Installation

Install Julia (v1.11 or newer) using https://github.com/JuliaLang/juliaup

curl -fsSL https://install.julialang.org | sh

After restarting your shell you should be able to start the Julia REPL via the command julia.

In the REPL you can add (the release version of) ISOKANN.jl to your project by entering the package mode (type ]) and typing

pkg> add ISOKANN
pkg> test ISOKANN

If you want the newest features you can instead install the newest version using pkg> add https://github.com/axsk/ISOKANN.jl instead.

Note that this can take a while on the first run as Julia downloads and precompiles all dependencies.

ISOKANN is using OpenMM for sampling, which is being called through PyCall.jl - a library facilitating python calls from withing julia. PyCall can install OpenMM automatically if it is using a conda environment managed by Julia through Conda.jl. This is the default on Windows on Mac systems, on Linux however you would need to install OpenMM via pip yourself or instruct Julia to use the Conda.jl environment by running

Then instruct PyCall to use the Conda.jl environment by calling

julia> ENV["PYTHON"] = ""
pkg> build PyCall

To use a shared Conda environment, e.g. because of quota limitations, you can configure it using prior to building PyCall:

julia> ENV["CONDA_JL_HOME"] = "/data/[...]/conda/envs/conda_jl"  # change this to your path, which contains bin/conda etc.
pkg> build Conda

See also the PyCall docs.

Development

If you want to make changes to ISOKANN you should clone it into a directory

git clone git@github.com:axsk/ISOKANN.jl.git

Then start Julia in that directory, activate it with ]activate ., instantiate the dependencies with ]instantiate.

See also the (almost mandatory read) on the Julia Pkg docs.

We strongly recommend using the Revise.jl package through using Revise before loading ISOKANN, so that your changes will automatically load in your current session.