Muni CLI

Muni is the command-line interface for the Muni platform. Use it to discover available tools, submit jobs, monitor runs, download outputs, and work with spaces and canvas nodes from your terminal.

Install

pipx install muni

Or install into an existing environment:

pip install muni

Requires Python 3.11 or newer.

Log in

muni login

On a server or SSH session without a browser:

muni login --device

Check the active account:

muni whoami

Common Workflow

Find a tool:

muni tools
muni tools --category protein-design
muni tools -q rfd3

Inspect tool inputs:

muni tool rfd3 --inputs
muni tool rfd3 --examples

Submit a job:

muni run rfd3 pdb_id=1UBQ num_designs=5

Submit and wait for completion:

muni run rfd3 pdb_id=1UBQ num_designs=5 --follow

Submit parameters from JSON:

muni run rfd3 --params-file params.json --follow

Run a batch from JSONL:

muni run ipsae --batch jobs.jsonl --follow
cat jobs.jsonl | muni run ipsae --batch - --follow

Check status and retrieve outputs:

muni status job_<uuid>
muni wait job_<uuid>
muni results job_<uuid>
muni results job_<uuid> --fields rank,sequence
muni files job_<uuid>
muni download-all job_<uuid> -o ./results/

Pipeline Workspaces

Create and validate an agent-ready pipeline workspace:

muni pipeline init ./my-pipeline
cd ./my-pipeline
muni pipeline check --json

The JSON check response is compact by default: it reports pipeline identity, tools, stage order, issues, compiler provenance, artifact digests, and written paths. The complete manifest and run plan are still written under .muni/build/; use muni pipeline check --json --full when those large values must also be returned on stdout. muni pipeline dashboard push compiles and saves dashboard source through the canonical Muni app/Canvas path, then writes the full server-returned artifact locally while printing only a bounded hash/version/diagnostics summary. Successful checks record a short-lived server receipt, and muni pipeline release obtains and submits a fresh receipt before publishing.

Spaces and Canvas Nodes

List and choose a workspace:

muni spaces
muni spaces -q protein --limit 50
muni spaces --roles       # show your email and role in each space
muni spaces --all --json  # fetch every matching page
muni space use             # choose interactively
muni space use "My Space"  # or pass a name/ID
muni page use              # choose a page in the active space

Once selected, muni run, muni job materialize, muni nodes, and muni node default to that active space/page. Canvas-targeted muni run creates and submits a real job node so completion can add deterministic result nodes to the canvas. Use --space-id or --page-id to override one command, or muni space use none / muni run ... --no-space for API-only jobs.

Control result-node creation explicitly when needed:

muni run rfd3 pdb_id=1UBQ --auto-materialize
muni run rfd3 pdb_id=1UBQ --no-auto-materialize

--auto-materialize requires a selected space/page and cannot be combined with --no-space, --no-nodes, or the legacy --no-result-nodes flag. Omitting both Boolean flags preserves the existing default.

List nodes on the active page:

muni nodes
muni nodes search "PXDesign"

Create or inspect nodes:

muni node create table "Results"
muni node create structure "TREM2 rank 1" --file ./rank_1.cif
muni node read <node_id>
muni node submit <node_id> --wait

Command Reference

Command What it does
muni login Authenticate the CLI
muni whoami Show the current account
muni balance Show credit balance
muni tools List available tools
muni tool <name> Show details for one tool
muni run <tool> KEY=VALUE Submit a job
muni jobs List recent jobs
muni jobs --tool ipsae Filter recent jobs by tool
muni status <job_id> Check a job
muni wait <job_id> Wait for one or more jobs
muni results <job_id> Print job results
muni files <job_id> List job output files
muni download <job_id> <path> Download one output file
muni download-all <job_id> Download all output files
muni spaces List spaces with pagination
muni spaces -q <query> Search spaces by name or member email
muni spaces --roles List spaces with your email and role
muni space <subcommand> Manage a space
muni nodes List canvas nodes
muni node <subcommand> Create, read, edit, connect, or run nodes

Run muni --help or muni <command> --help for the full set of options.

License

MIT

Project links

Data verified by PyPI on Jul 26, 2026
Data provided by the project maintainers, verified at the time the release was uploaded to PyPI.

Key dates

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  • Released:
Newer release available (0.2.3)

1 maintainer

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Avatar for dereka from gravatar.com dereka

Credits

Author: BioArena

GitHub Statistics

Data verified by PyPI on Jul 26, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License expression

MIT
View SPDX License List

Requires

Python >=3.11

Tags

bioarena muni cli bioinformatics protein-design

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