Epic: Migrate copick-mcp to OME-Zarr 0.5 and Zarr v3 #52

Goal

Adopt the published copick 2.0 ecosystem on the v2.0 branch while keeping copick-mcp storage-format-neutral, completing the CLI/plugin contract, and establishing the prerelease path. OME-Zarr 0.4/v0.5 and Zarr v2/v3 interoperability is owned and tested by copick core; MCP consumes Copick entities and does not parse those formats.

Project: https://github.com/orgs/copick/projects/1

Published prerequisites

• copick==2.0.0-alpha.1
• copick-utils==2.0.0-alpha.1
• optional copick-torch==2.0.0-alpha.1

Alpha metadata uses >=2.0.0-alpha.1,<3 floors. Stable floors change to >=2.0.0,<3 only during the coordinated ecosystem stable cutover.

Correction

The initial record said an MCP fixture proved logical parity across legacy and migrated OME-Zarr/Zarr projects. Review established that the fixture never reads Zarr metadata. #55 and #58 now record the correct, narrower claim: equivalent Copick entity trees exercise format-neutral MCP discovery, while actual storage interoperability remains core coverage.

Completed work

1. Establish the copick-mcp test, transport, and packaging gate #53 — deterministic focused behavior suite, lockfile, and Python 3.11-3.14 workflow.
2. Adopt copick 2.0 alphas and complete CLI plugin discovery #54 — published 2.0 floors, authoritative plugin discovery, and safe CLI parsing.
3. Verify format-neutral MCP entity discovery #55 — format-neutral entity discovery without false storage-format claims.
4. Validate installed MCP transport, optional torch integration, and backends #56 — focused optional torch command discovery; broader stdio/backend work excluded by revised scope.
5. Complete copick-mcp documentation, artifact gates, and 2.0 release #57 — documentation, exact-commit release validation, and prerelease setup.
6. fix: restore CLI introspection contracts #60, fix: harden metadata exploration behavior #62, and chore: align v2.0 maintenance and documentation #63 — alpha.1 review remediation.
7. fix: synchronize package version in releases #64 — Release Please package-version synchronization.
8. chore: release copick-mcp 2.0.0-alpha.3 #65 — successful copick-mcp==2.0.0a3 release after alpha.2 was superseded.

Repository state

• v2.0 is protected by active ruleset 21015564.
• Pull requests are required and py3.11, py3.12, py3.13, and py3.14 must pass.
• Release Please maintains separate stable and alpha configurations and validates the exact released SHA.
• The package version source is explicitly updated with the release manifest.

Acceptance criteria

• Focused tests cover public exploration/CLI behavior and all setup target variants on Python 3.11-3.14.
• Alpha metadata excludes Python 3.10 and pre-migration Copick packages.
• Authoritative installed plugin groups, including setup and download, are discoverable.
• CLI validation does not invoke callbacks and captures Click output.
• Equivalent Copick entity trees return equivalent logical results without being presented as Zarr parity tests.
• Exact optional torch alpha command metadata was verified without model execution.
• Exact release commits are tested before publication.
• copick-mcp==2.0.0a3 is published to PyPI.

Revised-scope exclusions

• Structural/source guards and exact dependency-declaration tests.
• Artifact-content tests.
• A torch-extra CI dependency job.
• Real stdio and remote-backend MCP integration tests.
• Direct Zarr reads/writes, OME metadata construction, store conversion, format switches, or GPU/model execution.