Installation

Sugar requires a Python version >=3.11. The package is hosted on PyPi and can be installed with pip:

pip install rnajena-sugar

To upgrade an existing installation, use the -U flag, e.g. pip install rnajena-sugar -U.

Note, that the package name is different from the import name sugar.

Inside a conda environment

If you want to install sugar in a dedicated conda environment, you may want to install most of its dependencies using conda first, e.g.

conda install -c conda-forge matplotlib pandas platformdirs pytest requests seaborn
pip install rnajena-sugar

Development version

If you want to install the latest bleeding-edge version you can clone the GitHub repository and install the code with pip, one way to do this, is:

pip install git+https://github.com/rnajena/sugar.git

Editable install

If you want to contribute code or want to hack into sugar quickly, an editable install is generally preferable:

git clone https://github.com/rnajena/sugar.git
pip install -e sugar

Minimal install

For advanced users, it is possible to get a base installation of sugar using pip’s --no-deps flag. A subset of dependencies can be installed manually, depending on the functionality needed.

Running the test suite

After installation, the test suite can be run with:

sugar test

You may want to check out its options with sugar test -h and pytest -h. Note that tests that require an Internet connection are skipped by default, this behavior can be turned off with the --web option. Also, depending on the installation and platform, some tests may be skipped or have an expected failure, to see details about the reasons please use the --verbose flag.