eli-project-template

For dependency management, I make use of poetry. This is a great tool for managing dependencies and virtual environments. I highly recommend using it for your projects. If you are not familiar with poetry, I suggest reading the documentation.

General Setup

Poetry reccomends using a virtual environment to install Poetry inside of to avoid conflicts and Poetry updates. To do this, run the following:

conda create -n eli-project-template python=3.11 -y
conda activate eli-project-template
python3 -m pip install --user pipx
python3 -m pipx ensurepath

This creates a conda environment called eli-project-template and activates it. You can name the environment whatever you want, but I suggest using the name of the project. This way, you can easily see which environment is for which project.

Once you have your environment setup, you can install poetry with the following command:

pipx install poetry

Project Setup

This project comes with a pyproject.toml file. This file is used to manage your project's dependencies and virtual environment. If you want to generate a new one and follow along with the rest of the setup, you can run the following command, or you can just edit the file directly:

poetry init

This will initialize the poetry project and create a pyproject.toml file. This file is used to manage your project's dependencies and virtual environment. At this point, you can edit the pyproject.toml file to add your dependencies and add your project's information..

You can add your dependencies to the pyproject.toml file and then run the following command to install them (this also installs your package so you can use it in your code):

poetry install --with dev

This will create a virtual environment and install your dependencies, including the development group dependencies. This will ensure that everyone is working with the same versions of the same packages. This is great for reproducibility and avoiding conflicts. On SuperPOD, you don't need the --with-dev flag, since this is more for MKDocs and other development tools. SuperPOD should be more about just running your code.

Now, edit your ./code_package to be an appropriate name (and reflect this in you pyproject.toml). Once you have that done

Installing Packages

Instead of using pip install, you can use poetry add to add a package to your project. This will add the package to your pyproject.toml file and install it in your virtual environment. For example, to install pandas, you would run the following command:

poetry add pandas

This will add pandas to your pyproject.toml file and install it in your virtual environment.

MKDocs

This project uses MKDocs to generate documentation. Under the docs directory, you can add markdown files to create your documentation. Once you have added your markdown files, you can run the following command to generate the documentation and serve it locally:

mkdocs serve

For more details on how to use MKDocs, I suggest reading the documentation.