Add Singularity/Apptainer quick-start guide and update image refs

[t0mdavid-m]

Summary

This PR adds comprehensive documentation for running OpenDiaKiosk with Singularity/Apptainer container runtimes, updates all image references to use the correct repository name, and removes the "simple" variant from CI builds.

Key Changes

• New Singularity/Apptainer quick-start section: Added a new "Alternative: run with Singularity" section in the main README with clear instructions for pulling and running SIF images via ORAS, including bind-mount semantics and port forwarding details
• Updated image repository references: Corrected all GHCR image references from openms/streamlit-template to openms/opendiakiosk throughout the HPC documentation section
• Simplified variant matrix: Removed the "simple" variant from the CI build matrix, now only building the "full" variant for SIF images
• Consistent tag documentation: Updated tag scheme documentation to reflect that only latest, main-full, v*-full, and per-commit SHAs are available (removed references to -simple variants)

Implementation Details

• The new Singularity section mirrors the Docker setup workflow but uses ORAS transport for direct SIF pulls, eliminating the need for on-the-fly OCI→SIF conversion
• Documentation clarifies HPC-specific considerations (read-only root filesystem, unprivileged runtime, runtime-state relocation) with a reference to a dedicated HPC section
• All references now consistently use opendiakiosk as the image name, matching the actual repository structure

https://claude.ai/code/session_01BBxwxciydgHsT9xha8NV69

Summary by CodeRabbit

• Documentation

  • Added Singularity deployment guide for prebuilt images with volume mount instructions.
  • Updated Apptainer/Singularity documentation with new image sources and tag scheme information.

• Chores

  • Modified container image publishing configuration.

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📥 Commits

Reviewing files that changed from the base of the PR and between 42ae5b2 and 719fa7b.

📒 Files selected for processing (1)

• README.md

📝 Walkthrough

Walkthrough

This PR restricts Apptainer SIF image publishing to the full variant in CI, and adds comprehensive Singularity/Apptainer deployment documentation for both self-hosted and HPC environments, describing how to pull and run prebuilt SIF images from GHCR using the OpenDIAKiosk image with a defined tag scheme.

Changes

Apptainer publishing and deployment documentation

Layer / File(s)	Summary
Restrict Apptainer publishing to full variant .github/workflows/build-and-test.yml	The publish-apptainer job matrix is restricted to variant: [full], removing the simple variant from SIF publishing to GHCR.
Singularity/Apptainer deployment documentation README.md	README adds a self-hosted Singularity/Apptainer alternative subsection describing ORAS-based SIF pull and bind-mount configuration (/mounted-data read-only, /workspaces-streamlit-template read-write). HPC section updated to reference OpenDIAKiosk SIF from ghcr.io/openms/opendiakiosk/sif:latest, documents available tags (latest, main-full, v*-full, per-commit SHAs), and updates the on-the-fly conversion fallback to use docker://ghcr.io/openms/opendiakiosk:<tag>.

Possibly related PRs

• OpenMS/OpenDIAKiosk#17: Both PRs modify the README's self-hosted deployment documentation—Add self-hosted Docker deployment guide to README #17 adds the Docker self-hosted section, while this PR extends the same area with Singularity/Apptainer guidance and updated HPC instructions.

🐰 A workflow refined, images now lean and mean,
Just the full variant, the finest you've seen!
Docs now guide the way, with ORAS in hand,
Singularity and Apptainer, across every land.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately summarizes the main changes: adding Singularity/Apptainer documentation and updating image references in both the README and CI workflow.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch claude/add-singularity-deployment-zNDIT

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