[mbreiser]

Summary

LAB-227 Phase 4: the Studio, the Pattern Designer and the data-browser dashboard now default to the lab's private data repo reiserlab/arena-experiments. The CSHL course repo reiserlab/cshl-2026-course stays usable by typing it into the Repo field (course benches and rig03-sr still write there).

• Default repo flip — Studio.DEFAULT_COURSE_REPO, the Designer's new DEFAULT_DATA_REPO (a fresh browser lists the lab repo in Open from Repo… / Save to Repo… without a Studio visit), the dashboard's DEFAULT_REPO + its repo field, link and local-path default. tests/test-studio-shell.js pins the three strings equal.
• "Bench id" → "Rig id" in the Studio and Designer UI (label, placeholder, titles, banners, roster log lines). The localStorage key studio_bench_id and the code identifiers keep their names.
• ?repo= signed-out bug (ww18, 2026-10-29) — root cause: the Studio had no ?repo= override at all; ?repo= was honored only together with p or replay, so the page-start shared-pattern listing always used the stored/default repo (the log said "course repo: 52 shared pattern preview(s)" for the DEFAULT repo). Now Studio.sessionRepo is parsed in the classic shell and courseSettings() returns it ahead of the stored repo and the default — a tab-scoped override, like the Pattern Designer's, never written to localStorage, in force before the page-start listings, for reads and writes, signed in or out. encodeApp({sessionRepo}) keeps a bare ?repo= across the canonical URL rewrite so a refresh stays on the requested repo; the ⚙ Settings Repo field shows the override (hover explains it) and typing a repo ends it. The listing log line now names the repo, and a signed-out 404 says "sign in if this repository is private".
• Patterns ↗ passes ?repo= from courseSettings() — default, stored or ?repo= override — instead of only a stored value.
• Replay — a signed-out 404 on a run log or run id says "sign in if this repository is private" instead of "not found" (mirrors the Studio's course-repo open message).
• Per-rig vocabularies (the optional item) — fetchCourseGenotypes / fetchCourseVocab read protocols/<rig-id>/<file>.yaml before the repo-root file (readCourseVocabFile); a missing rig-level file is silent, the source link and log name the file actually used. protocols/ was already a readable prefix.
• Docs — docs/development/data-repo-token-runbook.md (default repo, Rig id, course benches overwrite the field), dashboard/data-browser/README.md, one CLAUDE.md paragraph on the ?repo= override rule.

Deferred (not in this PR): the remaining "course repo" vocabulary in Studio copy and function names (Save → course repo, Course-repo open failed, fetchCourse*) — a wording pass, no behavior.

Linear: LAB-227 (Phase 4).

Tier

next candidate

Release notes

Studio

• The data repo defaults to the lab's private reiserlab/arena-experiments. Course benches keep typing reiserlab/cshl-2026-course into ⚙ Settings → Repo; a ?repo=owner/name link now switches that tab to the named repo for everything (pattern previews, Open from Repo, saves, replay), signed in or out, without changing the stored setting.
• "Bench id" is now "Rig id" in ⚙ Settings and every message that mentions it.
• Pattern previews name their source repo in the log, and a signed-out private repo says so instead of staying silent.
• A rig can keep its own genotype, age, sex and fly-number lists at protocols/<rig-id>/<file>.yaml; the repo-root lists remain the lab-wide fallback.
• Replay says "sign in if this repository is private" when a signed-out read of a run log fails, instead of "not found".

Pattern Designer

• Open from Repo… and Save to Repo… default to reiserlab/arena-experiments in a browser that has not set a repo; the Studio's Patterns ↗ link always hands over the repo the Studio is on.

Dashboard

• The repository field, the header link and the local-path default point at reiserlab/arena-experiments; type reiserlab/cshl-2026-course to browse the 2026 course logs.

Test plan

• pixi run test — 73/73 files green (new checks in tests/test-studio-shell.js and tests/test-studio-url-state.js)
• Local server, storage wiped: ⚙ Settings → Repo shows reiserlab/arena-experiments; the log says the shared library is not readable signed out (HTTP 404) — sign in if private; Patterns ↗ → pattern_editor.html?arena=…&repo=reiserlab%2Farena-experiments
• Signed out, ?repo=reiserlab/cshl-2026-course: log "shared pattern library: 52 preview(s) wired from reiserlab/cshl-2026-course/patterns/"; courseSettings().repo = course repo; the canonical URL keeps ?repo=; Patterns ↗ carries the course repo
• Pattern Designer with no stored repo: Open from Repo… lists reiserlab/arena-experiments
• Dashboard: repo field, "Data repo" link and local path default to the lab repo
• On a rig PC with a stored token: per-rig protocols/<rig-id>/genotypes.yaml is picked up (not bench-tested; the root-file path is unchanged)

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