fix: consider config.yml as configuration filename

[fbartusch]

fixes #80

Summary by CodeRabbit

• New Features

  • Enhanced the deployment process by introducing dynamic configuration file selection. The workflow now automatically recognizes an alternate configuration option at runtime, providing greater flexibility during deployments.

• Tests

  • Expanded test coverage to ensure that both default and alternative configuration file scenarios are handled correctly.

[coderabbitai]

📝 Walkthrough

Walkthrough

This pull request updates the deployment process by enhancing configuration file handling. The WorkflowDeployer.deploy_snakefile method now checks for two potential configuration files (config.yaml and config.yml), defaulting to config.yaml if neither is found. The Snakemake template is modified to accept a dynamic config path, and the test suite is extended to cover both configuration scenarios.

Changes

File(s)	Change Summary
snakedeploy/deploy.py snakedeploy/templates/use_module.smk.jinja	Updated configuration file handling: the deployment method now checks for both config.yaml and config.yml (defaulting to config.yaml if neither exists), and the Snakemake template now uses a dynamic {{ config }} placeholder.
tests/test_client.sh	Added new test cases to verify that the deployment correctly handles both the default (config.yaml) and alternative (config.yml) configuration file names.

Sequence Diagram(s)

sequenceDiagram
    participant U as User
    participant WD as WorkflowDeployer
    participant FS as FileSystem
    participant TR as Template Renderer

    U->>WD: deploy_snakefile(tmpdir, name, config)
    WD->>FS: Check if "config.yaml" exists
    alt "config.yaml" exists
        FS-->>WD: "config.yaml" found
    else Not found
        WD->>FS: Check if "config.yml" exists
        alt "config.yml" exists
            FS-->>WD: "config.yml" found
        else Not found
            WD-->>WD: Default to "config.yaml"
        end
    end
    WD->>TR: Render template with selected config path
    TR-->>WD: Rendered Snakefile
    WD-->>U: Return deployment result

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[coderabbitai]

Actionable comments posted: 0

🧹 Nitpick comments (1)

snakedeploy/deploy.py (1)

214-223: Good implementation for supporting both config file formats.

The implementation correctly checks for both config.yaml and config.yml files, with a sensible fallback to the default config.yaml if neither is found. This approach maintains backward compatibility while adding support for the additional format.

Consider adding a brief comment explaining the fallback logic - why we default to config.yaml when neither file exists (likely because a dummy config.yaml will be created in deploy_config).

📜 Review details

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Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between f52f7ef and 6a0f098.

📒 Files selected for processing (3)

• snakedeploy/deploy.py (2 hunks)
• snakedeploy/templates/use_module.smk.jinja (1 hunks)
• tests/test_client.sh (1 hunks)

🧰 Additional context used

📓 Path-based instructions (1)

`**/*.py`: Do not try to improve formatting. Do not suggest ...

**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

• snakedeploy/deploy.py

🔇 Additional comments (4)

snakedeploy/templates/use_module.smk.jinja (1)

7-7: Good change that enhances configuration flexibility.

Replacing the hardcoded configuration path with a dynamic template variable allows the template to support both config.yaml and config.yml file extensions. This is a clean way to implement the feature without duplicating code.

tests/test_client.sh (2)

56-57: Good test to verify backward compatibility.

This test ensures that the fix for issue #80 doesn't affect previous functionality by checking that config.yaml is still correctly handled in the generated Snakefile.

---

59-64: Excellent comprehensive test for the new feature.

This test effectively validates the fix for issue #80 by:

1. Deploying a repository known to use config.yml
2. Verifying that the generated Snakefile correctly references config.yml

Good choice of repository to test with, and the test is clear and focused.

snakedeploy/deploy.py (1)

233-233: LGTM - correctly passes the dynamic config path to the template.

This change properly integrates with the Jinja template modification, ensuring the determined configuration path is used when rendering the Snakefile.

[johanneskoester]

Thanks a lot!