Reported issues for OpenHCS

Pod holds 20 of 37 GitHub reports that passed its relevance review. This can include external user reports, maintainer-confirmed bugs, and concrete feature gaps. Treat them as evidence to inspect, not a count of distinct defects.

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Most discussed

Expose compiled materialized results to MCP inventory and viewer review

OpenHCS 0.8.6: with PipelineConfig.materialization_results_path set to an absolute output directory, a successful headless run wrote typed measurement CSVs and per-plane ROI ZIPs. The compiled artifact plan listed candidate paths, but openhcs_query_plate_files on the output plate returned zero result records because that directory is outside metadata-declared results_dir. openhcs_stream_plate_files_to_viewer rejected an exact persisted ROI ZIP path as "not found in the plate"; the MCP surface…

Read the thread · 2026-09-28 · open · 10 comments

Canonical custom-function ID is visible remotely but absent from in-process source lookup

Named diagnosis owner: knowledge lazy-conversion sidecar, branch fix/knowledge-lazy-conversion-20261001 / PR377; parent owns installed engineering acceptance. This is related to376 by the local declaration/catalogue boundary, but distinct from its timeout.

Original installed request: remote owned5993 registration succeeded once for openhcs:engineering_calibration_classification_fixture, returned stable import openhcs.processing.custom_functions.engineering_calibration_classification_fixture.…

Read the thread · 2026-10-01 · open · 6 comments

MCP dev-client response decoder raises JsonValue NameError after successful function-step mutation

Independent decoder owner: fix/mcp-inherited-dto-decoder-20261001, persistent worktree /home/ts/wt/openhcs-mcp-inherited-dto-decoder-20261001, based on main791650087e01c9d25766f12802a37296851f37cf. Current owners/open PRs checked; no decoder overlap found.

Fresh installed3d58912 persistent MCP dev-client shell called openhcs_add_function_step with pipeline_id=pipeline-1, function_id=skimage:exposure.adjust_gamma, name=paired350_identity, kwargs gamma=1/gain=1, napari_streaming_config…

Read the thread · 2026-10-01 · closed · 6 comments

Retained viewer schema mismatch prevents MCP visual QA despite healthy client handshake

Observed on retained isolated H002,30September2026. Engineering integration owner: parent blind-analysis thread. Shared viewer protocol/lifecycle implementation owner already registered: openhcs-pr159-viewer-bind-owner (PR159). Primary geometry author is not yet identified; do not create a competing shared-file patch or silently expand PR159 scope.

Reproducer through the exposed MCP tool, no OS input:…

Read the thread · 2026-09-30 · open · 4 comments

Preserve MCP call-boundary failures without post-dispatch transport fallback

Owner: OpenHCS blind-analysis coordinator (this thread). Reproduced through the owned installed OpenHCS 0.8.6 MCP dev-client/resident socket; reviewed production code 9f37cb66d, equivalent to merged #177 on main abb8b6116b.

A first source artifact-plan inspection of one 128x128 synthetic field with one registered callable hit the existing 10-second transport-inactivity limit at call_tool. Server PID 4141724 remained healthy and the warmed exact readonly inspection returned a sound plan later.…

Read the thread · 2026-09-29 · closed · 4 comments

Napari rejects valid one- and two-channel source-channel carriers as invalid RGB

Native viewer rejects a valid singleton source-channel carrier

Integration owner: parent. Source repair owner: Schrodinger. Checkpoint: remote main 58ee773b0c0d615e213ba5431513f5ee8c98223c, ordinary private installed OpenHCS 0.8.7 including merged PR437 and PR446. PR394 checked before assignment: head d4e800a7552623c8d5a55522aadea42728ecea6e; its current changed-file roster does not contain napari_streaming_handlers.py. Confirm…

Read the thread · 2026-10-02 · closed · 3 comments

Selected official30 knowledge conversion exceeds the MCP observation deadline

Source repair owner: managed-viewer sidecar, now distinct knowledge lazy-conversion boundary owner, branch fix/knowledge-lazy-conversion-20261001 in /home/ts/wt/openhcs-knowledge-lazy-conversion-20261001; base main6ace57656. Parent owns installed acceptance and the occupied native slot.

Retained installed reproducer: openhcs_get_knowledge_document(document_id=openhcs_official30_benchmark_recipes, section_id=cp-tutorial-pixel-based-classification-openhcs-python, max_chars=50000) returns…

Read the thread · 2026-10-01 · open · 3 comments

Admit custom-function persistence before dispatch and preserve execution endpoint ownership

Verified defect

Custom-function persistence can cross a restricted MCP write-root boundary and reach an unrelated shared execution endpoint. A timeout does not undo that mutation or prove it absent.

Integration owner: OpenHCS issue-batch coordinator. Implementation owner: Lovelace, using the existing function-catalog request/service, execution endpoint and CustomFunctionManager declarations. No alternate registry or runner.

Reproducer and evidence

Fresh installed OpenHCS source…

Read the thread · 2026-09-29 · closed · 3 comments

Most recent

MCP silently drops undeclared connection intent and submits to default endpoint

Verified cause

Fresh H002 candidate03 supplied execution routing as an unadvertised nested connection object to openhcs_create_orchestrator_session_from_pipeline_source; successful candidate02 used advertised flat host/port/transport_mode/persistent fields.

The actual paired FastMCP ArgModelBase silently ignores extra keys. The nested object is discarded before the original OpenHCS FromFields binding sees it. Request defaults therefore select localhost / omitted port / omitted…