Molecules

Molecules are work graphs: epics whose children flow through bd ready as dependency-ordered steps. They are usually instantiated from formulas, but a formula is optional — any epic with children is a molecule.

What is a Molecule?

A molecule is a persistent instance of a proto (a cooked formula):

Contains steps with dependencies
Persistent beads in the issue database, synced like any other bead
Steps map to issues with parent-child relationships

Under the hood, a molecule is just an epic — a parent bead with children — plus workflow semantics:

Term	Meaning	When to use
Epic	Parent issue with children	General term for hierarchical work
Molecule	Epic with execution intent	When discussing workflow traversal
Proto	Epic with the `template` label	Reusable pattern (optional)

Protos and formulas are optional layers for reusable patterns and complex composition — most work needs only epics and dependencies.

Creating Molecules

From a Formula

# Cook the formula into a proto, then pour the proto into a molecule
bd cook release.formula.toml
bd mol 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)

Without a Formula

Create the epic and wire the dependencies directly:

bd create "Feature X" -t epic
bd create "Design" -t task --parent <epic-id>
bd create "Implement" -t task --parent <epic-id>
bd create "Test" -t task --parent <epic-id>
bd dep add <implement-id> <design-id>   # implement needs design
bd dep add <test-id> <implement-id>     # test needs implement

If the epic carries a size/effort label, see Labels for keeping it off the steps. If an ad-hoc epic turns out to be worth repeating, extract a reusable formula from it with bd mol distill <epic-id> <formula-name>.

Finding Molecules

bd mol current           # Where you are in the molecule you're working
bd mol stale             # Complete-but-still-open molecules
bd mol wisp list         # Ephemeral molecules (wisps)

Viewing a Molecule

bd mol show <molecule-id>             # Structure and variables
bd mol show <molecule-id> --parallel  # Highlight steps that can run concurrently
bd dep tree <molecule-id>             # Shows full hierarchy

Working with Molecules

The Execution Model

An agent picks up a molecule and executes ready children in parallel until everything closes:

epic-root (assigned to agent)
├── child.1 (no deps → ready)      ← execute in parallel
├── child.2 (no deps → ready)      ← execute in parallel
├── child.3 (needs child.1) → blocked until child.1 closes
└── child.4 (needs child.2, child.3) → blocked until both close

Children are parallel by default. Only explicit dependencies create sequence. The multi-session loop:

Get ready work: bd ready --mol <molecule-id>
Claim it: bd update <id> --claim
Do the work
Close it: bd close <id>
Repeat until the molecule is done

Dependency Types

Only some dependency types block execution:

Type	Semantics	Use case
`blocks`	B can’t start until A closes	Sequencing work
`parent-child`	If the parent is blocked, children are blocked	Hierarchy (children parallel by default)
`conditional-blocks`	B runs only if A fails	Error-handling paths
`waits-for`	B waits for all of A’s dynamic children	Fan-in gates — see Gates

Non-blocking types (related, discovered-from, replies-to) link issues without affecting execution.

Step Dependencies

In a formula, steps declare needs:

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

On live issues, add the edge directly — the dependent comes first:

bd dep add <B-id> <A-id>   # B depends on A (B needs A)

The bd ready command respects these:

bd ready --mol <molecule-id>  # Only shows steps with completed dependencies

Progressing Through Steps

# 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 --mol bd-xyz

Viewing Progress

# See blocked steps
bd blocked

# Step-by-step status: [done] / [current] / [ready] / [blocked] / [pending]
bd mol current <molecule-id>

# Progress summary: completed/total, rate, ETA
bd mol progress <molecule-id>

Molecule Lifecycle

Formula (template source)
    ↓ bd cook
Proto (template epic)
    ↓ bd mol pour
Molecule (instance)
    ↓ work steps
Completed Molecule
    ↓ optional cleanup
Closed / Squashed / Burned

Closing the last child does not close the molecule root — epics stay open as close-eligible work until closed explicitly (bd epic close-eligible sweeps them). For cleanup of the beads themselves:

bd mol squash <id> condenses a molecule’s ephemeral children into a permanent digest issue.
bd mol burn <id> deletes a molecule outright, no digest — for abandoned or test runs.

See Wisps for the ephemeral lifecycle these commands usually serve.

Bonding: Connecting Work Graphs

Bond means creating a dependency between two work graphs. When molecule A blocks molecule B, completing A unblocks B and an agent can continue from A into B — one compound workflow that can span days.

bd mol bond A B                    # B depends on A (sequential by default)
bd mol bond A B --type parallel    # B runs alongside A
bd mol bond A B --type conditional # B runs only if A fails

The command is polymorphic over its operands:

Operands	What happens
proto + proto	Compound proto (reusable template)
proto + molecule	Spawns the proto as new issues, attached to the molecule
molecule + molecule	Joins them into a compound molecule
formula + anything	The formula is cooked inline first

Spawned issues follow the target’s phase (persistent or ephemeral) by default. Override with --pour (force persistent) or --ephemeral (force ephemeral) — see Wisps.

Dynamic Bonding

When the number of children isn’t known until runtime, bond in a loop with --ref to get readable child IDs instead of random hashes:

# One arm per discovered worker
bd mol bond mol-worker-arm bd-patrol --ref arm-{{name}} --var name=ace
# Creates: bd-patrol.arm-ace (and children like bd-patrol.arm-ace.capture)

Advanced Features

Bond Points

Formulas can define bond points — named attachment sites for composition. Each names a step to attach before_step or after_step (with optional parallel = true):

[[compose.bond_points]]
id = "entry"
description = "Attach setup work here"
before_step = "design"

Hooks

Step-completion hooks are not currently exposed as runnable formula actions. The historical on_complete.run example was invalid: run is not a formula field, and on_complete runtime expansion is tracked separately until it is wired end to end.

Assigning Molecules

Assign the molecule root to an agent at pour time, then track where each agent is:

bd mol pour mol-feature --assignee <agent>   # Assign on creation
bd mol current --for <agent>                 # Where that agent is

Agent Pitfalls

Temporal language inverts dependencies. “Phase 1 comes before Phase 2” tempts bd dep add phase1 phase2 — backwards. Use requirement language: “Phase 2 needs Phase 1” is bd dep add phase2 phase1. Verify with bd blocked.
Numbered steps don’t create sequence. Steps named “Step 1/2/3” still run in parallel until you add dependencies between them.
Forgetting to close work. Blocked issues stay blocked forever if their blockers aren’t closed: bd close <id> --reason "Done".

Example Workflow

# 1. Create molecule from formula
bd cook feature-workflow.formula.toml
bd mol 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 --mol bd-xyz  # Shows next steps

# 5. Continue until complete

Getting Started

Core Concepts

Architecture

Workflows

Recovery

Multi-Agent

Integrations

Community

Reference

What is a Molecule?

Creating Molecules

From a Formula

Without a Formula

Finding Molecules

Viewing a Molecule

Working with Molecules

The Execution Model

Dependency Types

Step Dependencies

Progressing Through Steps

Viewing Progress

Molecule Lifecycle

Bonding: Connecting Work Graphs

Dynamic Bonding

Advanced Features

Bond Points

Hooks

Assigning Molecules

Agent Pitfalls

Example Workflow

See Also

​What is a Molecule?

​Creating Molecules

​From a Formula

​Without a Formula

​Finding Molecules

​Viewing a Molecule

​Working with Molecules

​The Execution Model

​Dependency Types

​Step Dependencies

​Progressing Through Steps

​Viewing Progress

​Molecule Lifecycle

​Bonding: Connecting Work Graphs

​Dynamic Bonding

​Advanced Features

​Bond Points

​Hooks

​Assigning Molecules

​Agent Pitfalls

​Example Workflow

​See Also

What is a Molecule?

Creating Molecules

From a Formula

Without a Formula

Finding Molecules

Viewing a Molecule

Working with Molecules

The Execution Model

Dependency Types

Step Dependencies

Progressing Through Steps

Viewing Progress

Molecule Lifecycle

Bonding: Connecting Work Graphs

Dynamic Bonding

Advanced Features

Bond Points

Hooks

Assigning Molecules

Agent Pitfalls

Example Workflow

See Also