To do

Work planned, in order. Each item: what it is, what « done » means. Behaviour is unchanged by the reorganisation: the window tests (python tests/gui/screens.py) pass before and after each milestone.

Reorganisation of the code for more modules (SPEC.md 3.4)

1. gui/ and core/: done (2026-11-13)

• The shared window (Qt) in src/spam_gui/gui/: window, windows, controls, widgets, dialogs, busy, steps, plotting, points, layers.
• Without Qt or napari, in src/spam_gui/core/: parts, volumes, io (reading images), phi (Φ conversions).
• layers.py split into core/io.py, core/phi.py, gui/layers.py.

2. modules/mmr/: one file per step (not a priority)

• modules/mmr.py (about 3,900 lines) split into modules/mmr/: __init__.py (MultimodalRegistrationModule), state.py (MMRState), one file per step (load, eye, crop, histogram, phasediagram, registration, summary), phipane.py (Current Φ).
• What only MMR uses moved into it: phases.py (its phase layers), PhaseVolume and PhaseMask (from core/volumes.py), quantise, fields, registrationMemory (from core/parts.py).
• Done when: modules/mmr.py and phases.py are gone, the imports follow, SPEC.md 3.4 and specs/modules/mmr.md give the new paths, and the tests pass at the three sizes.

3. Tests

• The unit tests (tests/test_*.py) in tests/unit/.
• The window test split: the checks of the shared window (whatever the module) in tests/gui/window.py, the MMR workflow in tests/gui/modules/mmr.py.
• A screenshot script, tests/gui/screenshots.py: done (2026-11-13).
• Done when: pytest tests and python tests/gui/screens.py run them all, and SPEC.md section 6 gives the new paths.

Shared steps (modules/common/): when the next module is known

• Load two images, eye registration, crop: the steps of MMR that another module would share, made shared (modules/common/, specs/common-steps.md: what they need from a module's state, what they give).
• Waits for: which module of spam-gui comes next (OPEN_QUESTIONS.md, D5).