NDI-python: 2026-06 audit remediation + app frameworks + interactive spike sorter (review — do not merge)#57

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audriB wants to merge 62 commits into

Waltham-Data-Science:mainfrom

audriB:fix/app-residuals

Commits on Jun 10, 2026

Remove find/replace corruption from the class-rename commit
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Rebuild cloud sync engine for correctness (C1-C4)
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Fix cloud API contract drift and add 5xx retry
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Make ndi.neuron constructable so sorted units round-trip (C8b)
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Port time-conversion branches, rule daqsystem, and VHSB I/O (C5, C7, C8)
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Port addunderlyingepochs + missing-node retry + dest time filter (C6, C5 branch 3)
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Add session/dataset isIngested, convertLinkedSessionToIngested, stimulator pairOnOff
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Merge branch 'fix/time-system' into fix/element-addmultiple
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Add ndi.element.timeseries.addMultiple — batched bulk element creation
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DAQ parity: epochprobemap header/arrays (C10), mfdaq analog-event types, VHAudreyBPod transform
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epoch parity: epochgraph (cost,mapping) + matchedepochtable hash (§3.4-6); numeric _t threshold
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sync parity: port ndi.time.fun trigger-train/random-trigger alignment (§3.4-7)
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core docs + ndi_common parity: dependency fallback, dup-file error, 9 defs, definition cache
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ontology: add Uberon/NCIT/EDAM/IAO/STATO/SchemaOrg providers + extend registry (§3.4-14)
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security: harden secrets, eval, XML, downloads, packaging + CI (§3.5/§3.6)
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docs: reconcile bridge contracts + porting-guide/audit hygiene (§5, §3.6)
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feat(app): implement spike + tuning app compute methods from MATLAB (§3.4-13, part 1)
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feat(fun/probe): port the Kilosort import pipeline from MATLAB (decision 5)
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feat(app): markgarbage identifyvalidintervals + valid_interval array/struct storage (§3.4-13 pt2)
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Commits on Jun 11, 2026

Commits on Jun 12, 2026

Commits on Jun 17, 2026

Commits on Jun 21, 2026