SciducTainer

Minimal example (template) repo which includes files to interface with Sciduct job service.

This one happens to only depend on Python, with it's top-level (E.g. only things in import statments which are not in the Python standard library) dependencies and Python version specified in environment.yml. That should have any dependencies added (with pinned versions) to be able to run without containerization. E.g.

micromamba env create --file environment.yml
micromamba activate app_env001
./src/app_script001.py --name Sue
# Sue's age is 33.

The example app script shows a way to provide parameters via a config file (E.g. app_script001_config.json). An example file is provided as a starter. E.g.

cp src/app_script001_config_example.json app_script001_config.json

Those will be overridden by any explicit parameters passed in on the command line.

To use this, just click "Use this template". Create new repository with a name relevant for your app(s). Then change file and app names as appropriate (E.g. src/app_script001.py and in apps.scif).

This system uses Github Actions to build and publish a container, triggered by a git tag push of the form v<major>.<minor>.<patch> (See: Semantic Versioning for a quick explanation of what those mean).

E.g.

git add -u
git commit -m "useful commit message"
git pull --rebase && git push
git tag v0.1.1
git push origin v0.1.1

To enable Github Actions to build and publish this to the Github Container Resgistry (GHCR), someone will need to create an authentication token with via their Github account having "repo" and "write:packages" permissions. If a private repo needs to be accessed, a "GH_TOKEN" with "repo" priveleges also needs to be added.

The tokens and username needs to be saved as a repository secret (in "https://github.com/user-or-org-name/repo-name/settings/secrets/actions"), with names matching the ones in .github/workflows/build_docker.yml

Make sure to change your container image name to match your repo name (E.g. here).

Pulling and Running (testing) the Container via Apptainer (Docker bootstrap)

Note: adjust names to match your actual container and repo name, NOT SciducTainer.

git clone git@github.com:NSSAC/SciducTainer.git
cd SciducTainer
# module load apptainer
apptainer pull docker://ghcr.io/nssac/sciductainer:0.1.0
mkdir -p data
apptainer run --bind=data:/scif/data sciductainer_0.1.0.sif run app001 --age 42
# [app001] executing /bin/bash /scif/apps/app001/scif/runscript --age 42
# Running app_script001.py --outdir /scif/data/app001 --age 42
# Bob's age is 42.

If you want to also test changes to script files in the repository, and have the container use those, you can additionally --bind your local repo files directory in ("mounting" over the read-only copy of that in the container image). E.g.

# Change to 'age: int = 34' in src/app_script001.py
apptainer run --bind=data:/scif/data,src:/scif/apps/app001/lib sciductainer_0.1.5.sif run app001