Files that changed from the base of the PR and between 151216a and 154eb19.

• snakemake/deployment/conda.py (3 hunks)
• snakemake/persistence.py (1 hunks)
• snakemake/sourcecache.py (4 hunks)

snakemake/persistence.py (1)

Line range hint 1-1023: Overall assessment of changes to conda environment cleanup

The modifications to the conda_cleanup_envs method represent a positive step towards more efficient management of conda environments in Snakemake. The focus on cleaning up non-named environments and their associated YAML files is a good approach.

However, as noted in the previous comment, there's room for improvement in terms of error handling, logging specificity, and potentially adding a dry-run option. These enhancements would make the cleanup process more robust and informative for users.

The changes align well with the PR objectives of fixing the conda environment cleanup process. They should contribute to better management of conda environments within the Snakemake framework.

snakemake/sourcecache.py (8)

28-28: Importing logger for logging retry attempts

The addition of from snakemake.logging import logger is necessary for logging retry attempts, which enhances debugging and monitoring capabilities.

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374-374: Setting retries=1 in exists method

By setting retries=1 when calling _cache in the exists method, the code ensures that the existence check is quick and avoids unnecessary delays from multiple retries. This seems appropriate for a rapid existence check.

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395-395: Adding retries parameter to _cache method

Introducing the retries parameter with a default value of 3 in the _cache method allows for flexibility in controlling the number of retry attempts during caching operations, enhancing robustness against transient errors.

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398-398: Propagating retries to _do_cache method

Passing the retries parameter to _do_cache ensures consistent retry behavior throughout the caching process, maintaining alignment with the specified number of retries.

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401-401: Including retries in _do_cache method signature

Adding the retries parameter to the _do_cache method allows it to control the retry logic when opening the source file, which enhances error handling during caching.

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403-403: Passing retries to _open_local_or_remote

By passing retries to _open_local_or_remote, the code ensures that the retry logic is applied when opening the source file, which is critical for handling transient I/O errors.

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428-430: Modifying _open_local_or_remote to accept retries

Including the retries parameter in the _open_local_or_remote method signature provides control over the number of retry attempts when opening files, enhancing the method's flexibility and robustness.

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437-442: Utilizing retry_call with logging for retries

Using retry_call with the logger parameter enables logging of retry attempts, which aids in debugging and monitoring. The specified tries, delay, and backoff parameters provide a balanced retry strategy.

snakemake/deployment/conda.py (6)

98-105: Implemented _path_or_uri_prefix method to extract file prefix

The new method _path_or_uri_prefix correctly extracts the prefix from the conda environment file path, handling files that end with .yaml or .yml. It returns the prefix without the extension or None if the file has a different extension. This enhances code modularity and reusability.

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108-112: Refactored pin_file property to use _get_aux_file

The pin_file property now utilizes the _get_aux_file method, centralizing the logic for locating auxiliary files related to the conda environment. This refactoring improves maintainability by reducing code duplication.

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117-122: Refactored post_deploy_file property to use _get_aux_file

Similarly, the post_deploy_file property has been refactored to use _get_aux_file. This change further centralizes auxiliary file retrieval, enhancing code consistency and reusability.

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124-140: Added _get_aux_file method to centralize auxiliary file retrieval

The new _get_aux_file method encapsulates the logic for retrieving auxiliary files based on a given suffix and a custom omission message. It checks if the environment file exists, extracts the prefix, and constructs the auxiliary file path. It also logs a warning if the environment file does not have the expected .yaml or .yml extension. This addition improves code modularity and simplifies future maintenance.

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Line range hint 602-606: Ensured execution of post-deploy script after environment creation

The code now executes the post-deployment script if it is present after the conda environment is created. This change ensures that any necessary post-deployment steps are performed, enhancing the functionality of the deployment process.

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628-629: Added cleanup of temporary pin files

Temporary pin files are now properly removed after the environment creation process. This cleanup prevents leftover temporary files, reducing potential clutter and conflicts in the environment directory.

Files that changed from the base of the PR and between 154eb19 and 55fbf8d.

• snakemake/persistence.py (2 hunks)