Chapter 14 Creating Packages with Python

Another response of the wizards, when faced with a new and unique situation, was to look through their libraries to see if it had ever happened before. This was…a good survival trait. It meant that in times of danger you spent the day sitting very quietly in a building with very thick walls.

— Terry Pratchett

The more software we write, the more we come to think of programming languages as a way to build and combine libraries. Every widely-used language now has an online repository from which people can download and install those libraries. This lesson shows you how to use Python’s tools to create and share libraries of your own.

We will continue with our Zipf’s Law project, which should include the following files:

zipf/
├── .gitignore
├── .travis.yml
├── CONDUCT.md
├── CONTRIBUTING.md
├── KhanVirtanen2020.md
├── LICENSE.md
├── Makefile
├── README.md
├── environment.yml
├── requirements.txt
├── bin
│   ├── book_summary.sh
│   ├── collate.py
│   ├── countwords.py
│   ├── plotcounts.py
│   ├── plotparams.yml
│   ├── script_template.py
│   ├── test_zipfs.py
│   └── utilities.py
├── data
│   ├── README.md
│   ├── dracula.txt
│   └── ...
├── results
│   ├── dracula.csv
│   ├── dracula.png
│   └── ...
└── test_data
    ├── random_words.txt
    └── risk.txt

14.1 Creating a Python Package

A package consists of one or more Python source files in a specific directory structure combined with installation instructions for the computer. Python packages can come from various sources: some are distributed with Python itself as part of the language’s standard library, but anyone can create one, and there are thousands that can be downloaded and installed from online repositories.

Terminology

People sometimes refer to packages as modules. Strictly speaking, a module is a single source file, while a package is a directory structure that contains one or more modules.

A generic package folder hierarchy looks like this:

pkg_name
├── pkg_name
│   ├── module1.py
│   └── module2.py
├── README.md
└── setup.py

The top-level directory is named after the package. It contains a directory that is also named after the package, and that contains the package’s source files. It is initially a little confusing to have two directories with the same name, but most Python projects follow this convention because it makes it easier to set up the project for installation.

__init__.py

Python packages often contain a file with a special name: __init__.py (two underscores before and after init). Just as importing a module file executes the code in the module, importing a package executes the code in __init__.py. Packages had to have this file before Python 3.3, even if it was empty, but since Python 3.3 it is only needed if we want to run some code as the package is being imported.

If we want to make our Zipf’s Law software available as a Python package, we need to follow the generic folder hierarchy. A quick search of the Python Package Index (PyPI) reveals that the package name zipf is already taken, so we will need to use something different. Let’s use pyzipf and update our directory names accordingly:

$ mv ~/zipf ~/pyzipf
$ cd ~/pyzipf
$ mv bin pyzipf

Updating GitHub’s Repository Name

We won’t do it in this case (because it would break links/references from earlier in the book), but now that we’ve decided to name our package is pyzipf, we would normally update the name of our GitHub repository to match. After changing the name at the GitHub website, we would need to update our git remote so that our local repository could still be synchronized with GitHub:

$ git remote set-url origin 
  https://github.com/amira-khan/pyzipf.git  

Python has several ways to build an installable package. We will show how to use setuptools, which is the lowest common denominator and will allow everyone, regardless of what Python distribution they have, to use our package. To use setuptools, we must create a file called setup.py in the directory above the root directory of the package. (This is why we require the two-level directory structure described earlier.) setup.py must have exactly that name, and must contain lines like these:

from setuptools import setup


setup(
    name='pyzipf',
    version='0.1.0',
    author='Amira Khan',
    packages=['pyzipf'])

The name and author parameters are self-explanatory. Most software projects use semantic versioning for software releases. A version number consists of three integers X.Y.Z, where X is the major version, Y is the minor version, and Z is the patch version. Major version zero (0.Y.Z) is for initial development, so we have started with 0.1.0. The first stable public release would be version 1.0.0, and in general, the version number is incremented as follows:

  • Increment major every time there’s an incompatible externally-visible change
  • Increment minor when adding new functionality in a backwards-compatible manner (i.e. without breaking any existing code)
  • Increment patch for backwards-compatible bug fixes that don’t add any new features

Finally, we specify the name of the directory containing the code to be packaged with the packages parameter. This is straightforward in our case because we only have a single package directory. For more complex projects, the find_packages function from setuptools can automatically find all packages by recursively searching the current directory.

14.2 Virtual Environments

We can add additional information to our package later, but this is enough to be able to build it for testing purposes. Before we do that, though, we should create a virtual environment to test how our package installs without breaking anything in our main Python installation. We exported details of our environment in Chapter 13 as a way to document the software we’re using; in this section, we’ll use environments to make the software we’re creating more robust.

A virtual environment is a layer on top of an existing Python installation. Whenever Python needs to find a package, it looks in the virtual environment before checking the main Python installation. This gives us a place to install packages that only some projects need without affecting other projects.

Virtual environments also help with package development:

  • We want to be able to easily test install and uninstall our package, without affecting the entire Python environment.
  • We want to answer problems people have with our package with something more helpful than “I don’t know, it works for me”. By installing and running our package in a completely empty environment, we can ensure that we’re not accidentally relying on other packages being installed.

We can manage virtual environments using conda (Appendix I). To create a new virtual environment called pyzipf we run conda create, specifying the environment’s name with the -n or --name flag and including pip and our current version of python in the new environment:

$ conda create -n pyzipf pip python=3.7.6
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/amira/anaconda3/envs/pyzipf

  added / updated specs:
    - pip
    - python=3.7.6


The following packages will be downloaded:
...list of packages...

The following NEW packages will be INSTALLED:
...list of packages...

Proceed ([y]/n)? y

...

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate pyzipf
#
# To deactivate an active environment, use
#
#     $ conda deactivate

conda creates the directory /Users/amira/anaconda3/envs/pyzipf, which contains the subdirectories needed for a minimal Python installation, such as bin and lib. It also creates /Users/amira/anaconda3/envs/pyzipf/bin/python, which checks for packages in these directories before checking the main installation.

conda Variations

As with many of the other tools we’ve explored in this book, the behavior of some conda commands differ depending on operating system. There are multiple ways to accomplish some of the tasks we present in this chapter. The options we present here represent the approaches most likely to work across multiple platforms.

Additionally, the path for Anaconda differs among operating systems. Our examples show the default path for Anaconda installed via the Unix shell on MacOS (/Users/amira/anaconda3), but for the MacOS graphical installer it is /Users/amira/opt/anaconda3, for Linux it is /home/amira/anaconda3 and on Windows it is C:\Users\amira\Anaconda3. During the installation process users can also choose a custom location if they like (Section 1.3).

We can switch to the pyzipf environment by running:

$ conda activate pyzipf

Once we have done this, the python command runs the interpreter in pyzipf/bin:

(pyzipf)$ which python
/Users/amira/anaconda3/envs/pyzipf/bin/python

Notice that every shell command displays (pyzipf) when that virtual environment is active. Between Git branches and virtual environments, it can be very easy to lose track of what exactly we are working on and with. Prompts like this can make it a little less confusing; using virtual environment names that match the names of your projects (and branches, if you’re testing different environments on different branches) quickly becomes essential.

We can now install packages safely. Everything we install will go into the pyzipf virtual environment without affecting the underlying Python installation. When we are done, we can switch back to the default environment using conda deactivate:

(pyzipf)$ conda deactivate
$ which python
/usr/bin/python

14.3 Installing a Development Package

Let’s install our package in this virtual environment. First we re-activate it:

$ conda activate pyzipf

Next, we go into the upper pyzipf directory that contains our setup.py file and install our package:

(pyzipf)$ cd ~/pyzipf
(pyzipf)$ pip install -e .
Obtaining file:///Users/amira/pyzipf
Installing collected packages: pyzipf
  Running setup.py develop for pyzipf
Successfully installed pyzipf

The -e option indicates that we want to install the package in “editable” mode, which means that any changes we make in the package code are directly available to use without having to reinstall the package; the . means “install from the current directory”.

If we look in the location containing package installations (e.g., /Users/amira/anaconda3/envs/pyzipf/lib/python3.7/site-packages/), we can see the pyzipf package beside all the other locally-installed packages. If we try to use the package at this stage, though, Python will complain that some of the packages it depends on, such as pandas, are not installed. We could install these manually, but it is more reliable to automate this process by listing everything that our package depends on using the install_requires parameter in setup.py:

from setuptools import setup


setup(
    name='pyzipf',
    version='0.1',
    author='Amira Khan',
    packages=['pyzipf'],
    install_requires=[
        'matplotlib',
        'pandas',
        'scipy',
        'pyyaml',
        'pytest'])

We don’t have to list numpy explicitly because it will be installed as a dependency for pandas and scipy.

Versioning Dependencies

It is good practice to specify the versions of our dependencies and even better to specify version ranges. For example, if we have only tested our package on pandas version 1.1.2, we could put pandas==1.1.2 or pandas>=1.1.2 instead of just pandas in the list argument passed to the install_requires parameter.

Next, we can install our package using the modified setup.py file:

(pyzipf)$ cd ~/pyzipf
(pyzipf)$ pip install -e .
Obtaining file:///Users/amira/pyzipf
Collecting matplotlib
  Downloading matplotlib-3.3.3-cp37-cp37m-macosx_10_9_x86_64.whl
     |████████████████████████████████| 8.5 MB 3.1 MB/s 
Collecting cycler>=0.10
  Using cached cycler-0.10.0-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1
  Downloading kiwisolver-1.3.1-cp37-cp37m-macosx_10_9_x86_64.whl 
     |████████████████████████████████| 61 kB 2.0 MB/s 
Collecting numpy>=1.15
  Downloading numpy-1.19.4-cp37-cp37m-macosx_10_9_x86_64.whl
     |████████████████████████████████| 15.3 MB 8.9 MB/s 
Collecting pillow>=6.2.0
  Downloading Pillow-8.0.1-cp37-cp37m-macosx_10_10_x86_64.whl
     |████████████████████████████████| 2.2 MB 6.3 MB/s 
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3
  Using cached pyparsing-2.4.7-py2.py3-none-any.whl
Collecting python-dateutil>=2.1
  Using cached python_dateutil-2.8.1-py2.py3-none-any.whl
Collecting six
  Using cached six-1.15.0-py2.py3-none-any.whl
Collecting pandas
  Downloading pandas-1.1.5-cp37-cp37m-macosx_10_9_x86_64.whl
     |████████████████████████████████| 10.0 MB 1.4 MB/s 
Collecting pytz>=2017.2
  Using cached pytz-2020.4-py2.py3-none-any.whl
Collecting pytest
  Using cached pytest-6.2.1-py3-none-any.whl
Collecting attrs>=19.2.0
  Using cached attrs-20.3.0-py2.py3-none-any.whl
Collecting importlib-metadata>=0.12
  Downloading importlib_metadata-3.3.0-py3-none-any.whl
Collecting pluggy<1.0.0a1,>=0.12
  Using cached pluggy-0.13.1-py2.py3-none-any.whl
Collecting py>=1.8.2
  Using cached py-1.10.0-py2.py3-none-any.whl
Collecting typing-extensions>=3.6.4
  Downloading typing_extensions-3.7.4.3-py3-none-any.whl
Collecting zipp>=0.5
  Downloading zipp-3.4.0-py3-none-any.whl
Collecting iniconfig
  Using cached iniconfig-1.1.1-py2.py3-none-any.whl
Collecting packaging
  Using cached packaging-20.8-py2.py3-none-any.whl
Collecting pyyaml
  Using cached PyYAML-5.3.1.tar.gz
Collecting scipy
  Downloading scipy-1.5.4-cp37-cp37m-macosx_10_9_x86_64.whl
     |████████████████████████████████| 28.7 MB 10.7 MB/s 
Collecting toml
  Using cached toml-0.10.2-py2.py3-none-any.whl
Building wheels for collected packages: pyyaml
  Building wheel for pyyaml (setup.py) ... done
  Created wheel for pyyaml:
    filename=PyYAML-5.3.1-cp37-cp37m-macosx_10_9_x86_64.whl
    size=44626
    sha256=5a59ccf08237931e7946ec6b526922e4
           f0c8ee903d43671f50289431d8ee689d
  Stored in directory: /Users/amira/Library/Caches/pip/wheels/5e/
    03/1e/e1e954795d6f35dfc7b637fe2277bff021303bd9570ecea653
Successfully built pyyaml
Installing collected packages: zipp, typing-extensions, six,
pyparsing, importlib-metadata, toml, pytz, python-dateutil, py,
pluggy, pillow, packaging, numpy, kiwisolver, iniconfig, cycler,
attrs, scipy, pyyaml, pytest, pandas, matplotlib, pyzipf
  Attempting uninstall: pyzipf
    Found existing installation: pyzipf 0.1.0
    Uninstalling pyzipf-0.1.0:
      Successfully uninstalled pyzipf-0.1.0
  Running setup.py develop for pyzipf
Successfully installed attrs-20.3.0 cycler-0.10.0
importlib-metadata-3.3.0 iniconfig-1.1.1 kiwisolver-1.3.1
matplotlib-3.3.3 numpy-1.19.4 packaging-20.8 pandas-1.1.5
pillow-8.0.1 pluggy-0.13.1 py-1.10.0 pyparsing-2.4.7 pytest-6.2.1
python-dateutil-2.8.1 pytz-2020.4 pyyaml-5.3.1 pyzipf scipy-1.5.4
six-1.15.0 toml-0.10.2 typing-extensions-3.7.4.3 zipp-3.4.0

(The precise output of this command will change depending on which versions of our dependencies get installed.)

We can now import our package in a script or a Jupyter notebook just as we would any other package. For example, to use the function in utilities, we would write:

from pyzipf import utilities as util


util.collection_to_csv(...)

To allow our functions to continue accessing utilities.py, we need to change that line in both countwords.py and collate.py.

However, the useful command-line scripts that we used to count and plot word counts are no longer accessible directly from the Unix shell. Fortunately there is an alternative to changing the function import as described above. The setuptools package allows us to install programs along with the package. These programs are placed beside those of other packages. We tell setuptools to do this by defining entry points in setup.py:

from setuptools import setup


setup(
    name='pyzipf',
    version='0.1',
    author='Amira Khan',
    packages=['pyzipf'],
    install_requires=[
        'matplotlib',
        'pandas',
        'scipy',
        'pyyaml',
        'pytest'],
    entry_points={
        'console_scripts': [
            'countwords = pyzipf.countwords:main',
            'collate = pyzipf.collate:main',
            'plotcounts = pyzipf.plotcounts:main']})

The right side of the = operator is the location of a function, written as package.module:function; the left side is the name we want to use to call this function from the command line. In this case, we want to call each module’s main function, which as it stands requires an input argument args containing the command-line arguments given by the user (Section 5.2). For example, the relevant section of our countwords.py program is:

def main(args):
    """Run the command line program."""
    word_counts = count_words(args.infile)
    util.collection_to_csv(word_counts, num=args.num)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description=__doc__)
    parser.add_argument('infile', type=argparse.FileType('r'),
                        nargs='?', default='-',
                        help='Input file name')
    parser.add_argument('-n', '--num',
                        type=int, default=None,
                        help='Output only n most frequent words')
    args = parser.parse_args()
    main(args)

We can’t pass any arguments to main when we define entry points in our setup.py file, so we need to change our script slightly:

def parse_command_line():
    """Parse the command line for input arguments."""
    parser = argparse.ArgumentParser(description=__doc__)
    parser.add_argument('infile', type=argparse.FileType('r'),
                        nargs='?', default='-',
                        help='Input file name')
    parser.add_argument('-n', '--num',
                        type=int, default=None,
                        help='Output only n most frequent words')
    args = parser.parse_args()
    return args


def main():
    """Run the command line program."""
    args = parse_command_line()
    word_counts = count_words(args.infile)
    util.collection_to_csv(word_counts, num=args.num)


if __name__ == '__main__':
    main()

The new parse_command_line function handles the command line arguments, so that main() no longer requires any input arguments.

Once we have made the corresponding change in collate.py and plotcounts.py, we can re-install our package:

(pyzipf)$ pip install -e .
Defaulting to user installation because normal site-packages is
  not writeable
Obtaining file:///Users/amira/pyzipf
Requirement already satisfied: matplotlib in
  /usr/lib/python3.7/site-packages (from pyzipf==0.1) (3.2.1)
Requirement already satisfied: pandas in
  /Users/amira/.local/lib/python3.7/site-packages
  (from pyzipf==0.1) (1.0.3)
Requirement already satisfied: scipy in
  /usr/lib/python3.7/site-packages (from pyzipf==0.1) (1.4.1)
Requirement already satisfied: pyyaml in
  /usr/lib/python3.7/site-packages (from pyzipf==0.1) (5.3.1)
Requirement already satisfied: cycler>=0.10 in
  /usr/lib/python3.7/site-packages
  (from matplotlib->pyzipf==0.1) (0.10.0)
Requirement already satisfied: kiwisolver>=1.0.1 in
  /usr/lib/python3.7/site-packages
  (from matplotlib->pyzipf==0.1) (1.1.0)
Requirement already satisfied: numpy>=1.11 in
  /usr/lib/python3.7/site-packages
  (from matplotlib->pyzipf==0.1) (1.18.2)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,
!=2.1.6,>=2.0.1 in
  /usr/lib/python3.7/site-packages
  (from matplotlib->pyzipf==0.1) (2.4.6)
Requirement already satisfied: python-dateutil>=2.1 in
  /usr/lib/python3.7/site-packages
  (from matplotlib->pyzipf==0.1) (2.8.1)
Requirement already satisfied: pytz>=2017.2 in
  /usr/lib/python3.7/site-packages
  (from pandas->pyzipf==0.1) (2019.3)
Requirement already satisfied: six in
  /usr/lib/python3.7/site-packages
  (from cycler>=0.10->matplotlib->pyzipf==0.1) (1.14.0)
Requirement already satisfied: setuptools in
  /usr/lib/python3.7/site-packages
  (from kiwisolver>=1.0.1->matplotlib->pyzipf==0.1) (46.1.3)
Installing collected packages: pyzipf
  Running setup.py develop for pyzipf
Successfully installed pyzipf

The output looks slightly different than the first run because pip could re-use some packages saved locally by the previous install rather than re-fetching them from online repositories. (If we hadn’t used the -e option to make the package immediately editable, we would have to uninstall it before reinstalling it during development.)

We can now use our commands directly from the Unix shell without writing the full path to the file and without prefixing it with python.

(pyzipf)$ countwords data/dracula.txt -n 5
the,8036
and,5896
i,4712
to,4540
of,3738

Tracking pyzipf.egg-info?

Using setuptools automatically creates a new folder in your project directory named pyzipf.egg-info. This folder is another example of information generated by a script that is also included in the repository, so it should be included in the .gitignore file to avoid tracking with Git.

14.4 What Installation Does

Now that we have created and installed a Python package, let’s explore what actually happens during installation. The short version is that the contents of the package are copied into a directory that Python will search when it imports things. In theory we can “install” packages by manually copying source code into the right places, but it’s much more efficient and safer to use a tool specifically made for this purpose, such as conda or pip.

Most of the time, these tools copy packages into the Python installation’s site-packages directory, but this is not the only place Python searches. Just as the PATH environment in the shell contains a list of directories that the shell searches for programs it can execute (Section 4.6), the Python variable sys.path contains a list of the directories it searches (Section 11.2). We can look at this list inside the interpreter:

import sys
sys.path
['',
'/Users/amira/anaconda3/envs/pyzipf/lib/python37.zip',
'/Users/amira/anaconda3/envs/pyzipf/lib/python3.7',
'/Users/amira/anaconda3/envs/pyzipf/lib/python3.7/lib-dynload',
'/Users/amira/.local/lib/python3.7/site-packages',
'/Users/amira/anaconda3/envs/pyzipf/lib/python3.7/site-packages',
'/Users/amira/pyzipf']

The empty string at the start of the list means “the current directory”. The rest are system paths for our Python installation, and will vary from computer to computer.

14.5 Distributing Packages

Look But Don’t Execute

In this section we upload the pyzipf package to TestPyPI and PyPI:

https://test.pypi.org/project/pyzipf

https://pypi.org/project/pyzipf/

You won’t be able to execute the twine upload commands below exactly as shown (because Amira has already uploaded the pyzipf package), but the general sequence of commands in this section is an excellent resource to refer back to when you are uploading your own packages. If you want to try uploading your own pyzipf package via twine, you could edit the project name to include your name (e.g. pyzipf-yourname) and use the TestPyPI repository for the upload.

An installable package is most useful if we distribute it so that anyone who wants it can run pip install pyzipf and get it. To make this possible, we need to use setuptools to create a source distribution (known as an sdist in Python packaging jargon):

(pyzipf)$ python setup.py sdist
running sdist
running egg_info
creating pyzipf.egg-info
writing pyzipf.egg-info/PKG-INFO
writing dependency_links to pyzipf.egg-info/dependency_links.txt
writing entry points to pyzipf.egg-info/entry_points.txt
writing requirements to pyzipf.egg-info/requires.txt
writing top-level names to pyzipf.egg-info/top_level.txt
writing manifest file 'pyzipf.egg-info/SOURCES.txt'
package init file 'pyzipf/__init__.py' not found
(or not a regular file)
reading manifest file 'pyzipf.egg-info/SOURCES.txt'
writing manifest file 'pyzipf.egg-info/SOURCES.txt'
running check
warning: check: missing required meta-data: url

warning: check: missing meta-data: if 'author' supplied, 
                'author_email' must be supplied too

creating pyzipf-0.1
creating pyzipf-0.1/pyzipf
creating pyzipf-0.1/pyzipf.egg-info
copying files to pyzipf-0.1...
copying README.md -> pyzipf-0.1
copying setup.py -> pyzipf-0.1
copying pyzipf/collate.py ->
  pyzipf-0.1/pyzipf
copying pyzipf/countwords.py ->
  pyzipf-0.1/pyzipf
copying pyzipf/plotcounts.py ->
  pyzipf-0.1/pyzipf
copying pyzipf/script_template.py ->
  pyzipf-0.1/pyzipf
copying pyzipf/test_zipfs.py ->
  pyzipf-0.1/pyzipf
copying pyzipf/utilities.py ->
  pyzipf-0.1/pyzipf
copying pyzipf.egg-info/PKG-INFO ->
  pyzipf-0.1/pyzipf.egg-info
copying pyzipf.egg-info/SOURCES.txt ->
  pyzipf-0.1/pyzipf.egg-info
copying pyzipf.egg-info/dependency_links.txt ->
  pyzipf-0.1/pyzipf.egg-info
copying pyzipf.egg-info/entry_points.txt ->
  pyzipf-0.1/pyzipf.egg-info
copying pyzipf.egg-info/requires.txt ->
  pyzipf-0.1/pyzipf.egg-info
copying pyzipf.egg-info/top_level.txt ->
  pyzipf-0.1/pyzipf.egg-info
Writing pyzipf-0.1/setup.cfg
creating dist
Creating tar archive
removing 'pyzipf-0.1' (and everything under it)

This creates a file named pyzipf-0.1.tar.gz, located in a new directory in our project, dist/ (another directory to add to .gitignore). These distribution files can now be distributed via PyPI, the standard repository for Python packages. Before doing that, though, we can put pyzipf on TestPyPI, which lets us test the distribution of our package without having things appear in the main PyPI repository. We must have an account, but they are free to create.

The preferred tool for uploading packages to PyPI is called twine, which we can install with:

(pyzipf)$ pip install twine

Following the Python Packaging User Guide, we upload our distribution from the dist/ folder using the --repository option to specify the TestPyPI repository:

$ twine upload --repository testpypi dist/*
Uploading distributions to https://test.pypi.org/legacy/
Enter your username: amira-khan
Enter your password: *********
Uploading pyzipf-0.1.0.tar.gz
100%|█████████████████| 5.59k/5.59k [00:01<00:00, 3.27kB/s]

View at:
https://test.pypi.org/project/pyzipf/0.1/
Our new project on TestPyPI.

Figure 14.1: Our new project on TestPyPI.

and view the results at the new test project webpage (Figure 14.1). In the exercises, we will explore additional metadata that can be added to setup.py so that it appears on the project webpage.

We can test that everything works as expected by creating a virtual environment and installing our package from TestPyPI (the --extra-index-url reference to PyPI below accounts for the fact that not all of our package dependencies are available on TestPyPI):

(pyzipf)$ conda create -n pyzipf-test pip python=3.7.6
(pyzipf)$ conda activate pyzipf-test 
(pyzipf-test)$ pip install --index-url
  https://test.pypi.org/simple 
  --extra-index-url https://pypi.org/simple pyzipf
Looking in indexes: https://test.pypi.org/simple,
                    https://pypi.org/simple
Collecting pyzipf
  Downloading pyzipf-0.1.tar.gz (5.5 kB)
Collecting matplotlib
  Using cached matplotlib-3.3.3-cp37-cp37m-macosx_10_9_x86_64.whl
...collecting other packages...
Building wheels for collected packages: pyzipf
  Building wheel for pyzipf (setup.py) ... done
  Created wheel for pyzipf:
    filename=pyzipf-0.1-py3-none-any.whl
    size=6836
    sha256=62a23715379b71ad5a6b124444fab194
           596d094c7df293c4019d33bdd648aff1
  Stored in directory: /Users/amira/Library/Caches/pip/wheels/c6/
    d6/08/f16cf80ec82a9c70ab8a5d9c8acc7ab35c9a01009539aeb2be
Successfully built pyzipf
Installing collected packages: zipp, typing-extensions, six,
pyparsing, importlib-metadata, toml, pytz, python-dateutil, py,
pluggy, pillow, packaging, numpy, kiwisolver, iniconfig, cycler,
attrs, scipy, pyyaml, pytest, pandas, matplotlib, pyzipf
Successfully installed attrs-20.3.0 cycler-0.10.0
importlib-metadata-3.3.0 iniconfig-1.1.1 kiwisolver-1.3.1
matplotlib-3.3.3 numpy-1.19.4 packaging-20.8 pandas-1.1.5
pillow-8.0.1 pluggy-0.13.1 py-1.10.0 pyparsing-2.4.7 pytest-6.2.1
python-dateutil-2.8.1 pytz-2020.4 pyyaml-5.3.1 pyzipf-0.1
scipy-1.5.4 six-1.15.0 toml-0.10.2 typing-extensions-3.7.4.3
zipp-3.4.0

Once again, pip takes advantage of the fact that some packages already existing on our system (e.g., they are cached from our previous installs) and doesn’t download them again. Once we are happy with our package at TestPyPI, we can go through the same process to put it on the main PyPI repository.

Python Wheels

When we installed our package from TestPyPI, the output said that it collected our source distribution and then used it to build a wheel for pyzipf. This build takes time (especially for large, complex packages), so it can be a good idea for package authors to create and upload wheel files (.whl) to PyPI along with the source distribution. pip will use the appropriate wheel file if it’s available at PyPI instead of building it from the source distribution, which makes the installation process faster and more efficient. Check out the Real Python guide to wheels for details.

conda Installation Packages

Given the widespread use of conda for package management, it can be a good idea to post a conda installation package to Anaconda Cloud. The conda documentation has instructions for quickly building a conda package for a Python module that is already available on PyPI. See Appendix I for more information about conda and Anaconda Cloud.

14.6 Documenting Packages

Now that our package has been distributed, we need to think about whether we have provided sufficient documentation. Docstrings (Section 5.3) and READMEs are sufficient to describe most simple packages, but as our code base grows larger we will want to complement these manually written sections with automatically generated content, references between functions, and search functionality. For most large Python packages, such documentation is generated using a documentation generator called Sphinx, which is often used in combination with a free online hosting service called Read The Docs. In this section we will update our README file with some basic package-level documentation, before using Sphinx and Read The Docs to host that information online along with more detailed function-level documentation. For further advice on writing documentation for larger and more complex packages, see Appendix G.

14.6.1 Including package-level documentation in the README

When a user first encounters a package, they usually want to know what the package is meant to do, instructions on how to install it, and examples of how to use it. We can include these elements in the README.md file we started in Chapter 7. At the moment it reads as follows:

$ cat README.md
# Zipf's Law

These Zipf's Law scripts tally the occurrences of words in text
files and plot each word's rank versus its frequency.

...

This file is currently written in Markdown, but Sphinx uses a format called reStructuredText (reST), so we will switch to that. Like Markdown, reST is a plain-text markup format that can be rendered into HTML or PDF documents with complex indices and cross-links. GitHub recognizes files ending in .rst as reST files and displays them nicely, so our first task is to rename our existing file:

$ git mv README.md README.rst

We then make a few edits to the file formatting: titles are underlined and overlined, section headings are underlined, and code blocks are set off with two colons (::) and indented. We can also add some context about why to use the package, as well as updated information about package installation:

The ``pyzipf`` package tallies the occurrences of words in text
files and plots each word's rank versus its frequency together 
with a line for the theoretical distribution for Zipf's Law.

Motivation
----------

Zipf's Law is often stated as an observational pattern seen in the
relationship between the frequency and rank of words in a text:

`"…the most frequent word will occur approximately twice as often
as the second most frequent word,
three times as often as the third most
frequent word, etc."`
`wikipedia <https://en.wikipedia.org/wiki/Zipf%27s_law>`_

Many books are available to download in plain text format
from sites such as
`Project Gutenberg <https://www.gutenberg.org/>`_,
so we created this package to qualitatively explore how well
different books align with the word frequencies predicted by
Zipf's Law.

Installation
------------

``pip install pyzipf``

Usage
-----

After installing this package, the following three commands will
be available from the command line

- ``countwords`` for counting the occurrences of words in a text.
- ``collate`` for collating multiple word count files together.
- ``plotcounts`` for visualizing the word counts.

A typical usage scenario would include running the following from
your terminal::

    countwords dracula.txt > dracula.csv
    countwords moby_dick.txt > moby_dick.csv
    collate dracula.csv moby_dick.csv > collated.csv
    plotcounts collated.csv --outfile zipf-drac-moby.jpg

Additional information on each function
can be found in their docstrings and appending the ``-h`` flag,
e.g. ``countwords -h``.

Contributing
------------

Interested in contributing?
Check out the CONTRIBUTING.md
file for guidelines on how to contribute.
Please note that this project is released with a
Contributor Code of Conduct (CONDUCT.md).
By contributing to this project,
you agree to abide by its terms.
Both of these files can be found in our
`GitHub repository. <https://github.com/amira-khan/zipf>`_

14.6.2 Creating a web page for documentation

Now that we’ve added package-level documentation to our README file, we need to think about function-level documentation. We want to provide users with a list of all the functions available in our package along with a short description of what they do and how to use them. We could achieve this by manually cutting and pasting function names and docstrings from our Python modules (i.e. countwords.py, plotcounts.py, etc), but that would be a time consuming process prone to errors as more functions are added over time. Instead, we can use a documentation generator called Sphinx that is capable of scanning Python code for function names and docstrings and can export that information to HTML format for hosting on the web.

To start, let’s install Sphinx and create a docs/ directory at the top of our repository:

$ pip install sphinx
$ mkdir docs
$ cd docs

We can then run Sphinx’s quickstart tool to create a minimal set of documentation that includes the package-level information in the README.rst file we just created and the function-level information in the docstrings we’ve written along the way. It asks us to specify the project’s name, the name of the project’s author, and a release; we can use the default settings for everything else.

$ sphinx-quickstart
Welcome to the Sphinx 3.1.1 quickstart utility.

Please enter values for the following settings (just press Enter
to accept a default value, if one is given in brackets).

Selected root path: .

You have two options for placing the build directory for Sphinx
output. Either, you use a directory "_build" within the root
path, or you separate "source" and "build" directories within the
root path.
> Separate source and build directories (y/n) [n]: n
The project name will occur in several places in the built
documentation.
> Project name: pyzipf
> Author name(s): Amira Khan
> Project release []: 0.1
If the documents are to be written in a language other than
English, you can select a language here by its language code.
Sphinx will then translate text that it generates into that
language.

For a list of supported codes, see
https://www.sphinx-doc.org/en/master/usage/configuration.html
> Project language [en]:
Creating file /Users/amira/pyzipf/docs/conf.py.
Creating file /Users/amira/pyzipf/docs/index.rst.
Creating file /Users/amira/pyzipf/docs/Makefile.
Creating file /Users/amira/pyzipf/docs/make.bat.

Finished: An initial directory structure has been created.

You should now populate your master file
/Users/amira/pyzipf/docs/index.rst and create other documentation
source files. Use the Makefile to build the docs, like so:
   make builder
where "builder" is one of the supported builders, e.g. HTML,
LaTeX or linkcheck.

quickstart creates a file called conf.py in the docs directory that configures Sphinx. We will make two changes to that file so that another tool called autodoc can find our modules (and their docstrings). The first change relates to the “path setup” section near the head of the file:

# -- Path setup -------------------------------------------------

# If extensions (or modules to document with autodoc) are in
# another directory, add these directories to sys.path here. If the
# directory is relative to the documentation root, use
# os.path.abspath to make it absolute, like shown here.

Relative to the docs/ directory, our modules (i.e. countwords.py, utilities.py, etc) are located in the ../pyzipf directory. We therefore need to uncomment the relevant lines of the path setup section in conf.py to tell Sphinx where those modules are:

import os
import sys
sys.path.insert(0, os.path.abspath('../pyzipf'))

We will also change the “general configuration” section to add autodoc to the list of Sphinx extensions we want:

extensions = ['sphinx.ext.autodoc']

With those edits complete, we can now generate a Sphinx autodoc script that generates information about each of our modules and puts it in corresponding .rst files in the docs/source directory:

sphinx-apidoc -o source/ ../pyzipf
Creating file source/collate.rst.
Creating file source/countwords.rst.
Creating file source/plotcounts.rst.
Creating file source/test_zipfs.rst.
Creating file source/utilities.rst.
Creating file source/modules.rst.

At this point, we are ready to generate our webpage. The docs sub-directory contains a Makefile that was generated by sphinx-quickstart. If we run make html and open docs/_build/index.html in a web browser we’ll have a website landing page with minimal documentation (Figure 14.2). If we click on the Module Index link we can access the documentation for the individual modules (Figures 14.3 and 14.4).

The default website landing page.

Figure 14.2: The default website landing page.

The module index.

Figure 14.3: The module index.

The countwords documentation.

Figure 14.4: The countwords documentation.

The landing page for the website is the perfect place for the content of our README file, so we can add the line .. include:: ../README.rst to the docs/index.rst file to insert it:

Welcome to pyzipf's documentation!
==================================

.. include:: ../README.rst

.. toctree::
   :maxdepth: 2
   :caption: Contents:

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

If we re-run make html, we now get an updated set of web pages that re-uses our README as the introduction to the documentation (Figure 14.5).

The new landing page showing the contents of README.rst.

Figure 14.5: The new landing page showing the contents of README.rst.

Before going on, note that Sphinx is not included in the installation requirements in requirements.txt (Section 11.8). Sphinx isn’t needed to run, develop, or even test our package, but it is needed for building the documentation. To note this requirement, but without requiring everyone installing the package to install Sphinx, let’s create a requirements_docs.txt file that contains this line (where the version number is found by running pip freeze):

Sphinx>=1.7.4

Anyone wanting to build the documentation (including us, on another computer) now only needs run pip install -r requirements_docs.txt

14.6.3 Hosting documentation online

Now that we have generated our package documentation, we need to host it online. A common option for Python projects is Read The Docs, which is a community-supported site that hosts software documentation free of charge.

Just as continuous integration systems automatically re-test things (Section 11.8), Read The Docs integrates with GitHub so that documentation is automatically re-built every time updates are pushed to the project’s GitHub repository. If we register for Read The Docs with our GitHub account, we can login at the Read The Docs website and import a project from our GitHub repository. Read The Docs will then build the documentation (using make html just as we did earlier) and host the resulting files.

For this to work, all of the source files generated by Sphinx need to be checked into your GitHub repository: in our case, this means docs/source/*.rst, docs/Makefile, docs/conf.py, and docs/index.rst. We also need to create and save a Read the Docs configuration file in the root directory of our pyzipf package:

$ cd ~/pyzipf
$ cat .readthedocs.yml
# .readthedocs.yml
# Read the Docs configuration file
# See https://docs.readthedocs.io/en/stable/config-file/v2.html
# for details

# Required
version: 2

# Build documentation in the docs/ directory with Sphinx
sphinx:
  configuration: docs/conf.py

# Optionally set the version of Python and requirements required
# to build your docs
python:
  version: 3.7
  install:
    - requirements: requirements.txt

The configuration file uses the now-familiar YAML format (Section 10.1 and Appendix H) to specify the location of the Sphinx configuration script (docs/conf.py) and the dependencies for our package (requirements.txt).

Amira has gone through this process and the documentation is now available at:

https://pyzipf.readthedocs.io/

14.7 Software Journals

As a final step to releasing our new package, we might want to give it a DOI so that it can be cited by researchers. As we saw in Section 13.2.3, GitHub integrates with Zenodo for precisely this purpose.

While creating a DOI using a site like Zenodo is often the end of the software publishing process, there is the option of publishing a journal paper to describe the software in detail. Some research disciplines have journals devoted to describing particular types of software (e.g., Geoscientific Model Development), and there are also a number of generic software journals such as the Journal of Open Research Software and the Journal of Open Source Software. Packages submitted to these journals are typically assessed against a range of criteria relating to how easy the software is to install and how well it is documented, so the peer review process can be a great way to get critical feedback from people who have seen many research software packages come and go over the years.

Once you have obtained a DOI and possibly published with a software journal, the last step is to tell users how to cite your new software package. This is traditionally done by adding a CITATION file to the associated GitHub repository (alongside README, LICENSE, CONDUCT and similar files discussed in Section 1.1.1), containing a plain text citation that can be copied and pasted into email as well as entries formatted for various bibliographic systems like BibTeX.

$ cat CITATION.md
# Citation

If you use the pyzipf package for work/research presented in a
publication, we ask that you please cite:

Khan, A., and Virtanen, S., 2020. pyzipf: A Python package for word
count analysis. *Journal of Important Software*, 5(51), 2317,
https://doi.org/10.21105/jois.02317

### BibTeX entry

    @article{Khan2020,
        title={pyzipf: A Python package for word count analysis.},
        author={Khan, Amira and Virtanen, Sami},
        journal={Journal of Important Software},
        volume={5},
        number={51},
        eid={2317},
        year={2020},
        doi={10.21105/jois.02317},
       url={https://doi.org/10.21105/jois.02317},
    }

14.8 Summary

Thousands of people have helped write the software that our Zipf’s Law example relies on, but their work is only useful because they packaged it and documented how to use it. Doing this is increasingly recognized as a credit-worthy activity by universities, government labs, and other organizations, particularly for research software engineers. It is also deeply satisfying to make strangers’ lives better, if only in small ways.

14.9 Exercises

14.9.1 Package metadata

In a number of places on our TestPyPI webpage, it says that no project description was provided (Figure 14.1). How could we edit our setup.py file to include a description? What other metadata would you add?

Hint: The setup() args documentation might be useful.

14.9.2 Separating requirements

As well as requirements_docs.txt, developers often create a requirements_dev.txt file to list packages that are not needed by the package’s users, but are required for its development and testing. Pull pytest out of requirements.txt and put it in a new requirements_dev.txt file.

14.9.3 Software review

The Journal of Open Source Software has a checklist that reviewers must follow when assessing a submitted software paper. Run through the checklist (skipping the criteria related to the software paper) and see how the Zipf’s Law package would rate on each criteria.

14.9.4 Packaging quotations

Each chapter in this book opens with a quote from the British author Terry Pratchett. This script quotes.py contains a function random_quote which prints a random Pratchett quote:

import random


quote_list = ["It's still magic even if you know how it's done.",
              "Everything starts somewhere, "\
              "though many physicists disagree.",
              "Ninety percent of most magic merely consists "\
              "of knowing one extra fact.",
              "Wisdom comes from experience. "\
              "Experience is often a result of lack of wisdom.",
              "There isn't a way things should be. "\
              "There's just what happens, and what we do.",
              "Multiple exclamation marks are a sure sign "\
              "of a diseased mind.",
              "+++ Divide By Cucumber Error. "\
              "Please Reinstall Universe And Reboot +++",
              "It's got three keyboards and a hundred extra "\
              "knobs, including twelve with ‘?' on them.",
             ]


def random_quote():
    """Print a random Pratchett quote."""
    print(random.choice(quote_list))

Create a new conda development environment called pratchett and use pip to install a new package called pratchett into that environment. The package should contain quotes.py, and once the package has been installed the user should be able to run:

from pratchett import quotes


quotes.random_quote()

14.10 Key Points

  • Use setuptools to build and distribute Python packages.
  • Create a directory named mypackage containing a setup.py script as well as a subdirectory also called mypackage containing the package’s source files.
  • Use semantic versioning for software releases.
  • Use a virtual environment to test how your package installs without disrupting your main Python installation.
  • Use pip to install Python packages.
  • The default respository for Python packages is PyPI.
  • Use TestPyPI to test the distribution of your package.
  • Use a README file for package-level documentation.
  • Use Sphinx to generate documentation for a package.
  • Use Read The Docs to host package documentation online.
  • Create a DOI for your package using GitHub’s Zenodo integration.
  • Publish the details of your package in a software journal so that others can cite it.