feat: per-rule task timeout via aws_batch_task_timeout resource

[nh13]

Adds a per-rule aws_batch_task_timeout resource that overrides the workflow-level --aws-batch-task-timeout setting, mirroring the existing per-rule batch_queue pattern.

• Precedence: the per-rule resource wins over the global flag; falls back to the flag when the resource is absent; omits the timeout entirely when neither is set (preserving the no-default-timeout behavior from fix: don't apply a 300s default task timeout to every job #41).
• Validation: the value is coerced to an integer and must be ≥ 60 s (the AWS minimum). Errors name the source (resource vs flag) so the cause is unambiguous.

rule align:
    resources:
        aws_batch_task_timeout=14400  # 4 h
    ...

Depends on #41 (conditional task-timeout), now merged. Documented under a new "Task Timeout" section in docs/further.md.

Testing

New TestPerRuleTaskTimeout covers precedence, resource-only, fallback, both-absent, < 60, non-numeric, and the exact-60 boundary. Full suite: 61 unit tests pass; black + flake8 clean.

Summary by CodeRabbit

Release Notes

• New Features

  • Support for per-rule AWS Batch task timeout configuration, which takes precedence over workflow-level settings.
  • Workflow-level timeout control with minimum 60-second validation (AWS requirement); omitted if not configured.

• Documentation

  • Added "Task Timeout" section with configuration examples and behavior clarification.

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Run ID: 404f3302-dc99-440f-b212-f8097db9e588

📥 Commits

Reviewing files that changed from the base of the PR and between 1d7d6e6 and e08476b.

📒 Files selected for processing (3)

• docs/further.md
• snakemake_executor_plugin_aws_batch/batch_job_builder.py
• tests/test_batch_job_builder.py

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📝 Walkthrough

Walkthrough

This PR adds support for per-rule task timeout overrides in AWS Batch job definitions. Rules can now set aws_batch_task_timeout to override the workflow-level setting, with integer coercion and AWS minimum validation, and tests verify all timeout selection and validation paths.

Changes

Per-Rule Task Timeout Override Feature

Layer / File(s)	Summary
Per-rule timeout override and validation in job builder snakemake_executor_plugin_aws_batch/batch_job_builder.py	build_job_definition now checks per-rule aws_batch_task_timeout resource before falling back to workflow-level settings.task_timeout. When a timeout exists, it is coerced to an integer and validated to be ≥60 seconds with source-specific error messages. If both sources are absent, the timeout field is omitted so AWS applies its default.
Test helper and comprehensive test suite tests/test_batch_job_builder.py	Introduces _make_builder_with_rule_timeout helper to construct a builder with configurable global and per-rule timeouts, and TestPerRuleTaskTimeout test class with seven cases asserting resource override precedence, fallback behavior, omission when absent, and validation of integer type and 60-second minimum.
Task timeout documentation and usage examples docs/further.md	Adds "Task Timeout" section explaining the --aws-batch-task-timeout workflow-wide flag (60-second minimum) and per-rule aws_batch_task_timeout resource (which takes precedence), with a concrete rule example and clarification of default behavior when neither is set.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~12 minutes

Possibly related PRs

• snakemake/snakemake-executor-plugin-aws-batch#41: Both PRs modify BatchJobBuilder.build_job_definition to control the AWS Batch job-definition timeout (omitting it when unset and validating >=60), and both extend/change tests/test_batch_job_builder.py around timeout behavior—main PR further adds the per-rule aws_batch_task_timeout override.
• snakemake/snakemake-executor-plugin-aws-batch#40: Both PRs touch BatchJobBuilder.build_job_definition's AWS Batch job-definition timeout/task_timeout handling and its validation (min 60s behavior), so the main PR's timeout precedence/coercion builds directly on the retrieved PR's timeout logic/tests.

Suggested reviewers

• cademirch

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately describes the main feature: adding a per-rule task timeout capability via the aws_batch_task_timeout resource, which is the primary change across the modified files.
Docstring Coverage	✅ Passed	Docstring coverage is 90.00% which is sufficient. The required threshold is 80.00%.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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• Create PR with unit tests

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