Split longitudinal CLI into nested per-stage subcommands (Stage 3 of #301)#313
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…301) Replace the legacy `rbc longitudinal process --anatomical --functional` flag flow with dedicated `rbc longitudinal {template,anatomical,functional, metrics,qc,all}` subcommands. `rbc long` stays as an alias for the parent group. `metrics`, `qc`, and `all` register for discoverability but raise `NotImplementedError` until Stage 6 lands. CLI args now hang off `LongitudinalBaseArgs` (in `cli/longitudinal/_base.py`), which adds `--fs-license` on top of `BaseArgs`. Orchestration gains per-stage `run()` entrypoints in `orchestration/longitudinal/{anatomical,functional, metrics,qc,all}.py`; the shared subject/session iteration primitive moves to `orchestration/longitudinal.iter_sessions_with_template`. Unit tests now cover each subcommand's `validate_namespace`, the parent subparser + `long` alias help output, and per-stage orchestration dispatch.
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The per-stage orchestration `run()` entrypoints previously imported the shared iteration helper via a function-local import because the package `__init__.py` already imported those modules at top level. Moving the helper into a dedicated `_iter.py` module lets both sides import it cleanly at module scope. Test patch paths updated accordingly.
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Tracker: #301 — Stage 3.
Summary
rbc longitudinal process --anatomical --functionalflag flow with a nested subparser group:rbc longitudinal {template,anatomical,functional,metrics,qc,all}.rbc longstays registered as an alias for the parent command (aliases=["long"]).cli/longitudinal/_base.py::LongitudinalBaseArgson top ofBaseArgs, adding--fs-license. Every longitudinal subcommand accepts--fs-licensefor a consistent surface, even though onlytemplateconsumes it today.cli/longitudinal/process.py.metrics,qc, andallso they surface in--help, but their orchestration entrypoints raiseNotImplementedErroruntil Stage 6 lands. This keeps the discoverable shape stable while leaving the implementation to later stages.run()into per-stage entrypoints inorchestration/longitudinal/{anatomical,functional,metrics,qc,all}.py, sharing subject/session iteration via a newiter_sessions_with_templatehelper in the package__init__.py.validate_namespace, the parent subparser +longalias help output, and per-stage orchestration dispatch.rbc longitudinal …row to workflow table, flag Stage 6 gap) anddocs/data_dictionary.md.Stage 3 checklist (#301)
cli/longitudinal/{template,anatomical,functional,metrics,qc,all}.pyexist with nested subparsers.__init__.pyregisterslongitudinalwithaliases=["long"].cli/longitudinal/_base.pydefinesLongitudinalBaseArgswith--fs-licenseon top ofBaseArgs.cli/longitudinal.py(the--anatomical --functionalshape) is deleted — here, the Stage-2 holding pencli/longitudinal/process.py.cli/main.pyalready registers the longitudinal subparser group; this PR leaves it unchanged.NotImplementedErrorwith a pointer to Longitudinal pipeline: refactor and release readiness (tracker) #301.docs/data_dictionary.mdupdated.Test plan
uv run pytest -m unit— 767 passed, 1 skipped.uv run ruff check src/ tests/— clean.uv run ruff format --check src/ tests/— clean.uv run mypy src/ tests/— clean (166 files).uv run rbc longitudinal --helpshows all six stages.uv run rbc long --helpmatches.