@iowarp/clio-coder 0.4.5 → 0.4.7

package/library/plugins/materio/assets/templates/VIRTUAL-LAB.md

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+# Virtual Lab
+
+## Experimental Facilities
+
+### Labs Accessible
+| Lab Type | Location/Name | Access Level | Notes |
+|----------|--------------|--------------|-------|
+| [Chemistry/wet lab] | [building/room] | [daily | scheduled | limited] | [] |
+| [Mechanical testing] | [building/room] | [daily | scheduled | limited] | [] |
+| [Microscopy suite] | [building/room] | [daily | scheduled | limited] | [] |
+| [Cleanroom] | [building/room] | [daily | scheduled | limited] | [] |
+| [Processing/synthesis] | [building/room] | [daily | scheduled | limited] | [] |
+
+### Equipment Inventory
+
+#### Characterization
+| Equipment | Model/Capability | Access | Booking | Limitations |
+|-----------|-----------------|--------|---------|-------------|
+| SEM | [model, kV range, EDS?] | [in-house|external] | [yes/no, lead time] | [sample size, conductivity] |
+| TEM/STEM | [model, EELS/EDS?] | [in-house|external] | [yes/no, lead time] | [sample prep required] |
+| XRD | [model, Cu/Mo source, SAXS?] | [in-house|external] | [yes/no] | [powder/bulk/thin film] |
+| XPS | [model] | [in-house|external] | [yes/no] | [] |
+| APT | [model] | [in-house|external] | [yes/no] | [] |
+| Raman | [model] | [in-house|external] | [yes/no] | [] |
+| DSC/TGA | [model, temp range] | [in-house|external] | [yes/no] | [] |
+
+#### Mechanical Testing
+| Equipment | Capability | Access | Max Load | Temperature Range |
+|-----------|-----------|--------|----------|-------------------|
+| Universal testing machine | [tensile/compression/fatigue] | [in-house|external] | [kN] | [°C] |
+| Fatigue tester | [load-controlled, displacement] | [in-house|external] | [kN] | [] |
+| Hardness tester | [Vickers/Rockwell/nano] | [in-house|external] | [] | [] |
+| Nanoindenter | [model] | [in-house|external] | [mN] | [] |
+| DMA | [model, freq range] | [in-house|external] | [] | [] |
+
+#### Processing / Synthesis
+| Equipment | Type | Capability | Access |
+|-----------|------|-----------|--------|
+| Furnace | [box/tube/vacuum] | [max temp °C, atmosphere] | [in-house|external] |
+| Arc melter | [] | [button size, inert gas] | [in-house|external] |
+| Electrospinning | [] | [] | [in-house|external] |
+| Sputtering/PVD | [] | [targets, substrate size] | [in-house|external] |
+| 3D printer / SLM | [material, build volume] | [] | [in-house|external] |
+
+---
+
+## Computational Resources
+
+### HPC Systems
+| System Name | Cores Available | RAM/Node | Storage | Scheduler | Key Software |
+|-------------|----------------|---------|---------|-----------|-------------|
+| [cluster name] | [N cores/job] | [GB] | [TB quota] | [SLURM|PBS|SGE] | [VASP, LAMMPS, Abaqus, etc.] |
+
+### Local Workstations
+| Machine | CPU | GPU | RAM | OS | Special Use |
+|---------|-----|-----|-----|----|-------------|
+| [desktop/laptop] | [cores, GHz] | [model, VRAM] | [GB] | [Linux/Win] | [primary workstation] |
+
+### Cloud / External Compute
+| Resource | Type | Cost Model | Access Method |
+|----------|------|-----------|---------------|
+| [AWS/GCP/Azure/XSEDE/ACCESS] | [CPU/GPU cluster] | [$/hr or allocation] | [always|limited] |
+
+---
+
+## Software Licenses
+| Software | Purpose | License | Version | Notes |
+|----------|---------|---------|---------|-------|
+| VASP | DFT | [group|institutional] | [6.x] | [] |
+| LAMMPS | MD | open-source | [] | [] |
+| Thermo-Calc / Pandat | CALPHAD | [group|institutional] | [] | [] |
+| Abaqus | FEM | [group|institutional] | [] | [] |
+| VESTA | Crystal viz | free | [] | [] |
+| Python (numpy, scipy, pymatgen, ASE) | Analysis | open-source | [] | [] |
+| MATLAB | Analysis | [institutional] | [] | [] |
+| OriginPro | Plotting | [group|institutional] | [] | [] |
+
+---
+
+## External Facilities & Collaborations
+| Facility | Type | Access Route | Typical Lead Time | Contact |
+|----------|------|-------------|-------------------|---------|
+| [National lab, e.g., APS, NSLS-II] | [synchrotron XRD] | [proposal|collaborator] | [months] | [] |
+| [University core facility] | [] | [fee-for-service] | [weeks] | [] |
+| [Industry collaborator] | [] | [MOU|collaboration] | [] | [] |
+
+---
+
+## Materials & Consumables
+- **Budget**: [$/month or total project budget]
+- **Material sourcing**: [in-house synthesis | purchased (supplier) | collaborator-provided]
+- **Typical lead time**: [days/weeks for material procurement]
+- **Storage**: [controlled atmosphere | cryogenic | ambient]
+
+---
+
+## Human Resources
+- **Personnel**: [PI only | + grad students (N) | + postdoc | + technician | + undergrads]
+- **Time on this project**: [hours/week]
+- **Key skills in lab**: [list relevant expertise]
+- **Skills gaps**: [techniques nobody in the lab knows yet]
+
+---
+
+## Constraints & Blockers
+- [Equipment currently down or unavailable]
+- [Booking backlogs or seasonal access issues]
+- [Safety certifications required but not yet held]
+- [Export control or IP restrictions on certain materials/software]
+
+---
+
+## Resource-to-Task Mapping
+*Auto-generated during define-virtual-lab; maps available resources to WORKFLOW.md task types*
+
+| Task Type | Required Resource | Available? | Alternative if Not |
+|-----------|-----------------|------------|-------------------|
+| XRD characterization | In-house XRD | [yes/no] | [external facility X] |
+| DFT calculation | HPC with VASP | [yes/no] | [cloud compute, QE open-source] |
+| Tensile testing | UTM | [yes/no] | [external lab Y] |

package/library/plugins/materio/assets/templates/WORKFLOW.md

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+# Research Workflow
+
+## Research Type
+[experimental | computational | mixed | literature-only]
+
+## Overview
+[2-3 sentences describing the overall research strategy]
+
+## Tasks
+
+### Task 01: [name]
+- **Type**: literature | experimental | computational | analytical | data-analysis | writing
+- **Description**: [what needs to be done; specific and actionable]
+- **Assumptions**:
+  - [assumption 1; what is taken as given]
+  - [assumption 2]
+- **Inputs**: [data, information, or prior task outputs required]
+- **Expected Outputs**: [what this task produces; specific artifacts]
+- **Dependencies**: [task numbers that must complete first, or "none"]
+- **Estimated Effort**: [hours | days | weeks]
+- **Status**: ☐ pending
+- **Notes**: []
+
+---
+
+### Task 02: [name]
+- **Type**: [type]
+- **Description**: []
+- **Assumptions**: []
+- **Inputs**: [outputs from Task 01]
+- **Expected Outputs**: []
+- **Dependencies**: Task 01
+- **Status**: ☐ pending
+- **Notes**: []
+
+---
+
+## Archived Tasks
+[Tasks removed from active workflow but preserved for reference]
+
+## Workflow Decisions
+[Key decisions made during define-research-tasks; why certain steps were included/excluded]

package/library/plugins/materio/assets/templates/config.json

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+{
+	"web_search": false,
+	"auto_checkpoint": true,
+	"commit_research": false
+}

package/library/plugins/materio/evals/scripts.yaml

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+version: 2
+suite:
+  id: materio-script-contracts
+  title: Materio offline script contracts
+  visibility: public
+  description: Deterministic tests of research state, physics checks, Python parsing, and offline citation handling. No model quality claim.
+matrix:
+  dimensions: []
+  targets:
+    - id: default
+  repeats: 1
+tasks:
+  - id: offline-scripts
+    tags: [materio, deterministic, offline]
+    workspace:
+      kind: temp-copy
+      path: ..
+      excludes: [__pycache__]
+    runner:
+      kind: external-command
+      command: python3 -m unittest discover -s tests -p 'test_*.py'
+    verify:
+      assertions:
+        - metric: result.pass
+          op: eq
+          value: true
+    metrics:
+      collect: [result.pass, verifier.exitCode]
+    timeoutMs: 60000