Ship prebuilt Docker deployment - #14

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ClePol wants to merge 29 commits into

mainfrom

monolith_refactor

ClePol commented Jul 23, 2026

Member

Summary

ship the monolithic application as a prebuilt GHCR Docker image
simplify Linux installation and startup to Docker-only shell scripts
support Apple Silicon through explicit linux/amd64 emulation
move frontend deployment settings to runtime configuration
remove default FreeSurfer license handling and temporarily hide manual labeling
update vulnerable Python and npm dependencies
make npm and Python vulnerability scans blocking
configure Dependabot for the root uv project

Verification

npm run lint
npm run test:node (63 passed)
npm run build
.venv/bin/pyright
.venv/bin/pytest tests/ -v (278 passed, 26 skipped)
npm audit --audit-level=low (0 vulnerabilities)
uvx pip-audit --path .venv/lib/python3.12/site-packages (0 known vulnerabilities)
production Docker image build
container health check at http://localhost:8000

Notes

NIIVUE_REPORT.md is intentionally excluded.
Dependabot alerts on the default branch will close after this PR is merged.

ClePol and others added 17 commits

June 18, 2026 03:14


          Add monolith refactor plan

76db102

Document the plan to collapse the 6-service Compose stack to a single
process with two deployment profiles (desktop + shared/web), an in-process
DB-backed JobWorker replacing Celery/Redis, SQLite/WAL replacing Postgres,
and Apptainer (prebuilt arch-matched SIFs, docker:// fallback) as the tool
runtime for both native and privileged-container app deployments.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>


          docker compose setup

3cea149


          changes to dockerized monolith architecture

e90eee5


          feat: integrate Niivue case viewer

1e4075e


          Merge remote-tracking branch 'origin/niivue' into monolith_refactor

92f8bf5

# Conflicts:
#	.gitignore


          fix: improve viewer interaction timing

5d1984b


          performance optmiziation & refactor

c74a462


          optimize niivue windowing refresh

9dc1f4b


          fix: preserve niivue layer compositing

83203c0


          fix: defer niivue layer display refreshes

cbcb40e


          feat: simplify Docker install and runtime tools

198418f


          fix: render segmentation labels as voxel-exact RGBA

f68e312


          fix: remove managed FreeSurfer license setup

10282da


          fix: hide manual labeling controls

ab2fc1d


          feat: add orientation label toggle

4623b85


          feat: ship prebuilt Docker deployment

9e101c7


          fix: update vulnerable dependencies

d639eba

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ClePol mentioned this pull request

Bump python-multipart from 0.0.27 to 0.0.31 in the pip group across 1 directory #13

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View reviewed changes

api-service/api_service/main.py Fixed

api-service/api_service/main.py Fixed


          ci: remove obsolete runtime tools job

a7cb55f

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ClePol added 2 commits

July 24, 2026 01:21


          fix: register jobs explicitly

4b47246


          chore: remove stale viewer notes

15d99cb

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          ci: enforce Python linting

8b6bee2

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api-service/api_service/runtime_tools/handlers.py Fixed


          refactor: export stats handler directly

69ea96f

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          fix: keep viewer loading during case open

78544ce

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ClePol added 6 commits

July 24, 2026 20:25


          refactor: migrate viewer to NiiVue 1.0

84d1205


          fix: restore NiiVue FreeSurfer rendering

2aa0bc1


          fix: stabilize NiiVue rendering and loading

d4a1f01


          refactor: streamline NiiVue viewer integration

8f8cd03


          fix: stabilize NiiVue reference framing

ae4b0e7


          fix: stabilize NiiVue reference and viewer controls

e290d01

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github-code-quality Bot found potential problems

View reviewed changes

client/src/neurocadeViewer/fixedReferenceRuntime.ts

+                  try {
+                    return await creation;
+                  } finally {
+                    if (state.creation === creation) state.creation = undefined;

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