feat: support snakemake 9#50
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The executor talks to snakemake exclusively through snakemake-interface-executor-plugins, whose contract is identical across snakemake 8 and 9, so no source changes are required. This documents and tests support for both majors: - widen the dev snakemake dependency to >=8.30,<10; - add a CI test matrix over snakemake 8 and 9 (each leg resolves a different snakemake-interface-storage-plugins major via snakemake-storage-plugin-s3, so both must be exercised); - state supported versions in the docs and make the container-image storage-plugin guidance symmetric across snakemake 8 and 9.
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📝 WalkthroughWalkthroughThe 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. ChangesSnakemake compatibility
Estimated code review effort: 2 (Simple) | ~10 minutes Possibly related PRs
🚥 Pre-merge checks | ✅ 5✅ Passed checks (5 passed)
✨ Finishing Touches🧪 Generate unit tests (beta)
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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 devsnakemakepin^8.30.0→>=8.30,<10(dev-only; no end-user effect).ci_mocked_api.yml: add asnakemake: ["<9", ">=9,<10"]test matrix. Each leg does a full re-resolve viapoetry add --group dev --lockrather than an overlay install, because the Snakemake major dictates thesnakemake-interface-storage-pluginsmajor (3.x vs 4.x), which selects a compatiblesnakemake-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 asaws-batchin Snakemake 9'sExecutorPluginRegistry, and passes all 101test_batch_job_builder.pyunit tests. Both matrix legs resolve to consistent sets:<9>=9,<10Out of scope
No runtime-dependency changes: the existing
snakemake-storage-plugin-s3 >=0.2,<0.4pin 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