fix: ensure ExecutableRunner stderr goes somewhere by default

[clintval]

This doesn't fully solve:

• There should be a way to view the logs that bwa emits #41

But it should solve the issue where the stderr PIPE's buffer may become full and deadlock the process.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 96.76%. Comparing base (364a9dc) to head (234f236).
Report is 1 commits behind head on main.

Additional details and impacted files

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  Coverage   96.76%   96.76%           
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  Files          26       26           
  Lines        1701     1701           
  Branches      326      326           
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  Hits         1646     1646           
  Misses         29       29           
  Partials       26       26           

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[coderabbitai]

Walkthrough

The changes in this pull request focus on the ExecutableRunner class located in the prymer/util/executable_runner.py file. The primary modification involves the constructor's signature, specifically the default value assigned to the stderr parameter. Previously, the default value for stderr was set to subprocess.PIPE, which allowed the standard error output of the subprocess to be captured in a pipe. This has been changed to subprocess.DEVNULL, which redirects the standard error output to a null device, effectively discarding it. This change does not affect other aspects of the class, as the overall structure, methods, and properties remain unchanged. The functionality for managing subprocesses and validating executable paths continues to operate as before, with the only difference being the handling of standard error output.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant ExecutableRunner

    User->>ExecutableRunner: Initialize with command
    ExecutableRunner->>subprocess: Create subprocess
    alt stderr is DEVNULL
        subprocess-->>ExecutableRunner: Redirect stderr to DEVNULL
    else stderr is PIPE
        subprocess-->>ExecutableRunner: Capture stderr in PIPE
    end
    ExecutableRunner-->>User: Return subprocess object

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📥 Commits

Files that changed from the base of the PR and between 364a9dc and 234f236.

📒 Files selected for processing (1)

• prymer/util/executable_runner.py (1 hunks)

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🔇 Additional comments (1)

prymer/util/executable_runner.py (1)

45-45: Approve change with suggestions for documentation and verification.

The change from subprocess.PIPE to subprocess.DEVNULL as the default value for stderr addresses the PR objective of preventing potential deadlocks due to a full stderr buffer. This is a good fix for the issue described in GitHub issue #41.

However, to ensure clarity and maintain backwards compatibility, consider the following suggestions:

1. Add a comment explaining the rationale behind this change, e.g.:

   # Default to DEVNULL to prevent potential deadlocks due to full stderr buffer
   # See GitHub issue #41 for more details
   stderr: int = subprocess.DEVNULL,

2. Update the class docstring to reflect this new default behavior, mentioning that stderr is discarded by default and how users can capture it if needed.

3. Verify if this change affects any existing tests or usage in the codebase that might rely on capturing stderr without explicitly setting it.

To verify the impact of this change, run the following script:

This script will help identify areas of the codebase that might need attention due to the change in default stderr behavior.

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[clintval]

No longer needed due to merging:

• feat: redirect BwaAlnInteractive stderr to debug logging #74