Issues

• sim: no conformer search or ensemble averaging for molecular properties (single conformer only)

  enhancement
  ziatdinovmax/SciLink#792 · Filter by author sarah-allec opened on Oct 21, 2026
  

• sim: a successful run_complete_workflow returns no answer to the research goal — persist the final assessment and return structured results

  enhancement
  ziatdinovmax/SciLink#788 · Filter by author sarah-allec opened on Oct 20, 2026
  

• structure: coherent interfaces between mismatched lattices come out incoherent and mis-oriented — generation prompt routes them to lowest-strain ZSL matching on primitive cells; validator is told not to flag interface contacts

  bugenhancement
  ziatdinovmax/SciLink#787 · Filter by author sarah-allec opened on Oct 20, 2026
  

• Health gate: derive system-aware plausible bounds from the goal/references, not fixed frontmatter numbers

  enhancement
  ziatdinovmax/SciLink#783 · Filter by author sarah-allec opened on Oct 10, 2026
  

• Autonomous runs need an engine-neutral health gate + per-member watchdog

  enhancement
  ziatdinovmax/SciLink#781 · Filter by author sarah-allec opened on Oct 9, 2026
  

• Swarm reactions act on one finding; a swarm item's plan cannot be revised with later evidence

  ziatdinovmax/SciLink#773 · Filter by author ziatdinovmax opened on Oct 7, 2026

• Follow-ups from #768: RMS as a measured quantity, error-metric prefixes, a cancel test through a real wait

  ziatdinovmax/SciLink#771 · Filter by author ziatdinovmax opened on Oct 7, 2026

• Simulation swarm shapes: replica ensembles, method sweeps, and convergence ladders as items on the HPC placement

  enhancement
  ziatdinovmax/SciLink#767 · Filter by author sarah-allec opened on Oct 6, 2026
  2

  

• Parallel fan-out members: concurrent dispatch for campaign stages (the run_many seam)

  enhancement
  ziatdinovmax/SciLink#745 · Filter by author sarah-allec opened on Oct 4, 2026
  2

  

• Hyperspectral series: the replay gate's plausible-range rule rejects a correctly tracked drift, costing a refit per dataset

  ziatdinovmax/SciLink#731 · Filter by author ziatdinovmax opened on Oct 3, 2026

• Design: shared replay gate and verdict record across the analysis agents (extract, then fix #711, #710, #699)

  ziatdinovmax/SciLink#712 · Filter by author ziatdinovmax opened on Oct 1, 2026
  10

• Meta-driven simulations cannot submit to HPC (no connection reaches the simulation specialist or swarm workers)

  bug
  ziatdinovmax/SciLink#696 · Filter by author ziatdinovmax opened on Sep 30, 2026
  

• Closing the observable-convergence loop (follow-up to #447, after #680)

  ziatdinovmax/SciLink#682 · Filter by author sarah-allec opened on Sep 29, 2026
  2

  

• Support .pptx uploads and reading (meta, knowledge, document readers)

  ziatdinovmax/SciLink#672 · Filter by author ziatdinovmax opened on Sep 26, 2026

• Claude Code integration: bidirectional MCP bridge for code execution and domain tools

  enhancement
  ziatdinovmax/SciLink#663 · Filter by author sarah-allec opened on Sep 22, 2026
  1

  

• simulate: route_simulation blocks input generation when engine binary is missing

  bug
  ziatdinovmax/SciLink#661 · Filter by author sarah-allec opened on Sep 22, 2026
  

• Deterministic per-grain lattice-symmetry + orientation tool (LLM FFT-spot reading is unreproducible)

  ziatdinovmax/SciLink#653 · Filter by author ziatdinovmax opened on Sep 17, 2026

• Proxy path drops tool-result images even on vision backends (Claude/Gemini via base_url) — model never sees them

  ziatdinovmax/SciLink#648 · Filter by author ziatdinovmax opened on Sep 15, 2026

• Feature request: enable provider-side prompt caching in the LLM client layer to cut API costs

  ziatdinovmax/SciLink#647 · Filter by author jenna1701 opened on Sep 15, 2026

• Generalize the execution-environment probe beyond the image agent (#581 follow-up)

  ziatdinovmax/SciLink#613 · Filter by author ziatdinovmax opened on Sep 12, 2026

• run_analysis on a 3-D .npy stack file fails after file prep: 'Expected 1D or 2D curve data, got 3D'

  bug
  ziatdinovmax/SciLink#603 · Filter by author ziatdinovmax opened on Sep 9, 2026

• atomic_stem: generated scripts save map_polarization()['xy'] (cell positions) as the displacement / polarization arrays

  bug
  ziatdinovmax/SciLink#602 · Filter by author ziatdinovmax opened on Sep 9, 2026

• Volume-Analysis foundation agent for 3D volumes (tomography, serial sectioning, z-stacks)

  enhancement
  ziatdinovmax/SciLink#528 · Filter by author ziatdinovmax opened on Sep 3, 2026

• Orphaned-result adoption + incremental per-item flush (artifact-level salvage for killed pipeline runs)

  ziatdinovmax/SciLink#523 · Filter by author ziatdinovmax opened on Aug 31, 2026

• Structure-prep steps (H-addition, solvation, ion placement) leave unrelaxed sub-Å clashes

  bug
  ziatdinovmax/SciLink#496 · Filter by author sarah-allec opened on Aug 23, 2026