feat: add CaDecon Python bridge for automated deconvolution export#108
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Enable `calab.decon(traces, fs)` to open CaDecon in the browser and receive structured results (activity matrix + per-cell scalars + kernel params) back to Python via a two-POST binary transport pattern. - Add npy-writer.ts (inverse of npy-parser) for binary activity export - Extend bridge server with /api/v1/results/activity (.npy) and /api/v1/results (JSON) endpoints, plus configurable app param - Add decon() orchestrator, CaDeconResult NamedTuple, biexp waveform builder, and `calab cadecon` CLI subcommand - Wire ExportButton in CaDecon UI with loading/disabled states - 22 new tests (7 npy-writer, 5 bridge endpoints, 7 CaDeconResult, 3 waveform) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Extract shared _run_bridge() helper from tune()/decon() to eliminate ~60 lines of duplicated polling/heartbeat/shutdown boilerplate. Extract sortedCellIndices() in export-utils to avoid double-sorting lookup keys. Remove postActivityToBridge/postResultsToBridge from public io exports since they're internal to exportCaDeconToBridge. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Summary
calab.decon(traces, fs)— new Python bridge that opens CaDecon in the browser and returns structuredCaDeconResult(activity matrix, per-cell alphas/baselines/PVEs, kernel waveforms, metadata).npy(potentially 10s of MB) followed by JSON scalars/metadata, mirroring the inbound data flowcalab cadeconCLI — new subcommand for file-based automated deconvolution with optional output savingNew files
packages/io/src/npy-writer.tspackages/io/src/__tests__/npy-writer.test.tsapps/cadecon/src/lib/export-utils.tspython/tests/test_decon.pyModified files
packages/io/src/bridge.tspostActivityToBridge,postResultsToBridge,exportCaDeconToBridgepackages/io/src/index.tsapps/cadecon/.../GroundTruthControls.tsxpython/.../_{compute,server,apps,cli,init}CaDeconResult, server endpoints,decon(), CLIpython/tests/test_bridge.pyTest plan
npm run format)calab.decon(traces, fs=30, app_url="http://localhost:5175/")→ run solver → Export to Python → verify result fields🤖 Generated with Claude Code