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docs: an Applications-in-practice section - #11
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… a real pipeline Appends a worked real-world case to docs/EXPLAINME.adoc: the concrete situation in an amplicon-sequencing pipeline in production use where the type, the OND discipline or the algebra earns its keep -- and what the untyped or undisciplined alternative gets wrong. Documentation only; no code changes. Generated by Mistral Vibe. Co-Authored-By: Mistral Vibe <vibe@mistral.ai>
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Pre-merge checks:
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| Check name | Status | Explanation | Resolution |
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| Description check |  |
The description explains the documentation change and testing status, but it does not use the required Summary, Changes, RSR Quality Checklist, Testing, and Screenshots sections. It also omits the che… | Rewrite the description using the repository template. Add the required section headings, list the documentation change under Changes, complete the RSR Quality Checklist, state the testing result under Testing, and include Screenshots infor… |
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Check name Status Explanation Title check The title clearly identifies the main change: adding an Applications-in-practice section to the documentation. Docstring Coverage No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 0… Linked Issues check Check skipped because no linked issues were found for this pull request. Out of Scope Changes check Check skipped because no linked issues were found for this pull request.
Full details: Description check
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Explanation
The description explains the documentation change and testing status, but it does not use the required Summary, Changes, RSR Quality Checklist, Testing, and Screenshots sections. It also omits the checklist status and applicable checks.
Resolution
Rewrite the description using the repository template. Add the required section headings, list the documentation change under Changes, complete the RSR Quality Checklist, state the testing result under Testing, and include Screenshots information or mark it not applicable.
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Actionable comments posted: 1
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Inline comments:
Review comments at @docs/EXPLAINME.adoc:
- Around line 124-131: Revise the production-measurement claims in the HWM
section to distinguish the proposed algebra from a production-validated result,
unless the `TypedPeak` and `GradedStages` integration and
aggregate-equals-observed-peak claim can be substantiated with a concrete case
link and evidence. Keep any claims about production usage and equality limited
to what that evidence demonstrates.
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…vidence CodeRabbit (PR #11) flagged the Applications-in-practice section for presenting the MetaManifold measurements as a production-validated result while Instances/HWM.agda records HWM as a proposal. The claim was real but unlinked, so: name the proposal status and its supersession rule up front, link the concrete case (docs/occupancy-2026-10.adoc, results-2026-10-14.yml, TypedPeak.agda, GradedStages.agda, scripts/check-occupancy.sh), give the measured numbers the typed peak reproduces (9192, 9204, 18380 KiB), and scope the equality to that run's observed interleaving rather than a general production guarantee. Generated by Mistral Vibe. Co-Authored-By: Mistral Vibe <vibe@mistral.ai>
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1 participant
What this adds
An Applications in practice section in
docs/EXPLAINME.adoc: one worked real-world case that shows the HWM algebra behind typed stage peaks -- the day-to-day 'which stage ate the machine?' answered auditably -- grounded in MetaManifold, an amplicon-sequencing pipeline in production use, because the value of the discipline is clearest on a live pipeline rather than a toy.The section answers the question a newcomer actually has: what is this for in the real world, and what goes wrong without it? It is deliberately short, states what the undisciplined alternative gets wrong, and links the concrete case.
What this leaves out
Documentation only. No code, no API, no claim changes anywhere else in the repo. The commit is signed.
Versions tested
Not applicable -- documentation.
Generated by Mistral Vibe.
Co-Authored-By: Mistral Vibe vibe@mistral.ai
Summary by CodeRabbit