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[docs] Add an AI usage policy and align the agent contracts
area:agentsClaude Code, Codex, or other AI-agent tooling and contractsClaude Code, Codex, or other AI-agent tooling and contractsarea:documentationREADME, Sphinx docs, changelog, or docstringsREADME, Sphinx docs, changelog, or docstringstype:docsImprovements or additions to documentationImprovements or additions to documentationStatus: Open.[release] Evaluate MDAKit packaging and a JOSS submission
area:packagingpyproject, distribution metadata, build, or release artifactspyproject, distribution metadata, build, or release artifactstype:questionOpen question or decision that needs resolvingOpen question or decision that needs resolvingtype:releaseRelease preparation, tagging, or release notesRelease preparation, tagging, or release notesStatus: Open.[analyze] Verify the MAICoS local volume-fraction gap before building
area:analyzeObservables, statistics, binning, and histogramsObservables, statistics, binning, and histogramstype:questionOpen question or decision that needs resolvingOpen question or decision that needs resolvingStatus: Open.[analyze] Port polymer and crowding observables from the research codebase
area:analyzeObservables, statistics, binning, and histogramsObservables, statistics, binning, and histogramstype:featureNew feature or user-facing improvementNew feature or user-facing improvementStatus: Open.[manage] Decide whether manage builds on signac or stays internal
area:manageParser, organizer, lineage, and simulation data managementParser, organizer, lineage, and simulation data managementtype:questionOpen question or decision that needs resolvingOpen question or decision that needs resolvingStatus: Open.[manage] Move per-project constants from the organizer onto parser classes
area:manageParser, organizer, lineage, and simulation data managementParser, organizer, lineage, and simulation data managementbreaking-changeIncompatible change to the public API or documented behaviorIncompatible change to the public API or documented behaviortechnical-debtCleanup or improvement that reduces future maintenance costCleanup or improvement that reduces future maintenance costtype:refactorCode restructuring without intended behavior changeCode restructuring without intended behavior changeStatus: Open.[docs] Document time and space complexity for the organizer reducers
area:manageParser, organizer, lineage, and simulation data managementParser, organizer, lineage, and simulation data managementtype:docsImprovements or additions to documentationImprovements or additions to documentationStatus: Open.[analyze] Add autocorrelation-aware error estimation for correlated frames
area:analyzeObservables, statistics, binning, and histogramsObservables, statistics, binning, and histogramstype:featureNew feature or user-facing improvementNew feature or user-facing improvementStatus: Open.[organizer] Raise test coverage from 13 percent to at least 85 percent
area:manageParser, organizer, lineage, and simulation data managementParser, organizer, lineage, and simulation data managementtype:testTests, doctests, examples, or regression coverageTests, doctests, examples, or regression coverageStatus: Open.[release] Tag and archive v0.4.0
area:packagingpyproject, distribution metadata, build, or release artifactspyproject, distribution metadata, build, or release artifactstype:releaseRelease preparation, tagging, or release notesRelease preparation, tagging, or release notesStatus: Open.[organizer] Replace skipped doctests with executable examples
area:manageParser, organizer, lineage, and simulation data managementParser, organizer, lineage, and simulation data managementtype:docsImprovements or additions to documentationImprovements or additions to documentationtype:testTests, doctests, examples, or regression coverageTests, doctests, examples, or regression coverageStatus: Open.