Docs menu
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.
Last updated
Levels combine evidence from several areas. Open a level for its own requirements; higher levels also need the levels below.
L0Materials incompleteA confirmed material gap
L0 has no requirements of its own: it records that an essential material is confirmed missing. Fix it with the Materials guide.
L1Materials availableRequirements for this level
The necessary code, inputs and software are accounted for within the assessed scope, with evidence of availability or a credible access route.
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
L2Workflow documentedRequirements for this level
L1 plus complete instructions, versions, preparation and result mapping. Confirmed manuscript contradictions block this level.
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 L2Methods, parameters, statistics and reported numbers match what the code does.
Assessment areaManuscript consistencyLevel relationshipConfirmed contradictions block L2
Separate assessmentsDo not raise the level
Automation, access and preservation, software reuse, and policy and good practice stay visible beside the level. They never replace required materials or documentation.
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 levelThe 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”.