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INSTALLING_WITH_PIP.md

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Installing python packages

BioDendro is a python program which can be used as a python module or via a command-line interface. It can be installed from PyPI https://pypi.org/project/BioDendro/ using pip.

It is tested to work with python 3.6+, and it depends on several packages:

The install procedures below will install these for you automatically.

Typical install with pip

python3 -m pip install --user BioDendro

The --user flag tells pip to install to a user directory rather than a system directory (e.g. somewhere under /usr/ or Program Files). To install as root or in Windows you can omit the --user flag, but you may need root or administrator permission.

Note that the --user subdirectory containing scripts (<userdir>/bin on linux/mac or <userdir>\Scripts on Windows), may not automatically be on your path. The user directory installed to is given by the python command import site; print(site.USER_BASE). Generally on linux this is ~/.local. You can change this directory by setting the $PYTHONUSERBASE environment variable. You can then add the Script or bin subdirectory to your $PATH environment variable (e.g. Linux and MacOS, or Windows, or just google it ;) ).

Power users and sys-admins may also be interested in the pip install --prefix flag, but this will also require you to update your $PYTHONPATH environment variable or use .pth files . Nonetheless, it's useful for module software management.

Installing in a virtualenv

Generally it's a good idea to install python packages in a python virtual environment This protects versions of packages required for your operating system to work, from being updated (potentially breaking older code).

Here's a basic rundown of the virtualenv workflow.

# If it isn't installed already run one of these
# Try to use the system package managers if possible to avoid mixing up system dependencies.
# Mac users may be interested in homebrew.
sudo python3 -m pip install virtualenv
sudo apt install python3-virtualenv # Ubuntu and probably Debian
sudo dnf install python3-virtualenv # Fedora 24+

# Change dir to where you want the envronment to live (usually a project dir).
cd my_project

# Create a virtualenv in a folder ./env
# python3 can be substituted with your version of python.
python3 -m venv env

# Loads the virtualenv (essentially this changes PYTHONPATH and some other environment variables).
source env/bin/activate

which python3
# ./env/bin/python3

python3 -m pip install BioDendro

BioDendro --help

This time we don't need to use sudo or tell pip to install as --user because it will install all files in the ./env folder. Note however, that whenever you start a new terminal and want to use this environment you'll need to repeat the source env/bin/activate. If you want to exit the virtual environment, you can type deactivate on the command line or just start a new terminal.

Installing from git repository.

To install most recent commit on the master branch:

python3 -m venv env
source env/bin/activate
python3 -m pip install git+https://github.com/ccdmb/BioDendro.git

Note that we installed the package in a virtual environment, which is always recommended. See the section above for more details.

You can also clone the repository yourself and then install from that.

git clone https://github.com/ccdmb/BioDendro.git ./BioDendro
cd BioDendro

python3 -m venv env
source env/bin/activate

python3 -m pip install .

This is particularly useful if you want to modify the code. You can install the module in a way that allows changes you make to be automatically installed.

# Use this after cloning.
python3 -m venv env
source env/bin/activate

python3 -m pip install -e ".[dev,test]"

The [dev,test] thing just installs some extra packages used for testing etc.