build, run: Run Snakemake with --benchmark-extended#513
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This only applies to --cores and --resources, not --local-storage-prefix.
This is more consistent with the run and view commands.
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--benchmark-extended--benchmark-extended
Parallels IMAGE_FEATURE for Docker.
Preparing for reuse.
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| def supports_benchmark_extended(opts) -> bool: | ||
| """ | ||
| Check if the runner's image or environment supports Snakemake's | ||
| ``--benchmark-extended`` option (requires Snakemake ≥8.11.0). | ||
| """ | ||
| if opts.__runner__ in (docker, aws_batch, singularity): | ||
| image = runner.configured_image(opts) | ||
| if opts.__runner__ is singularity: | ||
| image = remove_prefix("docker://", image) | ||
| return docker.image_supports(docker.IMAGE_FEATURE.benchmark_extended, image) | ||
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| if opts.__runner__ is conda: | ||
| return conda.env_supports(conda.ENV_FEATURE.benchmark_extended) | ||
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| return False |
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What happens on ambient? Is directly interrogating the snakemake version acceptable?
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It returns False and doesn't automatically add --benchmark-extended.
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We could run snakemake --version and parse that, but I don't think it's worth the added complexity because this is currently all happening before actual invocation of Snakemake.
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Thanks for working on this! I only left a small comment.
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Commands used to find compatible versions for Docker¹ and Conda²:
curl -s "https://registry.hub.docker.com/v2/repositories/nextstrain/base/tags?page_size=1000" \
| jq -r '.results[].name | select(startswith("build-20250717"))'
micromamba search -c nextstrain "nextstrain-base >20250716,<20250718"
¹ nextstrain/docker-base@0d9577d
² nextstrain/conda-base@0d7a87f
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This PR contains 4 prep commits, 1 main commit that closes #467, and 1 follow-up commit.
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Locally tested both
buildandrunwith measlesLocally tested compatibility with Snakemake v7
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