docs: tutorial notebook `05_planning_minimal_edits.ipynb`

[AbdelStark]

Context

Planner demo.

Scope

• CEM from a pathogenic variant to a benign latent neighborhood.
• Visualize edit sequence.

Out of Scope

Design Reference

• examples/README.md

Acceptance Criteria

• Plan completes within RFC-0008 latency targets

Parent tracking issue: #20

[AbdelStark]

Blocked (session-scoped): tutorial depends on APIs that have not yet shipped.

Tutorial notebooks demonstrate the end-to-end user journey through geno_lewm.{encoder,score_variant,plan,read_receipt,...}. Those APIs themselves depend on the ML stack that this session could not bring up (see comments on the encoder / predictor / training / surprise / planning issues). Writing a tutorial against missing APIs would either:

• Hard-code expected outputs against code that does not exist (false demo), or
• Ship a notebook that does not execute (broken docs).

Notebook(s) that ARE buildable today (might be picked up in a follow-up):

• 07_verify_receipt.ipynb (docs: tutorial notebook 07_verify_receipt.ipynb #99) is the closest to feasibility because geno-lewm-verify and geno_lewm.provenance already ship (provenance: implement content-addressed model IDs + manifest schema #74, provenance: implement input commitment #75, provenance: implement checksum receipt writer/reader #76, provenance: implement geno-lewm-verify CLI (checksum mode) #77 merged this session). A tutorial showing manifest/receipt round-trip is constructible against the current package; what's missing is a real (non-mock) receipt produced by an actual scoring call, which still depends on the ML stack.

To pick up: wait for the relevant upstream issue (#62 / #65 / #59 / #66 / etc.) to land, then implement.

[AbdelStark]

Blocked on the planner and scoring/predictor runtime.

Evidence:

• This notebook requires running CEM planning from a pathogenic variant toward a benign latent neighborhood within RFC-0008 latency targets.
• geno_lewm/cli/plan.py is still a Phase 1 stub pointing to planning: implement geno-lewm-plan CLI #61.
• The underlying CEM solver/API issue planning: implement CEM solver and plan() API #59 and plan CLI issue planning: implement geno-lewm-plan CLI #61 are already marked status:blocked.
• The planner also depends on predictor/scoring behavior that is not implemented in the current runtime.

Why not write the notebook now:

• A scripted edit sequence would not exercise the planner or latency target.
• A notebook importing/calling the current planner CLI would only demonstrate the stub, not the acceptance criterion.

To unblock:

• Land the CEM solver, plan() API, geno-lewm-plan, and a tiny deterministic planning fixture with a documented latency target.

[AbdelStark]

Current blocker reconciliation after v0.1 publication:

The first release unblocks artifact-backed scoring demos, but this planner notebook still depends on the planner API/CLI work in #59 and #61 plus the v0.2 rollout substrate tracked by #197.

Keep it blocked until those planning pieces exist and have measured, claim-bounded evidence.