fix: add apptainer source, yml formatting

[m-jahn]

closes #44

Summary by CodeRabbit

• New Features

  • Conditional Apptainer installation step added (includes PPA setup) for workflows.
  • Consolidated and improved containerization test step for CI.

• Bug Fixes

  • Added input validation that returns clear error messages for invalid task values.

[coderabbitai[bot]]

📝 Walkthrough

Walkthrough

Updated action inputs' quote style, added task validation that errors on invalid values, and added a conditional "Install Apptainer" step (adds Apptainer PPA then installs) plus workflow adjustments to call the action with install-apptainer when containerizing.

Changes

Cohort / File(s)	Change Summary
Action metadata and runtime action.yml	Normalized default-value quoting to double quotes; added task validation step that prints an explicit error and exits on invalid task; added conditional "Install Apptainer" step which adds the Apptainer PPA then installs; adjusted step ordering and removed trailing blank line
Workflow invocation .github/workflows/main.yml	Upgraded actions/checkout from v1 to v4; added/updated test steps to run the local action including a "Test run" and a consolidated "Test containerize" step passing install-apptainer: true and task: "containerize"; adjusted ancillary steps (e.g., show Dockerfile) for new flow

Sequence Diagram(s)

sequenceDiagram
    actor User
    participant GH as GitHub Action
    participant V as Validator
    participant A as Apptainer Installer
    participant S as Snakemake Workflow

    User->>GH: dispatch with inputs (task, install-apptainer, ...)
    GH->>V: validate `task` input
    alt invalid task
        V-->>User: print error message
        GH-->>GH: exit non-zero
    else valid task
        V-->>GH: validation ok
        alt install-apptainer == true
            GH->>A: add Apptainer PPA && apt install apptainer
            A-->>GH: install result
            alt install failed
                GH-->>User: install error and exit
            end
        else install-apptainer == false
            GH-->>GH: skip apptainer install
        end
        GH->>S: run requested task (e.g., containerize)
        S-->>User: task completes
    end

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

• Areas to focus during review:
  • action.yml — validate the exact conditional expressions and exit behavior for task validation.
  • action.yml — verify the PPA add-command and apt-install steps (order, sudo usage, idempotence).
  • .github/workflows/main.yml — ensure the upgraded checkout action and updated test steps correctly pass inputs and behave on runners.

Suggested reviewers

• johanneskoester

Pre-merge checks and finishing touches

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'fix: add apptainer source, yml formatting' accurately reflects the main changes: adding Apptainer PPA source configuration and YAML formatting updates.
Linked Issues check	✅ Passed	The PR successfully addresses issue #44 by introducing a new Install Apptainer step that adds the apptainer PPA repository before installation, resolving the Ubuntu package source issue.
Out of Scope Changes check	✅ Passed	Changes are within scope: Apptainer PPA addition addresses issue #44, YAML formatting is supporting change, and GitHub Actions version upgrade is reasonable maintenance.

✨ Finishing touches

🧪 Generate unit tests (beta)

• [ ] Create PR with unit tests
• [ ] Post copyable unit tests in a comment
• [ ] Commit unit tests in branch fix_apptainer

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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 d43836421bf60df7a1a6c151738fe43ce5bd5a2d and 6e90b21979036d48983ed4126f6c0e3da9c8912f.

📒 Files selected for processing (1)

• .github/workflows/main.yml (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). (1)

• GitHub Check: build

🔇 Additional comments (4)

.github/workflows/main.yml (4)

15-15: Good: checkout action upgraded to v4.

Using a current version of the checkout action is important for security and compatibility. v1 is significantly outdated.

---

17-22: New "Test run" step looks good.

The step correctly uses the local action with appropriate parameters to test the basic workflow functionality before containerization.

---

33-35: "Show Dockerfile" step looks good.

The step correctly references the generated Dockerfile for inspection after containerization.

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24-31: All inputs are correctly defined and PPA installation logic is properly implemented.

Verification confirms:

• install-apptainer input is defined in action.yml (line 37)
• task input is defined in action.yml (line 31)
• The action correctly adds the Apptainer PPA repository (sudo add-apt-repository -y ppa:apptainer/ppa, line 60) before installation, as required by the PR objectives

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[m-jahn]

note to revs: the file diff looks more complicated then it is -- the only line that was added and that is important is sudo add-apt-repository -y ppa:apptainer/ppa.

[johanneskoester]

Thanks a lot!