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feat: load builtin snakemake executor plugins #73

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merged 2 commits into from
Oct 4, 2024

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johanneskoester
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@johanneskoester johanneskoester commented Oct 4, 2024

This enables simpler code when loading the registry and wanting to also use Snakemake's internal executor plugins (local, dryrun, touch).

Summary by CodeRabbit

  • New Features

    • Introduced a method for collecting and registering plugins, enhancing plugin management capabilities.
  • Bug Fixes

    • Improved error handling for missing dependencies, ensuring smoother operation when the snakemake package is not available.

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Walkthrough

The changes introduce a new method called collect_plugins to the ExecutorPluginRegistry class within the snakemake_interface_executor_plugins/registry/__init__.py file. This method is responsible for collecting plugins and registering them by invoking the register_plugin method for each identified plugin. It first calls the superclass's method to maintain existing functionality and attempts to import specific executors from the snakemake.executors module, handling any import errors gracefully.

Changes

File Path Change Summary
snakemake_interface_executor_plugins/registry/init.py Added collect_plugins method to ExecutorPluginRegistry class.

Sequence Diagram(s)

sequenceDiagram
    participant Client
    participant ExecutorPluginRegistry
    participant SnakemakeExecutors

    Client->>ExecutorPluginRegistry: call collect_plugins()
    ExecutorPluginRegistry->>ExecutorPluginRegistry: call superclass collect_plugins()
    ExecutorPluginRegistry->>SnakemakeExecutors: try to import local, dryrun, touch
    alt Import Successful
        ExecutorPluginRegistry->>ExecutorPluginRegistry: iterate over executors
        ExecutorPluginRegistry->>ExecutorPluginRegistry: register_plugin(executor_name, executor_module)
    else Import Failed
        ExecutorPluginRegistry->>Client: exit without adding plugins
    end
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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)
snakemake_interface_executor_plugins/registry/__init__.py (1)

61-74: LGTM with suggestions for improvement

The new collect_plugins method is a good addition that extends the functionality of the ExecutorPluginRegistry class. It successfully loads built-in Snakemake executor plugins when available. Here are some suggestions for improvement:

  1. Consider adding a check to ensure that the register_plugin method is only called if the executor module has a __name__ attribute.
  2. It might be beneficial to add error handling around the register_plugin calls to catch and log any unexpected issues during registration.
  3. To prevent potential side effects from multiple calls, consider adding a flag to track whether the built-in plugins have already been loaded.

Here's a suggested implementation incorporating these improvements:

def collect_plugins(self):
    """Collect plugins and call register_plugin for each."""
    super().collect_plugins()

    if hasattr(self, '_builtin_plugins_loaded'):
        return

    try:
        from snakemake.executors import local as local_executor
        from snakemake.executors import dryrun as dryrun_executor
        from snakemake.executors import touch as touch_executor
    except ImportError:
        # snakemake not present, proceed without adding these plugins
        return

    for executor in [local_executor, dryrun_executor, touch_executor]:
        if hasattr(executor, '__name__'):
            try:
                self.register_plugin(executor.__name__, executor)
            except Exception as e:
                # Log the error or handle it as appropriate for your use case
                print(f"Failed to register plugin {executor.__name__}: {str(e)}")

    self._builtin_plugins_loaded = True

This implementation adds checks for the __name__ attribute, includes error handling for the register_plugin calls, and uses a flag to prevent multiple loadings of the built-in plugins.

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 56b8c84 and c7198a6.

📒 Files selected for processing (1)
  • snakemake_interface_executor_plugins/registry/init.py (1 hunks)
🧰 Additional context used
📓 Path-based instructions (1)
snakemake_interface_executor_plugins/registry/__init__.py (1)

Pattern **/*.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.

@johanneskoester johanneskoester merged commit 03ee96b into main Oct 4, 2024
5 checks passed
@johanneskoester johanneskoester deleted the feat/load-builtin-snakemake-plugins branch October 4, 2024 14:42
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