Remove unused GITHUB_TOKEN build argument from Dockerfiles

[t0mdavid-m]

Summary

Removes the unused GITHUB_TOKEN build argument from both Dockerfile and Dockerfile.arm. This argument was declared but never referenced in the build process.

Changes

• Removed ARG GITHUB_TOKEN declaration and its associated comment from Dockerfile
• Removed ARG GITHUB_TOKEN declaration and its associated comment from Dockerfile.arm

Details

The GITHUB_TOKEN argument was previously documented as being used "to download latest OpenMS executable for Windows from Github action artifact," but this functionality is not actually utilized in the current Docker build configuration. The GITHUB_USER and GITHUB_REPO arguments remain, as they are still in use for artifact downloads.

This cleanup reduces unnecessary build arguments and potential security concerns around token handling in Docker builds.

https://claude.ai/code/session_015kE3xopcwc6muQr9dfrLtY

Summary by CodeRabbit

Chores

• Updated Docker build configuration to support configurable OpenMS source repository, branch, and container port settings.

[coderabbitai]

Caution

Review failed

The pull request is closed.

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: db0dfad4-11be-41b7-a726-c39b0a668652

📥 Commits

Reviewing files that changed from the base of the PR and between 7d4e58b and 625d2c0.

📒 Files selected for processing (2)

• Dockerfile
• Dockerfile.arm

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📝 Walkthrough

Walkthrough

Build arguments across Docker stages are reorganized to improve configuration scoping. The main Dockerfile adds OpenMS repository, branch, and port configuration arguments to the setup-build-system stage, while removing GITHUB_TOKEN from that stage where it is unused. Dockerfile.arm removes the same token argument from setup-build-system. The token is redeclared only in the run-app stage where it is consumed.

Changes

Docker Build Configuration

Layer / File(s)	Summary
Dockerfile build argument refactoring Dockerfile	The setup-build-system stage adds build arguments for OPENMS_REPO, OPENMS_BRANCH, and default PORT=8501, and removes the unused GITHUB_TOKEN declaration (which is redeclared in the run-app stage where it is needed).
Dockerfile.arm build argument cleanup Dockerfile.arm	The setup-build-system stage removes the GITHUB_TOKEN argument declaration, narrowing its scope to stages that actually consume it.

Possibly related PRs

• OpenMS/FLASHApp#65: Similar Docker build argument refactoring to remove GITHUB_TOKEN from the setup-build-system stage and redeclare it only in stages where the token is used for GitHub operations.

Poem

🐰 Tokens scattered far and wide,
Now bundled where they're needed inside,
Build stages clean, their scopes refined—
A Docker dance, perfectly aligned! 🎯

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch claude/update-repo-docs-GSnc8

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