projio 0.1.2

Project knowledge orchestrator and MCP server for research repositories

projio

Project knowledge orchestrator and MCP server for research repositories.

Turns a research repository into a queryable knowledge environment for humans and AI agents. Provides structured, machine-accessible knowledge layers by integrating code, papers, notes, pipelines, figures, and documentation through a unified MCP server interface.

Install

pip install projio                # core orchestrator + MCP server
pip install "projio[all]"         # all ecosystem packages

For development:

git clone https://github.com/arashshahidi1997/projio.git
cd projio
make dev

Quick start

# Scaffold .projio/ workspace
projio init .

# Scaffold a study or tool project
projio init . --kind study
projio init . --kind tool

# Show project status
projio status -C .

# Start MCP server (stdio)
projio mcp -C .

# Site operations
projio site build
projio site serve

Ecosystem

Projio orchestrates six specialized packages:

Package	Domain	Description
projio	orchestration	Workspace scaffold, site workflows, MCP entrypoint
indexio	retrieval	Corpus indexing, chunking, embedding, semantic search
biblio	literature	Bibliography management, citekey resolution, paper context
notio	notes	Structured notes, idea capture, manuscript assembly & rendering
codio	code	Library registry, code reuse discovery, implementation strategy
pipeio	pipelines	Pipeline authoring, contracts, notebook lifecycle, Snakemake flows
figio	figures	Declarative figure specs, panel rendering, SVG/PDF composition

Install individual extras: pip install "projio[biblio]", pip install "projio[pipeio]", etc.

MCP tools

The MCP server exposes 70+ tools across all subsystems:

Category	Tools	Examples
Retrieval	6	rag_query, rag_query_multi, corpus_list, indexio_build
Bibliography	26	biblio_ingest, citekey_resolve, paper_context, biblio_compile
Notes	10	note_create, note_list, note_search, notio_reindex
Manuscripts	16	manuscript_build, manuscript_assemble, manuscript_cite_check
Code	11	codio_list, codio_discover, codio_add, codio_registry
Pipelines	51	pipeio_flow_new, pipeio_run, pipeio_nb_exec, pipeio_dag_export
Figures	5	figio_build, figio_inspect, figio_validate
Project	10	project_context, ecosystem_status, site_build, datalad_save

See the MCP tools reference for the full list.

Configuration

Project-local defaults live in .projio/config.yml. Optional user defaults in ~/.config/projio/config.yml are merged first, with project config taking precedence.

# Scaffold user config
projio config init-user

# Show merged config
projio config -C . show

Claude Code / MCP config

{
  "mcpServers": {
    "projio": {
      "command": "/path/to/python",
      "args": ["-m", "projio.mcp.server"],
      "env": { "PROJIO_ROOT": "/path/to/your/project" }
    }
  }
}

Documentation

Full docs at arashshahidi1997.github.io/projio.

License

MIT