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Install the software

Install the software#

We recommend using the latest version of Python and Java, jp²rt is tested under Python 3.10 and Java 17; the Python package includes a precompiled version of the Java package, so you don’t need to install it separately.

Virtual environments#

It’s suggested to use a virtual environment to manage Python dependencies: virtual environments are independent groups of Python libraries, one for each project; packages installed for one project will not affect other projects or the operating system’s packages.

Create an environment#

Python 3 comes bundled with the :mod:venv module to create virtual environments. Create a project folder and a :file:venv folder within:

$ mkdir myproject
$ cd myproject
$ python3 -m venv venv

On Windows:

> py -3 -m venv venv

Activate the environment#

Every time you decide to use the library, activate the environment:

$ . venv/bin/activate

On Windows:

> venv\Scripts\activate

Install the package#

Within the activated environment, use the following command to install the full version of the package:

$ pip install jp2rt[plot]

If you plan to use the package on a system with no graphic support (for instance, on an headless high-performance computing cluster), you can install the package without the optional dependencies for plotting as:

$ pip install jp2rt

To check the installation just run

$ jp2rt --help

it should print the help message, including the list of available subcommands:

Usage: jp2rt [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  compute-descriptors  Computes molecular descriptions.
  estimate-model       Estimates a model using the given ensemble regressor.
  list-descriptors     List the known molecular descriptors.
  list-models          List the known ensemble models.
  predict-rt           Uses the model to predict the retention time.

Install just the Java library#

If you need to run just the descriptors computation on a system where it would be difficult to setup a Python environment (for instance, on a high performance computing cluster), you can install just the Java library as follows:

  • manually downloading a fat jar (containing all the dependencies) from the Releases page of the jp²rt repository, or

  • using the GitHub Apache Maven registry of the jp²rt repository; beware that authentication is needed, so please check the instructions.

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