feat: pass tempdir to EnvBase

[johanneskoester]

Summary by CodeRabbit

• New Features
  • Added an option to specify a temporary directory during environment initialization, allowing for more flexible management of temporary files.
• Bug Fixes
  • Enhanced the environment class instantiation by including a temporary directory path for improved temporary file handling.

[coderabbitai]

📝 Walkthrough

Walkthrough

The change updates the constructor of the EnvBase class in the software deployment plugins. A new parameter, tempdir (of type Path), is introduced immediately after the shell_executable argument. Within the constructor, the tempdir value is assigned to self.tempdir. Additionally, the _get_env method in the TestSoftwareDeploymentBase class is modified to include this tempdir in the args dictionary, enhancing the arguments passed for environment class instantiation.

Changes

File(s)	Change Summary
snakemake_interface_software_deployment_plugins/__init__.py	Added a new parameter tempdir: Path to the __init__ of EnvBase and assigned it to self.tempdir in the method.
snakemake_interface_software_deployment_plugins/tests.py	Updated _get_env in TestSoftwareDeploymentBase to include tempdir in the args dictionary, set to tempfile.gettempdir().

Sequence Diagram(s)

Possibly related PRs

• feat: make deploy async #11: The changes in the main PR, which add a tempdir parameter to the EnvBase class constructor, are related to the modifications in the retrieved PR that introduce the tempdir key in the args dictionary of the TestSoftwareDeploymentBase class, as both involve the handling of the tempdir parameter for environment class instantiation.

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• snakemake_interface_software_deployment_plugins/tests.py (2 hunks)

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• snakemake_interface_software_deployment_plugins/tests.py

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🔇 Additional comments (2)

snakemake_interface_software_deployment_plugins/tests.py (2)

4-4: LGTM: Import of tempfile module for use in _get_env.

This import is appropriate for accessing the tempfile.gettempdir() function.

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122-125: Type conversion needed for tempdir parameter.

The tempdir parameter is expected to be of type Path in the EnvBase constructor according to the PR description, but tempfile.gettempdir() returns a string. Consider converting it to a Path object to ensure type consistency.

-            "tempdir": tempfile.gettempdir(),
+            "tempdir": Path(tempfile.gettempdir()),

Also, don't forget to import Path from pathlib if not already imported elsewhere in the file.

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Actionable comments posted: 0

🧹 Nitpick comments (2)

snakemake_interface_software_deployment_plugins/__init__.py (2)

128-129: New required parameter introduces backward compatibility consideration

The addition of tempdir: Path as a required parameter (without a default value) means that all existing code instantiating EnvBase or its subclasses will need to be updated to provide this parameter. This is a breaking change that needs careful consideration.

Consider whether this parameter should have a default value (e.g., None or a temporary directory from the system) to maintain backward compatibility with existing code.

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136-137: New instance variable for temporary directory

The code now stores the provided temporary directory path as an instance variable, which can be accessed by methods in this class or its subclasses. However, there's no documentation about how this temporary directory should be used.

Consider adding a docstring or comment explaining the purpose and expected usage of this temporary directory. This would help future developers understand when and how to interact with this new variable.

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📥 Commits

Reviewing files that changed from the base of the PR and between cbdd798 and 0514347.

📒 Files selected for processing (1)

• snakemake_interface_software_deployment_plugins/__init__.py (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.

• snakemake_interface_software_deployment_plugins/__init__.py

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

• GitHub Check: linting