Run page: channel and replicate IDs, no-problems icon, plan card, mask kinds - #241

Summary

The Step 3 run-page label fixes the owner approved on 2026-11-09 (UX proposal Q4: a separate small PR, before the rearrangement). Notebook only; no change to the run, the table or any file written.

• run_labels.py (new): RunLabels, built from the published morphobricks.toml through description_from_bytes. recorded_labels(output) uses the file only when its SHA-256 equals the one the run's manifest recorded in experiment_description.
• notebook_plots.py / notebook_run.py:
  1. Plot tabs, plot titles and the findings table name channels by ID (DNA/ACTIN/PHASE) in a described run. A channel position whose units do not all declare the same ID keeps C<n>. Undescribed runs keep C0/C1/C2. The tabs are 96 px wide so PHASE is not cut off.
  2. The box-plot axis and the curve legends use the replicate ID (drug / rep2, legend rep2) instead of the folder name (drug / day2). The condition stays the folder label, as the description's condition IDs are not part of this fix.
  3. The run tile shows a tick for "no problems found" and keeps the warning sign when there are issues.
  4. "What will happen" is hidden after a successful run (it described that run) and returns when a setting changes. It stays after a run that wrote nothing.
• mask_text.py, mask_answers.py, notebook_mask_step.py, notebook_masks_screen.py: Describe the masks has one Mask column (the ID, with the folder name in brackets only when it differs), and a Declared kind column (objects/regions, the user's answer) beside Kind (suggested). A type with no answer says "not described yet".
• pyproject.toml declares the new module's layer (io); AGENTS.md repo map and CHANGELOG.md updated.

Decisions

• Only data the run already records is used: IDs come from the published description, checked against the manifest's recorded SHA-256. Nothing is guessed: no description, an edited file or disagreeing units give the table's own names.

Notes for review

• Not changed (follow-ups): the "Image or biological repeat" column of the findings table, step 4's plots, and the relationship tables of the mask step still show folder/type names.
• The box-plot label keeps the condition (drug / rep2) because a replicate ID alone repeats across conditions.
• Looked at in headless Chromium (deviceScaleFactor 2) with tests/channel_images.py images and standalone embed_minimal_html, which lacks JupyterLab styles and icons; not looked at in a real JupyterLab.

Tests

• tests/test_run_page_labels.py (new, 13 tests): channel tabs/titles, undescribed run, edited description, disagreeing units, replicate IDs, folder names kept, icons, plan card hidden/shown, declared kind, single Mask column, undescribed mask and differing ID. 9 of the new or changed tests fail on main; the rest guard the unchanged behaviour. tests/test_notebook_mask_step.py updated for the new columns.
• python tools/check.py with .[dev,notebook,zarr]: ruff check and format clean, code rules pass (shrink-only baseline untouched), 4843 passed, 4 skipped (file-mode and case-sensitivity tests that skip on this file system).

🤖 Generated with Claude Code

https://claude.ai/code/session_01G3qp9AxjpGPw9xfWAUJNqc