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Installation guide

Conventions

We assume that the following are available:

  • A Unix-based shell. For example, the terminal emulator on Linux, BSD, MacOS or the WSL terminal on Windows.
  • A Python 3.11 (or newer) installation. It can be obtained by using e.g., Micromamba.

We use the convention that $ represents the command line prompt. For example,

$ run command
means that one should type run command into the command line shell.

Installation instructions

To install Covvfit, ensure that you have Python installed and run:

$ pip install covvfit

This installs:

  • The command line program covvfit, which can be run on deconvolved data to estimate fitness advantages.
  • The Python package covvfit, which can be used to create more complex automated workflows or employed to build other tools.

Checking if the installation works

Run 

$ covvfit check

If the program outputs [Status: OK], then the tool is installed properly.

However, if you see any message with [Status: Error], then it means there is a problem with installation.

It is possible, that an incompatible version of the JAX package has been downloaded. In this case, consult this installation guide. In any other case, please report the problem by filling an issue on our bug tracker, including the output in the description of the problem.