Installation

Note

In its current incarnation paquo requires QuPath version 0.2.1 or higher. This is mainly because we’re developing and testing against this version right now. But this is bound to change (and other versions might already be supported). Follow Paquo Issue #19 to be notified when we’re starting to work on this.

There’s multiple ways to install paquo. We offer pypi packages and will soon provide conda packages too. Right now the easiest way to help develop is to setup your environment via conda.

Install paquo’s dev environment

Tip

This is currently the best way to get started 🐍

While we’re rushing towards getting our first official release out, we’re constantly changing and improving the way paquo operates. If you think you have what it takes to live on the bleeding edge of paquo development, the easiest way is to make sure you have git and conda and conda-devenv installed and then run:

user@computer:~$ git clone https://github.com/bayer-science-for-a-better-life/paquo.git
user@computer:~$ cd paquo
user@computer:paquo$ conda devenv --env PAQUO_DEVEL=True --print > environment.yml
user@computer:paquo$ conda env create -f environment.yml

This will create a paquo conda environment with everything you need to get started. It installs a special conda-packaged QuPath that we’re currently using to develop paquo and also installs all the other things required to let you get started. You should be able to run:

user@computer:paquo$ conda activate paquo
(paquo) user@computer:paquo$ pytest

And you should see that all the tests pass ❤️

Install paquo via conda

paquo will be installable via conda-forge when we publish the first conda packages.

Install paquo via pip

paquo is installable via pypi. Run:

user@computer:~$ pip install paquo

To get the latest release. You will have to install QuPath on your machine for paquo to work correctly. Also if you want the latest development version, you can install via pip and a direct reference to the github repository:

user@computer:~$ pip install git+https://github.com/bayer-science-for-a-better-life/paquo.git

This will also require you to install QuPath. Make sure that for now, you install QuPath version 0.2.1 or newer (get it here). As long as you install in the default directory paquo should be able to find it. If you have to install it somewhere else you need to configure paquo so that it can find it. Check out the Configuration section to learn more.