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Installation

BAT.jl is written in the Julia programming language. To use BAT.jl, you will need to install Julia itself, the BAT.jl Julia package, and some additional Julia packages. Depending on your use case, you may also want to need a Python installation with certain Python packages (optional).

Table of contents:

Installing Julia

Julia is available for Linux, OS-X and Windows, and easy to install:

  • Download Julia.

  • Extract the archive (Linux), resp. drag Julia into Applications (OS-X) or run the installer (Windows).

  • You may want to add the Julia bin directory to your $PATH. To get the location of the Julia bin directory on OS-X or Windows, start a Julia session (via applications menu) and run the Julia command Sys.BINDIR.

Note

BAT.jl requires Julia >= v1.6, we strongly recommend to use the latest Julia version for optimal performance.

BAT.jl is provided as a registered Julia package. To install it, simply run

julia> using Pkg
julia> pkg"add BAT"

However, you will likely need other Julia packages too. We recommend that you install certain statistics, plotting, I/O and array packages as well:

julia> using Pkg
julia> pkg"add BAT ArraysOfArrays Distributions ElasticArrays IntervalSets Parameters Plots StatsBase Tables TypedTables"

In addition, these packages will need to be installed and loaded (using PackageName or import PackageName) to enable some optional BAT algorithms/functionalities:

julia> pkg"add AutoDiffOperators AdvancedHMC Cuba Folds HDF5 NestedSamplers Optim"

To install the latest development version of BAT (main branch) instead of the latest stable release, use

julia> pkg"add BAT#main"

Installing Visual Studio Code and Jupyter (Optional)

Please download and install the lastest Julia release.

You may also want to install Visual Studio Code with the VS-Code Julia extension and/or a have a working Jupyter installation. JupyterLab Desktop is easy to install (but a full Anaconda or custom Python installation with Jupyter will work too, of course). For details regarding Julia and Jupyter, see the IJulia.jl documentation.

IJulia (Jupyter Julia kernel)

To use the the Julia Jupyter kernel, you need to add the package "IJulia.jl":

On Linux, simply use

pkg"add IJulia"

On OS-X, if you have an existing Jupyter installation (e.g. via Anaconda) and would like Julia to use it (instead of an internal Conda installation, see above), use (e.g.)

ENV["JUPYTER"] = "$(homedir())/opt/anaconda3/bin/jupyter"; pkg"add IJulia"

On Windows, if would like Julia to use an existing Jupyter installation (see above), use something like

ENV["JUPYTER"] = "DRIVE:/path/to/your/anaconda/.../jupyter.exe"; pkg"add IJulia"

Julia will remember the chosen Jupyter installation permanently, ENV["JUPYTER"] only needs to be set the first time you run pkg"add IJulia".

Environment variables

You may want/need to set the following environment variables:

  • $PATH: Include the Julia bin-directory in your binary search path, see above. On OS-X and Windows, Visual Studio Code should detect the path your Julia binary automatically, if installed in the default location.

  • $JULIA_NUM_THREADS: Number of threads to use for Julia multi-threading

  • $JULIA_DEPOT_PATH and JULIA_PKG_DEVDIR: If you want Julia to install packages in another location than $HOME/.julia.

See the Julia manual for a description of other Julia-specific environment variables.

Additional customization options

Note: If you want Julia to install packages in another location than $HOME/.julia, set the environment variables JULIA_DEPOT_PATH and JULIA_PKG_DEVDIR (see above).