@iowarp/clio-coder 0.4.5 → 0.4.7

package/library/plugins/materio/plugin.json

@@ -0,0 +1,530 @@
+{
+	"$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json",
+	"name": "materio",
+	"version": "0.1.0",
+	"description": "Materio: materials research interviews, supplied-corpus synthesis, lab feasibility, task execution and verified paper handoff.",
+	"author": {
+		"name": "IOWarp; domain workflow adapted from Daisy Quach"
+	},
+	"repository": "https://github.com/iowarp/clio-coder",
+	"keywords": ["materials-science", "research", "characterization", "scientific-workflows"],
+	"extensions": {
+		"ai.iowarp.clio": {
+			"manifestVersion": 1,
+			"compatibility": {
+				"clio": ">=0.4.7"
+			},
+			"resources": {
+				"skills": "skills",
+				"prompts": "ai.iowarp.clio/prompts",
+				"agents": "ai.iowarp.clio/agents",
+				"fleets": "ai.iowarp.clio/fleets"
+			},
+			"components": [
+				{
+					"kind": "resource",
+					"id": "research-domains",
+					"path": "assets/references/research-domains.md",
+					"requires": []
+				},
+				{
+					"kind": "resource",
+					"id": "traditional-workflows",
+					"path": "assets/references/traditional-workflows.md",
+					"requires": []
+				},
+				{
+					"kind": "resource",
+					"id": "research-policy",
+					"path": "assets/references/research-policy.md",
+					"requires": ["script:research-state", "script:check-physics", "script:check-scripts", "script:verify-citations"]
+				},
+				{
+					"kind": "resource",
+					"id": "clio-execution",
+					"path": "ai.iowarp.clio/references/execution.md",
+					"requires": ["resource:research-policy", "script:research-state"]
+				},
+				{
+					"kind": "resource",
+					"id": "research-template",
+					"path": "assets/templates/RESEARCH.md",
+					"requires": []
+				},
+				{
+					"kind": "resource",
+					"id": "virtual-lab-template",
+					"path": "assets/templates/VIRTUAL-LAB.md",
+					"requires": []
+				},
+				{
+					"kind": "resource",
+					"id": "workflow-template",
+					"path": "assets/templates/WORKFLOW.md",
+					"requires": []
+				},
+				{
+					"kind": "resource",
+					"id": "config-template",
+					"path": "assets/templates/config.json",
+					"requires": []
+				},
+				{
+					"kind": "script",
+					"id": "check-physics",
+					"path": "assets/scripts/check_physics.py",
+					"requires": []
+				},
+				{
+					"kind": "script",
+					"id": "check-scripts",
+					"path": "assets/scripts/check_scripts.py",
+					"requires": []
+				},
+				{
+					"kind": "script",
+					"id": "research-state",
+					"path": "assets/scripts/research_state.py",
+					"requires": []
+				},
+				{
+					"kind": "script",
+					"id": "verify-citations",
+					"path": "assets/scripts/verify_citations.py",
+					"requires": []
+				},
+				{
+					"kind": "resource",
+					"id": "action-add-task",
+					"path": "assets/actions/add-task.md",
+					"requires": ["resource:research-policy", "script:research-state"]
+				},
+				{
+					"kind": "resource",
+					"id": "action-archive-task",
+					"path": "assets/actions/archive-task.md",
+					"requires": ["resource:research-policy", "script:research-state"]
+				},
+				{
+					"kind": "resource",
+					"id": "action-checkpoint",
+					"path": "assets/actions/checkpoint.md",
+					"requires": ["resource:research-policy", "script:research-state"]
+				},
+				{
+					"kind": "resource",
+					"id": "action-define-research-tasks",
+					"path": "assets/actions/define-research-tasks.md",
+					"requires": [
+						"resource:research-policy",
+						"resource:traditional-workflows",
+						"resource:workflow-template",
+						"script:research-state"
+					]
+				},
+				{
+					"kind": "resource",
+					"id": "action-define-virtual-lab",
+					"path": "assets/actions/define-virtual-lab.md",
+					"requires": [
+						"resource:research-domains",
+						"resource:research-policy",
+						"resource:virtual-lab-template",
+						"script:research-state"
+					]
+				},
+				{
+					"kind": "resource",
+					"id": "action-execute-task",
+					"path": "assets/actions/execute-task.md",
+					"requires": [
+						"resource:research-policy",
+						"script:check-physics",
+						"script:check-scripts",
+						"script:research-state",
+						"script:verify-citations"
+					]
+				},
+				{
+					"kind": "resource",
+					"id": "action-help",
+					"path": "assets/actions/help.md",
+					"requires": ["resource:research-policy"]
+				},
+				{
+					"kind": "resource",
+					"id": "action-identify-research",
+					"path": "assets/actions/identify-research.md",
+					"requires": [
+						"resource:config-template",
+						"resource:research-domains",
+						"resource:research-policy",
+						"resource:research-template",
+						"script:research-state"
+					]
+				},
+				{
+					"kind": "resource",
+					"id": "action-literature-review",
+					"path": "assets/actions/literature-review.md",
+					"requires": ["resource:research-policy", "script:research-state", "script:verify-citations"]
+				},
+				{
+					"kind": "resource",
+					"id": "action-pause-research",
+					"path": "assets/actions/pause-research.md",
+					"requires": ["resource:research-policy", "script:research-state"]
+				},
+				{
+					"kind": "resource",
+					"id": "action-progress",
+					"path": "assets/actions/progress.md",
+					"requires": ["resource:research-policy"]
+				},
+				{
+					"kind": "resource",
+					"id": "action-remove-task",
+					"path": "assets/actions/remove-task.md",
+					"requires": ["resource:research-policy", "script:research-state"]
+				},
+				{
+					"kind": "resource",
+					"id": "action-resume-research",
+					"path": "assets/actions/resume-research.md",
+					"requires": ["resource:research-policy", "script:research-state"]
+				},
+				{
+					"kind": "resource",
+					"id": "action-settings",
+					"path": "assets/actions/settings.md",
+					"requires": ["resource:research-policy", "script:research-state"]
+				},
+				{
+					"kind": "resource",
+					"id": "action-status",
+					"path": "assets/actions/status.md",
+					"requires": ["resource:research-policy"]
+				},
+				{
+					"kind": "resource",
+					"id": "action-upload-data",
+					"path": "assets/actions/upload-data.md",
+					"requires": ["resource:research-policy", "script:research-state"]
+				},
+				{
+					"kind": "resource",
+					"id": "action-wtfp",
+					"path": "assets/actions/wtfp.md",
+					"requires": ["resource:research-policy"]
+				},
+				{
+					"kind": "skill",
+					"id": "lab-definer",
+					"path": "skills/materio-lab-definer/SKILL.md",
+					"requires": [
+						"resource:action-define-virtual-lab",
+						"resource:research-domains",
+						"resource:research-policy",
+						"resource:virtual-lab-template"
+					]
+				},
+				{
+					"kind": "skill",
+					"id": "literature-reviewer",
+					"path": "skills/materio-literature-reviewer/SKILL.md",
+					"requires": [
+						"resource:action-literature-review",
+						"resource:research-domains",
+						"resource:research-policy",
+						"resource:research-template"
+					]
+				},
+				{
+					"kind": "skill",
+					"id": "research-explorer",
+					"path": "skills/materio-research-explorer/SKILL.md",
+					"requires": [
+						"resource:action-add-task",
+						"resource:action-archive-task",
+						"resource:action-checkpoint",
+						"resource:action-help",
+						"resource:action-identify-research",
+						"resource:action-pause-research",
+						"resource:action-progress",
+						"resource:action-remove-task",
+						"resource:action-resume-research",
+						"resource:action-settings",
+						"resource:action-status",
+						"resource:action-upload-data",
+						"resource:action-wtfp",
+						"resource:config-template",
+						"resource:research-domains",
+						"resource:research-policy",
+						"resource:research-template"
+					]
+				},
+				{
+					"kind": "skill",
+					"id": "task-executor",
+					"path": "skills/materio-task-executor/SKILL.md",
+					"requires": [
+						"resource:action-execute-task",
+						"resource:research-domains",
+						"resource:research-policy",
+						"resource:traditional-workflows",
+						"resource:virtual-lab-template",
+						"resource:workflow-template"
+					]
+				},
+				{
+					"kind": "skill",
+					"id": "task-verifier",
+					"path": "skills/materio-task-verifier/SKILL.md",
+					"requires": [
+						"resource:action-execute-task",
+						"resource:research-policy",
+						"resource:research-template",
+						"resource:workflow-template"
+					]
+				},
+				{
+					"kind": "skill",
+					"id": "workflow-planner",
+					"path": "skills/materio-workflow-planner/SKILL.md",
+					"requires": [
+						"resource:action-define-research-tasks",
+						"resource:research-policy",
+						"resource:research-template",
+						"resource:traditional-workflows",
+						"resource:virtual-lab-template",
+						"resource:workflow-template"
+					]
+				},
+				{
+					"kind": "agent",
+					"id": "lab-definer",
+					"path": "ai.iowarp.clio/agents/materio-lab-definer.md",
+					"requires": ["skill:lab-definer"]
+				},
+				{
+					"kind": "agent",
+					"id": "literature-reviewer",
+					"path": "ai.iowarp.clio/agents/materio-literature-reviewer.md",
+					"requires": ["skill:literature-reviewer"]
+				},
+				{
+					"kind": "agent",
+					"id": "research-explorer",
+					"path": "ai.iowarp.clio/agents/materio-research-explorer.md",
+					"requires": ["skill:research-explorer"]
+				},
+				{
+					"kind": "agent",
+					"id": "task-executor",
+					"path": "ai.iowarp.clio/agents/materio-task-executor.md",
+					"requires": ["skill:task-executor"]
+				},
+				{
+					"kind": "agent",
+					"id": "task-verifier",
+					"path": "ai.iowarp.clio/agents/materio-task-verifier.md",
+					"requires": ["skill:task-verifier"]
+				},
+				{
+					"kind": "agent",
+					"id": "workflow-planner",
+					"path": "ai.iowarp.clio/agents/materio-workflow-planner.md",
+					"requires": ["skill:workflow-planner"]
+				},
+				{
+					"kind": "prompt",
+					"id": "add-task",
+					"path": "ai.iowarp.clio/prompts/materio/add-task.md",
+					"requires": ["resource:clio-execution", "script:research-state"]
+				},
+				{
+					"kind": "prompt",
+					"id": "archive-task",
+					"path": "ai.iowarp.clio/prompts/materio/archive-task.md",
+					"requires": ["resource:clio-execution", "script:research-state"]
+				},
+				{
+					"kind": "prompt",
+					"id": "checkpoint",
+					"path": "ai.iowarp.clio/prompts/materio/checkpoint.md",
+					"requires": ["resource:clio-execution", "resource:research-policy", "script:research-state"]
+				},
+				{
+					"kind": "prompt",
+					"id": "define-research-tasks",
+					"path": "ai.iowarp.clio/prompts/materio/define-research-tasks.md",
+					"requires": [
+						"agent:workflow-planner",
+						"resource:clio-execution",
+						"resource:traditional-workflows",
+						"resource:workflow-template",
+						"script:research-state"
+					]
+				},
+				{
+					"kind": "prompt",
+					"id": "define-virtual-lab",
+					"path": "ai.iowarp.clio/prompts/materio/define-virtual-lab.md",
+					"requires": [
+						"agent:lab-definer",
+						"resource:clio-execution",
+						"resource:research-domains",
+						"resource:virtual-lab-template",
+						"script:research-state"
+					]
+				},
+				{
+					"kind": "prompt",
+					"id": "execute-task",
+					"path": "ai.iowarp.clio/prompts/materio/execute-task.md",
+					"requires": [
+						"agent:task-executor",
+						"agent:task-verifier",
+						"resource:clio-execution",
+						"script:check-physics",
+						"script:check-scripts",
+						"script:research-state",
+						"script:verify-citations"
+					]
+				},
+				{
+					"kind": "prompt",
+					"id": "help",
+					"path": "ai.iowarp.clio/prompts/materio/help.md",
+					"requires": ["resource:clio-execution"]
+				},
+				{
+					"kind": "prompt",
+					"id": "identify-research",
+					"path": "ai.iowarp.clio/prompts/materio/identify-research.md",
+					"requires": [
+						"agent:research-explorer",
+						"resource:clio-execution",
+						"resource:config-template",
+						"resource:research-domains",
+						"resource:research-template",
+						"script:research-state"
+					]
+				},
+				{
+					"kind": "prompt",
+					"id": "literature-review",
+					"path": "ai.iowarp.clio/prompts/materio/literature-review.md",
+					"requires": [
+						"agent:literature-reviewer",
+						"resource:clio-execution",
+						"script:research-state",
+						"script:verify-citations"
+					]
+				},
+				{
+					"kind": "prompt",
+					"id": "pause-research",
+					"path": "ai.iowarp.clio/prompts/materio/pause-research.md",
+					"requires": ["resource:clio-execution", "script:research-state"]
+				},
+				{
+					"kind": "prompt",
+					"id": "progress",
+					"path": "ai.iowarp.clio/prompts/materio/progress.md",
+					"requires": ["resource:clio-execution"]
+				},
+				{
+					"kind": "prompt",
+					"id": "remove-task",
+					"path": "ai.iowarp.clio/prompts/materio/remove-task.md",
+					"requires": ["resource:clio-execution", "script:research-state"]
+				},
+				{
+					"kind": "prompt",
+					"id": "resume-research",
+					"path": "ai.iowarp.clio/prompts/materio/resume-research.md",
+					"requires": ["resource:clio-execution", "script:research-state"]
+				},
+				{
+					"kind": "prompt",
+					"id": "settings",
+					"path": "ai.iowarp.clio/prompts/materio/settings.md",
+					"requires": ["resource:clio-execution", "script:research-state"]
+				},
+				{
+					"kind": "prompt",
+					"id": "status",
+					"path": "ai.iowarp.clio/prompts/materio/status.md",
+					"requires": ["resource:clio-execution"]
+				},
+				{
+					"kind": "prompt",
+					"id": "upload-data",
+					"path": "ai.iowarp.clio/prompts/materio/upload-data.md",
+					"requires": ["resource:clio-execution", "script:research-state"]
+				},
+				{
+					"kind": "prompt",
+					"id": "wtfp",
+					"path": "ai.iowarp.clio/prompts/materio/wtfp.md",
+					"requires": ["resource:clio-execution", "resource:research-policy"]
+				},
+				{
+					"kind": "fleet",
+					"id": "execute-task",
+					"path": "ai.iowarp.clio/fleets/materio-execute-task.md",
+					"requires": ["agent:task-executor", "agent:task-verifier"]
+				},
+				{
+					"kind": "script",
+					"id": "project-plugin",
+					"path": "assets/scripts/project_plugin.py",
+					"requires": []
+				}
+			],
+			"evals": {
+				"scripts": "evals/scripts.yaml"
+			}
+		},
+		"ai.iowarp.portability": {
+			"version": 1,
+			"core": "Agent Plugins 1.0.0",
+			"skills": {
+				"count": 6,
+				"mode": "host-neutral instructions with shared local assets and complete action guides"
+			},
+			"clio": {
+				"prompts": 17,
+				"agents": 6,
+				"fleets": 1,
+				"mode": "native resource graph"
+			},
+			"codex": {
+				"mode": "standard portable skills; host conversation and available delegation",
+				"nativeFleet": false
+			},
+			"claude": {
+				"mode": "generated native skills, command guides and agents",
+				"nativeFleet": false
+			},
+			"gemini": {
+				"mode": "generated skills and TOML command guides; roles execute through available host capabilities",
+				"nativeFleet": false
+			},
+			"scripts": {
+				"runtime": "Python >=3.10; bash for shell syntax checks",
+				"network": "optional Crossref only when configured",
+				"mcp": false
+			},
+			"externalIntegrations": [
+				{
+					"name": "wtfp",
+					"actions": ["new-paper", "progress", "map-project", "create-outline"],
+					"required": false,
+					"writes": "handoff text only; receiver owns paper state"
+				}
+			]
+		}
+	}
+}

package/library/plugins/materio/skills/materio-lab-definer/SKILL.md

@@ -0,0 +1,74 @@
+---
+name: materio-lab-definer
+description: "Structure resource interviews into a feasibility map with gaps and alternatives."
+---
+
+Interview the researcher about actual experimental and computational resources, software licenses, collaborators, people, budget, and access constraints. Write .research/VIRTUAL-LAB.md with available resources and the resource-to-task feasibility mapping. Surface blocked methods and realistic alternatives for researcher review.
+
+Read the [shared research policy](../../assets/references/research-policy.md) for
+state, provenance, execution boundaries, and advisory validation.
+
+Read the linked references when needed. Resolve links from this skill directory.
+If acting as a worker, return questions to the orchestrator; when acting as the
+interactive assistant, collect the researcher answers directly using the host's
+conversation facility.
+
+- [research-domains.md](../../assets/references/research-domains.md)
+- [VIRTUAL-LAB.md](../../assets/templates/VIRTUAL-LAB.md)
+
+## Resource Maps Should Be Targeted, Not Exhaustive
+
+A materials science researcher working on CALPHAD modeling does not need SEM sample prep rows filled in. A synthetic chemist does not need LAMMPS. Read LITERATURE.md's methodological landscape to learn which tools the field uses, and prioritize those when judging what is missing.
+
+## Feasibility Is the Goal
+
+VIRTUAL-LAB.md is used downstream by the workflow-planner to assign only tasks that can actually be done. Every resource entry must carry enough detail for that decision:
+- "SEM available" is not enough → need: EDS capability? Max sample size? Booking lead time?
+- "HPC available" is not enough → need: Which software is installed? How many cores per job? Queue wait?
+
+When a detail is missing, write `unspecified` in the table and add the item to the follow-up list in your return. Do not invent specifications.
+
+## Always Flag Gaps
+
+Cross-reference available resources against what the literature says is commonly used. If a common method in the field is NOT available, flag it explicitly with alternatives:
+- "No VASP license → can use Quantum ESPRESSO (free) or request time on national facility"
+- "No TEM in-house → external facility available at [university] core lab (lead time: 2-3 weeks)"
+
+
+
+For each common method in the field that is NOT available:
+```
+GAP: [method]; commonly used in [domain] research
+  Not available: [reason]
+  Alternatives:
+    A. [open-source or free alternative]
+    B. [external facility, if known]
+    C. [collaboration route]
+  Impact: [how this limits the research scope]
+```
+
+If a gap makes the stated research prompt infeasible with every listed alternative, return `needs_input: checkpoint:decision` now: the researcher must decide before planning.
+
+## Step 4: Build Resource-to-Task Mapping
+
+Generate the mapping table that links resource types to workflow task types. This is what the workflow-planner reads.
+
+Common mappings:
+- SEM/TEM → characterization tasks (microstructure, composition)
+- XRD → structural characterization tasks
+- UTM/fatigue tester → mechanical testing tasks
+- VASP/QE on HPC → DFT calculation tasks
+- LAMMPS on HPC → MD simulation tasks
+- Thermo-Calc → CALPHAD/phase diagram tasks
+- Abaqus → FEM simulation tasks
+- Python + data files → data-analysis tasks
+- No experimental equipment → literature + computational tasks only
+
+
+
+## Complete action guides
+
+Read only the guide for the requested operation; it contains its interview and
+state transitions. Resolve these links from this skill directory.
+
+- [define-virtual-lab](../../assets/actions/define-virtual-lab.md)

package/library/plugins/materio/skills/materio-literature-reviewer/SKILL.md

@@ -0,0 +1,64 @@
+---
+name: materio-literature-reviewer
+description: "Review supplied materials and provided URLs with citation provenance and explicit gaps."
+---
+
+For a materials literature review, read the confirmed research question and supplied corpus, confirm scope, synthesize what is supported, and write .research/LITERATURE.md. Include a Key Papers table, Sources Reviewed with inspection depth, evidence limitations, justified gaps (possibly none), and proposed keyword changes. Let the researcher decide question/keyword revisions and citation findings.
+
+Read the [shared research policy](../../assets/references/research-policy.md) for
+state, provenance, execution boundaries, and advisory validation.
+
+Read the linked references when needed. Resolve links from this skill directory.
+If acting as a worker, return questions to the orchestrator; when acting as the
+interactive assistant, collect the researcher answers directly using the host's
+conversation facility.
+
+- [research-domains.md](../../assets/references/research-domains.md)
+- [RESEARCH.md](../../assets/templates/RESEARCH.md)
+
+## What a Good Literature Review Produces
+
+1. **Knowledge map**; What is currently known, organized by sub-topic
+2. **Methodological landscape**; What approaches exist, their strengths and limits
+3. **Genuine gaps**; What remains unknown or contested, with justification
+4. **Keyword refinement**; More precise terms than the initial set
+5. **Key references**; Landmark papers and recent work (last 5 years)
+6. **Loop-back signal**; Whether the research prompt needs adjustment
+
+## Supplied Materials Come First
+
+Papers, BibTeX files, and notes the researcher registered under `.research/data/` are the primary corpus. They anchor the review in the group's actual reading; record unsupported formats honestly. Researcher-provided URLs can extend that corpus when allowed. If `<web_allowed>` is false or the web tools are unavailable, review the supplied materials only and say so plainly in Review Notes. A review built from supplied materials alone is complete and honest; a review padded with invented papers is neither.
+
+## Citation Integrity
+
+Only list papers you actually read (supplied) or actually found (web) and are confident are real. Put each paper title in "quotes" in the Key Papers table and include a DOI when you have one, so the orchestrator can machine-verify the list against Crossref. If you are unsure a specific paper exists or only vaguely recall it, do not invent bibliographic details: omit it, or mark it `[topic; unverified, ~YEAR]` and note it under Review Notes. Flagged entries are shown to the researcher for a decision; they are not silently removed.
+
+## Gap Quality
+
+A genuine research gap is:
+- **Specific**: "The fatigue behavior of HEAs at cryogenic temperatures" not "more research is needed"
+- **Justified**: Supported by absence of papers or explicit statements in existing literature
+- **Feasible**: Something the researcher's prompt could actually address
+
+Not a gap: "Nobody has studied exactly this material system" (often because it's not interesting)
+
+## Loop-Back Conditions
+
+Signal `loop_back:` if:
+- The prompt is already fully answered (>3 recent papers directly address it)
+- The prompt is so broad it spans multiple review articles without a clear angle
+- The prompt contains a false premise (assumed mechanism doesn't exist)
+
+Read supplied files and the data index first. Fetch only researcher-provided URLs
+when project policy and the available host retrieval capability permit it. Record
+actual inspection depth, failed/unreadable sources, and coverage. Metadata alone
+is not full-text inspection, and a restricted corpus does not establish global
+absence. Ask for usable text if an unreadable paper blocks the research.
+
+
+## Complete action guides
+
+Read only the guide for the requested operation; it contains its interview and
+state transitions. Resolve these links from this skill directory.
+
+- [literature-review](../../assets/actions/literature-review.md)