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lightcone-cli

lightcone-cli is Lightcone Research's agentic execution layer for ASTRA (Agentic Schema for Transparent Research Analysis). It ships the lc executable, a small set of Claude Code skills, and the provenance/integrity machinery that ties an astra.yaml spec to a tree of materialized outputs.

This site has two halves.

I'm a researcher and I want to use this thing

Start at the User Guide. Friendly, step-by-step, with worked examples. You will not need to read any Python.

The shortest possible path:

uv tool install lightcone-cli
lc init my-analysis && cd my-analysis
claude                                # then, inside Claude Code: /lc-new

pip install lightcone-cli
lc init my-analysis && cd my-analysis
claude                               # then, inside Claude Code: /lc-new

I work on lightcone-cli

Welcome — keep reading. The rest of this page is a fast tour for contributors and maintainers; deep dives live in the sub-trees of the nav.

Two packages, one toolchain

Layer Package Role
ASTRA astra-tools Pure specification: schema, validation, prior insights & findings, evidence verification helpers, the astra CLI.
lightcone-cli lightcone-cli Agentic layer: project scaffolding, Snakemake-based execution, Dask cluster management, container builds, Claude Code skills.

lightcone-cli depends on astra-tools. The astra CLI handles the spec itself (validation, paper management, evidence verification); the lc CLI handles execution and the agent surface.

Repository at a glance

src/lightcone/                  # PEP 420 namespace package — NO __init__.py
├── cli/                        # Click surface
│   ├── __init__.py             # exposes main()
│   ├── commands.py             # init, run, status, verify, build, export
│   └── plugin.py               # plugin source-dir discovery
├── engine/                     # execution substrate
│   ├── manifest.py             # write_manifest, sha256_dir, code_version
│   ├── snakefile.py            # generate .lightcone/Snakefile from astra.yaml
│   ├── container.py            # docker/podman/podman-hpc build + recipe wrap
│   ├── dask_cluster.py         # cluster lifecycle (local/SLURM/external)
│   ├── status.py               # manifest-driven status walker (no Snakemake)
│   ├── verify.py               # recompute hashes, walk the chain
│   ├── tree.py                 # sub-analysis tree helpers
│   ├── validation.py           # post-recipe output sanity checks
│   └── site_registry.py        # vestigial; not imported by active code
└── eval/                       # evaluation harness for the agent loop
    ├── cli.py harness.py sandbox.py graders.py build.py report.py models.py

src/snakemake_executor_plugin_dask/   # Snakemake executor → dask.distributed

.claude-plugin/                 # marketplace manifest (force-included into the wheel)
└── marketplace.json            # declares the `lightcone` plugin sourced from ./claude/lightcone

claude/lightcone/               # Claude Code plugin (force-included into the wheel)
├── .claude-plugin/plugin.json  # plugin manifest
├── skills/                     # lc-new, lc-from-code, lc-from-paper,
│                                # lc-feedback, ralph (+ bundle siblings);
│                                # reference skills: astra, lc-cli
├── agents/                     # lc-extractor (literature subagent)
├── hooks/hooks.json            # hook config (${CLAUDE_PLUGIN_ROOT}-rooted commands)
├── scripts/                    # hook scripts: venv, validate-on-save, session-start primer
└── templates/                  # project CLAUDE.md template

tests/                          # pytest, mirrors src/
pyproject.toml                  # hatchling + hatch-vcs; ASTRA + Snakemake as deps

The lightcone.* namespace is a PEP 420 implicit namespace package. Do not add src/lightcone/__init__.py — that would turn it into a regular package and break coexistence with future sibling distributions (lightcone-ui, etc.). Any new lightcone-* package must live under src/lightcone/<name>/ and ship only its own subpackage.

Execution flow

astra.yaml ── snakefile.generate() ──► .lightcone/Snakefile + .lightcone/snakefile-config.json
                                              │
                                       snakemake -s … -d … --executor dask
                                              │
                       ┌──────────────────────┼──────────────────────┐
                       │                      │                      │
                  DAG resolution         per-rule run:           dask scheduler
                  (Snakemake)            shell(recipe)           (LocalCluster /
                                         + write_manifest()       SLURM-srun /
                                                                  external)
                       │
                       └─► results/<u>/<o>/data
                           results/<u>/<o>/.lightcone-manifest.json

What Snakemake owns (we don't write it): DAG construction, topological execution, parallelism, dry-run, locking, retry, log capture, per-rule resources, --rerun-triggers for staleness detection.

What we own: a Snakefile generator, the manifest layer (write/read/verify), a status walker, a verify routine, the Dask cluster manager, the container-runtime layer, and a Snakemake executor plugin that submits each rule to a Dask scheduler.

What every materialized output gets

A sidecar .lightcone-manifest.json next to its data, recording:

  • code_version = sha256(recipe + container_image + decisions)
  • data_version = sha256_dir(output_dir) excluding the manifest itself
  • input_versions for each declared input (chained data_version when the input is another materialized output, mtime-size or sha256 for external files)
  • container_image, recipe, decisions, git_sha, lc_version, host, slurm_job_id, finished_at

lc verify recomputes data_version and walks the chain. Failures surface as tampered_data, broken_chain, or missing_manifest. lc status reads only manifests — works offline, no Snakemake or DB needed.

Development setup

just install        # uv sync --all-groups
just test           # uv run pytest
just lint           # ruff + mypy
just docs-serve     # live docs preview