4 Project Tour

Let’s take a tour of the project repository. We assume you have cloned the project repository as described in the setting up section of the documentation. For the tour, cd into the project. For example (assuming you cloned the repo in your home folder):

cd ~/ecoevolity-hyper-time

Here’s an overview of the contents of the project:

README.md file

This markdown-formatted file contains some basic information about the project, including the license.

conda-env.yml file

This is a YAML-formatted text file that specifies the project’s conda environment. This environment is created when you run the setup_project_env.sh script.

project_utils.sh shell file

This Bash file contains information that is used by other Bash scripts, like the specific commit ID of ecoevolity that needs to be installed, the name of the project’s conda environment, and what conda program to use (i.e., conda, mamba, or micromamba).

setup_project_env.sh script

This is a Bash script that will

Create a conda environment with all of the required software for this project.
Compile and install (locally, within the project directory) a specific commit of ecoevolity.

See the setup section of the documentation for instructions on using this script to setup the working environment for this project.

data directory

This directory contains data files in a file format (YAML) recognized by ecoevolity. All of the files with the naming scheme of comp##-#species-##genomes-#####chars.txt are “dummy” data files that will be used by the simcoevolity tool to simulate datasets. They are fully valid data files for ecoevolity, but are only meant to serve the purpose of “telling” simcoevolity the size of datasets to simulate.

docs directory

This directory contains the markdown-formatted source files that are used by quarto to create the HTML files for the project’s documentation website, which is hosted via GitHub Pages.

ecoevolity-configs directory

This directory contains all of the configuration files needed for the ecoevolity simulations and analyses. These configuration files specify where the data files are located, and all of the settings for analysis. These configs are discussed in the study design and hyper prior validation sections of the documentation.

plotting-configs directory

This directory contains some YAML-formatted files that are used when plotting some of the results for the project.

scripts directory

This contains some Bash scripts for some of the longer running analyses for the project, so they can be easily submitted to the queueing system of an HPC cluster.

bin directory

This directory is created when you run the setup_project_env.sh script, and contains the compiled and executable programs of the ecoevolity package.