G1: declare axes as a family; delete the component enums

[trissim]

Surface G1 (receipt: docs/refactor/consolidation-20261009/G1-axis-family.md).

What changed

• openhcs/core/axes.py: nominal Axis classes registered in an AxisFamily (AutoRegisterMeta). Roles are capability mixins with cardinality checked when a family is declared: PartitionAxis (exactly one), StackAxis (at most one), ColourAxis, TileAxis, TimeAxis, DefaultVariable, DefaultGroupBy (at most one). Value kinds are LabelValued and OrdinalValued. Ungrouped is the explicit absent-grouping declaration. A role-keyed strategy mixin replaces the strategies that were keyed by enum member.
• The microscopy family (site, channel, z_index, timepoint, well, with their current roles and order) lives in openhcs/domains/microscopy/axes.py. The product entry point (openhcs/__init__.py) activates it once per process. No kernel module imports the domain.
• Deleted: the five enums, _ComponentTemplate, ComponentConfiguration and its factory, the per-call get_openhcs_config, the GroupBy __eq__/__hash__ patch, convert_enum_by_value, ComponentSet.coerce*, the import-time DEFAULT_*/MULTIPROCESSING_AXIS, OpenHCSPlaneAddress.from_values, and every .value identity bridge.
• Kernel member references are now role queries:
  • source metadata projections, Zarr NGFF axes and viewer labels use role-keyed leaves;
  • viewer display configs have one mode field per role (partition_mode, tile_mode, colour_mode, stack_mode, time_mode);
  • plane filenames derive from the declared axis tokens;
  • function requirements declare roles (required_axis_roles, allowed_group_by_roles).
• Boundaries:
  • JSON and wire values use Axis.name, and group_by uses "none" for Ungrouped;
  • config documents spell Microscopy.Channel (new pycodify formatter);
  • form fields declare AnnotationChoices.
• Lockstep libraries: Add AnnotationChoices for declared finite choice sets python-introspect#17 (AnnotationChoices, type[X] validation) and Render AnnotationChoices fields; provider-owned grouping labels PyQT-reactive#16 (choice widgets; the provider now owns grouping labels instead of get_groupby_enum).

Durable state (owner decision G1-Q1)

Pickled pipelines are deprecated and not converted (F1 deletes the GUI pickle path). tools/cutover/g1_axis_family.py rewrites pycodify Python sources (.py pipelines, config documents, custom functions): enum members, GroupBy.NONE, per-member viewer mode fields, required_variable_components/allowed_group_by and their imports, keeping a .pre-g1 backup. tests/unit/test_g1_cutover_tool.py converts fixtures rendered by pre-G1 main and loads and validates them on G1. Tool, test and fixtures are deleted once the owner has migrated.

Verification

• Guards: tests/unit/test_axis_family_guards.py, 3/3 pass. The deleted names appear nowhere in openhcs/, tests/, benchmark/ or scripts/. Kernel modules neither import openhcs.domains nor name the microscopy family or its members. The product entry point activates Microscopy.
• Witness: tests/unit/test_axis_family_witness.py, 5/5 pass. A remote-sensing family (scene, tile, band, date; no stack axis) is activated in-process with zero kernel edits. These all follow it:
  • family queries;
  • ProcessingConfig defaults and validation;
  • Fiji/Napari mode projection and its wire round trip;
  • plane filenames;
  • step validation and the compiler's group-axis resolution.
  • A real pipeline was not run end to end: the openhcsdata handler (domain, G4) still writes microscopy-named metadata.
• Official30 parity (ZMQ): 29/30 equivalent. Only cp_tutorial_3d_monolayer fails, with the same .pkl serialization error as the baseline on main.
• Offscreen GUI import: OK. variable_components and sequential_components render as checkbox groups, group_by as a combo.
• Touched-module tests: every failure left is either one that also fails in the main baseline, an environment issue (pyclesperanto/torch not installed, subprocess import-root checks), or a test file that did not collect on main.

MCP schema changes (fixture regenerated)

All intended consequences of the per-role viewer mode fields:

• openhcs_stream_plate_files_to_viewer: the Napari display-config properties site_mode, channel_mode, z_index_mode, timepoint_mode, well_mode become tile_mode, colour_mode, stack_mode, time_mode, partition_mode (same enum, same defaults).
• openhcs_set_viewer_image_color: the description now says colour_mode=LAYER instead of channel_mode=LAYER.

No other tool, surface or resource changed.

Handoff

Recorded in the receipt:

• domain member references left for G2/G4;
• one(role) assumptions for G3/G4/G5;
• 24 axis-name string literals in kernel modules for G4/G7/G8;
• viewer slot families for G6;
• separating the grid role from the partition role (G8);
• merging the debug JSON switches (K6).

Production +2445/−2193. Net +252: the new kernel axes.py and role-keyed strategy leaves exceed the deleted factory and enum machinery. Tests +2656/−2403.

G1 · PR #1170 · guards 3/3 · production −2193 +2445 · tests −2403 +2656

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