Fix Docker Build

[t0mdavid-m]

Summary by CodeRabbit

• Chores
  • Build artifacts and source files are now retained in the Docker image, increasing container size while making these materials available within the runtime environment.

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[coderabbitai]

Walkthrough

A cleanup command in the Docker build stage is commented out, preserving build artifacts (src, doc, CMakeFiles) in the final image. Previously these directories were removed post-build; now they remain available, increasing the resulting image size.

Changes

Cohort / File(s)	Summary
Docker build stage cleanup Dockerfile	Commented out the RUN command that deleted build artifacts (src, doc, CMakeFiles), changing the build behavior to preserve these directories in the final image instead of removing them

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~2 minutes

• Single-line configuration change with straightforward intent
• Verify the decision to increase image size by preserving artifacts is intentional
• Confirm no unintended side effects from retaining build directories

Poem

A rabbit hops through build stages with glee,
"Leave the artifacts! Let them be, let them be!"
No more cleanup sweeping the floor,
The src and docs shall exist evermore. 🐰✨

Pre-merge checks and finishing touches

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Title check	❓ Inconclusive	The title 'Fix Docker Build' is vague and generic, lacking specificity about what was fixed in the Dockerfile.	Specify what was fixed, e.g., 'Preserve build artifacts in Docker image by commenting out cleanup command' or 'Disable artifact cleanup in Docker build stage'.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch fix_docker

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📜 Recent review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 2a74955 and 48f563f.

📒 Files selected for processing (1)

• Dockerfile (1 hunks)

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (2)

• GitHub Check: build-openms
• GitHub Check: build-full-app

🔇 Additional comments (1)

Dockerfile (1)

110-110: Clarify the root cause and verify this doesn't mask a deeper issue.

Commenting out the cleanup command works around a build failure, but the entire /openms-build directory is removed later at line 139 anyway. This suggests either:

1. The rm command is failing (permissions, non-existent paths), halting the build before reaching line 139, or
2. The commented command is now redundant due to subsequent cleanup.

If scenario 1 applies, the fix is pragmatic but temporary—it masks a permission or path issue that should be investigated. If scenario 2 applies, this line is unnecessary.

Please clarify:

• Why does the build fail with this rm command in place? (Permission denied, paths don't exist, etc.)
• Does the final image size actually change, or is this equivalent to the earlier behavior once line 139 executes?

If the issue is a missing/non-existent path, consider using rm -rf src doc CMakeFiles || true to gracefully handle missing targets without halting the build.

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