Installation

There are different ways to install cocoatree:

• Install the latest official release. This is the best approach for most users and will provide a stable version.

• Building the package from source. This is best for users who want the latest-and-greatest features and aren’t afraid of running brand-new code. This is also needed for users who wish to contribute to the project.

Install the latest release

Install a version of Python 3, for instance from https://www.python.org.

Then run:

pip install -U cocoatree

In order to check your installation you can use:

python -m pip show cocoatree # to see which version and where cocoatree is installed
python -m pip freeze # to see all packages installed in the active environment.

Note that in order to avoid potential conflicts with other packages it is strongly recommended to use a virtual environment, e.g. python3 virtualenv or conda environments.

Building the package from source

Building from source is required to work on a contribution (bug fix, new feature, code or documentation improvement).

1. Use Git to check out the latest source from the cocoatree repository on Github.:

   git clone git@github.com:TrEE-TIMC/cocoatree.git
   cd cocoatree
   

   If you plan on submitting a pull-request, you should clone from your fork instead.

2. Install the following dependencies if they are not already installed:

   • Python (>= 3.11)

   • NumPy (>= 2.1),

   • SciPy (>= 0.1dd9.1),

   • Matplotlib (>= 3.9),

   • scikit-learn

   • biopython

   • ete3

   • pyqt5

   • pandas

2. Optional (but recommended): create and activate a dedicated virtualenv or conda environment.

3. Build the project with pip in Editable mode:

   pip install --verbose --editable .
   

   If you run the development version, it is cumbersome to reinstall the package each time you update the sources. Therefore it is recommended that you install in with the pip install –editable . command, which allows you to edit the code in-place. This builds the extension in place and creates a link to the development directory (see the pip docs).

   This is fundamentally similar to using the command python setup.py develop (see the setuptool docs). It is however preferred to use pip.

   On Unix-like systems, you can equivalently type make in from the top-level folder. Have a look at the Makefile for additional utilities.

4. Check that the installed cocoatree has a version number ending with .dev0:

   python -c "import cocoatree; cocoatree.__version__"
   

Additional dependencies for building the documentation

In addition to the aforementioned dependencies for cocoatree, in order to build the documentation you will need:

• sphinx (>= 1.0)

• sphinx-gallery

• numpydoc

• pillow

These can be installed with pip using the command:

pip install -U sphinx sphinx-gallery numpydoc

Additional dependencies for running the tests

In addition to the aforementioned dependencies for cocoatree, in order to build the documentation you will need:

• pytest

• pytest-cov

• flake8

These can be installed with pip using the following command:

pip install -U pytest pytest-cov