OneZoom Tree Building repo

This repository contains everything that is needed to build the OneZoom tree and all the other files needed by the backend.

Setting up the environment

The first step to using this repo is to create a Python virtual environment and activate it:

# From the root of the repo, create a Python environment and activate it
python3 -m venv .venv
source .venv/bin/activate

# Install it
pip install -e .

After the first time, you just need to run the source .venv/bin/activate each time you want to activate it in a new shell.

Testing

To run the test suite, from the root of the repo, and from your activated environment, run

pytest

Building the latest tree from OpenTree

Setup

We assume that you want to build a OneZoom tree based on the most recent online OpenTree version. You can check the most recent version of both the synthetic tree (synth_id) and the taxonomy (taxonomy_version) via the API e.g. by running curl -X POST https://api.opentreeoflife.org/v3/tree_of_life/about. Later in the build, we use specific environment variables set to these version numbers. Assuming you are in a bash shell or similar, you can set them as follows:

OT_VERSION=14_9 #or whatever your OpenTree version is
OT_TAXONOMY_VERSION=3.6
OT_TAXONOMY_EXTRA=draft1 #optional - the draft for this version, e.g. `draft1` if the taxonomy_version is 3.6draft1

Download

Constructing the full tree of life requires various files downloaded from the internet. They should be placed within the appropriate directories in the data directory, as documented here.

Building the tree

Once data files are downloaded, you should be set up to actually build the tree and other backend files, by following these instructions.