abi-agent 0.2.0

Agent-Bioinformatics Interface: plugin-based abstraction for AI-driven bioinformatics analysis

ABI — Agent-Bioinformatics Interface

ABI is a Python interface layer for agent-driven bioinformatics workflows. It standardizes analysis plugins behind a common plan -> dry-run -> run -> inspect -> report lifecycle, with provenance, standard TSV tables, OpenAI-compatible tool descriptors, optional MCP transport, Nextflow export/runtime support, and a queue-backed HTTP Job Service.

Installation

pip install abi-agent

# Development install
pip install -e ".[dev]"

# Optional MCP server dependencies
pip install -e ".[dev,mcp]"

Python 3.10-3.13 is supported.

Quick Start

# List installed analysis plugins
abi list-types

# Initialize a plugin workspace
abi init --type metatranscriptomics --outdir ./workspace

# Build a plan without executing tools
abi plan --type metatranscriptomics --config config.yaml --sample-sheet samples.tsv

# Write dry-run provenance and table skeletons
abi dry-run --type metatranscriptomics --config config.yaml --sample-sheet samples.tsv

# Execute only after explicit confirmation
abi run --type metatranscriptomics --config config.yaml --sample-sheet samples.tsv \
  --confirm-execution

# Inspect and rebuild reports
abi inspect --result-dir results/
abi report --result-dir results/ --type metatranscriptomics

# Export agent/runtime interfaces
abi export-nextflow --type metatranscriptomics --output workflow.nf
abi export-openai-tools --type metatranscriptomics --format responses
abi export-agent-context --type metatranscriptomics --format json
abi doctor-agent --type metatranscriptomics

All agent-facing commands support --output-json.

Built-In Analysis Types

Type	Implementation	Notes
metatranscriptomics	Native ABI demo plugin	fastp -> STAR/HISAT2 -> featureCounts portability demo.
metagenomic_plasmid	Internal abi.autoplasm pipeline	Migrated from the former AutoPlasm development tree and bundled inside abi-agent.

The package also exposes an autoplasm command for the bundled plasmid pipeline:

autoplasm dry-run --config examples/config_minimal.yaml --profile dry_run

There is no top-level Python package named autoplasm; import the internal implementation as abi.autoplasm.

Agent Transports

ABIAgentInterface is the stable transport-neutral boundary used by:

• CLI JSON through --output-json
• OpenAI-compatible descriptors from abi export-openai-tools
• Optional MCP stdio server via python -m abi.mcp.server
• HTTP Job Service via abi job-service and abi job submit/list/status/artifacts/cancel

Execution tools require explicit confirmation. abi run, abi_run, and Job Service execution submissions return confirmation_required unless confirm_execution=true or --confirm-execution is provided.

Development

pip install -e ".[dev]"

ruff check src/ tests/
ruff format --check src/ tests/
mypy src/abi/ --ignore-missing-imports
pytest tests/ -v --tb=short

python -m build
python -m twine check dist/*

Repository-local bioinformatics environments are described under envs/ and resolved from .mamba/envs/<env_name>/bin. Set ABI_MAMBA_ROOT to override the default .mamba root; AUTOPLASM_MAMBA_ROOT remains accepted for compatibility.

More details:

• ABI Spec v0.1
• Agent Usage Guide
• Development Guide
• Plugin Development Guide
• OpenAI Interface Standard
• Job Service Guide
• Experiment Plan
• Metagenomic Plasmid Plugin
• Release Guide

Public SDK

Plugin authors should depend on these public modules:

Module	Contents
abi.interfaces	ABIPlugin, ABIDryRunPlugin, ABIInitializablePlugin
abi.schemas	ABISample, ABISampleContext, ABIPlanStep, ABIExecutionPlan
abi.tools	ToolRegistry, ToolSkill, GenericCommandSkill, RunResult
abi.errors	ABIError, ConfigError, SampleSheetError, ToolError
abi.testing	assert_plugin_contract

Register third-party plugins with:

[project.entry-points."abi.plugins"]
my_analysis = "my_package.plugins:MyPlugin"

License

MIT, see LICENSE.