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Requirements and guides
Find what a level requires, or what we examine in each area. Every requirement links to its section in the area’s guide.
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Areas describe what we examine. Each area has one guide: open an area for its requirements and their relationship to the levels.
MaterialsRequired for L1
Are the necessary code, inputs and software accounted for? Public, controlled and private access are identified separately.
Public code computes the values behind every key result.
Assessment areaMaterialsLevel relationshipRequired for L1Every file the code reads is shared, deposited or has a documented source.
Assessment areaMaterialsLevel relationshipRequired for L1Besides the authors’ own code, every package, tool and model it depends on, such as scanpy or a pretrained model, can be obtained, commercial ones included.
Assessment areaMaterialsLevel relationshipRequired for L1
DocumentationRequired for L2
Can a reviewer follow the workflow and identify its outputs? Discoverable instructions can live in the paper, repository or linked documentation.
A dependency file lists every imported package with a version or range.
Assessment areaDocumentationLevel relationshipRequired for L2An immutable code version is cited, and stated tool versions match the code.
Assessment areaDocumentationLevel relationshipRequired for L2Each dataset has a persistent, versioned identifier and a described access route.
Assessment areaDocumentationLevel relationshipRequired for L2Every input that shared code does not produce comes with its preparation steps.
Assessment areaDocumentationLevel relationshipRequired for L2Each key figure and table names the one script that produces it.
Assessment areaDocumentationLevel relationshipRequired for L2Instructions cover setup, where inputs go, the run order and manual steps.
Assessment areaDocumentationLevel relationshipRequired for L2Every documented command, file, option and install name matches the repository.
Assessment areaDocumentationLevel relationshipRequired for L2Result code has no paths from one computer and no unexplained platform lock.
Assessment areaDocumentationLevel relationshipRequired for L2
Manuscript consistencyA contradiction blocks L2
A Materials and workflow check compares the paper with the code and its outputs for every key result. Confirmed contradictions block L2; unresolved evidence stays visible.
Methods, parameters, statistics and reported numbers match what the code does.
Assessment areaManuscript consistencyLevel relationshipConfirmed contradictions block L2
AutomationSeparate from the level
Are entry points, environments, input retrieval and randomness handled? Static evidence of automation does not prove successful execution.
One documented command regenerates every key result without manual steps.
Assessment areaAutomationLevel relationshipSeparate from the levelExact versions of every package, the runtime and the base image are locked.
Assessment areaAutomationLevel relationshipSeparate from the levelThe run command fetches and verifies its inputs, with no manual downloads.
Assessment areaAutomationLevel relationshipSeparate from the levelRandom draws are seeded, and run-to-run variation is controlled or documented.
Assessment areaAutomationLevel relationshipSeparate from the level
Access & preservationSeparate from the level
How can materials be obtained, and are they preserved in a lasting archive? Public, controlled and private access are distinct from archiving. Review-reported access conditions are shown; archive verification is not yet assessed.
Software reuseSeparate axis · not assessed yet
Can a named algorithm or software package be used and adapted beyond this paper? This concerns the software component, not the completeness of the paper analysis. Not applicable requires an explicit scope reason. A reuse badge does not raise the readiness level.
Policy and good practiceDo not raise the level
Journal policies (a license, a citation file, source data) and good practice (a tidy repository, tests, a consistent paper). Their findings are Warnings: they never change the level.
The license, citation file and source data that journal policies ask for.
Assessment areaPolicy and good practiceLevel relationshipSeparate from the levelAdvice beyond the levels: a tidy repository, tests and a consistent paper.
Assessment areaPolicy and good practiceLevel relationshipSeparate from the level
What a check covers
A check reads the available code, paper, data and documentation; the code is not executed. Instructions can span the repository, the paper and linked supplements. Areas a check did not examine stay “Not assessed”.