fix(docker): fail build when atlas download stalls instead of hanging#38
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tabedzki wants to merge 2 commits into
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fix(docker): fail build when atlas download stalls instead of hanging#38tabedzki wants to merge 2 commits into
tabedzki wants to merge 2 commits into
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The build-time atlas pre-download hit the GIN server directly and would hang indefinitely when the server stalled mid-transfer, since check_latest=False only skips the version check, not the data download. Bound the download with `timeout` (ATLAS_FETCH_TIMEOUT, default 1200s) so a stalled GIN server fails the build instead of hanging it, and let download failures propagate so we never ship an image without atlases. Extract the fetch logic into fetch_atlases.py, shared by the build and by a startup re-verification in entrypoint.sh (a no-op in the normal case, but re-fetches if a runtime volume mount shadows ~/.brainglobe/). Assisted-by: ClaudeCode:claude-opus-4.8
…nced `uv run` syncs the environment with the default dependency groups (including dev) before executing. Since the image is built with `uv sync --no-dev`, the entrypoint's `uv run` calls were re-installing dev-only packages (sphinx, babel, ...) into the container at every startup. Pass --no-dev to match the build so startup neither re-syncs nor pulls dev dependencies. Assisted-by: ClaudeCode:claude-opus-4.8
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Problem
The Docker build pre-downloads the mouse/rat atlases from the GIN server so the app starts instantly. When GIN stalls mid-transfer,
docker buildhangs indefinitely —check_latest=Falseonly skips the remote version check, not the actual data download, and the download socket has no timeout.Change
Keep the requirement that atlases are baked into the image, but make a bad GIN server a bounded failure rather than an infinite hang:
timeout "${ATLAS_FETCH_TIMEOUT}" python /fetch_atlases.py(default 1200s) with no|| true. A stall trips the timeout and fails the build; a download error propagates and fails the build. Either way, we never ship an image without atlases.fetch_atlases.py(new) — idempotent fetch of the required atlases (skips ones already cached), non-zero exit if any is still missing. Shared by build and startup.entrypoint.sh— runs the same script at startup as a cheap safety net. It's a no-op in the normal case (atlases baked in) and only re-fetches if a runtime volume mount shadows~/.brainglobe/.REQUIRE_ATLASES=1(default) makes a missing atlas a hard startup failure; set0to warn and boot anyway.Verification
docker build -t pixelmap:build-test .succeeds; both atlases download during the build (allen_mouse_25um ~99 MB, whs_sd_rat_39um ~222 MB)./fetch_atlases.pyinside the built image reports both atlases already cached and exits 0 (startup check is a no-op as intended).🤖 Generated with Claude Code
https://claude.ai/code/session_01EQUz7NQenGjdZVVRbk3a2Y