Run any Skill in Manus with one click

Get Started

install

Stars41

Forks6

UpdatedMay 20, 2026 at 13:08

Use this skill if the required tools are not yet installed.

Installation

Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.

Run Skill in Manus

Source

int-brain-lab

int-brain-lab/ibl-ai-agent

View GitHub Repository View Creator Repositories

Download

Run Skill in Manus

Related occupationsSOC

Based on SOC occupation classification

Software DevelopersComputer and Mathematical Occupations·SOC 15-1252

SKILL.md

readonly

name	install
description	Use this skill if the required tools are not yet installed.

Preflight and Installation

Before the first research, report-writing, or publishing task in a fresh checkout, run a small setup preflight yourself. Check for a usable Python, uv, a project environment, core Python imports, Quarto for report rendering, Git/GitHub CLI for publishing, GitHub authentication when publishing is requested, and configured IBL data access or local dataset paths when data loading is needed.
If any of these items are missing STOP, do not proceed to scientific analyses. Even if the user has asked a scientific question, do not proceed with scientific analyses unless the user gives you explicit instructions to do so rather than completing installation.
Instead, interactively lead the user through installation of missing items, using uv unless explicitly instructed otherwise. Explain the missing item(s) and offer to install or configure them. Use tool calls to run the needed commands after approval when network, package installation, or external authentication is required.
Prefer uv for project setup. If uv is missing but Python is available, offer to install uv, then run UV_CACHE_DIR=.uv-cache uv sync --extra ibl --extra notebook --extra dev. Use uv run ... for project commands once the environment exists. Do not recommend plain pip install -e . as the primary setup path because brainwidemap is resolved through uv sources.
Verify Quarto, git, gh, and gh auth status, which are required for report publication.
For some packages such as Quarto, git, and gh, automatic installation may be difficult. In such cases, guide the user to appropriate websites to manually download and install what is needed.
If the BWM data shards are not yet present, ask the user if these files are already present on disk. If so, edit data_locations.local.yaml to point to them; if not, ask the user for a location to download to (defaulting to data/ within the current repo), download, then edit data_locations.local.yaml.

More from this repository

same repository

ibl-analyze

int-brain-lab/ibl-ai-agent

Use this skill for quantitative scientific analysis of IBL data after the always-on scientific workflow in `AGENTS.md` is active.

2026-06-2341

ibl-load

int-brain-lab/ibl-ai-agent

Use this skill when loading IBL data, preferring the smallest sufficient local or aggregate surface before session-level loaders.

2026-06-2341

scientific-coding-style

int-brain-lab/ibl-ai-agent

describes how to write code to be read and validated by human scientists.

2026-06-1341

ibl-neuropixel

int-brain-lab/ibl-ai-agent

Use this skill for raw Neuropixels binary access, destriping, compression, waveform extraction, and probe-level preprocessing based on the `int-brain-lab/ibl-neuropixel` repository.

2026-05-2641

exploration-confirmation

int-brain-lab/ibl-ai-agent

Use this skill to analyze scientific data: refine, formalize and test hypotheses.

2026-05-2041

ibl-access

int-brain-lab/ibl-ai-agent

Use this skill when a task needs IBL data access setup, ONE/Alyx authentication, or selecting between public and private data modes.

2026-05-1941

Preflight and Installation

Before the first research, report-writing, or publishing task in a fresh checkout, run a small setup preflight yourself. Check for a usable Python, uv, a project environment, core Python imports, Quarto for report rendering, Git/GitHub CLI for publishing, GitHub authentication when publishing is requested, and configured IBL data access or local dataset paths when data loading is needed.

If any of these items are missing STOP, do not proceed to scientific analyses. Even if the user has asked a scientific question, do not proceed with scientific analyses unless the user gives you explicit instructions to do so rather than completing installation.

Instead, interactively lead the user through installation of missing items, using uv unless explicitly instructed otherwise. Explain the missing item(s) and offer to install or configure them. Use tool calls to run the needed commands after approval when network, package installation, or external authentication is required.

Prefer uv for project setup. If uv is missing but Python is available, offer to install uv, then run UV_CACHE_DIR=.uv-cache uv sync --extra ibl --extra notebook --extra dev. Use uv run ... for project commands once the environment exists. Do not recommend plain pip install -e . as the primary setup path because brainwidemap is resolved through uv sources.

Verify Quarto, git, gh, and gh auth status, which are required for report publication.

For some packages such as Quarto, git, and gh, automatic installation may be difficult. In such cases, guide the user to appropriate websites to manually download and install what is needed.

If the BWM data shards are not yet present, ask the user if these files are already present on disk. If so, edit data_locations.local.yaml to point to them; if not, ask the user for a location to download to (defaulting to data/ within the current repo), download, then edit data_locations.local.yaml.