Python Package Set-Up#



  • What is the layout of a Python package?

  • How can I quickly create the structure of a Python package?

  • What license should I choose for my project?


  • Explain Python package structure.

  • Use the CMS CookieCutter to build a Python package.

For this workshop, we are going to create a Python package that performs analysis and creates visualizations for molecules. We will start with a Jupyter Notebook that has some functions and analysis. (You should have downloaded the Jupyter Notebook during setup (Set Up).

The idea is that we would like to take this Jupyter Notebook and convert the functions we have created into a Python package. That way, if anyone (a lab-mate, for example) would like to use our functions, they can do so by installing the package and importing it into their own scripts.

To start, we will first use a tool called CookieCutter, which will set up a Python package structure and several tools we will use during the workshop.

Examples of Python package structure#

If you look at the GitHub repositories for several large Python packages such as numpy, scipy, or scikit-learn, you will notice a lot of similarities between the directory layouts of these projects.

Having a similar way to lay out Python packages allows people to more easily understand and contribute to your code.

Creating a Python package using CookieCutter#

To create a skeletal structure for our project, we will use the MolSSI Computational Molecular Science (CMS) CookieCutter. The CMS CookieCutter is a special cookiecutter created specifically by MolSSI to use the tools and services we recommend in developing a Python project.

CookieCutter will not only create our directory layout, but will also set up many tools we will use including testing, continuous integration, documentation, and version control using git. We will discuss what all of these are later in the workshop.

Obtaining CookieCutter#

You should have the general CookieCutter installed, according to the directions given in the setup (Set Up) portion of this workshop. If you do not, please navigate to setup (Set Up) and follow the instructions given there.

Running CookieCutter#

Navigate to the molssi_best_practices directory created during setup (Set Up). (CookieCutter will generate the new project in a subdirectory.) Run the CMS CookieCutter to start your project:

 cookiecutter gh:molssi/cookiecutter-cms

This command runs the cookiecutter software (cookiecutter in the command) and tells cookiecutter to look at GitHub (gh) in the repository under molssi/cookiecutter-cms. This repository contains a template that cookiecutter uses to create your project, once you have provided some starting information.

Cookiecutter Template Location

When we use the command cookiecutter gh:molssi/cookiecutter-cms, we are using the Cookiecutter tool and telling it to use the GitHub repository as a template.

The gh is for GitHub, and the molssi/cookiecutter-cms is the repository name.

You could point to any location where there is a Cookiecutter template, including files on your local file system or other online repositories.

You will see an interactive prompt that asks questions about your project. Here, the prompt appears first, followed by the default value in square brackets. The first question will be on your project name. You have very cleverly decided to give it the name molecool (it’s like molecule, but with cool instead, because of your cool visualizations - get it?)

Answer the questions according to the following. If nothing is given after the colon (:), hit enter to use the default value.

project_name [ProjectName]: molecool
repo_name [molecool]:
first_module_name [molecool]: functions
author_name [Your name (or your organization/company/team)]: *YOUR_NAME_HERE*
author_email [Your email (or your organization/company/team)]: *YOUR_EMAIL_ADDRESS_HERE*
description [A short description of the project (less than one line).]: A Python package for analyzing and visualizing xyz files.

Select open_source_license:
1 - MIT
2 - BSD-3-Clause
3 - LGPLv3
4 - Not Open Source
Choose from [1/2/3/4] (1): 2

Select dependency_source:
1 - Prefer conda-forge with pip fallback
2 - Prefer default anaconda channel with pip fallback
3 - Dependencies from pip only (no conda)
Choose from [1/2/3] (1):

Select include_ReadTheDocs:
1 - y
2 - n
Choose from [1/2] (1):

Explanation of CookieCutter Questions#

The first two questions are for the project and repository name. The project name is the name of the project, while the repo name is the name of the folder that CookieCutter will create. Usually, you will leave these two to be the same thing. The repo_name is the name that you will use to import the package you eventually create, and because of that has some rules. The repo_name must be a valid Python module name and cannot contain spaces.

The next choice is about the first module name. Modules are the .py files that contain Python code. The default for this is the repo_name, but we will change this to avoid confusion (the module in a folder named molecool in a folder named molecool??). For now, we’ll just name our first module functions, and this is where we will put all of our starting functions.

Another thing that CookieCutter checks for is your email address. Be sure to provide a valid email address to cookiecutter. (It must have an @ symbol followed by a domain name, or cookiecutter will fail.) Note that your email address is not recorded or kept by the CookieCutter software, itself. cookiecutter inserts your email address into generated files so that people using your software will have contact information for you.

License Choice#

Choosing which license to use is often confusing for new developers. The MIT license (option 1) is a very common license and the default on GitHub. It allows anyone to use, modify, or redistribute your work with no restrictions (and also no warranty).

Here, we have chosen the BSD-3-Clause. The BSD-3-Clause license is an open-source, permissive license (meaning that few requirements are placed on developers of derivative works), similar to the MIT license. However, it adds a copyright notice with your name and requires redistributors of the code to keep the notice. It also prohibits others from using the name of the project or its contributors to promote derived products without written consent.

You can see more detailed information on each license at or by clicking the links below:

  1. MIT License

  2. BSD-3-Clause

  3. LGPLv3

  4. Not Open Source - In this case, the cookiecutter will not generate a license. You can add a custom license, or choose to not add a license. If there is no license in a repository, you should assume that the project is not open source, and you cannot modify or redistribute the software.

For most of your projects, it is likely that the license you choose won’t matter a great deal. However, remember that if you ever want to change a license, you may have to get permission of all contributors. So, if you ever start a project that becomes popular or has contributors, be sure to decide your license early!

Types of Open-Source Licenses

Open-source licenses can either be ‘permissive’ or ‘copy-left’. Copy-left licenses require that derivative works also be open source. Out of the choices given above, MIT and BSD-3-Clause are permissive, while LGPLv3 is a copyleft license.

We recommend that you spend some time reading about licensing. One place to start is this helpful guide from the Chodera Lab or the website

Dependency Source#

This determines some things in the setup for what will be used to install dependencies for testing. This mostly has consequences for the section on Continuous Integration. We have chosen to install dependencies from Anaconda with pip fallback. Don’t worry too much about this choice for now.

Support for ReadTheDocs#

This option is to choose whether you would like files associated with the documentation hosting service ReadTheDocs. Choose “yes” for this workshop.

Reviewing directory contents#

Now we can examine the project layout CookieCutter has set up for us. Navigate to the newly created molecool directory.

cd molecool

You should see the following directory structure.

├──              <- Code of Conduct for developers and users
├── LICENSE                         <- License file
├──                     <- Packaging information for pip
├──                       <- Description of the project which GitHub will render
├── molecool                        <- Basic Python Package import file
│   ├──                 <- Basic Python Package import file
│   ├──                <- Starting package module
│   ├── data                        <- Sample additional data (non-code) which can be packaged. Just an example, delete in production
│   │   ├──
│   │   └── look_and_say.dat
│   └── tests                       <- Unit test directory with sample tests
│       ├──
│       └──
├── devtools                        <- Deployment, packaging, and CI helpers directory
│   ├──
│   ├── conda-envs                  <- Conda environments for testing
│   │   └── test_env.yaml
│   └── scripts
│       └──     <- OS agnostic Helper script to make conda environments based on simple flags
├── docs                            <- Documentation template folder with many settings already filled in
│   ├── Makefile
│   ├──                   <- Instructions on how to build the docs
│   ├── _static
│   │   └──
│   ├── _templates
│   │   └──
│   ├── api.rst
│   ├──
│   ├── getting_started.rst
│   ├── index.rst
│   ├── make.bat
│   └── requirements.yaml           <- Documentation building specific requirements. Usually a smaller set than the main program
├── pyproject.toml                  <- Generic Python build system configuration (PEP-517).
├── readthedocs.yml
├── setup.cfg                       <- Near-master config file to make house INI-like settings for Coverage, Flake8, YAPF, etc.
├──                        <- Your package's setup file for installation with additional options that can be set
├── .codecov.yml                    <- Codecov config to help reduce its verbosity to more reasonable levels
├── .github                         <- GitHub hooks for user contribution, pull request guides, and GitHub Actions CI
│   ├──
│   ├──
│   └── workflows
│       └── CI.yaml
├── .gitignore                      <- Stock helper file telling git what file name patterns to ignore when adding files
└── .lgtm.yml

Visualizing the Directory Structure

To visualize your project like above you will use tree. If you do not have tree, you can get it using sudo apt-get install tree on Linux, or brew install tree on Mac. Note: tree will not show you the helpful labels after <- (those were added by us).

CookieCutter has created a lot of files!

If you have set up VSCode as your text editor as described in the setup (Set Up), you can open a VSCode project that contains the newly created molecool directory by typing

code .

This will open a new VSCode window with your current directory (.) the molecool directory as the root directory.

The files that Cookiecutter has created for us can be thought of as three sections. In the top level of our project, we have a folder for tools related to development (devtools), documentation (docs) and to the package itself (molecool). We will first be working in the molecool folder to build our package, and adding more things later.

├── molecool
│   ├──                 <- Basic Python Package import file
│   ├──                <- Starting package module
│   ├── data                        <- Sample additional data (non-code) which can be packaged
│   │   ├──
│   │   └── look_and_say.dat
│   ├── tests                       <- Unit test directory with sample tests
│   │   ├──
│   │   └──

This the only folder we actually have to work with to build our package. The other folders relate to “best practices”, which do not technically have to be used in order for your package to be working (but you should do them, and we will talk about them later). You could build this directory structure by hand, but we have just used cookiecutter to set it up for us. This directory will contain all of our Python code for our project, as well as sample data (in the data folder), and tests (in the tests folder.)

Packages and modules

What ‘packages’ or ‘modules’ are in Python may be confusing. In general, ‘module’ refers to a single .py file containing Python definitions and statements. It may be imported for use in another module or script. The module name is determined by the file name. A function defined in a module is used (once the module is imported) using the syntax module_name.function_name().

‘Package’ refers to a collection of Python modules. The package may also have an file. To read more about Python packages vs. modules, check out Python’s documentation.

The molecool directory#

We will first examine some files in the molecool directory. This is the directory that contains our package code.

The file#

The file is a special file recognized by the Python interpreter which makes a directory into a package. This file can be blank in some cases, however, we will use it to define how the user interacts with the functions in our package.

Contents of molecool/molecool/

"""A Python package for analyzing and visualizing xyz files."""

# Add imports here
from .functions import *

from ._version import __version__

The very first section of this file contains a string opened and closed with three quotations. This is a docstring, and has a short description of the file.

The section we will be concerned with is under # Add imports here. This is how we define the way functions from modules are used.

In particular, the line

from .functions import *

goes to the file, and brings everything that is defined there into the file. When we use our function defined in, that means we will be able to just say molecool.canvas() instead of giving the full path molecool.functions.canvas(). If that’s confusing, don’t worry too much for now. We will be returning to in a few minutes. For now, just note that it exists and makes our directory into a package.

Our first module#

Once inside the molecool folder (molecool/molecool), examine the files that are there. View the module ( in a text editor. We see a few things about this file. The top begins with a description of this module surrounded by three quotations ("""). Right now, that is the sentence “Provides the primary functions”. We will change this to be more descriptive later. CookieCutter has also created a placeholder function called canvas. At the start of the canvas function, we have a docstring (more about this in [documentation]), which describes the function.

We will be moving all of the functions we defined in the Jupyter notebook into python modules (.py files) like these.

Before proceeding, make sure your pip and setuptools packages are up-to-date

conda update pip setuptools

Installing from local source.#

You may be accustomed to pip automatically retrieving packages from the internet.

To develop this package, we will want to use what is called “development mode”, or an “editable install”, so that we can try out our functions and package as we develop it. We access development mode using the -e option to pip.

Reviewing the generated config files#

Return to the top directory (molecool). Two of the files CookieCutter generated are pyproject.toml and setup.cfg. These are the configuration files for our packaging and testing tools. pyproject.toml tells setuptools about your package (such as the name and version) as well as which code files to include. We’ll be using this file in the next section.

Installing your package#

A development install, also known as an “editable” install, will allow you to import your package and use it from anywhere on your computer. You will then be able to import your package into scripts in the same way you import matplotlib or numpy. This setup is particularly useful during development, as it ensures that any changes you make to your package’s code are immediately reflected in your Python environment, without the need for reinstallation.

To perform a development installation, you use pip with the -e option, which stands for “editable”. This tells pip to install the package in such a way that it links directly to your project’s source code.

pip install -e .

Here, the -e indicates that we are installing this project in editable mode (i.e. setuptools development mode), while . indicates to install from the local directory (you could also specify a path here).

When you install a Python package using either pip or conda, that package is installed in your Python environment’s site-packages folder. You can see where this is by checking your Python system path. To do this, open Python (type python into your terminal window), and type

>>> import sys
>>> sys.path

This will output a list of locations that Python searches for packages. One of these will typically end with site-packages, indicating the directory where Python looks for installed packages.

If you examine site-packages, you are likely to see a folder with your package’s name followed by a .dist-info. Inside, the direct_url.json file signifies an editable installation by pointing back to your project’s directory.

Python Packaging’s Rapidly Evolving Landscape

In recent years, the Python packaging ecosystem has seen the development of numerous tools designed to streamline the process. While the MolSSI CookieCutter primarily utilizes setuptools and pyproject.toml for packaging, alternatives like poetry and flit offer different features and workflows. Depending on your tool of choice or even your Python version, you may encounter various files or configurations within site-packages following an editable installation.

After our install, we can use our package from any directory, similar to how we can use other installed packages like numpy. Open Python, and type

>>> import molecool
>>> molecool.canvas()

This should print a quote.

'The code is but a canvas to our imagination.\n\t- Adapted from Henry David Thoreau'

A development installation inserts a link to your project into your Python site-packages folder so that updates are immediately available the next time you launch Python, without having to reinstall your package.

Check Your Understanding

What happens if we use conda deactivate and attempt to execute the code above?

What if we switch directories?

Final Repository State

You can see the final state of the repository after this section here.

You can also download a zip of the repository here.

Key Points#

Key Points

  • There is a common way to structure Python packages.

  • You can use the CMS CookieCutter to quickly create the layout for a Python package.

  • An editable installation allows you to use your package from anywhere on your computer, and with updates immediately available.