EcoOracle

EcoOracle is an MCP server plus registry pipeline for answering ecosystem questions across many R/Python packages. Primary goal: let users build new scripts outside package repos by retrieving canonical usage recipes and API cards.

It is designed so package onboarding is deterministic:

• package repo opts in with .ecosystem.yml
• package CI publishes atlas-pack.tgz at release tag eco-atlas
• eco-registry discovery updates registry.json nightly
• MCP server loads registry and serves eco_howto, eco_symbol, eco_packages, eco_where_used

Canonical registry repository: https://github.com/bbuchsbaum/eco-registry.

What Lives Here

• packages/eco-oracle-mcp: MCP server
• tools/eco_atlas_extract.R: extract symbols/snippets/edges
• tools/eco_atlas_distill.mjs: distill snippets into microcards
• tools/eco-atlas.yml: package-side workflow template that builds and publishes atlas-pack.tgz
• eco-registry: registry repo and nightly discovery workflow
• schemas: data contracts for cards, symbols, edges, manifest, registry

End-to-End Flow

1. Package repo includes .ecosystem.yml.
2. Package workflow builds atlas files and publishes atlas-pack.tgz to release tag eco-atlas.
3. eco-registry/.github/workflows/discover-registry.yml runs nightly at 04:00 UTC (and on manual dispatch).
4. Discovery script scans owner repos, finds .ecosystem.yml, resolves release assets, and writes eco-registry/registry.json.
5. MCP server refreshes from registry and caches atlas packs locally.
6. Claude/Codex sessions call the MCP tools to generate external scripts.

Add A New Package (Turnkey)

Do this in the target package repository.

Fastest path with an agent:

• ask: Add this package to the ecosystem
• if eco-join skill is available, it scaffolds the required files/workflow.

Fastest path from R:

# install.packages("remotes")
remotes::install_github("bbuchsbaum/eco-oracle")
library(ecooracle)

# initial scaffold
ecooracle::use_ecooracle()

# refresh workflow/tool templates later without hand edits
ecooracle::use_ecooracle(overwrite = TRUE)

# or run commit/push/workflow/discovery without prompts
ecooracle::use_ecooracle(
  commit = TRUE,
  push = TRUE,
  run_workflow = TRUE,
  run_discovery = TRUE
)

# check local onboarding health
ecooracle::check_health()

1. Add .ecosystem.yml at repo root:

ecosystem: true
package: mypkg
language: R
role: transform
tags: [domain-tag, canonicalization]
entrypoints:
  - mypkg::main_fn
  - mypkg::read_input
# optional overrides (defaults shown)
release_tag: eco-atlas
asset: atlas-pack.tgz

1. Add atlas tooling to the package repo:

• copy tools/eco_atlas_extract.R
• copy tools/eco_atlas_distill.mjs
• copy .github/workflows/eco-atlas.yml from tools/eco-atlas.yml

If you use ecooracle::use_ecooracle(), these files are scaffolded for you. Re-run it with overwrite = TRUE to refresh an existing package to the current template set. The helper also fills placeholder role/tags/entrypoints from DESCRIPTION and NAMESPACE, and in interactive sessions it can ask whether to commit, push, trigger eco-atlas.yml, and trigger registry discovery.

1. Configure package secrets:

• OPENAI_API_KEY for distillation step

1. Push to main (or run workflow manually):

• verify release tag eco-atlas contains asset atlas-pack.tgz

1. Wait for registry discovery (nightly) or trigger discover-registry manually in eco-registry.

Example manual trigger:

gh workflow run discover-registry.yml --repo bbuchsbaum/eco-registry

1. Verify package is in registry:

cat eco-registry/registry.json

1. Verify MCP can load it:

node packages/eco-oracle-mcp/dist/index.js
# then call eco_refresh and eco_packages from your MCP client

No manual registry edits should be required in normal operation.

Manual Hints: Exactly Where To Put Them

If you want package-specific guidance to improve retrieval quality, put it in the package repository, not in eco-registry/registry.json.

Hard rule:

1. Do not manually edit eco-registry/registry.json for package hints.
2. Nightly discovery rewrites registry.json.
3. Manual edits there are temporary and will be lost.

Put hints in durable source locations in the package repo:

1. .ecosystem.yml

• set role, tags, entrypoints

1. R/*.R

• add # ECO:howto ... markers above canonical snippets

1. README.Rmd / vignettes/*.Rmd

• include canonical code fences for real workflows

1. manual_cards.jsonl (optional, deterministic overrides)

• add hand-authored microcards that are merged into final atlas/cards.jsonl
• if id collides with generated card id, manual card wins

Manual cards file contract:

1. File path: manual_cards.jsonl at package repo root (default; override with ECO_ATLAS_MANUAL_CARDS_PATH)
2. One JSON object per line
3. Required fields per record:

• q, a, recipe, symbols

1. Optional fields:

• id, tags, package, language, sources

Example manual_cards.jsonl line:

{"id":"manual.bidser.load_project","q":"How do I load a BIDS project in R?","a":"Use bidser::bids_project() on the dataset root, then inspect scans with func_scans().","recipe":"library(bidser)\nproj <- bidser::bids_project('/path/to/bids')\nscans <- bidser::func_scans(proj)","symbols":["bidser::bids_project","bidser::func_scans"],"tags":["bids","ingest"]}

Example # ECO:howto snippet:

# ECO:howto How do I load a BIDS project?
library(bidser)
proj <- bidser::bids_project("/path/to/bids")
scans <- bidser::func_scans(proj)

What gets overwritten by automation:

1. eco-registry/registry.json is regenerated by discovery.
2. atlas/cards.jsonl and release atlas-pack.tgz are regenerated by package atlas workflow.

What does not get overwritten:

1. .ecosystem.yml committed in the package repo.
2. # ECO:howto markers and package docs committed in the package repo.

Operational flow for manual hints:

1. Commit hint changes in the package repo.
2. Run/push package eco-atlas workflow so a new atlas-pack.tgz is published.
3. Wait for nightly discovery (or trigger it manually).
4. Run eco_refresh in client and verify behavior with eco_howto / eco_symbol.

Registry Automation Setup (Do Once In eco-registry)

Set these in the eco-registry GitHub repo:

1. Secret: GH_ORG_PAT

• token must read target owner repositories and push to eco-registry

1. Variable: ECO_OWNER

• owner to scan, org or user (for example bbuchsbaum)

1. Optional variable: ECO_ORG

• backward-compatible fallback

Discovery supports both GitHub orgs and users.

Run The MCP Server Locally

From this repo:

npm install
npm run build --workspace=packages/eco-oracle-mcp
node packages/eco-oracle-mcp/dist/index.js

Environment:

• ECO_REGISTRY_URL or ECO_REGISTRY_PATH (set at least one)
• ECO_GITHUB_TOKEN (optional, needed for private release assets)
• ECO_CACHE_DIR (optional, default ~/.cache/eco-oracle)
• ECO_REFRESH_SECS (optional, default 600)

Use From Claude Code

User scope:

claude mcp add --transport stdio eco-oracle --scope user -- npx -y eco-oracle-mcp

Project scope (.mcp.json):

{
  "mcpServers": {
    "eco-oracle": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "eco-oracle-mcp"],
      "env": {
        "ECO_REGISTRY_URL": "https://raw.githubusercontent.com/bbuchsbaum/eco-registry/main/registry.json",
        "ECO_GITHUB_TOKEN": "${ECO_GITHUB_TOKEN}"
      }
    }
  }
}

Copy-Paste Directive: Ecosystem-First (Compatible with oh-my-claude)

Use this in CLAUDE.md, AGENTS.md, or as the first message in a fresh Claude/Codex session:

## Internal package policy (eco-oracle MCP only)

This policy refers only to the `eco-oracle` MCP server.
Do not activate or invoke any other skill/mode (including `oh-my-claudecode:ecomode`) unless the user explicitly asks.

For R code, prefer ecosystem packages discovered via eco-oracle MCP.
Workflow is mandatory:

1. Call `eco_howto` first for each "How do I...?" subtask.
2. Call `eco_symbol` for each function you plan to use.
3. Use ecosystem packages/functions in final code.

Do not introduce non-ecosystem packages (for example `RNifti`, `oro.nifti`, `ANTsR`) unless:
1. eco-oracle returns no viable result, and
2. you explicitly ask for user approval before using external packages.

When answering, include:
1. `Ecosystem packages used: ...`
2. `Functions used: ...`
3. `Fallback needed: yes/no`

Quick prompt to reinforce behavior in any new session:

Use eco-oracle MCP as source of truth. Do not enable oh-my-claude modes/skills unless I explicitly request them. Ecosystem-only solution unless no match exists; if no match, ask me before using external packages.

Shortcut session opener (equivalent):

Enter ecosystem mode.

Use From Codex

User scope:

codex mcp add eco-oracle -- npx -y eco-oracle-mcp

Or in ~/.codex/config.toml:

[[mcp_servers]]
name = "eco-oracle"
command = "npx"
args = ["-y", "eco-oracle-mcp"]

[mcp_servers.env]
ECO_REGISTRY_URL = "https://raw.githubusercontent.com/bbuchsbaum/eco-registry/main/registry.json"
ECO_GITHUB_TOKEN = "${ECO_GITHUB_TOKEN}"

MCP Tools

• eco_howto(query, ...)
• eco_symbol(symbol, ...)
• eco_packages(...)
• eco_where_used(symbol, ...)
• eco_refresh()

Operational Checklist

For each package:

1. .ecosystem.yml present and valid.
2. eco-atlas workflow runs on main.
3. Release tag eco-atlas has atlas-pack.tgz.

For registry:

1. Nightly discovery workflow succeeds.
2. registry.json updates automatically.
3. New packages appear without manual edits.

For clients:

1. MCP config points at correct registry URL/path.
2. eco_refresh() returns expected package/card/symbol counts.