Files that changed from the base of the PR and between c6187a4 and 3d6bd21.

• snakemake/common/init.py (2 hunks)
• snakemake/deployment/conda.py (3 hunks)

snakemake/common/__init__.py (1)

13-13: LGTM!

The shutil import is appropriately placed with other system imports and is required for the new functionality.

snakemake/deployment/conda.py (3)

34-34: LGTM: Clean import of the new function.

The import of copy_permission_safe is correctly placed within the existing snakemake.common imports block.

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544-544: Verify permission handling for environment files.

The replacement of shutil.copy with copy_permission_safe for environment files is a good security improvement. However, we should verify that this change handles all edge cases correctly.

✅ Verification successful

Let me gather more information about the copy_permission_safe function and its implementation to better understand the permission handling.

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Let me check one more thing to understand the copy_permission_safe implementation since it wasn't found in the previous search.

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Now I have enough information to provide the final response about the permission handling verification.

Permission handling for environment files is properly implemented

The copy_permission_safe function in snakemake/common/__init__.py implements a secure approach by:

1. Removing the destination file first to avoid permission-related conflicts
2. Using shutil.copy which preserves the file mode bits

The codebase also shows proper error handling:

• Permission errors are caught and reported with clear messages in the IO operations
• Windows-specific permission issues are properly handled with test cases

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check for any other direct usage of shutil.copy in the codebase that might need similar treatment
rg "shutil\.copy\(" --type py

# Look for any environment file related error handling
rg "(?i)permission.*(?:denied|error).*\.yaml" -A 5 -B 5

Length of output: 340

---

Script:

#!/bin/bash
# Check the implementation of copy_permission_safe
ast-grep --pattern 'def copy_permission_safe'

# Look for any error handling related to file copying in deployment/conda.py
rg "copy_permission_safe" -A 5 -B 5 snakemake/deployment/conda.py

# Check for any permission-related error handling in the codebase
rg "(?i)(permission|access).*error" -A 3 -B 3

Length of output: 3729

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Script:

#!/bin/bash
# Look for copy_permission_safe implementation in common module
cat snakemake/common/__init__.py

Length of output: 9696

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623-623: Verify permission handling for deployment scripts.

The use of copy_permission_safe for post-deployment scripts is appropriate. However, we should ensure proper error handling exists for permission-related failures.

✅ Verification successful

Let me gather more information about the error handling around the copy_permission_safe function and its usage.

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Let me check the broader error handling context around this deployment code section.

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Based on the gathered information, I can now provide a final response:

Permission handling for deployment scripts is adequately implemented

The copy_permission_safe function has proper built-in safety mechanisms:

• It removes the destination file first to avoid permission conflicts
• It's used within a broader error-handling context where deployment failures are caught
• The deployment script execution has explicit error handling for unsupported platforms

The implementation is safe and follows good practices for permission handling:

• Destination file cleanup before copying (os.unlink)
• Direct file copying with preserved permissions (shutil.copy)
• Platform-specific checks before deployment script execution

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check error handling around deployment script copying
ast-grep --pattern 'try {
  $$$
  copy_permission_safe($_, $_)
  $$$
} catch ($err) {
  $$$
}'

# Look for any deployment script related permission errors in the codebase
rg "(?i)permission.*(?:denied|error).*post-deploy\.sh" -A 5 -B 5

Length of output: 163

---

Script:

#!/bin/bash
# Check the implementation of copy_permission_safe
rg "def copy_permission_safe" -A 10

# Look for try-except blocks around deployment file operations
rg "try:.*?copy_permission" -A 10 --multiline

# Check broader context of the deployment file copying
rg "copy_permission_safe\(" -B 5 -A 5

Length of output: 3287

---

Script:

#!/bin/bash
# Check the broader context of the deployment function
rg "def execute_deployment_script" -A 15 -B 5

# Look for any error handling in the deployment section
rg "def create_conda_env" -A 50 -B 5

# Check for any exception handling patterns in the conda.py file
ast-grep --pattern 'try {
  $$$
} catch ($err) {
  $$$
}'

Length of output: 4725