add emacs-nox [bnm2717]

[broland-hat]

Description

• Add emacs-nox to image for developer velocity. It very helpful to have a command-line editor built-into the container for quick investigation.

Type of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Refactor
• Documentation update
• Other (please describe):

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# TODO: Add code snippet

Pre-submit Checklist

• [NA] I have tested these changes locally
• [NA] I have updated the documentation accordingly
• [NA] I have added/updated tests as needed
• [NA] All existing tests pass successfully

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[coderabbitai]

Walkthrough

Added emacs-nox to the apt-get install list in the bionemo2-base stage of the Dockerfile. No other changes were made.

Changes

Cohort / File(s)	Summary
Base image packages Dockerfile	Added emacs-nox to the apt-get install list in the bionemo2-base stage; no other modifications.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~2 minutes

Poem

I hop through layers, light and lean,
A new tool tucked in build routine—
emacs-nox, no windows flare,
Just terminal calm and tidy air.
Thump-thump! The image hums along,
My paws add one more editor strong.

✨ Finishing Touches

🧪 Generate unit tests

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch br_bnm2717_add_emacs_to_container

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[broland-hat]

/ok to test c88b6c2

[broland-hat]

/okay to test c88b6c2

[coderabbitai]

Actionable comments posted: 0

🧹 Nitpick comments (2)

Dockerfile (2)

45-56: Prefer installing editors only in dev images; add --no-install-recommends to keep base/release slim

Emacs in the base stage ships into release images, increasing size and CVE surface. Move it to the dev stage and disable APT recommends to reduce deps.

Apply in bionemo2-base (remove emacs and avoid recommends):

-apt-get install -qyy \
+apt-get install -qyy --no-install-recommends \
   libsndfile1 \
   ffmpeg \
   git \
   curl \
   pre-commit \
   sudo \
-  emacs-nox \
   gnupg \
   unzip \
   libsqlite3-dev

---

258-266: Install emacs-nox in the dev stage instead (developer-only), and use no-recommends

Keeps release images clean while delivering the intended developer velocity. Also reuses the best practice of trimming recommended packages.

 apt-get update -qy
-apt-get install -qyy \
-  sudo
+apt-get install -qyy --no-install-recommends \
+  sudo \
+  emacs-nox
 rm -rf /tmp/* /var/tmp/*

📜 Review details

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Review profile: CHILL

Plan: Pro

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📥 Commits

Reviewing files that changed from the base of the PR and between 4a47964 and c88b6c2.

📒 Files selected for processing (1)

• Dockerfile (1 hunks)

[pstjohn]

not a vim user 😆 ? but sure, fine with me

[broland-hat]

/okay to test 0b924d4

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 80.62%. Comparing base (4854165) to head (0b924d4).
⚠️ Report is 294 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1107   +/-   ##
=======================================
  Coverage   80.62%   80.62%           
=======================================
  Files         157      157           
  Lines       11079    11079           
=======================================
  Hits         8932     8932           
  Misses       2147     2147           

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