ tests/
• uv run ruff format src/ tests/
• uv run mypy src/ tests/
• uv run rbc longitudinal --help and rbc long template --help show the expected nested subparser output
• Tier-2 integration test deferred to a follow-up PR. Acceptance criterion called for an integration test on the ds000114 fixture, but the multi-session fixture infrastructure (download script, CI cache key, conftest) is substantial enough to deserve its own PR. The existing pytest -m "integration and not slow" lane is unaffected (collects 0 tests today, so the "passes" criterion is trivially satisfied). I'll file a follow-up issue.

Follow-ups referenced

• Evaluate noit=True in longitudinal robust template generation #302 -- noit=True quality spike (ported as-is here).
• New issue to file: ds000114 fixture infrastructure + tier-2 integration tests for rbc longitudinal template.
• Stage 3 (next PR) -- split rbc longitudinal process into dedicated anatomical/functional subcommands; remove the legacy --anatomical --functional flag shape.

[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
rbc
__init__.py	1	0	100%
context.py	25	1	96%	77
metadata.py	67	0	100%
rbc/bids
__init__.py	9	0	100%
_schema.py	585	4	99%	776, 782, 790, 1101
anatomical.py	24	3	87%	44, 47–48
builder.py	72	7	90%	233–235, 362, 364–365, 386
functional.py	42	5	88%	46–49, 84
metrics.py	23	1	95%	44
qc.py	17	0	100%
query.py	67	42	37%	103–107, 121–125, 127–128, 130–135, 137, 139, 153, 159–165, 198, 207, 209–216, 225, 257, 266–267
session.py	47	0	100%
rbc/bids/longitudinal
__init__.py	0	0	100%
anatomical.py	17	0	100%
functional.py	11	0	100%
template.py	27	0	100%
rbc/cli
__init__.py	1	0	100%
all.py	49	2	95%	84, 109
anatomical.py	25	2	92%	47, 63
base.py	71	9	87%	56, 62, 123–125, 131–133, 156
functional.py	33	2	93%	67, 87
main.py	42	0	100%
metrics.py	42	2	95%	77, 95
qc.py	25	2	92%	45, 61
rbc/cli/longitudinal
__init__.py	8	0	100%
process.py	27	2	92%	52, 69
template.py	23	0	100%
rbc/core
__init__.py	3	0	100%
common.py	26	12	53%	43–45, 62–70
fileops.py	27	4	85%	69–72
fsl2itk.py	42	0	100%
nifti.py	192	5	97%	236–237, 244–245, 524
niwrap.py	71	13	81%	59, 143–144, 146–148, 150–151, 156–157, 159, 161–162
rbc/core/anatomical
__init__.py	4	0	100%
registration.py	15	4	73%	59, 151, 166, 183
segmentation.py	24	8	66%	64, 74–76, 92, 114, 125, 141
rbc/core/functional
__init__.py	13	0	100%
coregistration.py	7	2	71%	44, 55
despiking.py	7	3	57%	32, 36–37
distortion.py	130	40	69%	269–271, 321, 324, 332–335, 341–346, 349, 352–353, 356, 365–369, 375–376, 387–388, 391, 397, 443–444, 447, 455, 461, 470–471, 474, 484, 491
erosion.py	32	1	96%	50
initialization.py	9	4	55%	35, 42–43, 63
masking.py	34	25	26%	53, 55–56, 58–59, 62–65, 69, 91, 134, 183, 197, 208, 223, 233, 249, 258, 271, 285, 296, 306, 319, 328
motion.py	57	37	35%	62, 64–67, 69, 71, 73, 76–77, 83–84, 86–87, 95–97, 99, 102, 105, 107, 124–125, 135–138, 159, 169, 171–172, 175, 177–179, 181, 183
nuisance.py	81	60	25%	78, 80–85, 87, 89–90, 93, 96–98, 100–102, 104–110, 112–116, 118, 163, 165, 167, 170–171, 173–175, 178, 181–182, 185–187, 190–193, 197, 203–205, 207, 235, 243, 269, 278, 307, 316, 322
regressors.py	89	6	93%	163, 193, 325–328
resampling.py	54	43	20%	37–42, 74–76, 78, 80–81, 85–87, 90, 93, 105, 107–108, 112, 114, 150–152, 154–155, 159, 161–162, 167–169, 173–174, 177, 180, 187, 199, 201–202, 207, 209
timing.py	16	11	31%	46–47, 49–53, 58, 60, 66–67
rbc/core/longitudinal
__init__.py	1	0	100%
freesurfer.py	35	0	100%
transform.py	46	7	84%	106–107, 165–168, 170
rbc/core/metrics
__init__.py	3	0	100%
alff.py	90	1	98%	265
reho.py	66	0	100%
smoothing.py	7	3	57%	36, 42–43
standardization.py	27	11	59%	64, 66–68, 70, 72–75, 77–78
timeseries.py	70	1	98%	147
rbc/core/qc
__init__.py	6	0	100%
dvars.py	26	0	100%
motion.py	31	0	100%
registration.py	41	0	100%
xcp.py	41	0	100%
rbc/orchestration
__init__.py	32	2	93%	90, 93
all.py	41	9	78%	131–132, 137, 145, 153–154, 171, 173–174
anatomical.py	37	22	40%	49–52, 57–58, 60–63, 85–87, 89–90, 94, 101, 104, 109–110, 116, 118
functional.py	41	12	70%	124–126, 128–129, 133, 139, 142, 147–148, 157, 159
metrics.py	46	30	34%	32–35, 38–40, 67, 75–76, 100–102, 104–106, 110, 118–121, 123–124, 130–132, 137, 145, 152, 154
qc.py	34	0	100%
rbc/orchestration/longitudinal
__init__.py	38	1	97%	78
anatomical.py	16	0	100%
functional.py	14	0	100%
template.py	51	5	90%	48, 53–55, 101
rbc/workflows
__init__.py	10	0	100%
anatomical.py	29	11	62%	88–91, 95–100, 105
functional.py	92	57	38%	108–109, 117, 122–123, 131, 202–203, 206–207, 210–211, 214, 217–220, 230–232, 242–243, 246, 249, 252–254, 260, 263, 267–268, 275–276, 283–284, 291–292, 295–297, 300–303, 315–316, 328, 330–333, 336–337, 346–347, 355, 362
metrics.py	41	18	56%	80, 83–84, 93–94, 99–102, 105–108, 112–115, 119
qc.py	55	34	38%	88–89, 92–93, 96, 99, 102–107, 110, 119–121, 125–128, 130–134, 136–137, 139–141, 144, 161, 167, 169
rbc/workflows/longitudinal
__init__.py	0	0	100%
anatomical.py	24	8	66%	80–83, 85–87, 91
functional.py	11	2	81%	66, 72
template.py	15	5	66%	54–55, 59–60, 68
rbc_resources
__init__.py	38	0	100%
TOTAL	3468	601	82%

Tests	Skipped	Failures	Errors	Time
757	0 💤	0 ❌	0 🔥	11.191s ⏱️