Command line¶
The help of every braino command, generated from the code.
braino eval compare¶
Usage: braino eval compare [OPTIONS] {before} {now}
Compare two evaluation reports: pass rate, and tasks fixed or broken.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * before <path> Earlier report (JSON) [required] │
│ * now <path> Later report (JSON) [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino eval list¶
Usage: braino eval list [OPTIONS]
List the evaluation tasks.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --include-large Also tasks that need large downloads │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino eval run¶
Usage: braino eval run [OPTIONS]
Run the evaluation tasks with an agent and score them.
Each task gets a fresh copy of its dataset and a scripted user who answers
questions and
decides on proposals. A task passes when all its required checks pass,
including that every
number in the answer comes from a tool result.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --agent <str> oracle, null, or module:factory for your │
│ own agent │
│ [default: oracle] │
│ --tasks <str> Comma-separated task ids; default all │
│ --include-large Also tasks that need large downloads │
│ --tier <str> Hardware tier this run stands for, e.g. │
│ minimum, gpu │
│ --model <str> Model name, for the report │
│ --workdir <path> Keep each task's data and transcript here │
│ --output -o <path> Write the report (JSON) here │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino import¶
Usage: braino import [OPTIONS] [source]
Import recordings into a BIDS dataset, removing personal details on the way.
Give one recording with --subject-id and --task, or many with --mapping.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ source <path> Recording to import (or use --mapping) │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --dataset <path> BIDS dataset to import into [default: .] │
│ --key <path> Subject key file (private; must be outside the │
│ dataset) │
│ --subject-id <str> The person's original ID (kept in the key) │
│ --task <str> Task label, e.g. rest │
│ --session <str> Session label │
│ --run <int> Run number │
│ --line-freq <float> Power-line frequency in Hz, if known │
│ --mapping <path> CSV with │
│ source,subject_id,task[,session,run,line_freq] │
│ --overwrite Replace recordings │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino inspect¶
Usage: braino inspect [OPTIONS]
Summarise a BIDS dataset: subjects, tasks, and each recording's channels and
events.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --dataset <path> Root of the BIDS dataset to work on [default: .] │
│ --json Print the full summary as JSON │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino model bench¶
Usage: braino model bench [OPTIONS]
Measure how fast the agent will be with the chosen model.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino model hardware¶
Usage: braino model hardware [OPTIONS]
Show this computer's CPU, RAM and GPUs, and the model tier BrainO proposes.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --json Print as JSON │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino model list¶
Usage: braino model list [OPTIONS]
List the models BrainO can run, and which are downloaded or fit here.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino model remove¶
Usage: braino model remove [OPTIONS] [model]
Delete a downloaded model or an installed llama.cpp build, to free disk space.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ model <str> Model id to delete │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --runtime <str> Delete an installed llama.cpp backend │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino model serve¶
Usage: braino model serve [OPTIONS]
Run the model server in the foreground until Ctrl+C (for development).
Prints the OpenAI-compatible base URL and this session's API key.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --port <int> Port (default: a free one) │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino model setup¶
Usage: braino model setup [OPTIONS]
Install llama.cpp and download the model for this computer, once.
Downloads are checked against pinned SHA-256 hashes and resume if interrupted.
Afterwards a
short benchmark tells you how fast the agent will be.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --model <str> Model id (default: the proposed one) │
│ --backend <str> cpu, vulkan, cuda or metal (default: │
│ auto) │
│ --bench --no-bench Measure the speed [default: bench] │
│ --yes -y Do not ask before downloading │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino model status¶
Usage: braino model status [OPTIONS]
Show the chosen model, what is installed, and the last benchmark.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino pipeline export¶
Usage: braino pipeline export [OPTIONS] {spec}
Export a pipeline's current results as a standalone Python script that re-runs
every step (including steps reused from earlier runs) and checks the results.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * spec <str> Spec file (.yaml/.json) or the name of a built-in spec │
│ [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --dataset <path> Root of the BIDS dataset to work on [default: .] │
│ --output -o <path> Write the script here instead of printing it │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino pipeline list¶
Usage: braino pipeline list [OPTIONS]
List the pipeline specs that come with BrainO.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino pipeline run¶
Usage: braino pipeline run [OPTIONS] {spec}
Run a pipeline over a dataset. Steps whose inputs and settings are unchanged
are skipped. Decision steps wait for your approval unless --auto-approve is
given; approve with 'braino proposals approve' and run again to continue.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * spec <str> Spec file (.yaml/.json) or the name of a built-in spec │
│ [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --dataset <path> Root of the BIDS dataset to work on │
│ [default: .] │
│ --subjects <str> Comma-separated subset of the subjects │
│ --from <str> Run this step and the ones after it again │
│ --auto-approve Approve every proposal as made, in your name │
│ (e.g. for validation runs) │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino pipeline show¶
Usage: braino pipeline show [OPTIONS] {spec}
Print a spec (e.g. a built-in one, to copy and adapt).
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * spec <str> Spec file (.yaml/.json) or the name of a built-in spec │
│ [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino pipeline status¶
Usage: braino pipeline status [OPTIONS] {spec}
Show, for each subject, which steps have a current result.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * spec <str> Spec file (.yaml/.json) or the name of a built-in spec │
│ [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --dataset <path> Root of the BIDS dataset to work on [default: .] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino pipeline validate¶
Usage: braino pipeline validate [OPTIONS] {spec}
Check a spec: its tools exist and accept the arguments given.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * spec <str> Spec file (.yaml/.json) or the name of a built-in spec │
│ [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino proposals approve¶
Usage: braino proposals approve [OPTIONS] {proposal_id}
Approve a proposal (optionally edited) and apply it.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * proposal_id <str> Proposal ID [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ * --dataset <path> Root of the BIDS dataset to work on [required] │
│ --edit <str> JSON object of proposal fields to change before │
│ applying │
│ --note <str> Reason for the decision │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino proposals list¶
Usage: braino proposals list [OPTIONS]
List proposals made by decision tools, oldest first.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ * --dataset <path> Root of the BIDS dataset to work on [required] │
│ --pending Only undecided proposals │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino proposals reject¶
Usage: braino proposals reject [OPTIONS] {proposal_id}
Reject a proposal; nothing is applied.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * proposal_id <str> Proposal ID [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ * --dataset <path> Root of the BIDS dataset to work on [required] │
│ --note <str> Reason for the decision │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino proposals show¶
Usage: braino proposals show [OPTIONS] {proposal_id}
Print a proposal and its decision, if any, as JSON.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * proposal_id <str> Proposal ID [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ * --dataset <path> Root of the BIDS dataset to work on [required] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino qc¶
Usage: braino qc [OPTIONS]
Check data quality: flat and noisy channels, line noise, and time with large
artifacts.
Changes nothing; per-channel tables are written to derivatives/braino/.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --dataset <path> Root of the BIDS dataset to work on [default: .] │
│ --subject <str> Subject label; omit to check every recording │
│ --task <str> Task label │
│ --session <str> Session label │
│ --run <str> Run number │
│ --json Print the summaries as JSON │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino runs export¶
Usage: braino runs export [OPTIONS] {run_id}
Export a run as a standalone Python script that re-runs it and checks its
results.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * run_id <str> Run ID, as printed by 'braino runs list' [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ * --dataset <path> Root of the BIDS dataset to work on [required] │
│ --output -o <path> Write the script here instead of printing it │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino runs list¶
Usage: braino runs list [OPTIONS]
List recorded runs, oldest first, with the tools each one called.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ * --dataset <path> Root of the BIDS dataset to work on [required] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino runs show¶
Usage: braino runs show [OPTIONS] {run_id}
Print the full provenance record of a run as JSON.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * run_id <str> Run ID, as printed by 'braino runs list' [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ * --dataset <path> Root of the BIDS dataset to work on [required] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino tools list¶
Usage: braino tools list [OPTIONS]
List the registered tools.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino tools run¶
Usage: braino tools run [OPTIONS] {name}
Run a tool and print its result as JSON.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * name <str> Tool name, e.g. system.info [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --args <str> Tool arguments as JSON [default: {}] │
│ --dataset <path> Root of the BIDS dataset to work on │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino tools schema¶
Usage: braino tools schema [OPTIONS] [name]
Print the LLM-facing JSON schema of one tool, or of all tools.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ name <str> Tool name; omit for all tools │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino validate erpcore¶
Usage: braino validate erpcore [OPTIONS] {component}
Run the built-in ERP CORE pipeline and compare with the published scores.
Downloads the data on first use (P3 2.2 GB, N170 3.4 GB for all 40
participants) into
$BRAINO_DATA (default ~/.cache/braino). Decisions are auto-approved in your
name.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * component <str> P3 or N170 [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --subjects <str> Comma-separated participants, e.g. 001,002; default │
│ all │
│ --json Print the full result as JSON │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
braino version¶
Usage: braino version [OPTIONS]
Print the BrainO version.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯