Installation

Conda (recommended)

Install Miniconda, follow the steps described here

Start the conda prompt

• Windows: Open the Anaconda Prompt via the Start menu

• macOS or Linux: Open a Terminal

Create a dimspy specific conda environment. This will install a the dependencies required to run dimspy:

$ conda create --yes --name dimspy dimspy -c conda-forge -c bioconda -c computational-metabolomics

Note

• The installation process will take a few minutes.

• Feel free to use a different name for the Conda environment

You can use the following command to remove a conda environment:

$ conda env remove -y --name dimspy

This is only required if something has gone wrong in the previous step.

Activate the dimspy environment:

$ conda activate dimspy

To test your dimspy installation, in your Conda Prompt, run the command:

$ dimspy --help

or:

$ python
import dimspy

Close and deactivate the dimspy environment when you’re done:

$ conda deactivate

PyPi

Install the current release of dimspy with pip:

$ pip install dimspy

Note

• The installation process will take a few minutes.

To upgrade to a newer release use the --upgrade flag:

$ pip install --upgrade dimspy

If you do not have permission to install software systemwide, you can install into your user directory using the --user flag:

$ pip install --user dimspy

Alternatively, you can manually download dimspy from GitHub or PyPI. To install one of these versions, unpack it and run the following from the top-level source directory using the Terminal:

$ pip install .

Testing

DIMSpy uses the Python pytest testing package. You can learn more about pytest on their homepage.