Habitat-Genome Compiler

Habitat-Genome Compiler is a safe, local-first mission compiler for speculative habitat and environmental bio-design programs. It turns a mission JSON spec into a ranked candidate set, a markdown dossier, and an auditable local run archive. The project now also includes a browser-based mission studio that can generate valid mission specs through a guided builder instead of requiring hand-authored JSON.

What is included

• A mission JSON compiler with biosafety-aware validation and refusal handling.
• A GUI mission builder that generates safe mission specs and keeps the JSON view in sync.
• A preset library for industrial, water, climate, and offworld mission scenarios.
• Local run persistence with manifest.json, mission.json, result.json, and report.md for every saved compile.
• A lightweight HTTP API plus CLI commands for compile, serve, list runs, and inspect archived artifacts.

Quick start

Clone the repository, then install the package in editable mode:

pip install -e .

For the GUI builder, make sure fastapi and uvicorn are available in your environment, then start the app:

python gui_app.py

Open http://127.0.0.1:8000 to use the mission studio.

CLI usage

Compile a bundled example and save the full run archive:

habitat-compiler compile examples/pfas_brine.json --save-run

List recent saved runs:

habitat-compiler runs

Inspect a saved markdown dossier:

habitat-compiler show-run <run_id> --artifact report

Run the lightweight API server:

habitat-compiler serve --host 127.0.0.1 --port 8080

Mission studio

The browser UI now includes:

• Preset cards with safe-first ordering and blocked-demo missions pushed to the end.
• A guided builder for name, domain, environment, stressors, objectives, and safety profile.
• Research-note cards that explain why extra control, containment, consortium, or offworld objectives were added.
• A live JSON panel so generated missions can still be reviewed and edited directly.
• Compile results that surface verdicts and the saved run ID for traceability.

Bundled presets

Current example missions include:

• examples/pfas_brine.json
• examples/desalination_brine_polishing.json
• examples/methane_biofilter.json
• examples/mine_tailings_recovery.json
• examples/mars_bioreactor.json
• examples/mars_regolith_biofertility.json
• examples/blocked_mission.json

Research-backed generator

The mission builder adds extra objectives and constraints using rules derived from published work on:

• Digital twins for bioprocess control
• Long-term microbial consortium homeostasis
• Layered biological containment
• Offworld resource loops and regolith-linked nutrient recycling

The applied source mapping is documented in docs/research-upgrades.md.

Saved runs

When a compile is saved, the run archive stores:

• manifest.json with metadata, timestamps, compiler version, and artifact references
• mission.json with the validated mission input
• result.json with the compiler output
• report.md with the rendered dossier

Runs are stored in ./runs by default, or in the directory pointed to by HABITAT_COMPILER_RUNS_DIR.

Safety model

This project is intentionally simulation-first. Unsafe mission requests are blocked, and the builder refuses pathogen, toxin, immune-evasion, transmissibility, and similar harmful capability framing. Generated missions bias toward containment, telemetry, shutdown logic, and review gates instead of actionable wet-lab instructions.

Verification

The current automated test suite passes with:

python -m pytest -q

Latest verified result: 75 passed.