1. Installation

1.1. Step 1

The easiest way to get eQuilibrator-API up and running is using virtualenv, PyPI, and Jupyter notebooks

virtualenv -p python3 equilibrator
source equilibrator/bin/activate
pip install equilibrator-api jupyter

If you are using a Windows environment, we recommend using conda instead of pip:

conda install -c conda-forge equilibrator-api

1.2. Step 2 (optional)

Run this command to initialize eQuilibrator:

python -c "from equilibrator_api import ComponentContribution; cc = ComponentContribution()"

Note, that this can take minutes or even up to an hour, since about 1.3 GBytes of data need to be downloaded from a remote website (Zenodo). If this command fails, try improving the speed of your connection (e.g. disabling your VPN, or using a LAN cable to connect to your router) and running it again.

Note that you don’t have to run this command before using eQuilibrator. It will simply download the database on the first time you try using it (e.g. inside the Jupyter notebook). In any case, after downloading the database the data will be locally cached and loading takes only a few seconds from then onwards.

1.3. Step 3 (optional)

Now, you are good to go. In case you want to see an example of how to use eQuilibrator-API in the form of a Jupyter notebook, run the following commands:

curl https://gitlab.com/equilibrator/equilibrator-api/-/raw/develop/scripts/equilibrator_cmd.ipynb > equilibrator_cmd.ipynb
jupyter notebook

and select the notebook called equilibrator_cmd.ipynb and follow the examples in it.

1.4. Dependencies

  • python >= 3.6

  • equilibrator-cache

  • component-contribution

  • numpy

  • scipy

  • pandas

  • python-Levenshtein-wheels

  • pint

  • path

  • appdirs

  • diskcache

  • httpx

  • tenacity

  • periodictable

  • uncertainties

  • pyzenodo3

  • python-slugify

  • cobra (optional)