Intro to Poetry

Setting up Poetry

We first need to install Poetry. The easiest way to do this is with pipx:

pipx install poetry

Your experience doing this with other operating systems may vary. Further details about installation can be found here.

Don't do this, but you can initialize a new project with poetry from scratch:

poetry new my-project-name

Typically you would do this from the start of your work.

Or you might have some existing work and an environment that you might want to continue developing using poetry:

poetry init

Since we already have some code, we use the later option for this project. Running poetry init will involve having to run through some basic setup steps to define out config file. Replace all instances of crsid with your own CRSID.

Package name [packaging-publishing]:  cancer-prediction-crsid
Version [0.1.0]:  
Description []:  A basic model to predict cancerous tumors based on certain properties.
Author [Ryan Daniels <31715811+rkdan@users.noreply.github.com>, n to skip]:  
License []:  GPL-3.0-or-later
Compatible Python versions [^3.10]:  

Would you like to define your main dependencies interactively? (yes/no) [yes] yes

We can then open the requirements file and just read them off. Do this for everything except streamlit. When we are asked to define development dependencies, we will add black, isort, and flake8. Confirm the generation, and that should create our pyproject.toml. We'll discuss this in more detail in the notes

File structure

Let's create the file directories according to the structure below. Don't worry if the order of the files and folders isn't the same.

cancer-prediction-crsid
├── venv
├── models
│   └── cancer_model.pkl
├── data
│   ├── breast_cancer_test.csv
│   ├── breast_cancer_train.csv
│   └── breast_cancer.csv
├── cancer_prediction
│   ├── __init__.py
│   ├── app.py
│   ├── cancer_model.py
│   └── streamlit_app.py
├── tests
│   └── __init__.py
├── pyproject.toml
├── README.md
├── LICENSE.md
├── .gitignore
├── requirements.txt
└── notebook.ipynb

Licensing

We also need to populate the LICENSE.md file. You can find out the details of licensing here

Warning

If you do not include a license, nobody else can copy, distribute, or modify your work without being at risk of take-downs, shake-downs, or litigation. If the work has other contributors, this includes YOU. The GitHub Terms of Service allow people to view or fork your code.

Warning

If software does not have a license, this generally means that you do not have permission to use, modify, or share the code. Forking and viewing code does not imply that you are permitted to use, modify or share it. Your best option is to nicely ask the authors to add a license, by either sending them an email, or opening an Issue on the repo.

Adding packages to your Poetry environment

Now let's add streamlit to our project. If you open the pyproject.toml file, you'll notice that there is a list of dependencies:

[tool.poetry.dependencies]
python = "^3.10"
pandas = "2.2.1"
scikit-learn = "1.4.1.post1"
matplotlib = "3.8.3"
numpy = "1.26.4"

If we want to add another package to our project, such as streamlit, we can just say,

poetry add streamlit

Notice that now streamlit has appeared in pyproject.toml! Poetry has also created a file called poetry.lock. This file essentially locks in all of your dependencies so someone external can recreate your environment. It is somewhat analogous to the conda environment.yml file. Generally, we never alter this file manually.

Now let's implement the command line interface (CLI).