Installation

Installation or Upgrade

Providing you have all the system requirements (see below), you can use the following command to install or upgrade DELINEATE directly from the package repositories:

python3 -m pip install -U git+https://github.com/jeetsukumaran/delineate.git

System Requirements

  • Python (3.7 or greater)

    Make sure you have Python 3.7 or higher available on your system. You can check this by typing the following in your operating system shell:

    $ python3

    If you get a response indicating that the operating system could not find or understand that command, or if it shows that the version is Python 3.6 or lesser, then please install an appropriate version of [Python3] from: https://www.python.org/downloads/ .

    (NOTE: I highly recommend that you consider using Anaconda instead of the system Python installation. As a general best practice, you should keep your operating system Python environments isolated from yours. Admittedly, this does require some extra effort and learning on your part (not just how to use Python, but how to manage Python environments using the Anaconda system). But it really is worth it! Please visit the Anaconda site for details on how to setup and use Anaconda on your system.)

  • pip (for Python 3, i.e. pip3)

    pip should be installed by default along with your Python for all newer Python versions (> 3.4), except, frustratingly enough, in the case of operating system Python’s for some flavors of Linux. As I note above, I really encourage all users to use Anaconda for their Python usage rather than the operating system Python. But if you do wish to use the operating system Python, then you will have to use your operating system package manager to install pip:

    sudo apt install python3-pip

    Note that, rather confusingly, Python 2 has its own version of pip, so if your operating system has Python 2 in addition to Python 3 side-by-side, you should ensure that you specifically have and will be running the Python 3 version by using the full version-qualified command name of pip3 rather than just pip. Type pip3 --version in your operation system shell to check:

    pip3 --version

Library Dependencies

DELINEATE makes use of the following Python libraries.

These dependencies should be installed automatically by running the pip command above. In case that does not work, you can manually install these dependencies yourself by running:

python3 -m pip install -U \
    scipy \
    numpy \
    git+https://github.com/jeetsukumaran/DendroPy.git