Reviewing files that changed from the base of the PR and between 378ec2d and 3258a46.

• src/snakemake/report/__init__.py (9 hunks)

src/snakemake/report/__init__.py (6)

6-6: Adding support for async operations.

Adding TaskGroup from asyncio enables concurrent execution of tasks, which will improve performance when retrieving multiple files from storage.

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114-114: Initialization change for report definitions.

Changed the initialization of the definitions variable to start with an empty JSON array.

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188-202: Converted function to async with concurrent file retrieval.

The function is now asynchronous and uses TaskGroup to concurrently retrieve files from storage, which is a significant performance optimization for workflows that handle multiple storage-based files.

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456-460: Properly modified expand_labels for async operation.

The function has been converted to async and properly awaits the result of expand_report_argument when processing labels, maintaining consistency with the overall async pattern.

Also applies to: 478-479

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599-599: Properly awaiting async register_file calls.

All calls to the now-async register_file function are correctly awaited, maintaining the async flow through the code.

Also applies to: 620-621, 643-644

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550-566:

Details

❓ Verification inconclusive

Potential issue with nested async function scope.

The nested async functions access outer scope variables (job and report_obj) without capturing them as parameters, which could lead to unexpected behavior if these variables change before the async functions are executed.

async def register_file(
    f,
    parent_path=None,
    wildcards_overwrite=None,
    aux_files=None,
    name_overwrite=None,
+   job=job,
+   report_obj=report_obj,
):
    wildcards = wildcards_overwrite or job.wildcards

    async def expand_cat_name(cat_name, wildcards=wildcards, job=job):
        if cat_name is not None:
            return await expand_report_argument(
                cat_name, wildcards, job
            )
        else:
            return cat_name

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🏁 Script executed:

#!/bin/bash
# Verify if this is a known pattern in the codebase
rg -A 3 "async def \w+\([^)]*\):" --type py | rg -B 1 -A 2 "^\s+async def"

Length of output: 76

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Action: Verify Closure Capture in Nested Async Functions

The modifications to capture outer scope variables (job and report_obj) by assigning them as default parameters in both register_file and its nested function expand_cat_name seem to address the potential issues raised. However, since our automated search for similar patterns returned no results, please verify manually that these changes reliably preserve the intended values in asynchronous contexts.

• File: src/snakemake/report/__init__.py (Lines: 550-566)
  • Updated register_file to include job=job, report_obj=report_obj in its parameters.
  • Modified the nested async function expand_cat_name to capture wildcards and job as default parameters.

Diff snippet:

async def register_file(
    f,
    parent_path=None,
    wildcards_overwrite=None,
    aux_files=None,
    name_overwrite=None,
+   job=job,
+   report_obj=report_obj,
):
    wildcards = wildcards_overwrite or job.wildcards

    async def expand_cat_name(cat_name, wildcards=wildcards, job=job):
        if cat_name is not None:
            return await expand_report_argument(
                cat_name, wildcards, job
            )
        else:
            return cat_name

Please confirm manually that these changes correctly capture the outer variables at the time of function definition, ensuring there are no unexpected side effects during asynchronous execution.

🧰 Tools

🪛 Ruff (0.8.2)

557-557: Function definition does not bind loop variable job

(B023)

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562-562: Function definition does not bind loop variable job

(B023)