fix: check for availability of module cmd

[johanneskoester]

Summary by CodeRabbit

• New Features
  • Introduced an early validation step during startup to verify that required environment modules are available, ensuring users receive clear notifications if dependencies are missing.
• Bug Fixes
  • Updated the environment specification handling in tests to accommodate new parameters, enhancing the accuracy of the testing framework.

[coderabbitai]

📝 Walkthrough

Walkthrough

The changes introduce a new method check in the Env class, decorated with @EnvBase.once. This method checks for the availability of the "module" command using self.run_cmd("type module", stdout=sp.PIPE, stderr=sp.PIPE). If the command is not found, it raises a WorkflowError indicating that environment modules must be available on the system. Additionally, a __post_init__ method is added to the Env class, which calls the check method after instance initialization. The import statements are updated to include subprocess as sp and WorkflowError from snakemake_interface_common.exceptions.

Changes

File(s) Changed	Summary of Changes
src/snakemake_software_deployment_plugin_envmodules/__init__.py	- Added a check method (decorated with @EnvBase.once) in the Env class to verify the "module" command availability using self.run_cmd("type module", stdout=sp.PIPE, stderr=sp.PIPE). - Introduced a __post_init__ method that calls check after initialization. - Updated import statements to include subprocess as sp and WorkflowError.
tests/test_plugin.py	- Modified the return statement in the get_env_spec method of the TestSoftwareDeployment class to include a fallback parameter set to None when creating EnvSpec.

Sequence Diagram(s)

sequenceDiagram
    participant E as Env Instance
    participant P as __post_init__
    participant C as check Method
    participant R as run_cmd
    participant W as WorkflowError

    E->>P: __post_init__()
    P->>C: call check()
    C->>R: Execute self.run_cmd("type module")
    alt Command Found
        R-->>C: Return command path
        C-->>P: Successful check
        P-->>E: Instance initialized
    else Command Not Found
        R-->>C: Return error
        C->>W: Raise WorkflowError with error message
    end

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📥 Commits

Reviewing files that changed from the base of the PR and between aa7103b and bf8dc03.

⛔ Files ignored due to path filters (1)

• pyproject.toml is excluded by !pyproject.toml

📒 Files selected for processing (1)

• src/snakemake_software_deployment_plugin_envmodules/__init__.py (2 hunks)

🚧 Files skipped from review as they are similar to previous changes (1)

• src/snakemake_software_deployment_plugin_envmodules/init.py

⏰ Context from checks skipped due to timeout of 90000ms (1)

• GitHub Check: linting

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