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Replace remaining clone-based worker package installs with local build context #147

Description

@arjunrajlab

Several older worker Docker builds still clone arjunrajlaboratory/ImageAnalysisProject during image build and then install annotation_utilities / worker_client from that clone. This means branch builds can silently pick up default-branch package code instead of the checked-out branch being built.

Remaining clone-based builds found after fixing Cellpose/Cellpose-SAM/StarDist in PR #145:

  • workers/annotations/piscis/predict/Dockerfile
  • workers/annotations/piscis/train/Dockerfile
  • workers/annotations/sam_automatic_mask_generator/Dockerfile
  • workers/annotations/sam_automatic_mask_generator/Dockerfile_M1

Suggested fix:

  • Build these images from a repo-root Docker context where needed.
  • Replace RUN git clone https://github.com/arjunrajlaboratory/ImageAnalysisProject/ with COPY ./annotation_utilities /annotation_utilities and, where needed, COPY ./worker_client /worker_client.
  • Update the relevant build helper/compose files so the Dockerfile paths still resolve from repo-root context.
  • Verify with the affected Docker build commands or at least docker build syntax/context checks.

Context: this came up while reviewing PR #145, where entrypoints used helper code added in the PR but some Dockerfiles would have installed default-branch package code.

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