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iowarp/clio-kit

iowarp/clio-kit · 28 stars · 72 plugins

Marketplace

Install

In Claude Code
/plugin marketplace add iowarp/clio-kit

Run inside Claude Code, then install plugins from it. Check the repo's README before you run it.

Open the repo

Plugins 72

After adding the marketplace, install one with /plugin install <name>@clio-kit.

  1. 1clio-adiosFetch and analyze BP5 data files using ADIOS2. Access scientific data, metadata, and attributes for research and analysis purposes./plugin install clio-adios@clio-kitv2.2.5scientific
  2. 2clio-arxivSearch arXiv by topic, author, title or date, read paper details, and export BibTeX or PDFs./plugin install clio-arxiv@clio-kitv2.2.5scientific
  3. 3clio-chronologRecord and retrieve agent interactions in a ChronoLog log store./plugin install clio-chronolog@clio-kitv2.0.3scientific
  4. 4clio-compressionCompress and decompress files with gzip and report the compression ratio./plugin install clio-compression@clio-kitv2.2.5general
  5. 5clio-darshanDarshan I/O profiler MCP server for analyzing I/O trace files/plugin install clio-darshan@clio-kitv2.2.5scientific
  6. 6clio-geoMCP server for rendering GeoJSON vector layers into map images with basemaps/plugin install clio-geo@clio-kitv2.3.1scientific
  7. 7clio-hdf5Open HDF5 files, browse groups, inspect datasets and attributes, and read or summarize data in chunks./plugin install clio-hdf5@clio-kitv2.2.6scientific
  8. 8clio-jarvisJARVIS-CD MCP with a compact user pipeline contract and explicit admin compatibility profiles/plugin install clio-jarvis@clio-kitv3.7.4scientific
  9. 9clio-lmodList, search and inspect Lmod environment modules, and save or restore module collections./plugin install clio-lmod@clio-kitv3.0.1scientific
  10. 10clio-ndpNational Data Platform (NDP) MCP server for searching and discovering datasets across multiple CKAN instances/plugin install clio-ndp@clio-kitv2.2.5scientific
  11. 11clio-node-hardwareReport CPU, memory, disk, network, GPU and process information for local or remote nodes./plugin install clio-node-hardware@clio-kitv2.3.0scientific
  12. 12clio-pandasLoad tabular data, then clean, filter, group, merge and summarize it with pandas./plugin install clio-pandas@clio-kitv2.3.0scientific
  13. 13clio-parallel-sortSort, filter and summarize large log files by timestamp, level or keyword./plugin install clio-parallel-sort@clio-kitv2.3.0scientific
  14. 14clio-paraviewVisualize simulation results in ParaView: load fields, then slice, contour, color and render them./plugin install clio-paraview@clio-kitv2.2.5scientific
  15. 15clio-parquetSummarize Parquet files, preview columns, read row slices and aggregate values./plugin install clio-parquet@clio-kitv2.2.5scientific
  16. 16clio-plotDraw line, bar, scatter, histogram, heatmap and time-series plots from tabular data./plugin install clio-plot@clio-kitv2.2.5scientific
  17. 17clio-scientific-catalogOperator-owned scientific dataset discovery for remote agents/plugin install clio-scientific-catalog@clio-kitv1.1.4scientific
  18. 18clio-seismologyMCP server for analyzing SAC seismic-waveform files and TAR archives: inspect members, compute per-trace statistics, and plot traces/plugin install clio-seismology@clio-kitv2.3.1scientific
  19. 19clio-slurmSubmit, list, inspect and cancel Slurm jobs, and describe the cluster./plugin install clio-slurm@clio-kitv3.0.2scientific
  20. 20clio-spackStructured Spack discovery and installation tools for scientific agents/plugin install clio-spack@clio-kitv2.3.1scientific
  21. 21clio-terrainMCP server for terrain analysis: DEM slope/aspect/suitability and point-cloud reading/gridding/plugin install clio-terrain@clio-kitv2.2.5scientific
  22. 22clio-webProvider-fixed web search plus transparent URL, DOI, and document fetching/plugin install clio-web@clio-kitv2.1.3general
  23. 23clio-hpc-skillsSkills for the clio-hpc workflow: install a code, wrap it in a pipeline, submit it, and follow it on a cluster./plugin install clio-hpc-skills@clio-kitv1.0.2skills
  24. 24clio-hpcInstall a code, wrap it in a pipeline, submit it, and follow it on a cluster./plugin install clio-hpc@clio-kitv1.0.2workflow
  25. 25clio-performance-skillsSkills for the clio-performance workflow: work out why a finished job was slower than it should have been./plugin install clio-performance-skills@clio-kitv1.0.3skills
  26. 26clio-performanceWork out why a finished job was slower than it should have been./plugin install clio-performance@clio-kitv1.0.3workflow
  27. 27clio-scientific-io-skillsSkills for the clio-scientific-io workflow: open a scientific data file, see its structure, and read part of it./plugin install clio-scientific-io-skills@clio-kitv1.0.6skills
  28. 28clio-scientific-ioOpen a scientific data file, see its structure, and read part of it./plugin install clio-scientific-io@clio-kitv1.0.6workflow
  29. 29clio-analysis-skillsSkills for the clio-analysis workflow: turn a dataset into summary statistics and a figure./plugin install clio-analysis-skills@clio-kitv1.0.7skills
  30. 30clio-analysisTurn a dataset into summary statistics and a figure./plugin install clio-analysis@clio-kitv1.0.7workflow
  31. 31clio-geoscience-skillsSkills for the clio-geoscience workflow: inspect and map geospatial features, terrain models, and waveform archives./plugin install clio-geoscience-skills@clio-kitv1.0.2skills
  32. 32clio-geoscienceInspect and map geospatial features, terrain models, and waveform archives./plugin install clio-geoscience@clio-kitv1.0.2workflow
  33. 33clio-research-skillsSkills for the clio-research workflow: find papers on a topic and the datasets behind them./plugin install clio-research-skills@clio-kitv1.0.4skills
  34. 34clio-researchFind papers on a topic and the datasets behind them./plugin install clio-research@clio-kitv1.0.4workflow
  35. 35clio-skillsSkills for primary scientific workflows, without MCP servers./plugin install clio-skills@clio-kitv1.0.0skills
  36. 36clio-agentsScientific workflow planning and independent evidence review agents./plugin install clio-agents@clio-kitv1.0.2agents
  37. 37clio-coder-skillsOptional Clio Coder coding and research skills, including Materio procedures. Native Clio agents and fleets require Clio Coder./plugin install clio-coder-skills@clio-kitv1.1.2skills
  38. 38archifyValidated interactive system maps and diagrams as standalone HTML from a typed JSON spec, for one of five diagram types (architecture, workflow, sequence, dataflow, lifecycle). Use when the user asks to visualize architecture, a workflow, a call sequence, a data pipeline, or a state machine, or to map this repository. Not for ad hoc drawings or slide art, and not for Mermaid output; use the artifact tool for plain Markdown./plugin install archify@clio-kitv0.1.0planning
  39. 39architectureDecides the engineering approach for an intent in an interactive session: investigates, proposes two or three genuinely different approaches with trade-offs, recommends, lets the user decide, and writes the decision doc. Not a task-by-task plan; use cut-it. Not a multi-perspective debate; use design-council. Not product intent; use product-intent. Not a typed implementation handoff; use tech-spec./plugin install architecture@clio-kitv0.4.1planning
  40. 40arxiv-literatureSearches arXiv, summarizes or compares papers, and builds a compact literature survey as citation-ready, source-linked paper cards. Prefer the Researcher shadow agent for noisy multi-paper retrieval./plugin install arxiv-literature@clio-kitv0.5.1research
  41. 41ast-grepStructural code search with ast-grep rules: finds code by shape when grep on text is too noisy, and never rewrites it. Not for plain string or filename lookups; use grep or find./plugin install ast-grep@clio-kitv0.3.0coding
  42. 42backlogTurns a finished PRD or architecture doc into a ticket backlog of small stories with verifiable acceptance criteria, confirmed, then created as GitHub issues or in another configured tracker. Not for local sprint slicing into a SPRINT.md; use cut-it./plugin install backlog@clio-kitv0.4.1planning
  43. 43branch-closeoutProves merged work on the canonical base, inspects and removes associated worktrees through Git, deletes local branches safely, and audits surviving repository refs. Not for creating worktrees; use worktree-create. Not for integrating branches; use worktree-merge./plugin install branch-closeout@clio-kitv0.1.0git
  44. 44clio-coder-devGoverns changes to Clio Coder's own source and harness (TUI, skills, agents, tools, prompts, domains): what may change freely, what needs explicit user intent, and how to change it without breaking the architecture. Not for verifying a change against the harness; use clio-coder-test./plugin install clio-coder-dev@clio-kitv0.4.0meta
  45. 45clio-coder-testVerifies a Clio Coder source change against the current contract, smoke, boundary, and application test lanes, including temporary-state and local-provider harnesses. Not for deciding what may change; use clio-coder-dev./plugin install clio-coder-test@clio-kitv0.3.1meta
  46. 46coding-standardsCorrect-by-construction TypeScript rules (errors as values, parse don't validate, illegal states unrepresentable, deep modules) for writing or refactoring TypeScript when the project has not pinned its own standards./plugin install coding-standards@clio-kitv0.4.0coding
  47. 47context-handoffWrites a durable, redacted, reference-not-copy handoff document when a session winds down or context is about to be compacted or lost, so the next session or agent can continue. Not for orienting at the start of a session; use context-prime./plugin install context-handoff@clio-kitv0.5.1context
  48. 48context-primeOrients a fresh session in a repository by loading the last handoff, git state, the project constitution, and active-work signals before acting. Not for writing the handoff; use context-handoff./plugin install context-prime@clio-kitv0.4.1context
  49. 49credentialsHandles API keys, tokens, and facility credentials (kerberos tickets, globus and scheduler tokens, ssh agents, netrc) before a tool needs one, after an auth error, when a new secret is supplied, or when one may have leaked. Not for provider target configuration; use clio-coder auth and target settings./plugin install credentials@clio-kitv0.2.0meta
  50. 50cut-itSlices an existing plan, PRD, or milestone into an executable sprint of dependency-ordered vertical slices sized for one agent run each, with done-when verification per slice; never fabricates a plan. Not for deciding the approach; use architecture./plugin install cut-it@clio-kitv0.4.1workflow
  51. 51design-councilConvenes several expert perspectives that challenge each other on a design decision with real trade-offs before code is written; quick mode runs a single round. Not for a one-question-at-a-time interrogation of a plan; use grill-me. Not for splitting implementation across workers; use dispatch directly./plugin install design-council@clio-kitv0.6.0workflow
  52. 52experiment-protocolPre-registers a performance study, numerical comparison, parameter sweep, or benchmark: thresholds, tolerances, environment pins, and verdict conditions locked into the validation contract before any measurement. Not for diagnosing a stalled bug; use scientific-debugging./plugin install experiment-protocol@clio-kitv0.3.1research
  53. 53file-ticketTurns something noticed mid-session into a tracker issue: captures evidence, dedups against existing issues, composes a labeled issue with acceptance criteria, confirms, and creates it via gh. Not for batch ticket creation from a PRD; use backlog. Not for diagnosing an existing issue; use fix-issue./plugin install file-ticket@clio-kitv0.3.0git
  54. 54find-skillsFinds published skills and prepares their Library installation for the operator when the user asks whether a capability exists as a skill. Not for authoring a new skill; use skill-craft./plugin install find-skills@clio-kitv0.2.1meta
  55. 55fix-issueResolves a tracker issue end to end: fetches it, diagnoses only when the issue does not name the code, fixes test-first, and self-reviews against the acceptance criteria, leaving a verified uncommitted change. Not for filing; use file-ticket. Not for committing or PRs; use ship./plugin install fix-issue@clio-kitv0.3.0git
  56. 56grill-meStress-tests a plan, design, or idea through a phased one-question-at-a-time interview before code is written, ending in a compact decision log. Not for a multi-perspective debate; use design-council./plugin install grill-me@clio-kitv0.5.1workflow
  57. 57herdrLaunches, drives, or inspects another agent or command in a Herdr pane, tab, or workspace, including a second Clio Coder instance; requires HERDR_ENV=1. Not for background work a plain shell or dispatch already covers./plugin install herdr@clio-kitv0.2.0meta
  58. 58materioMaterio: materials research interviews, supplied-corpus synthesis, lab feasibility, task execution and verified paper handoff./plugin install materio@clio-kitv0.1.0
  59. 59prdTurns an idea into a product requirements document through a phase-gated interview, ending in PRD.md plus per-milestone prompt files ready to drive a coding agent. Not for the problem-first product thesis; use product-intent./plugin install prd@clio-kitv0.4.1planning
  60. 60product-intentWrites a problem-first product document for a greenfield effort: interviews for the problem, evidence, and a falsifiable hypothesis, with zero engineering decisions. Not for engineering decisions; use architecture. Not for turning a locked idea into milestone build prompts; use prd./plugin install product-intent@clio-kitv0.4.1planning
  61. 61prototypeAnswers a design question with throwaway code: a clearly marked, runnable, no-persistence prototype whose verdict is kept and whose code is discarded. Not for pre-registered performance experiments; use experiment-protocol. Not for production implementation./plugin install prototype@clio-kitv0.4.0coding
  62. 62resolve-merge-conflictsResolves a merge, rebase, or cherry-pick stopped on conflicts by reconstructing both sides' intent, validating with the project's own checks, and completing the operation. Not for integrating many branches; use worktree-merge./plugin install resolve-merge-conflicts@clio-kitv0.4.0git
  63. 63scientific-debuggingDiagnoses stalled or cross-system failures and wrong, NaN, nondeterministic, or unexpectedly slow scientific results through falsifiable hypotheses across distinct fault classes, with evidence-cited verdicts before any fix. Not for designing benchmarks or pre-registered experiments; use experiment-protocol./plugin install scientific-debugging@clio-kitv0.3.1research
  64. 64scientific-modernizationModernizes, ports, rewrites, packages, or replaces established scientific software in independently validated stages against an external scientific oracle, settling compatibility and upstream stewardship before calling it complete. Not for an isolated benchmark; use experiment-protocol. Not for diagnosing wrong results; use scientific-debugging./plugin install scientific-modernization@clio-kitv0.4.1research
  65. 65shipShips finished work: writes one reviewed atomic commit, keeps maintainer branches local, or pushes a contributor branch to their fork and opens a PR only on explicit intent. Not for producing the change; use fix-issue./plugin install ship@clio-kitv0.5.0git
  66. 66skill-craftWrites, reviews, or prunes a SKILL.md, judging whether its description, body, and length earn their cost. Not for packaging a workflow that just happened; use workflow-distiller./plugin install skill-craft@clio-kitv0.3.1meta
  67. 67tddBuilds a feature or fix test-first, red to green at pre-agreed public seams, one vertical slice at a time. Not for designing benchmark criteria; use experiment-protocol./plugin install tdd@clio-kitv0.4.0coding
  68. 68tech-specWrites a typed call-stack architecture handoff: code-shaped contracts plus execution flows, implementation-ready for another engineer. User-invoked only. Not for weighing approaches or deciding the design; use architecture first./plugin install tech-spec@clio-kitv0.3.1planning
  69. 69workflow-distillerPackages a workflow that just happened into a reusable SKILL.md: reconstructs it from the session record, checks overlap with installed skills, gates on approval, then writes it following skill-craft. Not for authoring a skill with no prior workflow; use skill-craft./plugin install workflow-distiller@clio-kitv0.4.2workflow
  70. 70worktree-createStands up one or more git worktrees for parallel work, each on its own branch with gitignored config copied in, dependencies installed, and a verified health check. Not for merging finished worktrees; use worktree-merge. Not for closeout; use branch-closeout./plugin install worktree-create@clio-kitv0.6.0git
  71. 71worktree-mergeIntegrates finished worktree branches through one throwaway integration branch, testing after each merge and running the full suite before the main line moves, with exact rollback on failure. Not for creating worktrees; use worktree-create. Not for closeout; use branch-closeout./plugin install worktree-merge@clio-kitv0.6.0git
  72. 72clio-dataset-reportTurn a small HDF5 dataset into a report with a CSV, figure, checked statistics and evidence review./plugin install clio-dataset-report@clio-kitv1.0.0workflow

Files

README.md

CLIO Kit

License: BSD-3-Clause PyPI version Python FastMCP CI Coverage

MCP Servers Ruff Type Checked Package Manager Security Audit

CLIO Kit is the IoWarp meta-marketplace for scientific computing. It brings together MCP servers, workflow skills, plugins, agent definitions, and community contributions—including plugins from external marketplaces—and enables AI agents to interact with HPC resources, scientific data formats, and research datasets.

Choose individual MCPs, skills, agents and hooks—or a plugin that bundles what your workflow needs. A plugin can include any of these components; it does not need all four.

Website | IOWarp

Documentation · For agents: read here.

Chat with us on Zulip or join us

Developed by GRC Logo Gnosis Research Center

❌ Without CLIO Kit

Working with scientific data and HPC resources requires manual scripting and tool-specific knowledge:

  • ❌ Write custom scripts for every HDF5/Parquet file exploration
  • ❌ Manually craft Slurm job submission scripts
  • ❌ Switch between multiple tools for data analysis
  • ❌ No AI assistance for scientific workflows
  • ❌ Repetitive coding for common research tasks

✅ With CLIO Kit

Install workflow bundles, use skills to guide your agent, and discover community tools:

  • ✅ "Analyze the temperature dataset in this HDF5 file" - HDF5 MCP does it
  • ✅ "Submit this simulation to Slurm with 32 cores" - Slurm MCP handles it
  • ✅ "Find papers on neural networks from ArXiv" - ArXiv MCP searches
  • ✅ "Plot the results from this CSV file" - Plot MCP visualizes
  • ✅ "Optimize memory usage for this pandas DataFrame" - Pandas MCP optimizes
  • ✅ Workflow guidance - Skills explain tool sequences; optional agents help plan and review results
  • ✅ Community contributions - Discover external plugins and marketplace collections

MCP servers · Skills · Plugins · Agents · Hooks · Community marketplaces

CLIO Kit is part of the IoWarp platform's tooling ecosystem for AI agents. Its meta-marketplace brings tools and reusable workflows together for scientific computing—from exploring HDF5 datasets and managing Slurm jobs to analyzing results and finding research papers. Built by researchers, for researchers, at Illinois Institute of Technology with NSF support.

Part of IoWarp Platform: CLIO Kit is the platform's meta-marketplace and tooling layer, bringing together MCP servers, skills, workflow plugins, agent definitions, and community marketplace collections.

One launcher for MCP servers. Individual components or workflow bundles. BSD-3-Clause licensed, with automated checks and real installation, MCP, and HPC workflow tests. See the validation guide for tested coverage and environment requirements.

🚀 Quick Installation

git clone https://github.com/iowarp/clio-kit.git
cd clio-kit

Recommended: Ask your agent:

Read setup.md and set up CLIO Kit for me.

Manual setup: Install this checkout's launcher, then choose an option below. For the no-clone release route (2.11.0 or newer), see selective installation.

uv tool install --force --reinstall --editable ".[verification]"

Claude Code

Install a workflow plugin (bundle) with its MCP servers and skills:

claude plugin marketplace add "$PWD"
claude plugin install clio-hpc@clio-kit
claude mcp list

Restart Claude Code after installation and confirm the servers connect. First launches download dependencies; see startup recovery if a server exceeds the client's connection timeout.

Or install an individual MCP or a skill collection:

claude plugin install clio-hdf5@clio-kit                  # HDF5 server
claude plugin install clio-scientific-io-skills@clio-kit  # Scientific I/O skills

Claude Code uses plugin install for component packages too. CLIO Kit lists those separately from workflow plugins; see components and plugins.

Codex and Other Agents

Install a workflow's skills and MCP configuration together:

clio-kit plugin install clio-scientific-io --client codex --project /path/to/project

Also supports opencode, cursor, antigravity, vscode and claude-code. This sets up project components; native agents and hooks need client-specific adapters. See client installation and limits.

Install a bundle or one skill into your project:

# Bundle
clio-kit skill install --bundle clio-scientific-io --target /path/to/project/.agents/skills
# Individual skill
clio-kit skill install dataset-explore --target /path/to/project/.agents/skills

Configure the required MCP servers using setup.md. Use your agent’s supported skill directory.

Install Skills with npm

Requires Node.js 22.20.0+. From your working project:

# All skills
npx skills@1.5.25 add /path/to/clio-kit --skill '*' --agent codex --copy
# Individual skill
npx skills@1.5.25 add /path/to/clio-kit --skill dataset-explore --agent codex --copy

Replace codex with claude-code or antigravity. MCP servers require separate configuration.

Choose either the Python or npm installer for each skill. See the skills CLI guide for selecting skills, updates and removal.

One Command for Any Server

# From the CLIO Kit checkout, install the CLI in a persistent tool environment
uv tool install --force --reinstall --editable .
# If uv's executable directory is not on PATH:
uv tool update-shell

# List all 22 available MCP servers
clio-kit mcp-servers

# Run an individual server
clio-kit mcp-server hdf5
clio-kit mcp-server pandas
clio-kit mcp-server slurm

Once 2.11.0 is published, install it with uv tool install 'clio-kit>=2.11.0' (2.11.0 or newer; earlier releases lack the skill, plugin and doctor commands). uv tool install creates a persistent, isolated environment; use uvx --from 'clio-kit>=2.11.0' clio-kit ... for a temporary, one-shot invocation.

The release separates the small launcher from component downloads: one MCP fetches only that server, one skill fetches only its files, and a workflow selects its components. Server dependencies stay isolated and locked. See selective installation for release, checkout and native plugin routes. The --branch option is for development, not an immutable release installation.

The wheel also includes machine-readable tool contracts for JARVIS, Slurm, Spack and Scientific Catalog, with SHA-256 digests for downstream verification:

clio-kit mcp-contracts
clio-kit mcp-contract clio-kit-jarvis-user-v3.7.2
clio-kit mcp-contract clio-kit-slurm-user-v3
clio-kit mcp-contract clio-kit-spack-user-v2.3
clio-kit mcp-contract clio-kit-scientific-catalog-user-v1.1

Workflow Bundles

These are broad workflow plugins. Each combines its MCP servers and skills.

Bundle Purpose MCP servers
clio-hpc Build software and run cluster jobs spack, lmod, jarvis, slurm, node-hardware
clio-performance Diagnose slow jobs and inspect logs darshan, chronolog, parallel-sort
clio-scientific-io Explore scientific data files hdf5, adios, parquet, compression
clio-analysis Analyze results and create figures pandas, plot, paraview
clio-geoscience Work with maps, terrain and waveforms geo, terrain, seismology
clio-research Find papers and datasets arxiv, ndp, scientific-catalog, web

Some servers require additional system software. See setup and prerequisites. See plugin composition for primary bundles and task plugins that combine components across them.

For a complete dataset-report workflow—HDF5, Pandas, Plot, a skill, evidence review and a verification hook:

claude plugin install clio-dataset-report@clio-kit

See dataset reports for inputs and verification limits.

Skills and Agents

Skills provide workflow instructions and guidance for interpreting results. Claude Code users can install skills or agent definitions separately:

claude plugin install clio-skills@clio-kit
claude plugin install clio-agents@clio-kit

The shared installer supports Codex, Claude Code, OpenCode, Cursor, Antigravity and VS Code. Codex, Claude Code and OpenCode also have adapters for the scientific agents and Dataset Report hooks. See client support.

Add the optional Clio Coder coding and research skills, including Materio procedures:

clio-kit skill install --bundle clio-coder --target .agents/skills
# Or through Claude Code:
claude plugin install clio-coder-skills@clio-kit

Individual skills also work: clio-kit skill install clio-kit-scientific-debugging --target .agents/skills. Adapted Clio Coder skills use the clio-kit- prefix to distinguish them from upstream originals. See Clio Coder integration for upstream packages and native plugin support.

Contribute Servers, Skills or Plugins

Contribute a package folder under plugins/, skills/, agents/ or hooks/; website builds and CI update the catalogues automatically. See the folder contribution guide.

Add skills here, or list a plugin maintained in your own repository:

clio-kit plugin init my-plugin
clio-kit plugin validate my-plugin
clio-kit plugin submit my-plugin --repo owner/name

submit generates a community entry for a pull request. External servers can use any language; servers hosted inside CLIO currently support Python, Node.js and Go.

Add an optional Claude Code hook with clio-kit plugin init my-plugin --hook. See the hook guide.

See the contribution guide and community guide for requirements and submission details.

Install in Cursor

Add to .cursor/mcp.json in your project, or ~/.cursor/mcp.json:

{
  "mcpServers": {
    "clio-hdf5": { "command": "clio-kit", "args": ["mcp-server", "hdf5"] },
    "clio-adios": { "command": "clio-kit", "args": ["mcp-server", "adios"] },
    "clio-parquet": { "command": "clio-kit", "args": ["mcp-server", "parquet"] },
    "clio-compression": { "command": "clio-kit", "args": ["mcp-server", "compression"] }
  }
}

Install the workflow skills from your project:

clio-kit skill install --bundle clio-scientific-io --target .cursor/skills

See Cursor MCP docs and skills docs.

Install in Claude Code

From the CLIO Kit checkout, install the workflow plugin with its MCPs and skills:

claude plugin marketplace add "$PWD"
claude plugin install clio-scientific-io@clio-kit
claude mcp list

Skills-only and agent plugins:

claude plugin install clio-skills@clio-kit    # scientific workflow skills, no MCP servers
claude plugin install clio-agents@clio-kit    # workflow planner and evidence reviewer

See setup.md for details.

Install in VS Code

Add to .vscode/mcp.json for GitHub Copilot:

{
  "servers": {
    "clio-hdf5": { "type": "stdio", "command": "clio-kit", "args": ["mcp-server", "hdf5"] },
    "clio-adios": { "type": "stdio", "command": "clio-kit", "args": ["mcp-server", "adios"] },
    "clio-parquet": { "type": "stdio", "command": "clio-kit", "args": ["mcp-server", "parquet"] },
    "clio-compression": { "type": "stdio", "command": "clio-kit", "args": ["mcp-server", "compression"] }
  }
}

Install the workflow skills from your project:

clio-kit skill install --bundle clio-scientific-io --target .github/skills

Start the servers with MCP: List Servers. The Codex extension uses the Codex configuration below. See VS Code MCP docs and skills docs.

Install in Claude Desktop

Edit claude_desktop_config.json through Settings → Developer → Edit Config:

{
  "mcpServers": {
    "clio-hdf5": { "command": "clio-kit", "args": ["mcp-server", "hdf5"] },
    "clio-adios": { "command": "clio-kit", "args": ["mcp-server", "adios"] },
    "clio-parquet": { "command": "clio-kit", "args": ["mcp-server", "parquet"] },
    "clio-compression": { "command": "clio-kit", "args": ["mcp-server", "compression"] }
  }
}

Restart Claude Desktop. This config adds MCP servers only; CLIO's native skill and agent plugins target Claude Code. See Claude Desktop MCP docs.

Install in Codex

Add the MCP servers for Codex CLI or its IDE extension:

codex mcp add clio-hdf5 -- clio-kit mcp-server hdf5
codex mcp add clio-adios -- clio-kit mcp-server adios
codex mcp add clio-parquet -- clio-kit mcp-server parquet
codex mcp add clio-compression -- clio-kit mcp-server compression
codex mcp list

Install the workflow skills from your project:

clio-kit skill install --bundle clio-scientific-io --target .agents/skills

Check /mcp and /skills in Codex. To install a complete supported workflow, use clio-kit plugin install clio-dataset-report --client codex --project .; review its hooks with /hooks before running it. See Codex MCP docs and skills docs.

Install in Antigravity

Open MCP Servers → Manage MCP Servers → View raw config and add:

{
  "mcpServers": {
    "clio-hdf5": { "command": "clio-kit", "args": ["mcp-server", "hdf5"] },
    "clio-adios": { "command": "clio-kit", "args": ["mcp-server", "adios"] },
    "clio-parquet": { "command": "clio-kit", "args": ["mcp-server", "parquet"] },
    "clio-compression": { "command": "clio-kit", "args": ["mcp-server", "compression"] }
  }
}

Install the workflow skills from your project:

clio-kit skill install --bundle clio-scientific-io --target .agents/skills

Reload the MCP configuration. For Antigravity CLI, start the first session from this project with agy --new-project so its local skills and MCP configuration are loaded. Reopen it with agy --project <project-name-or-id>. Reuse .agents/skills if already installed for Codex. CLIO does not yet ship a native Antigravity plugin. See Antigravity MCP docs and skills docs.

Available Packages

The version below identifies each MCP server's contract and runtime release, independently of the containing clio-kit wheel version. JARVIS 3.7 and SLURM 3.0 have contracts redesigned for agent use. Spack is at 2.3, while the other contracts retain their existing 2.x identities until a focused upgrade.

The Spack install contract makes concretization explicit: reuse=true passes spack install --reuse, while reuse=false passes spack install --fresh. Agents should discover first, install only when needed, then pass the exact spack_locate result to JARVIS for runtime loading. A find with no installed match is normal typed data (count=0, packages=[]); locate reports the distinct not_installed semantic, while real Spack failures remain errors.

📦 Package 📌 Ver 🔧 System 📋 Description ⚡ Install Command
adios 2.2.5 Data I/O Read data using ADIOS2 engine clio-kit mcp-server adios
arxiv 2.2.5 Research Fetch research papers from ArXiv clio-kit mcp-server arxiv
chronolog 2.0.3 Logging Log and retrieve data from ChronoLog clio-kit mcp-server chronolog
compression 2.2.5 Utilities File compression with gzip clio-kit mcp-server compression
darshan 2.2.5 Performance I/O performance trace analysis clio-kit mcp-server darshan
geo 2.3.1 Geospatial Render GeoJSON vector layers with basemaps clio-kit mcp-server geo
hdf5 2.2.6 Data I/O HPC-optimized scientific data with 27 tools, AI insights, caching, streaming clio-kit mcp-server hdf5
jarvis 3.7.4 Workflow Durable pipeline, bounded package discovery, progress, artifact, and service-runtime management clio-kit mcp-server jarvis
lmod 3.0.1 Environment Environment module management clio-kit mcp-server lmod
ndp 2.2.5 Data Protocol Search and discover datasets across CKAN instances clio-kit mcp-server ndp
node-hardware 2.3.0 System System hardware information clio-kit mcp-server node-hardware
pandas 2.3.0 Data Analysis CSV data loading and filtering clio-kit mcp-server pandas
parallel-sort 2.3.0 Computing Large file sorting clio-kit mcp-server parallel-sort
paraview 2.2.5 Visualization Scientific 3D visualization and analysis clio-kit mcp-server paraview
parquet 2.2.5 Data I/O Read Parquet file columns clio-kit mcp-server parquet
plot 2.2.5 Visualization Generate plots from CSV data clio-kit mcp-server plot
seismology 2.3.1 Seismology Analyze SAC waveforms and archives clio-kit mcp-server seismology
scientific-catalog 1.1.4 Discovery Operator-owned scientific dataset discovery clio-kit mcp-server scientific-catalog
slurm 3.0.2 HPC Job submission and management clio-kit mcp-server slurm
spack 2.3.1 Package Management Structured package discovery, installation, and location clio-kit mcp-server spack
terrain 2.2.5 Geospatial Analyze DEMs and terrain point clouds clio-kit mcp-server terrain
web 2.1.3 Web Web search and URL fetch, with queryable, cancellable fetch tasks; DOI and document conversion need a remote service clio-kit mcp-server web

📖 Usage Examples

HDF5: Scientific Data Analysis

"What datasets are in climate_simulation.h5? Show me the temperature field structure and read the first 100 timesteps."

Tools used: open_file, analyze_dataset_structure, read_partial_dataset, list_attributes

Slurm: HPC Job Management

"Submit simulation.py to Slurm with 32 cores, 64GB memory, 24-hour runtime. Monitor progress and retrieve output when complete."

Tools used: slurm_submit, slurm_list, slurm_describe

ArXiv: Research Discovery

"Find the latest papers on diffusion models from ArXiv, get details on the top 3, and export citations to BibTeX."

Tools used: search_arxiv, get_paper_details, export_to_bibtex, download_paper_pdf

Pandas: Data Processing

"Load sales_data.csv, clean missing values, compute statistics by region, and save as Parquet."

Tools used: load_data, handle_missing_data, groupby_operations, save_data

Plot: Data Visualization

"Create a line plot showing temperature trends over time from weather.csv with proper axis labels."

Tools used: line_plot, data_info

🚨 Troubleshooting

Server Not Found Error

If clio-kit mcp-server <server-name> fails:

# Verify server name is correct
clio-kit mcp-servers

# Common names: hdf5, pandas, slurm, arxiv (not hdf5-mcp, pandas-mcp)
Import Errors or Missing Dependencies

For development or local testing:

cd mcp-servers/hdf5
uv sync --all-extras --dev
uv run hdf5-mcp
uv or clio-kit Command Not Found

Install uv package manager:

# Linux/macOS
curl -LsSf https://astral.sh/uv/install.sh | sh

# Windows
powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

# Or via pip
pip install uv

Then install CLIO Kit persistently and expose uv's tool directory:

uv tool install --force --reinstall --editable .
uv tool update-shell

Open a new shell after update-shell, then check it resolved:

clio-kit mcp-servers

Team

Sponsored By

NSF Logo NSF (National Science Foundation) - Supporting scientific computing research and AI integration initiatives

we welcome more sponsorships. please contact the Principal Investigator

Ways to Contribute

  • Submit Issues: Report bugs or request features via GitHub Issues
  • Build MCP Servers: Contribute Python, Node.js or Go servers (guide)
  • Write Skills: Share reusable scientific workflows (guide)
  • Share Plugins or Marketplaces: List tools maintained in your own repository (guide)
  • Improve Documentation: Help make guides clearer
  • Share Use Cases: Tell us how you're using CLIO Kit in your research

Full Guide: CONTRIBUTING.md

Community & Support

Facts

Kind
Marketplace
Repo
iowarp/clio-kit
Group
Uncategorized
Stars
28
Marketplace name
clio-kit
Owner
IoWarp Team - Gnosis Research Center
License
BSD-3-Clause
Language
Python
Created
2025-04-30
Last push
2026-10-08
Forks
25
Homepage
toolkit.iowarp.ai
Topics
ai4hpc, ai4science, hpc, hpc-ai, mcp, mcp-tools, clio, clio-kit
Plugins
72

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