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Molecules

website/docs/workflows/molecules.md

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Molecules

Molecules are work graphs created from formulas.

What is a Molecule?

A molecule is a persistent instance of a formula:

  • Contains steps with dependencies
  • Tracked in .beads/ (syncs with git)
  • Steps map to issues with parent-child relationships

Creating Molecules

From Formula

bash
# Pour a formula into a molecule
bd pour <formula-name> [--var key=value]

Example:

bash
bd pour release --var version=1.0.0

This creates:

  • Parent issue: bd-xyz (the molecule root)
  • Child issues: bd-xyz.1, bd-xyz.2, etc. (the steps)

Listing Molecules

bash
bd mol list
bd mol list --json

Viewing a Molecule

bash
bd mol show <molecule-id>
bd dep tree <molecule-id>  # Shows full hierarchy

Working with Molecules

Step Dependencies

Steps have needs dependencies:

toml
[[steps]]
id = "implement"
title = "Implement feature"
needs = ["design"]  # Must complete design first

The bd ready command respects these:

bash
bd ready  # Only shows steps with completed dependencies

Progressing Through Steps

bash
# Start a step
bd update bd-xyz.1 --claim

# Complete a step
bd close bd-xyz.1 --reason "Done"

# Check what's ready next
bd ready

Viewing Progress

bash
# See blocked steps
bd blocked

# See molecule stats
bd stats

Molecule Lifecycle

Formula (template)
    ↓ bd pour
Molecule (instance)
    ↓ work steps
Completed Molecule
    ↓ optional cleanup
Archived

Advanced Features

Bond Points

Formulas can define bond points for composition:

toml
[compose]
[[compose.bond_points]]
id = "entry"
step = "design"
position = "before"

Hooks

Execute actions on step completion:

toml
[[steps]]
id = "build"
title = "Build project"

[steps.on_complete]
run = "make build"

Pinning Work

Assign molecules to agents:

bash
# Pin to current agent
bd pin bd-xyz --start

# Check what's pinned
bd hook

Example Workflow

bash
# 1. Create molecule from formula
bd pour feature-workflow --var name="dark-mode"

# 2. View structure
bd dep tree bd-xyz

# 3. Start first step
bd update bd-xyz.1 --claim

# 4. Complete and progress
bd close bd-xyz.1
bd ready  # Shows next steps

# 5. Continue until complete

See Also