fix(atlas): make graph init required and independent of the atlas binary#113
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The dominant reason a research session never created an Atlas graph. The
prompt told the agent to run 'atlas doctor' FIRST and, if it failed, to
'skip Atlas silently' — which a model reads as skipping step 2
('openscience project init') too. But project init is the actual
find-or-create and it runs entirely off the managed session, independent
of the atlas binary. Install channels that skip the launcher's
'npm i -g @synsci/atlas' have no atlas binary, so 'atlas doctor' fails
and the whole Atlas setup (including the working init) was suppressed.
Reorder and decouple: step 1 is 'openscience project init' — REQUIRED,
run it even if atlas is unavailable, and only skip Atlas when init itself
returns project_id:null with an error kind (relaying the actionable fix).
'atlas doctor' + nodes:list becomes an optional step 2 for loading prior
graph state, which no longer gates graph creation.
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The dominant root cause of "Atlas doesn't create the graph."
Problem
The research prompt told the agent, at the start of a task:
atlas doctor; if it fails, skip Atlas silently.openscience project init(the actual find-or-create).A model reads "if doctor fails, skip Atlas" as skip step 2 as well. But
openscience project initis the graph-create and it runs entirely off the managed session — it does not touch theatlasbinary at all. The binary is only present when the launcher'snpm i -g @synsci/atlasran; install channels that skip the wizard have noatlas, soatlas doctorfails → the agent skips the whole block → no graph is ever created, even though a directopenscience project initwould have succeeded. The step was also purely advisory (no BLOCKING/REQUIRED language), so it got skipped on short tasks too.Fix
Reorder and decouple:
openscience project init, REQUIRED, run even ifatlasis unavailable. Only skip Atlas when init itself printsproject_id: nullwith anerrorkind, and then relay the matching fix (unauthenticated/plan/unreachable).atlas doctor+nodes:list, optional/best-effort for loading prior graph state. A failed doctor no longer undoes step 1's creation.Prompt-only change; no code paths altered. Full backend suite (922 tests) green; no test snapshots
research.txt.