Install

Below we assume you have the default Python environment already configured on your computer and you intend to install RerF inside of it. We strongly encourage the use of Python virtual environments, please follow instructions on venv and virtual environments.

Make sure you have the latest version of pip (the Python package manager) installed. If you do not, refer to the Pip documentation and install pip first.

Currently RerF is available on Linux and MacOS, and requires Python 3.8 or newer.

From PyPI

pip install rerf

https://pypi.org/project/rerf

From source

Requirements

Linux

Make sure you have the appropriate build tools

sudo apt-get install build-essential cmake python3-dev libomp-dev   # Ubuntu/Debian

Mac

  • Install the SDK headers (Mojave update removes SDK headers)

    open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg

  • Get brew

    /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

  • Get Python 3

    brew install python3

  • Get openmp (for multiprocessing)

    brew install libomp

  • Get llvm

    brew install llvm

  • Set up paths to use llvm’s clang

    echo ‘export PATH=“/usr/local/opt/llvm/bin:$PATH”’ >> ~/.bash_profile

    Source your .bash_profile

    source ~/.bash_profile

Install (from source)

From PyPI

pip install --no-binary rerf rerf

From GitHub

pip install -e "git+https://github.com/neurodata/RerF.git@staging#egg=rerf&subdirectory=Python"

Build from source

  • Get the source files

    git clone https://github.com/neurodata/RerF.git

  • Navigate to Python directory

    cd RerF/Python

  • Clean out old installation (skip if fresh install)

    rm -rf build

  • Build using pip

    pip install -e .