Python Scripts and Modules

Overview

Questions

• What is a ‘module’ in Python? How does this differ from a ‘script’?
• What are the benefits of modularising our Python code?

Objectives

• Introduce the example library used in this lesson.
• Understand the limitations of scripts.
• Understand what happens when we import something.
• Learn how to convert a simple script into a reusable module.

Python as a Scripting Language

---

Python is frequently used as a scripting language by scientists and engineers due to its expressiveness, simplicity, and its rich ecosystem of third-party libraries. There isn’t a hard line between a scripting language and a non-scripting language, but some differences include:

• Scripts are not compiled to an executable or library object (such as .so or .dll) before use, and are instead interpreted directly from the source code. A non-scripting language, such as C++, must be compiled to machine code before it can be used.
• Scripts must be run using some other compiled program, such as python or bash.
• Scripts are typically short programs that leverage the power of complex libraries to accomplish some task. They focus more on gluing together existing tools than performing their own low-level computations.

Python is a very general-purpose language, and it meets the criteria of both a scripting language and a non-scripting language depending on how we choose to use it:

• Python can be run as an interactive session simply by calling python at the command line. This is typical of a scripting language.
• It is possible to write a linear series of Python expressions in a file, and run this using the Python interpretter –again, like a scripting language.
• Python code can be bundled in modules and packages which can then be import-ed into other Python programs/scripts. These are typically pre-compiled into ‘bytecode’ to improve performance. This is closer to the behaviour of a fully compiled language.

Typically, a Python project will begin as something that is inarguably a ‘script’, but as it develops it will take on the character of a ‘program’. A single file containing a linear series of commands may develop into a module of reusable functions, and this may develop further into a package of related modules. Developing our software in this way allows our programs to grow in complexity in a much more sustainable manner, and grants much more flexibility to how users can interact with our code.

Throughout this course, we’ll develop an example library that might be used for epidemiology modelling, though it isn’t necessary to understand how this works in order to follow the course. We’ll begin where many new Python projects start: with a simple script. This one solves a SIR model, which models the number of Susceptible, Infected, and Recovered individuals as a pathogen spreads through a population. The general pattern of the code – set up inputs, solve a problem, plot the results – should be familiar to those working in a data-oriented field. It uses the popular plotting library Matplotlib to generate a figure.

PYTHON

import matplotlib.pyplot as plt

# Inputs
# Total number of susceptible people at the start of an outbreak
pop_size = 8000000
# Average no. of new infections per infected person per day
beta = 0.5
# Inverse of the average number of days taken to recover
gamma = 0.1
# Number of days to run the simulation for
days = 150
# Number of infected people at the start of the simulation
I_0 = 10

# Initialise data
S = [] # Number of susceptible people each day
I = [] # Number of infected people each day
R = [] # Number of recovered people each day
S.append(pop_size - I_0)
I.append(I_0)
R.append(0)

# Solve model
for i in range(days):
    # Get rate of change of S, I, and R
    dS = - beta * S[i] * I[i] / pop_size
    dR = gamma * I[i]
    dI = -(dS + dR)
    # Get values on next day
    S.append(S[i] + dS)
    I.append(I[i] + dI)
    R.append(R[i] + dR)

# Plot results
plt.plot(range(len(S)), S, label="S")
plt.plot(range(len(I)), I, label="I")
plt.plot(range(len(R)), R, label="R")
plt.xlabel("Time /days")
plt.ylabel("Population")
plt.legend()
plt.show()

If we save this script to the file SIR_model_script.py, it can then be run from the command line as follows:

BASH

$ python3 SIR_model_script.py

If everything works as expected, it should produce the following result:

SIR model results

So far so good, but there are some limitations to this coding style.

Challenge

Can you think of any drawbacks to writing scripts like the one shown above? Think about the general structure of the code and how the user interacts with it rather than the details of the implementation.

Show me the solution

There are many possible answers to this. Here are some examples:

• If the user wants to change the model inputs, they have to open the script file and modify some lines of code before running again. This is difficult to automate and it’s possible that the user might overwrite something they didn’t intend to.
• If we wish to expand on this functionality or do something different with the output data, we must either overwrite our original script, or copy the code across to a new scipt. If we choose to copy the script, it would take a lot of effort to update all versions every time we wish to adjust the core routine, and this is likely to introduce bugs.
• The user must know where the script is stored on their system, navigate to that directory, and call it from there. This makes it challenging to string scripts together to make more complex programs.

It’s important to note that there’s nothing strictly wrong with writing scripts in this way, and it’s often a good starting point for a new project. However, as we develop our project further, we might find it useful to bundle up the reusable bits of our code into a module that we can import from other Python programs, just as we import-ed Matplotlib in our own script.

What is a ‘Module’?

---

A module is simply any file containing Python statements, so, technically, the script we defined above is already a module. The name of a module is the same as the file name, only without the .py extension. If we were to open a new Python interpretter session and call the following:

PYTHON

>>> import SIR_model_script

then the script would run as if we’d run it from the command line. However, the variables we defined in the script will be accessible within the namespace SIR_model_script:

PYTHON

>>> import SIR_model_script
>>> print(SIR_model_script.S)

The current namespace includes all of the objects defined in our interpretter session, plus all built-in Python functions and types. When we import our script, we add the name of the script to the current namespace, but not the variables defined within it; those are defined within the scope of SIR_model_script, and are only accessible using the dot operator. If we wanted to bring everything within the script to the current namespace, but not the module itself, we can instead call:

PYTHON

>>> from SIR_model_script import *
>>> print(S)

Alternatively, if we only want a few objects brought into the current namespace, we can use:

PYTHON

>>> from SIR_model_script import S, I, R
>>> print(S, I, R)

The dangers offrom module import *

Using from module import * is considered harmful by many developers, as objects can be unintentionally overwritten if there are any name clashes between modules. It can also make it difficult for people reading you code to tell which modules your functions and classes have come from. In general, it’s better to be explicit about what you’re import-ing.

It is also possible to assign an alias to a module name using the as keyword:

PYTHON

>>> import SIR_model_script as script
>>> print(type(script.S))

Something to note about import is that it runs the code found within the module only the first time it is imported, so if we were to import our script multiple times, it would only create a plot once.

While we’ve shown that our script is importable, so far it doesn’t seem to provide many advantages over simply running it on the command line. The next section will explain what features can make a module more versatile and useful.

Challenge

Let’s save the following code in the file my_module.py:

PYTHON

x = 10

Then we open an interpetter and call the following:

PYTHON

>>> import my_module
>>> my_module.x += 5
>>> import my_module
>>> print(my_module.x)

What is the result?

Show me the solution

The result is 15, as the second import does not run the code in my_module.py, and therefore my_module.x is not reset back to 10.

Making a Reusable Module

---

A good Python module will tend to do the following:

• Define functions, classes and constants that the user might want to use.
• Not rely on global variables (those defined within the module but not inside of functions/classes), except in a few scenarios where it only makes sense for a single instance of the an object to exist.
• Avoid performing runtime calculations at the import stage.

Most Python modules shouldn’t do anything if we try to run them from the command line, and instead they should provide import-able tools that can be used in the Python interpretter, by other Python modules, or by dedicated scripts. We’ll see later how to write a reusable Python module that doubles as a runnable script.

Most scripts can be converted into reusable modules using the following steps:

• Identify each major stage of our data processing. Examples may include reading in data, running a model, processing results, creating plots, etc.
• For each stage, identify what data is an input, and what is an output.
• Bundle each processing stage into a function that takes the input data as arguments and returns the output data.

For example, the script SIR_model_script has two stages that can be bundled into functions. The first stage runs the SIR model, and it takes the following input parameters:

Parameter	Type	Description
pop_size	int	Total number of susceptible people at the start of an outbreak
beta	float	Average no. of new infections per infected person per day
gamma	float	Inverse of the average number of days taken to recover
days	int	Number of days to run the simulation for
I_0	int	Number of infected people at the start of the simulation

The output data from this stage is:

Parameter	Type	Description
S	List[float]	Number of susceptible people each day
I	List[float]	Number of infected people each day
R	List[float]	Number of recovered people each day

We can therefore bundle this portion of the script into the function SIR_model:

PYTHON

def SIR_model(pop_size, beta, gamma, days, I_0):
    """
    Solves a SIR model numerically using a simple integration scheme.

    Parameters
    ----------
    pop_size: int
        Total number of susceptible people at the start of an outbreak.
    beta: float
        Average number of new infections per infected person per day.
    gamma: float
        Inverse of the average number of days taken to recover.
    days: int
        Number of days to run the simulation for.     
    I_0: int
        Number of infected people at the start of the simulation.

    Returns
    -------
    S: List[float]
        Number of susceptible people on each day.
    I: List[float]
        Number of infected people on each day.
    R: List[float]
        Number of recovered people on each day.
    """
    # Initialise data
    S = [] # Number of susceptible people each day
    I = [] # Number of infected people each day
    R = [] # Number of recovered people each day
    S.append(pop_size - I_0)
    I.append(I_0)
    R.append(0)

    # Solve model
    for i in range(days):
        # Get rate of change of S, I, and R
        dS = - beta * S[i] * I[i] / pop_size
        dR = gamma * I[i]
        dI = -(dS + dR)
        # Get values on next day
        S.append(S[i] + dS)
        I.append(I[i] + dI)
        R.append(R[i] + dR)

    return S, I, R

Note that we’ve provided a nice docstring, so that users of our function can understand how to use it. The second stage of our script takes the results of the SIR model as input data, and produces a plot. We can therefore bundle the plotting parts of the script as follows:

PYTHON

# Note: imports should go at the top of the file
import matplotlib.pyplot as plt

def plot_SIR_model(S, I, R):
    """
    Plot the results of a SIR simulation.

    Parameters
    ----------
    S: List[float]
        Number of susceptible people on each day.
    I: List[float]
        Number of infected people on each day.
    R: List[float]
        Number of recovered people on each day.

    Returns
    -------
    None
    """
    plt.plot(range(len(S)), S, label="S")
    plt.plot(range(len(I)), I, label="I")
    plt.plot(range(len(R)), R, label="R")
    plt.xlabel("Time /days")
    plt.ylabel("Population")
    plt.legend()
    plt.show()

If we save the two code blocks above to a file called SIR_model.py, we can then open up a Python interpreter and run the following:

PYTHON

>>> from SIR_model import SIR_model, plot_SIR_model
>>> S, I, R = SIR_model(
        pop_size=8000000, beta=0.5, gamma=0.1, days=150, I_0=10
    )
>>> plot_SIR_model(S, I, R)

This should give us the same results as when we ran the script earlier, and we can run the SIR_model function with different inputs without needing to change the input parameters in the file itself. The functions in our script are now therefore ‘reusable’, and can be integrated in other workflows. The nice docstrings we added can be viewed using the built-in help() function:

PYTHON

>>> help(SIR_model)

However, the script-like behaviour has been lost:

BASH

$ python3 SIR_model.py
$ # Nothing happens!

In the next section, we’ll show how to maintain script-like behaviour, and write reusable modules in the same file.

Maintaining Script-Like Functionality

---

If we wish, we can also maintain the script-like behaviour using the if __name__ == "__main__".py idiom at the bottom of the file SIR_model.py. Here, we create a special if block at the bottom of our module, and within this we call each of our functions in turn, using the outputs of one as inputs to the next:

PYTHON

# file: SIR_model.py

# Add this after our function definitions
if __name__ == "__main__":
    S, I, R = SIR_model(
        pop_size=8000000, beta=0.5, gamma=0.1, days=150, I_0=10
    )
    plot_SIR_model(S, I, R)

With this is place, we can still run the module as if it were a script:

BASH

$ python3 SIR_model.py

However, this section will not run if we import the file. Let’s break down how this works:

• Each Python module is automatically assigned a variable __name__, and this is usually set to the name of the file without the .py extension.

PYTHON

>>> import SIR_model
>>> print(SIR_model.__name__)

OUTPUT

"SIR_model"

• The exception to the rule is when we run a Python module as a script. In this case, the top-level file instead has its __name__ variable set to "__main__".

Therefore, the code written under if __name__ == "__main__" will run if we use the module as a script, but not if we import the file.

Challenge

If we create the the file name_test.py, which contains only the following line:

PYTHON

print(__name__)

What happens if we run the following on the command line?

BASH

$ python3 name_test.py

Show me the solution

It prints "__main__"

Challenge(continued)

What if instead we open an interpreter and import it?

PYTHON

>>> import name_test

Show me the solution

It prints "name_test"

As we’ll see later, it can also be handy to bundle the contents of our if __name__ == "__main__" block into a function, as then we can import that function and access our script-like behaviour in another way. This function can take any name, but is often called main:

PYTHON

# file: SIR_model.py

def main():
    S, I, R = SIR_model(
        pop_size=8000000, beta=0.5, gamma=0.1, days=150, I_0=10
    )
    plot_SIR_model(S, I, R)

if __name__ == "__main__":
    main()

We’ll use this format later when discussing ways to make runnable packages.

Managing PYTHONPATH

---

Our script is now import-able, so the SIR_model function can be used from any other Python script, module, or interpretter session. However, we still need to know where the module is stored on our file system, which can make it difficult to reuse the functions in a separate project. A simple solution is to set the PYTHONPATH environment variable on our system. On Linux machines, this can be achieved using:

BASH

$ export PYTHONPATH="${PYTHONPATH}:/path/to/my/module/directory"

If you want this to be set every time you open a terminal, you can add the line to the file ~/.bashrc.

However, this is not recommended as a long-term solution, as a custom PYTHONPATH can cause dependency conflicts between different packages on our system and can be difficult to debug. In a later chapter, we will show how to install our own modules using the pip package manager, which gives us much more control over how we integrate our modules into our Python environments (which may be managed using tools such as venv or conda), and also allows us to install packages from a remote repository. We’ll also show how to upload our own packages to the remote repository PyPI, and therefore allow others to download and install our code from the command line!

Extra: Better Automation with Matplotlib

---

Earlier, we converted the plotting section of our script into a function that the user can call. There are two issues with the implementation as it stands:

• The use of plt.show() interrupts the flow of the program and requires the user to manually save the figure or discard it. This makes it difficult to automate the production of figures.
• As it calls plt.plot() without first creating a new figure, it may interfere with our user’s Matplotlib code.

We can improve the function with a few changes:

• Rather than using Matplotlib’s ‘implicit’ API (such as by using plt.plot()), which manages global Matplotlib objects, use the ‘explicit’ API, sometimes called the ‘object-oriented’ API. This requires handling Figure and Axes objects directly.
• Optionally take in an Axes object. This way, the user can choose to set up their own Figure and Axes, and our function can write to it.
• Return the Axes object that we worked on, so that the user can make further changes if they wish.
• Only use plt.show() if the user requests it. Also provide an option to save the figure.

Here is an example of an improved function:

PYTHON

import matplotlib.pyplot as plt

def plot_SIR_model(S, I, R, ax=None, save_to=None, show=False):
    """
    Plot the results of a SIR simulation.

    Parameters
    ----------
    S: List[float]
        Number of susceptible people on each day.
    I: List[float]
        Number of infected people on each day.
    R: List[float]
        Number of recovered people on each day.
    ax: Optional[plt.Axes], default None
        Axes object on which to create the plot.
        A new Axes is created if this is None.
    save_to: Optional[str], default None
        Name of the file to save the plot to.
        Does not save if None.
    show: bool, default False
        If True, call plt.show() on completion.

    Returns
    -------
    plt.Axes
        The axes object the results have been plotted to.
    """
    # Use plt.subplots to create Figure and Axes objects
    # if one is not provided.
    if ax is None:
        fig, ax = plt.subplots()

    # Create plot
    ax.plot(range(len(S)), S, label="S")
    ax.plot(range(len(I)), I, label="I")
    ax.plot(range(len(R)), R, label="R")
    ax.set_xlabel("Time /days")
    ax.set_ylabel("Population")
    ax.legend()

    # Optionally save the figure
    if save_to is not None:
        fig = ax.get_figure()
        fig.savefig(save_to)

    # Optionally show the figure
    if show:
        plt.show()

    return ax

This gives our users much more control over how to create plots, and it allows our function to be used as part of a larger automated pipeline that runs without needing human input. There are many further ways we could improve this function and allow our users to finely control what’s plotted, such as by allowing the user to overwrite axis/line labels or interact with legend placement, but we’ll move on from this topic for now.

Extra: Better scripting with argparse

---

We showed earlier how to maintain script-like functionality in our modules. We’ll update that code to include our updated plotting function, so we’ll automatically save to a file if the user runs our script:

PYTHON

# file: SIR_model.py

def main():
    S, I, R = SIR_model(
        pop_size=8000000, beta=0.5, gamma=0.1, days=150, I_0=10
    )
    plot_SIR_model(S, I, R, save_to="SIR_model.png")

if __name__ == "__main__":
    main()

An issue with our example is that it still requires the user to manually edit the file if they wish to change the input or outputs. This problem can be solved by instead taking arguments from the command line. A simple interface can be created using sys.argv, which is a list of command line arguments in the form of strings:

PYTHON

# file: SIR_model.py
import sys

def main():
    # Note: sys.argv[0] is the name of our program!
    pop_size = int(sys.argv[1])
    beta = float(sys.argv[2])
    gamma = float(sys.argv[3])
    days = int(sys.argv[4])
    I_0 = int(sys.argv[5])
    output = sys.argv[6]

    S, I, R = SIR_model(
        pop_size=pop_size,
        beta=beta,
        gamma=gamma,
        days=days,
        I_0=I_0,
    )
    plot_SIR_model(S, I, R, save_to=output)

if __name__ == "__main__":
    main()

However, this requires the user to provide every argument in order, and doesn’t allow default arguments. We can achieve a better interface using the built-in argparse library. The comments in the code below explain how this works:

PYTHON

# file: SIR_model.py
from argparse import ArgumentParser

def main():
    # Create an argument parser object. We can provide
    # some info about our program here.
    parser = ArgumentParser(
        prog="SIR_model",
        description="Solves SIR model and creates a plot",
    )

    # Add each argument to the parser. We can specify
    # the types of each argument. Optional arguments
    # should have single character names with a hypen,
    # or longer names with a double dash.
    parser.add_argument(
        "-p", "--pop_size", type=int, default=10000000,
        help="Total population size",
    )
    parser.add_argument(
        "-b", "--beta", type=float, default=0.5,
        help="Average no. of new infections per infected person per day",
    )
    parser.add_argument(
        "-g", "--gamma", type=float, default=0.1,
        help="Inverse of average number of days taken to recover",
    )
    parser.add_argument(
        "-d", "--days", type=int, default=150,
        help="Number of days to run the simulation",
    )
    parser.add_argument(
        "-i", "--i0", type=int, default=10,
        help="Number of infected people at the start of the simulation",
    )
    parser.add_argument(
        "-o", "--output", default="SIR_model.png",
        help="Output file to save plot to",
    )

    # Get each argument from the command line
    args = parser.parse_args()

    # Run our code
    S, I, R = SIR_model(
        pop_size=args.pop_size,
        beta=args.beta,
        gamma=args.gamma,
        days=args.days,
        I_0=args.i0,
    )
    plot_SIR_model(S, I, R, save_to=args.output)

if __name__ == "__main__":
    main()

We can now run our script using inputs from the command line:

BASH

$ python3 SIR_model.py --pop_size=1000 --days=10 -o mymodel.png

We defined each option with a default, so we don’t need to provide all of them if we don’t want to. Each option has a long form with two dashes (--output, --beta), and a short form with one dash (-o, -b), which are interchangeable (if we wish, we could provide only the short form or the long form). Note that we can use either an equals = or a space to separate the option name from its value.

If we had provided options without preceeding dashes, they would become ‘positional’ arguments, and would be required. The order positional arguments should be supplied is given by the order in which they are added to the parser. For example, if we had added beta and gamma as follows:

PYTHON

    parser.add_argument(
        "beta", type=float,
        help="Average no. of new infections per infected person per day",
    )
    parser.add_argument(
        "gamma", type=float,
        help="Inverse of average number of days taken to recover",
    )

We would need to supply these arguments in order when running our code. Positional arguments are not specified by name on the command line:

BASH

$ python3 SIR_model.py 0.5 0.1 --pop_size=1000 --days=10 -o mymodel.png

If we forget how our script is supposed to be run, argparse automatically provides a nice help message if we run it with -h or --help:

BASH

$ python3 SIR_model.py --help

usage: SIR_model [-h] [-p POP_SIZE] [-b BETA] [-g GAMMA] [-d DAYS] [-i I0] [-o OUTPUT]

Solves SIR model and creates a plot

optional arguments:
  -h, --help            show this help message and exit
  -p POP_SIZE, --pop_size POP_SIZE
                        Total population size
  -b BETA, --beta BETA  Average no. of new infections per infected person per day
  -g GAMMA, --gamma GAMMA
                        Inverse of average number of days taken to recover
  -d DAYS, --days DAYS  Number of days to run the simulation
  -i I0, --i0 I0        Number of infected people at the start of the simulation
  -o OUTPUT, --output OUTPUT
                        Output file to save plot to

There are many ways to control our command line interface in more detail, such as constraining the possible user input choices, parsing lists of inputs, and using ‘sub-parsers’ to split functionality across a number of sub-commands, much like how pip handles its many utilities:

BASH

$ pip install --upgrade mypkg myotherpkg
$ pip list --exclude numpy

Here, install and list are sub-commands, which each handle a different set of their own args. We’ll show how to achieve this in the next lesson, where we’ll expand our code from a single module to a collection of modules known as a ‘package’.

Key Points

• Any Python file can be considered a ‘module’, and can be import-ed. This just runs the code in the file, and makes the names of any objects in the module accessible using dot-notation.
• If we bundle our Python scripts into a collection of functions, we can reuse those functions in other modules or in the Python interpretter.
• After turning our scripts into reusable modules, we can maintain script-like behaviour using the idiom if __name__ == "__main__".
• argparse can be used to create sophisticated command line interfaces.