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Installation Guide

kreview is built to be a high-performance evaluation environment. It depends on DuckDB, XGBoost, SHAP, and scientific Python libraries.

Requirements

  • Python ≥ 3.10
  • pip (latest)

Environment Setup

[!IMPORTANT] Quarto is strictly required for programmatic dashboard generation. Because quarto-cli wrapper packages are unreliable across Python environments, kreview assumes the Quarto executable is installed dynamically on your OS or container.

The easiest way to run kreview without managing external dependencies is to use our pre-built Docker container (hosted on GHCR). It natively ships with Python 3.12, all ML libraries, and the underlying quarto linux binaries configured flawlessly: 

docker pull ghcr.io/msk-access/kreview:latest
docker run -v /your/data:/data ghcr.io/msk-access/kreview:latest \
  kreview run --cancer-samplesheet /data/cancer.csv ...
For more complex execution commands (e.g., binding multiple access paths), see the Docker Operations Guide.

Option 2: Local Install (Pip)

First, you must separately install Quarto via your OS manager: Follow the official Quarto Installation Guide (e.g. brew install quarto on macOS).

Then clone the repository. kreview is developed entirely using nbdev, so the source notebooks (nbs/) act as the active execution environment.

git clone https://github.com/msk-access/kreview.git
cd kreview

2. Install the Package

Install the core package with all runtime dependencies:

pip install -e .

Install with all linting, testing, CI, and documentation tools bundled: 

pip install -e '.[all]'

Optional Sub-Packages

If you only need specific toolchains instead of the full all suite: - Jupyter Only: pip install -e '.[jupyter]' - Testing Only: pip install -e '.[test]' - Docs Only: pip install -e '.[docs]'

3. Install Git Hooks

Development Hook

If you are contributing code, install the pre-commit hooks to automatically strip Jupyter notebook metadata and run linters before each commit:

nbdev-install-hooks
pre-commit install

4. Verification Check

To quickly verify that the CLI was successfully mapped:

kreview --help

You should see an output tree listing run, label, features-list, and report. If so, you're clear to proceed to Configuration!

Listing Registered Features

You can immediately verify all 26 feature evaluators are discoverable: 

kreview features-list