Lecture 7 Exercises — Containers (Docker & Apptainer) (1-week workload)

Objective: containerize the Python VWCE example from Lecture 6, including its pytest suite. Build a Docker image from scratch (no pre-made course image), run the app and tests inside the container, and optionally convert to Apptainer for HPC. Keep a lab log (codes/lab07/lab-notebook.md) with build/run commands and notes.

Exercise 1 — Prep and copy sources¶

1. In your sspa-sandbox, create codes/lab07/<name.surname>/.

2. Copy the Lecture 6 Python materials (source + tests you wrote) into that folder: cp -r /path/to/lab06/<name.surname>/python codes/lab07/<name.surname>/.

3. Confirm the code and tests still run on the host: pytest -q.

Exercise 2 — Write the Dockerfile from scratch¶

1. Create Dockerfile in codes/lab07/<name.surname>/ with a small base (e.g., python:3.11-slim).

2. Add a non-root user, set WORKDIR, copy the code, install Python deps (at least pytest; pin versions via requirements.txt if you have one), and set a sensible default CMD (e.g., ["python", "-m", "main", "--csv", "vwce_2024.csv"]).

3. Add a build target or stage for tests so you can run pytest inside the image without polluting the final runtime layer. Document the target name (e.g., --target test).

4. Include a .dockerignore to keep images lean (no __pycache__, .git, large CSVs if unnecessary).

Exercise 3 — Build and run¶

1. Build the runtime image: docker build -t vwce:latest .

2. Run the app with a bind mount for your working directory:
   docker run --rm -v "$PWD":/app -w /app vwce:latest python -m main --csv vwce_2024.csv --out /app/out.dat

3. Verify output and logs; capture the command and output snippet in your notebook.

Exercise 4 — Run tests inside the container¶

1. Execute the test stage/target: docker build -t vwce:test --target test . or docker run --rm vwce:latest pytest -q.

2. Confirm the suite passes; if it fails, fix code/tests and rebuild.

3. Record failing/passing outputs in the notebook, along with the final commands used.

Exercise 5 — Optional: Apptainer for HPC¶

1. If Apptainer is available, convert your Docker image:
   apptainer build vwce.sif docker-daemon://vwce:latest

2. Run the CLI inside the .sif: apptainer exec vwce.sif python -m main --csv vwce_2024.csv.

3. Note any path binding requirements (-B) or permission quirks in the notebook.

Submission checklist¶

• codes/lab07/<name.surname>/Dockerfile (and .dockerignore/requirements.txt if used) plus the Python source/tests.

• lab-notebook.md with build/run commands, outputs, and any issues.

• Runtime image runs the VWCE script; test stage/command runs pytest successfully. Optional .sif if you tried Apptainer.