Installation and Requirements

Prerequisites

PyCoBi has been build and tested for Python >= 3.6. We recommend to use Anaconda to create a new python environment with Python >= 3.6. In addition, Auto-07p has to be installed manually, since it is not uploaded at PyPI or Anaconda at the moment. Below, you find standard installation instructions that should work on most systems. If you run into problems, check out the specific installation instructions of Auto-07p for your operating system.

Step 1:

Clone the Auto-07p github repository via the following command line call

git clone https://github.com/auto-07p/auto-07p

Step 2:

Go to the directory that you cloned the Auto-07p repository into and run the configuration script from command line

./configure

If this step fails (check the displayed output whether configuration was successful or not), one of the most likely issues is that no fortran compiler is installed on your system. In that case, see the Auto-07p documentation for required prerequisites for your operating system (you will not need to install prerequisites for the plotting/user interface functionalities).

Step 3:

In the same directory, execute the installation of Auto-07p via the following command line call

make

Step 4:

Finally, still in the same directory, install the Python package of Auto-07p via

python setup.py install

It is important that you use the Python interpreter that you also plan to use for installation of PyCoBi. After that, the installation instructions provided below should work independent of the operating system.

Dependencies

PyCoBi has the following hard dependencies:

  • pyrates

  • numpy

  • matplotlib

  • pandas

Following the installation instructions below, these packages will be installed automatically, if not already installed within the Python environment you are using.

Installation

PyCoBi can be installed via the pip command. Simply run the following line from a terminal with the target Python environment being activated:

pip install pycobi

You can install optional (non-default) packages by specifying one or more options in brackets, e.g.:

pip install pycobi[dev]

Currently, the only available option is dev (includes pytest and bump2version).

Alternatively, it is possible to clone this repository and run one of the following lines from the directory in which the repository was cloned:

python setup.py install

or

pip install .[<options>]