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questio phase 0: create questions.yml and milestones.yml for pixecog

Goal

Bootstrap the questio data model in pixecog by converting existing plan/ markdown to YAML.

Context

The questio design spec at docs/specs/research-orchestration/design.md defines the YAML schema for plan/questions.yml and plan/milestones.yml. Pixecog already has the data in markdown: - docs/plan/master/03-Questions-and-Hypotheses.md — 7 hypotheses (H1-H7) with citations - docs/plan/Milestones.md — milestone tables with status/pipeline/evidence columns - docs/plan/roadmap.md — mermaid dependency graph

This task converts those to machine-readable YAML following the spec schema.

Prompt

Convert pixecog's existing research plan to questio YAML format.

Step 1: Read the questio design spec at /storage2/arash/projects/projio/docs/specs/research-orchestration/design.md, sections 5.1 (questions schema) and 5.2 (milestones schema).

Step 2: Read pixecog's existing plan files: - /storage2/arash/projects/pixecog/docs/plan/master/03-Questions-and-Hypotheses.md - /storage2/arash/projects/pixecog/docs/plan/Milestones.md - /storage2/arash/projects/pixecog/docs/plan/roadmap.md

Step 3: Create plan/questions.yml in pixecog with all 7 hypotheses (H1-H7). For each: - text: the research question from Q1-Q7 - type: hypothesis (all are testable predictions) - prediction: the hypothesis statement - pipelines: list of pipeio flow names from the milestones table - milestones: list of milestone IDs (use kebab-case slugs matching milestones.yml) - manuscript_section: map to appropriate results subsection - status: derive from current milestone states (not_started unless milestones show progress) - depends_on: H7 depends on H6; others are independent - citations: extract citekeys from the markdown

Step 4: Create plan/milestones.yml in pixecog with all milestones from the tables. For each: - description: from the milestone name - pipelines: from the Pipeline column - depends_on: derive from the roadmap mermaid graph (e.g., swr-detection depends on preprocessing-stable) - status: from current Status column (in_progress or not_started) - evidence: empty list (no result notes exist yet)

Include milestones for all four sections: Preprocessing, Event Detection, Hypothesis Testing, Publication.

Step 5: Validate the YAML is well-formed (python -c "import yaml; yaml.safe_load(open('plan/questions.yml'))" etc.).

Step 6: Commit with message: "Add questio YAML data model (questions.yml + milestones.yml)"

Work in the pixecog project at /storage2/arash/projects/pixecog.

Acceptance Criteria

  • [ ] plan/questions.yml exists with H1-H7, all fields populated
  • [ ] plan/milestones.yml exists with all milestones, dependency graph correct
  • [ ] Both files parse as valid YAML
  • [ ] Committed to pixecog

Result

(Filled in after execution)

Batch Result

  • status: done
  • batch queue_id: f89dd756f3dc
  • session: e64cb29d-393c-4600-893b-02d62ca5ab92
  • batch duration: 356.5s