Installation

To install Jadex, open a Julia interactive session (see the Julia documentation's Getting Started page for further instructions) and then enter the package management mode by entering ] and then add Jadex:

julia> ]

pkg> add Jadex

and, optionally, to run the test suite call:

pkg> test Jadex

Alternatively, to install from the main branch hosted on GitHub, call:

pkg> add https://github.com/autocorr/autocorr/Jadex.jl

Installing in Python

To call Jadex from Python we can use the PyJulia Python package to call-out to our Julia environment. Following the PyJulia installation instructions:

(1) Ensure that Julia is installed and that the Julia executable is in one's PATH (a symbolic link is okay but not an alias).

(2) Install Jadex within Julia (see the previous section above).

Python installation without Anaconda

Now we need to install PyJulia, which can be imported as the Python julia module. If your system uses Anaconda, then please see the alternate instructions in the following section.

(3a) Install PyJulia in Python by calling python3 -m pip install --user julia from the command line.

(4a) Install the Julia dependencies of PyJulia (i.e., PyCall) from within Python by calling:

import julia
julia.install()

To import Jadex and call it, run:

from julia import Jadex
mol = Jadex.Specie("hco+@xpol", datadir="path/to/data")

Python installation with Anaconda

If using Anaconda, we need to mitigate a known limitation of PyJulia/PyCall for distributions of Python that use static linking, which is the case for Anaconda (see PyJulia's Troubleshooting page for more details).

(3b) Install PyJulia in Python by calling pip install julia from the conda environment you wish to use (i.e., after calling conda activate myenv or similar).

(4b) Before using PyJulia (i.e., import julia), turn off the Julia module compilation cache and then install the Julia dependencies of PyJulia:

from julia.api import Julia
jl = Julia(compiled_modules=False)
import julia
julia.install()