research-buddy 1.6.0

Structured AI research collaborator — generates high-fidelity HTML from versioned JSON or Markdown research documents.

Research Buddy v1.6.0

A structured AI research collaborator for any domain.

Format: v2 Markdown (recommended) and v1 JSON (legacy)

v2 Markdown is the recommended format for new projects as of 1.5. v1 JSON remains supported for existing projects but is on a deprecation path; new features land on v2 first.

• v2 Markdown (default for new work): YAML frontmatter + Markdown body with HTML-comment anchors (<!-- @anchor: ... -->, <!-- @rule: ... -->, <!-- @da: ... -->). Source of truth = *_v*-source.md (agent-edited, full framework). The reader-facing artifact is the clean view *_v*.md (framework stripped) or the rendered HTML. Each top-level ## H2 becomes a tab.
• v1 JSON (legacy): structured JSON with rich block types (callouts, verdicts, fixed-width tables). Source of truth = *_v*.json. Continue using for projects already on v1; migrate to v2 with research-buddy migrate-v1-to-v2.

build and validate dispatch on file extension. migrate-v1-to-v2 and clean operate on v2 only. upgrade is v1-only — v2 framework updates ship by editing starter.md and re-deriving downstream files.

How it works

The AI agent reads agent_guidelines embedded in the JSON and behaves as a Research Buddy for the full lifetime of the project. Every session produces an updated, versioned JSON file — the source of truth — and optionally a rendered HTML document for reading.

Session zero (first session with a new document): the agent introduces itself, asks 5 questions to understand the project, does discovery research, and proposes the initial structure — tabs, source tiers, queue items, and methodology rules tailored to your domain. Output: [file_name]_v1.0.json.

Subsequent sessions: upload the latest JSON, say "Continue research" — the agent picks up exactly where you left off and works through the queue one topic at a time in exactly 2 turns.

Install

For users (pip)

pip install research-buddy

PDF export is an optional extra (weasyprint is a large install with system-level dependencies, so it's not pulled in by default):

pip install "research-buddy[pdf]"

For development

uv sync --extra dev
# or:
pip install -e ".[dev]"

For AI Agents or AI users

If you are an AI agent or a user of a chatbot looking for the initial research template:

• Direct download: starter.json
• Package path: research_buddy.starter.json (when installed via pip)
• Source path: src/research_buddy/starter.json (in this repository)

Download this file and attach it into an AI chatbot session to start researching. The AI agent will know what to do.

Generating HTML

After each research session, to give the user a readable HTML document:

pip install research-buddy
research-buddy build your-project.json

The output will be your-project.html in the same directory.

Workflow

1. Session start: User uploads their JSON file. If new, ask them to run research-buddy init <project-name> first to get the starter template.
2. Session end: After making changes, run research-buddy build <json-file> to generate HTML. Tell the user the HTML is ready and they can download it.
3. Next session: Ask the user to upload the latest JSON file and say "Continue research".

The JSON file is always the source of truth — never the HTML.

Quick start

# Scaffold a new project
research-buddy init my-project/

# Upload my-project/source/research-document.json to your AI assistant
# The agent runs session_zero and produces [file_name]_v1.0.json

# Build HTML from the versioned output
research-buddy build my-project_v1.0.json

# Or point at the project directory — it finds the latest version automatically
research-buddy build my-project/

# Watch for changes
research-buddy build my-project/ --watch

# Open the result
open [file_name].html

Research protocol

Every session follows a strict, high-integrity 2-turn workflow:

1. Turn 1: Research & External Prompt
   • Agent performs discovery research using domain-appropriate Tier 1 sources with inline citations.
   • Agent prints findings, proposed decisions, and a prompt for other researchers.
   • CRITICAL: The agent then STOPS and waits for the user to provide results from other researchers (other AI agents, human experts, etc.).
2. Turn 2: Review & Finalize
   • User submits findings from other researchers.
   • Agent evaluates, labels (Gemini-1, Human-1, etc.), and compares them with its own research.
   • Agent performs an atomic write to the JSON file, bumps the version, and generates the final HTML (e.g., my-research_v2.3.html and my-research.html).
   • Any requests to add new research topics during these turns are integrated into the final JSON.

Failure modes are explicit: the document includes a failure_modes list that agents use to self-check before and after every action.

File naming

The script uses meta.file_name from your JSON to name the outputs.

File	Purpose
research-document.json	Unversioned template — never modified after init
[file_name]_v1.0.json	First project file, produced by session_zero
[file_name]_v1.1.json	After first research session
[file_name]_vX.Y.html	Versioned HTML build
[file_name].html	Latest stable HTML build

Batch Processing

You can process multiple JSON files in order. This is useful for projects with many versions:

# Processes files in the given order. The final [file_name].html 
# will be generated from the last file in the list.
research-buddy build v1.0.json v1.1.json v1.2.json

Commands

research-buddy init <dir>

Scaffold a new project. Creates source/research-document.json (Research Buddy v1.0 template) and versions/.

research-buddy init my-project/ [--title "Project Name"] [--subtitle "..."]

research-buddy build <path...>

Build HTML from document JSON(s) or Markdown file(s). Accepts files, directories, or both. Dispatches on file extension: .json → v1 pipeline, .md → v2 pipeline (same single-file chrome — tab bar, sidebar nav, theme toggle, hljs).

research-buddy build my-project/                    # latest version in source/
research-buddy build my-research_v1.5.json          # v1 JSON
research-buddy build my-research_v1.0-source.md     # v2 Markdown
research-buddy build a.json b.json                  # batch JSON IN ORDER
research-buddy build my-project/ --watch            # rebuild on change (.json only)
research-buddy build my-project/ --pdf              # + PDF (v1 only, requires weasyprint)
research-buddy build my-project/ --output master.html
research-buddy build my-project/ --validate-only    # v1 only

Mixing .json and .md inputs in a single invocation is rejected; --watch and --pdf are not yet supported for .md inputs. The MD build strips the framework block by default (matches the JSON build's "reader-facing" semantics — the framework is for the agent reading the source, not for HTML readers).

research-buddy validate <path...>

Validate JSON or Markdown documents. Dispatches on extension: .md → v2 mechanical validator (frontmatter, anchor pairing, link resolution, ID uniqueness); everything else → v1 JSON validator (schema + reference ordering + version compat).

research-buddy validate my-research_v1.0-source.md
research-buddy validate my-research_v1.1-source.md --prior my-research_v1.0-source.md

The optional --prior flag (v2 only) compares against an earlier version of the same file and enforces append-only invariants: anchors, Discarded Alternatives, References, and Changelog entries must never disappear.

research-buddy clean <path...> (v2)

Generate the shareable clean view from a v2 source file: strips the framework block (<!-- @anchor: framework.core --> … <!-- @end: framework.reference -->) and regenerates the title block from the YAML frontmatter. Output: {file_name}_v{version}.md alongside the source.

research-buddy clean my-research_v1.0-source.md
research-buddy clean my-research_v1.0-source.md -o /tmp/out.md

Refuses to run on a starter file (project.domain is null in the frontmatter) — there's nothing to clean until session zero fills in the project specification.

research-buddy migrate-v1-to-v2 <path...> (v2)

One-way migration from a v1 JSON document to a v2 Markdown source file. Maps meta.* + agent_guidelines.project_specific.* to YAML frontmatter; replaces the old framework with the v2 framework block copied from the bundled starter.md; promotes research-tab sections to top-level H2s; converts verdict blocks to @rule / @da blocks with stable IDs.

research-buddy migrate-v1-to-v2 my-research_v3.0.json     # writes my-research_v3.0-source.md
research-buddy migrate-v1-to-v2 old.json -o new-source.md
research-buddy migrate-v1-to-v2 old.json --force          # overwrite existing output

Refuses to overwrite an existing output unless --force is passed. After migration, run research-buddy validate <output>.md to confirm the result.

research-buddy upgrade <path...> (v1 only)

Re-sync a project JSON against the installed starter.json: replaces agent_guidelines.framework and agent_guidelines.session_protocol wholesale, preserves session_zero.note so initialized projects do not re-run session zero, leaves agent_guidelines.project_specific untouched, and bumps meta.research_buddy_version. Appends a dated migration entry to meta.format_note only when something actually changed.

research-buddy upgrade my-project/                # dry-run (exit 1 if changes needed)
research-buddy upgrade my-project/ --apply        # write + validate (exit 0 on clean apply)
research-buddy upgrade my-project/ --apply --no-validate

Exit codes: 0 clean (no changes or applied), 1 dry-run found changes, 2 error (bad path, validation failed, starter missing).

Project layout

my-project/
├── source/
│   └── research-document.json    # Template (agent uploads this for session_zero)
├── versions/                     # Versioned HTML builds
│   └── v1.0.html
├── [file_name].html              # Latest stable build (copy of most recent version)
└── theme.css                     # Optional CSS overrides

Multi-language support

The document language is set in session_zero based on the user's preference. meta.language accepts a string ("English") or an object ({"code": "es", "label": "Español"}). The HTML lang attribute is set automatically. agent_guidelines always stays in English.

UI labels ("OPEN", "✦ Researched", "Next Topic", etc.) are stored in meta.ui_strings and translated by the agent in session_zero — no hard-coded strings in document content.

Document format

The JSON schema is bundled with the package. For reference, see src/research_buddy/schema.json in the repository, or the matching path inside the installed wheel (research_buddy/schema.json).

Block types

Type	Key fields
p	md
h3, h4	md, id, badge
code	text, lang
callout	md, variant (blue|green|amber|red|purple), title
verdict	badge (adopt|reject|defer|pending), label, md
table	headers[], rows[][]
ul, ol	items[]
card_grid	cols (2|3), cards[{title, md}]
phase_cards	cards[{phase, title, items[]}]
usage_banner	title, items[]
references	items[{version, date, text}]
svg	html (raw SVG string)

Schema compatibility

meta.research_buddy_version is required in all documents. The validator warns if it is missing. When this version changes, schema or build script behaviour may change — always use the template that matches your installed version.

Version compatibility (tool ↔ document)

Research Buddy uses MAJOR.MINOR.PATCH semver. Every research-buddy build and research-buddy validate compares the installed CLI version against meta.research_buddy_version and reacts like this:

Comparison	Severity	What happens
Exact match	silent	Nothing to worry about.
Only PATCH differs (e.g. 1.0.3 vs 1.0)	silent	Patches are strictly backwards-compatible. Treated as equivalent.
Tool MINOR newer than doc (same MAJOR)	silent	No action required. Doc is fully compatible. The agent will bump meta.research_buddy_version on the next write. Nothing is printed; exit code stays 0.
Tool MINOR older than doc (same MAJOR)	warning	Doc may use features your tool does not render correctly. Run pip install --upgrade research-buddy.
MAJOR differs	error	Schema is not guaranteed to match. Either install the matching major (pip install 'research-buddy==1.*') or start an AI session and say "Migrate to research-buddy vX.Y" so the agent updates the document structure.

Algorithmic rule: for compatibility, the validator compares MAJOR.MINOR only. Patch-level differences are ignored — 1.0.3 and 1.0 behave the same.

What if my document is on an older version?

If you're upgrading the CLI to a newer minor (e.g. tool 1.1.0, doc 1.0.3) there is nothing to do: your build continues to produce HTML as before. The agent bumps meta.research_buddy_version the next time it writes to the document.

If you're moving across a major boundary, the CLI will tell you, point at CHANGELOG.md, and give you a copy-pasteable command to pin the matching major (if you want to keep your current doc as-is) or an instruction to hand to the agent (if you want to migrate).

Development

make sync           # Install dev dependencies
make lint           # ruff + mypy
make format         # Auto-fix + format
make test           # Run full test suite
make update-skills  # Pull latest shared Claude skills

Examples

The starter-example/ directory contains pre-built HTML outputs from the bundled starters:

• starter.html — built from starter.json (v1 JSON pipeline).
• starter-md.html — built from starter.md (v2 Markdown pipeline, framework stripped to match the v1 reader view).

Regenerate with:

make regen-example      # v1 only
make regen-md-example   # v2 only
make regen-examples     # both

License

MIT