Galaxy Notebooks (PR #22361): post-merge follow-up tracking

Umbrella tracking issue for work deferred out of galaxyproject/galaxy#22361 (“Galaxy Notebooks: Persistent Narrative for Human-AI Collaborative Science in Galaxy”). Companion PRs already merged: galaxyproject/galaxy#21942 (shared agent-operations layer), galaxyproject/galaxy#22625 (user-defined-tool agent operations).

Architecture reference: HISTORY_MARKDOWN_ARCHITECTURE.md.

mvdbeek’s review approved the PR with the caveat that some review threads are explicitly follow-up scope (“There are a lot more comments in there, some of that could be followup work.”). This issue tracks those + polish items we ourselves want to chase.

SHA caveat: commit SHAs cited below (and inside TEST_AGENT_TOOLS_ISSUE.md) are from the pre-final-rebase history_pages branch. After merge to dev they will only resolve via the PR’s GitHub merge commit, not on dev directly — refresh against the merge commit when filing the GH issue, or just link to the PR.

Sub-issues with full write-ups (in this folder)

TEST_AGENT_TOOLS_ISSUE.md — aiocop regression guard for agent tool dispatch. Drives the real PageAssistantAgent against a real DB via pydantic_ai.models.test.TestModel so the next sync-on-event-loop regression cannot slip past the test suite. Closes the gap mvdbeek flagged on the history_tools.py sync/async thread (discussion_r3268670909). Companion to jmchilton/galaxy-architecture#20.
CHAT_DIRECTIVE_PREVIEW_POLISH.md — chat panel renders raw ```galaxy directives as plain code. Behavior is correct (chat must not hydrate), presentation is unpolished. Recommend STYLED_CHIPS_AND_FENCE_PILL — small MarkdownIt post-process, no hydration, no new fetches.

Bullet-only follow-ups (no doc needed yet)

Split-pane editor vs Window Manager. mvdbeek asked whether the chat split view should use the window manager primitive instead of a hand-rolled split: https://github.com/galaxyproject/galaxy/pull/22361#discussion_r3268509099. Current PR refactored to Common/SplitView.vue via DraggableSeparator — answer for now is “split is correct for the inline two-pane editor, WM stays the right shape for detachable floating windows” — but worth revisiting after @ahmedhamidawan’s UI polish pass. (Window-manager chat is on arch doc §14’s long-term list and is partly integrated already.)
Agent displays markdown in chat instead of directly editing. Recurring UX paper-cut: assistant narrates the proposed markdown in chat prose rather than emitting a SectionPatchEdit / FullReplacementEdit. Already iteratively softened/sharpened in f866f7f7c9, e74becc73f, 5d277375cd, dff03eb5a0. Not fully solved by prompt tweaks — likely needs a structured-output rebalance or a programmatic “if you wrote >N markdown lines in response, emit a patch instead” check. Flag, do not fix yet.
Beta labeling decision (Ahmed + jmchilton on the PR conversation tab): Notebooks themselves are NOT beta — they are a long-planned thin model on top of Galaxy Markdown. Chat interface IS a candidate for beta across notebooks and reports. Pages → Reports language change is likely NOT beta — guerler accepted the rename in the same thread (“Galaxy Notebooks as the primary editable document and Galaxy Reports as invocation-generated starting points”). Ahmed’s suggestion to relocate the notebook button to the history options dropdown only makes sense if we mark chat beta, not notebooks — and the button still belongs at the counter level. Decision owner: jmchilton + @ahmedhamidawan, before/just-after merge.
Rename isChromeFree to a Galaxy-idiomatic term (PageView.vue:92, thread discussion_r3268492913). jmchilton committed to a follow-up rename — “chrome” is industry-standard UI lingo but not Galaxy-ish. Trivial.
Delete dead APPLY_PAGE_EDIT / INSERT_PAGE_SECTION enum values (client/src/composables/agentActions.ts:23-24, :225-226, client/src/components/ChatGXY/ActionCard.vue:62-63). The arch doc called these “not fully wired” — verified: handleAction switch (agentActions.ts:66) has no case for them and they fall through to default → handleContactSupport(). Page-edit flow uses structured output (FullReplacementEdit / SectionPatchEdit) rendered by ProposalDiffView / SectionPatchView, not action cards. These enum values are dead from an earlier design — delete, don’t wire.
Revive skipped test_router_with_test_model (test/unit/app/test_agents.py:286) — pydantic-ai API drift; small, adjacent to TEST_AGENT_TOOLS_ISSUE Q3.

Considered and not tracked

Items from the architecture doc §14 “Remaining Work” — kept in §14 as the long-term vision but not tracked under this umbrella because they predate the implementation and remain speculative:

Window Manager chat (chat already integrated into the editor in some form).
CodeMirror 6 migration.
Streaming agent responses.
Orchestrator integration.

Other items considered and dropped: concurrent edit protection (too speculative — no collision incidents to date on pages); stale chat exchanges after page soft-delete (reviewer-subagent inference, never observed, not verified in code).

Anything from the review not listed above?

guerler caught the one outright bug in the review (discussion_r3032429339) — chat API was reaching Page directly without an access check. Shipped in 88e66d6a5b (“access-check page in chat manager”, get_accessible_page in chat.py). Worth a sentence in the GH issue narrative.

All 20 unresolved mvdbeek review threads have replies and have been substantively addressed in code (typed pages client 83a3a0dc09, useWindowAwareNavigation 0433dbcbd0 + 3ebd44f695, Common/SplitView.vue refactor 0433dbcbd0, threadpool-offload c8b77adfde, manager-delegation + SQL pagination + implicit-conversion HID fix d4d12d30b9, element_count + nice_size reuse 392b130270, in-method import hoists ad0013a413, for_workflows tool tweaks reverted in a9773c0764 / 3608bf9e21). They are left “unresolved” in the GitHub UI only because mvdbeek has not clicked Resolve yet — there is no outstanding code work hidden in them.

Two threads point at known-followup work captured above:

discussion_r3268492913 → isChromeFree rename (bullet above).
discussion_r3268509099 → split-pane vs WM (bullet above).

Post-review user-facing polish that shipped during screencast prep (not from a reviewer, included so the GH issue narrative covers it): e1d519014e “fix empty-content save for notebooks and reports”, b513e3d4b9 “Default new history-attached page title to ‘Untitled Notebook’”, 65c69991b6 “Restore editor textarea full height in chat split view”, 8ec67b415b “Hide markdown toolbox when chat panel is open”.

Draft tracking-issue body (for filing on galaxyproject/galaxy)