Setup

ChemREL can be installed via the command line from the PyPI index using the pip install command. Once installed, the ChemREL CLI can be invoked from any directory in the command line using the chemrel command (but you should cd into the proper directory first, as described below).

Virtual Environment

To ensure that the chemrel keyword is recognized by your system, it is recommended that you create a new virtual environment before installing ChemREL. To do so, open the command line and run the following.

$ python -m venv venv

Next, if using a MacOS (unix-like) or Linux machine, activate the environment by running

$ source venv/bin/activate

or if using a Windows machine, run

$ venv\Scripts\activate

instead. Your virtual environment should now be active, and the prompt in the command line should be prefaced by the name of your environment, venv.

GPU Commands

If you plan to use ChemREL CLI commands to train on a CUDA-enabled GPU, you should install versions of Spacy and PyTorch which have been compiled with CUDA enabled before installing ChemREL. To do so, within the command line and within your virtual environment, run the installation commands generated by the PyTorch quickstart site and the Spacy quickstart site after selecting your applicable preferences. Once the PyTorch and Spacy installations have been completed, proceed to the next step.

Caution

If you do not install CUDA-enabled versions of Spacy and PyTorch before installing ChemREL, all GPU-related commands will fail by default.

Installation

Now, to install ChemREL in the environment, run the following.

$ pip install chemrel

Next, run the following to ensure that ChemREL has been properly installed. A help prompt should display.

$ chemrel --help

Before running any model-related commands, ChemREL must be initialized by downloading all necessary model and config files required by the package. To download the files to your desired directory, first enter the directory where you wish to save the files by running the cd command in the command line as follows, where [PATH] should be replaced with the directory path of your desired location. Hereinafter, this directory will be referred to as the ChemREL Initial Directory.

$ cd [PATH]

Note

Note that you will need to cd into the ChemREL Initial Directory before using ChemREL in the future.

You can then run the pwd command to print the path you have entered to verify that you are in the correct directory.

Next, run the following command to download the required files. The files will be downloaded in the folder path you previously entered. This may take a while to complete.

$ chemrel init

Tip

You can also install the files to a path relative to the currently focused directory by passing an additional argument into the command, e.g. chemrel init [ALTERNATE PATH]. Here, [ALTERNATE PATH] will serve as the Initial Directory.

Note for Windows installations

If the chemrel init command hangs while downloading required files, you can alternatively clone the contents of the chemrelmodels Hugging Face repository to the same Initial Directory.

Once the initialization is complete, you are ready to begin using ChemREL.