feat: support snakemake 9

[nh13]

Documents and tests support for Snakemake 9 alongside Snakemake 8. The plugin already worked under Snakemake 9 but was untested and undocumented against it; this makes that support explicit and guarded.

The executor interacts with Snakemake exclusively through snakemake-interface-executor-plugins, whose contract is identical across Snakemake 8 and 9 (both pin >=9.3.2,<10). No source-code or runtime-dependency changes are required.

Changes

• pyproject.toml: widen the dev snakemake pin ^8.30.0 → >=8.30,<10 (dev-only; no end-user effect).
• ci_mocked_api.yml: add a snakemake: ["<9", ">=9,<10"] test matrix. Each leg does a full re-resolve via poetry add --group dev --lock rather than an overlay install, because the Snakemake major dictates the snakemake-interface-storage-plugins major (3.x vs 4.x), which selects a compatible snakemake-storage-plugin-s3. Passing on one major does not imply the other.
• docs/: state supported versions (8 and 9) and make the container-image storage-plugin guidance symmetric across both majors.

Verified locally

Installed against Snakemake 9.23.1 (resolves s3 0.3.6 / storage-interface 4.4.1 / executor-plugins 9.4.0); plugin imports, subclasses RemoteExecutor, registers as aws-batch in Snakemake 9's ExecutorPluginRegistry, and passes all 101 test_batch_job_builder.py unit tests. Both matrix legs resolve to consistent sets:

leg	snakemake	s3	storage-interface
<9	8.30.0	0.3.1	3.5.0
>=9,<10	9.23.1	0.3.6	4.4.1

Out of scope

No runtime-dependency changes: the existing snakemake-storage-plugin-s3 >=0.2,<0.4 pin already resolves correctly for both majors. Re-pinning CI actions by SHA and any storage-dependency restructuring are left to separate PRs.

Summary by CodeRabbit

• Documentation
  • Clarified that the plugin supports Snakemake versions 8 and 9.
  • Updated container image guidance to explain compatibility requirements between Snakemake and storage-plugin versions.
• Tests
  • CI now validates the project against both supported Snakemake major-version ranges.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 7497b0b3-46a3-4bde-a3d4-8328adf13950

📥 Commits

Reviewing files that changed from the base of the PR and between 47e8027 and 7c89485.

⛔ Files ignored due to path filters (1)

• pyproject.toml is excluded by !pyproject.toml

📒 Files selected for processing (3)

• .github/workflows/ci_mocked_api.yml
• docs/further.md
• docs/intro.md

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📝 Walkthrough

Walkthrough

The CI workflow now tests Snakemake versions below 9 and from 9 to 10 using a matrix. Documentation describes Snakemake 8/9 support and requires container images to pre-install compatible storage-plugin versions.

Changes

Snakemake compatibility

Layer / File(s)	Summary
Snakemake version matrix .github/workflows/ci_mocked_api.yml	The testing job runs separate Snakemake version matrix legs and pins each selected version through Poetry while updating the lockfile.
Compatibility documentation docs/intro.md, docs/further.md	Documentation states support for Snakemake 8 and 9 and explains that container images must pin compatible Snakemake and storage-plugin versions.

Estimated code review effort: 2 (Simple) | ~10 minutes

Possibly related PRs

• snakemake/snakemake-executor-plugin-aws-batch#13: Both changes update the mocked-API CI workflow.
• snakemake/snakemake-executor-plugin-aws-batch#21: Both changes update the documentation in docs/further.md.

🚥 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 clearly summarizes the main change: adding Snakemake 9 support.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
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.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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