Chapter 4 Command Line Programs in Python

Multiple exclamation marks are a sure sign of a diseased mind.

— Terry Pratchett

The Jupyter Notebook, PyCharm, and other graphical interfaces are great for prototyping code and exploring data, but eventually we may need to apply our code to thousands of data files, run it with many different parameters, or combine it with other programs as part of a data analysis pipeline. The easiest way to do this is often to turn our code into a standalone program that can be run in the Unix shell just like other command-line tools (Taschuk and Wilson 2017).

In this chapter we will develop a command-line Python program that handles input and output in the same way as other shell commands, can be controlled by several option flags, and provides useful information when things go wrong. The result will have more scaffolding than useful application code, but that scaffolding stays more or less the same as programs get larger.

After the previous chapters, our Zipf’s Law project should have the following files and directories:

zipf/
├── bin
│   └── book_summary.sh
└── data
├── dracula.txt
├── frankenstein.txt
├── jane_eyre.txt
├── moby_dick.txt
├── sense_and_sensibility.txt
├── sherlock_holmes.txt
└── time_machine.txt

4.1 Programs and Modules

To create a Python program that can run from the command line, the first thing we do is to add the following to the bottom of the file:

if __name__ == '__main__':

This strange-looking check tells us whether the file is running as a standalone program or whether it is being imported as a module by some other program. When we import a Python file as a module in another program, the __name__ variable is automatically set to the name of the file. When we run a Python file as a standalone program, on the other hand, __name__ is always set to the special string "__main__". To illustrate this, let’s create the file print_name.py that prints the value of the __name__ variable:

print(__name__)

When we run this file directly, it will print __main__:

$python print_name.py __main__ But if we import print_name.py from another file or from the Python interpreter, it will print the name of the file, i.e. print_name. $ python
Python 3.8.1 | packaged by conda-forge | (default, Jan 29 2020, 14:55:04)
[GCC 7.3.0] on linux
>>> import print_name
print_name

Checking the value of the variable __name__ therefore tells us whether our file is the top-level program or not. If it is, we can handle command-line options, print help, or whatever else is appropriate; if it isn’t, we should assume that some other code is doing this.

We could put the main program code directly under the if statement like this:

if __name__ == "__main__":
# code goes here

but that is considered poor practice, since it makes testing harder (Chapter 11). Instead, we put the high-level logic in a function, then call that function if our file is being run directly:

def main():
# code goes here

if __name__ == "__main__":
main()

This top-level function is usually called main, but we can use whatever name we want.

4.2 Handling Command-Line Options

The first thing the main function usually does is parse any options the user gave the program on the command line. The most commonly used library for doing this in Python is argparse, which can handle options with or without arguments, convert arguments from strings to numbers or other types, display help, and many other things.

The simplest way to explain how argparse works is by example. Let’s create a short Python program called script_template.py:

import argparse

def main(args):
print('Input file:', args.infile)
print('Output file:', args.outfile)

if __name__ == '__main__':
USAGE = 'One-line description of what the script does.'
parser = argparse.ArgumentParser(description=USAGE)
args = parser.parse_args()
main(args)

If script_template.py is run as a standalone program at the command line then __name__ == '__main__' is true, so the program uses argparse to create an argument parser. It then specifies that it expects two command-line arguments: and input filename (infile) and output filename (outfile). The program uses parse_args() to parse the actual command-line arguments given by the user and stores the result in a variable called args, which it passes to main. That function can then get the values using the names specified in the parser.add_argument calls.

Specifying Types

We have passed type=str to add_argument to tell argparse that we want infile and outfile to be treated as strings. str is not quoted because it is not a string itself: instead, it is the built-in Python function that converts things to strings. As we will see below, we can pass in other functions like int if we want arguments converted to numbers.

If we run script_template.py at the command line the output shows us that argparse has successfully handled the arguments:

$python script_template.py in.csv out.png Input file: in.csv Output file: out.png It also displays an error message if we give the program invalid arguments: $ python script_template.py in.csv
usage: script_template.py [-h] infile outfile
script_template.py: error: the following arguments are required: outfile

Finally, it automatically generates help information (which we can get using the -h option):

$python script_template.py -h usage: script_template.py [-h] infile outfile One-line description of what the script does. positional arguments: infile Input file name outfile Output file name optional arguments: -h, --help show this help message and exit 4.3 Documentation Our template is a good starting point, but we can make one improvement right away. To start, let’s write a function that doubles a number, but add a bit of documentation: def double(num): 'Double the input.' return 2 * num The first line of this function is a string that isn’t assigned to a variable. Such a string is called a documentation string, or docstring for short. If we call our function it does what we expect: double(3) 6 However, we can also ask for the function’s documentation, which is stored in double.__doc__: double.__doc__ 'Double the input.' Python creates the variable __doc__ automatically for every function, just as it creates the variable __name__ for every file. If we don’t write a docstring for a function, __doc__’s value is an empty string. We can put whatever text we want into a function’s docstring, but it is usually used to provide online documentation. We can also put a docstring at the start of a file, in which case it is assigned to a variable called __doc__ that is visible inside the file. If we add documentation to our template, it becomes: """One-line description of what the script does.""" import argparse def main(args): """Run the program.""" print('Input file:', args.infile) print('Output file:', args.outfile) if __name__ == '__main__': parser = argparse.ArgumentParser(description=__doc__) parser.add_argument('infile', type=str, help='Input file name') parser.add_argument('outfile', type=str, help='Output file name') args = parser.parse_args() main(args) Note that docstrings are usually written using triple-quoted strings, since these can span multiple lines. Note also how we pass description=__doc__ to argparse.ArgumentParser. This saves us from typing the same information twice, but more importantly ensures that the help message provided in response to the -h option will be the same as the interactive help. Let’s try this out in an interactive Python session. (Remember, do not type the >>> prompt: Python provides this for us.) $ python
Python 3.8.1 | packaged by conda-forge | (default, Jan 29 2020, 14:55:04)
[GCC 7.3.0] on linux
>>> import script_template
>>> script_template.__doc__
'One-line description of what the script does.'
>>> help(script_template)
Help on module script_template:

NAME
script_template - One-line description of what the script does.

FUNCTIONS
main(args)
Run the program.

FILE
/Users/amira/script_template.py

As this example shows, if we ask for help on the module, Python formats and displays all of the docstrings for everything in the file. We’ll talk more about what to put in a docstring in Section 13.6.1.

4.4 Counting Words

Now that we have a template for command-line Python programs, we can use it to check Zipf’s Law for our collection of classic English novels. We start by moving the template into the directory where we store our runnable programs (Section 1.4.2):

$mv script_template.py ~/zipf/bin Next, let’s write a function that counts how often words appear in a file. Our function splits the text on whitespace characters (which is the default behavior of the string object’s split method), then strips leading and trailing punctuation. This isn’t completely correct—if two words are joined by a long dash like “correct” and “if” in this sentence, for example, they will be treated as one word—so we will explore better options in the exercises. We also use the Counter class from the collections library to count how many times each word occurs. If we give Counter a list of words, the result is an object that contains the number of times each one appears in the list: import string from collections import Counter def count_words(reader): """Count the occurrence of each word in a string.""" text = reader.read() chunks = text.split() stripped = [word.strip(string.punctuation) for word in chunks] word_list = [word.lower() for word in stripped if word] word_counts = Counter(word_list) return word_counts Let’s try our function on Dracula: with open('data/dracula.txt', 'r') as reader: word_counts = count_words(reader) print(word_counts) Counter({'the': 8036, 'and': 5896, 'i': 4712, 'to': 4540, 'of': 3738, 'a': 2961, 'in': 2558, 'he': 2543, 'that': 2455, 'it': 2141, 'was': 1877, 'as': 1581, 'we': 1535, 'for': 1534, ...}) If we want the word counts in a format like CSV for easier processing, we can write another small function that takes our Counter object, orders its contents from most to least frequent, and then writes it to standard output as CSV: import csv def collection_to_csv(collection): """Write out a collection of items and counts in csv format.""" collection = collection.most_common() writer = csv.writer(sys.stdout) writer.writerows(collection) Running this would print all the distinct words in the book along with their counts. This list could well be several thousand lines long, so to make the output a little easier to view on our screen, we can add an option to limit the output to the most frequent words. We set its default value to None so that we can easily tell if the caller hasn’t specified a cutoff, in which case we display the whole collection: def collection_to_csv(collection, num=None): """Write out a collection of items and counts in csv format.""" collection = collection.most_common() if num is None: num = len(collection) writer = csv.writer(sys.stdout) writer.writerows(collection[0:num]) collection_to_csv(word_counts, num=10) the,8036 and,5896 i,4712 to,4540 of,3738 a,2961 in,2558 he,2543 that,2455 it,2141 To make our count_words and collection_to_csv functions available at the command line, we need to insert them into our script template and call them from within the main function. Let’s call our program countwords.py and put it in the bin subdirectory of the zipf project: """Count the occurrences of all words in a text and output them in CSV format.""" import sys import string import argparse import csv from collections import Counter def collection_to_csv(collection, num=None): """Write out a collection of items and counts in csv format.""" collection = collection.most_common() if num is None: num = len(collection) writer = csv.writer(sys.stdout) writer.writerows(collection[0:num]) def count_words(reader): """Count the occurrence of each word in a string.""" text = reader.read() chunks = text.split() stripped = [word.strip(string.punctuation) for word in chunks] word_list = [word.lower() for word in stripped if word] word_counts = Counter(word_list) return word_counts def main(args): """Run the command line program.""" with open(args.infile, 'r') as reader: word_counts = count_words(reader) collection_to_csv(word_counts, num=args.num) if __name__ == '__main__': parser = argparse.ArgumentParser(description=__doc__) parser.add_argument('infile', type=str, help='Input file name') parser.add_argument('-n', '--num', type=int, default=None, help='Limit output to N most frequent words') args = parser.parse_args() main(args) Note that we have replaced the 'outfile' argument with an optional -n (or --num) flag to control how much output is printed and modified collection_to_csv so that it always prints to standard output (Section 2.10). If we want that output in a file, we can redirect with >. Let’s take our program for a test drive: $ python bin/countwords.py data/dracula.txt -n 10
the,8036
and,5896
i,4712
to,4540
of,3738
a,2961
in,2558
he,2543
that,2455
it,2141

4.5 Pipelining

Most of the Unix commands we have seen so far follow a useful convention: if the user doesn’t specify the names of any input files, they read from standard input. Similarly, if no output file is specified, the command sends its results to standard output. This makes it easy to use the command in a pipeline.

Our program always sends its output to standard output; as noted above, we can always redirect it to a file with >. If we want it to read from standard input, we only need to change the handling of infile in the argument parser and simplify main to match:

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

if __name__ == '__main__':
parser = argparse.ArgumentParser(description=__doc__)
default='-', help='Input file name')
help='Limit output to N most frequent words')
args = parser.parse_args()
main(args)

There are two changes to how add_argument handles infile:

1. Setting type=argparse.FileType('r') tells argparse to treat the argument as a filename and open that file for reading. This is why we no longer need to call open ourselves, and why main can pass args.infile directly to count_words.

2. The number of expected arguments (nargs) is set to ?. This means that if an argument is given it will be used, but if none is provided, a default of '-' will be used instead. argparse.FileType('r') understands '-' to mean “read from standard input”; this is another Unix convention that many programs follow.

After these changes, we can create a pipeline like this to count the words in the first 500 lines of a book:

$head -500 data/dracula.txt | python bin/countwords.py --num 10 the,227 and,121 of,116 i,98 to,80 in,58 a,49 it,45 was,42 that,41 4.6 Positional and Optional Arguments We have met two kinds of command-line arguments while writing countwords.py. Optional arguments are defined using a leading - or -- (or both), which means that all three of the following definitions are valid: parser.add_argument('-n', type=int, help='Limit output') parser.add_argument('--num', type=int, help='Limit output') parser.add_argument('-n', '--num', type=int, help='Limit output') The convention is for - to precede a short (single letter) option and -- a long (multi-letter) option. The user can provide optional arguments at the command line in any order they like. Positional arguments have no leading dashes and are not optional: the user must provide them at the command line in the order in which they are specified to add_argument (unless nargs='?' is provided to say that the value is optional). 4.7 Collating Results Ultimately, we want to save the word counts to a CSV file for further analysis and plotting. Let’s create a subdirectory to hold our results (following the structure described in Section 1.4): $ mkdir results

and then save the counts for various files:

$python bin/countwords.py data/dracula.txt > results/dracula.csv $ python bin/countwords.py data/moby_dick.txt > results/moby_dick.csv
$python bin/countwords.py data/jane_eyre.txt > results/jane_eyre.csv Now that we can get word counts for individual books we can collate the counts for several books. This can be done using a loop that adds up the counts of a word from the each of the CSV files created by countwords.py. Using the same template as before, we can write a program called collate.py: """Combine multiple word count CSV-files into a single cumulative count.""" import sys import csv import argparse from collections import Counter def collection_to_csv(collection, num=None): """Write out a collection of items and counts in csv format.""" collection = collection.most_common() if num is None: num = len(collection) writer = csv.writer(sys.stdout) writer.writerows(collection[0:num]) def update_counts(reader, word_counts): """Update word counts with data from another reader/file.""" for word, count in csv.reader(reader): word_counts[word] += int(count) def main(args): """Run the command line program.""" word_counts = Counter() for file_name in args.infiles: with open(file_name, 'r') as reader: update_counts(reader, word_counts) collection_to_csv(word_counts, num=args.num) if __name__ == '__main__': parser = argparse.ArgumentParser(description=__doc__) parser.add_argument('infiles', type=str, nargs='*', help='Input file names') parser.add_argument('-n', '--num', type=int, default=None, help='Limit output to n most frequent words') args = parser.parse_args() main(args) The loop in the main function iterates over each filename in infiles, opens the CSV file, and calls update_counts with the input stream as one parameter and the counter as the other. update_counts then iterates through all the words the CSV-files and increments the counts using the += operator. Note that we have not used type=argparse.FileType('r') here. Instead, we have called the option infiles (plural) and specified nargs='*' to tell argparse that we will accept zero or more filenames. We must then open the files ourselves. Passing the filename rather than having argparse read its content automatically is also useful when doing things like moving or coping files; we will look in the exercises at how to combine this with reading from standard input. Let’s give collate.py a try (using -n 10 to limit the number of lines of output): $ python bin/collate.py results/dracula.csv results/moby_dick.csv results/jane_eyre.csv -n 10
the,30505
and,18916
of,14908
to,14369
i,13572
a,12059
in,9547
that,6984
it,6821
he,6142

4.8 Writing Our Own Modules

countwords.py and collate.py both now contain the function collection_to_csv. Having the same function in two or more places is a bad idea: if we want to improve it or fix a bug, we have to find and change every single script that contains a copy.

The solution is to put the shared functions in a separate file and load that file as a module. Let’s create a file called utilities.py in the bin directory that looks like this:

"""Collection of commonly used functions."""

import sys
import csv

def collection_to_csv(collection, num=None):
"""
Write out a collection of items and counts in csv format.

Parameters
----------
collection : collections.Counter
Collection of items and counts
num : int
Limit output to N most frequent items
"""
collection = collection.most_common()
if num is None:
num = len(collection)
writer = csv.writer(sys.stdout)
writer.writerows(collection[0:num])

Note that we have written a much more detailed docstring for collection_to_csv: as a rule, the more widely used code is, the more it’s worth explaining exactly what it does.

We can now import our utilities into our programs just as we would import any other Python module using either import utilities (to get the whole thing) or something like from utilities import collection_to_csv (to get a single function). After making this change, countwords.py looks like this:

"""Count the occurrences of all words in a text and write them to a CSV-file."""

import re
import argparse
from collections import Counter
import utilities

"""Count the occurrence of each word in a string."""
chunks = text.split()
stripped = [word.strip(string.punctuation) for word in chunks]
word_list = [word.lower() for word in stripped if word]
word_counts = Counter(word_list)
return word_counts

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

if __name__ == '__main__':
parser = argparse.ArgumentParser(description=__doc__)
default='-', help='Input file name')
help='Limit output to n most frequent words')
args = parser.parse_args()
main(args)

collate.py is now:

"""Combine multiple word count CSV-files into a single cumulative count."""

import csv
import argparse
from collections import Counter
import utilities

"""Update word counts with data from another reader/file."""
word_counts[word] += int(count)

def main(args):
"""Run the command line program."""
word_counts = Counter()
for fn in args.infiles:
utilities.collection_to_csv(word_counts, num=args.num)

if __name__ == '__main__':
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('infiles', type=str, nargs='*', help='Input file names')
help='Limit output to n most frequent words')
args = parser.parse_args()
main(args)

Any Python source file can be imported by any other. This is why Python files should be named using snake case (e.g. some_thing) instead of kebab case (e.g. some-thing): an expression like import some-thing isn’t allowed because some-thing isn’t a legal variable name. When a file is imported, the statements in it are executed as it loads. Variables, functions, and items defined in the file are then available as module.thing, where module is the filename (without the .py extension) and thing is the name of the item.

The __pycache__ Directory

When we import a file, Python translates the source code into instructions called byte codes that it can execute efficiently. Since the byte codes only change when the source changes, Python saves the byte code in a separate file, and reloads that file instead of re-translating the source code the next time it’s asked to import the file (unless the file has changed, in which case Python starts from the beginning).

Python creates a subdirectory called __pycache__ that holds the byte code for the files imported from that directory. We typically don’t want to put the files in __pycache__ in version control, so we normally tell Git to ignore it as discussed in Section 5.9.

4.9 Plotting

The last thing for us to do is to plot the word count distribution. Recall that Zipf’s Law states the second most common word in a body of text appears half as often as the most common, the third most common appears a third as often, and so on. Mathematically, this might be written as “word frequency is proportional to 1/rank.”

The following code plots the word frequency against the inverse rank using the Pandas library:

import pandas as pd

input_csv = 'results/jane_eyre.csv'
df['rank'] = df['word_frequency'].rank(ascending=False, method='max')
df['inverse_rank'] = 1 / df['rank']
scatplot = df.plot.scatter(x='word_frequency', y='inverse_rank',
figsize=[12, 6], grid=True)
fig = scatplot.get_figure()
fig.savefig('results/jane_eyre.png')

4.10 Summary

Why is building a simple command-line tool so complex? One answer is that the conventions for command-line programs have evolved over several decades, so libraries like argparse must now support several different generations of option handling. Another is that the things we want to do genuinely are complex: read from either standard input or a list of files, display help when asked to, respect parameters that might not be there, and so on. As with many other things in programming (and life), everyone wishes it was simpler, but no one can agree on what to throw away.

The good news is that this complexity is a fixed cost: our template for command-line tools can be re-used for programs that are much larger than the examples shown in this chapter. Making tools that behave in ways people expect greatly increases the chances that others will find them useful.

4.11 Exercises

4.11.1 Running Python statements from the command line

We don’t need to open the interactive interpreter to run Python code. Instead, we can invoke Python with the command flag -c and the statement we want to run:

$python -c "print(2+3)" 5 When and why is this useful? 4.11.2 A better plotting program Using script_template.py as a guide, take the plotting code from Section 4.9 and write a new Python program called plotcounts.py. The script should: 1. Use the type=argparse.FileType('r'), nargs='?' and default='-' options for the input file argument (i.e. similar to the countwords.py script) so that plotcounts.py uses standard input if no csv file is given. 2. Include an optional --outfile argument for the name of the output image file. The default value should be plotcounts.png. 3. Include an optional --xlim argument so that the user can change the x-axis bounds. When you are done, generate a plot of the word counts for Jane Eyre: $ python bin/plotcounts.py results/jane_eyre.csv --outfile results/jane_eyre.png

Note: the solution to this exercise is used in following chapters.

4.12 Key Points

• Write command-line Python programs that can be run in the Unix shell like other command-line tools.
• If the user does not specify any input files, read from standard input.
• If the user does not specify any output files, write to standard output.
• Place all import statements at the start of a module.
• Use the value of __name__ to determine if a file is being run directly or being loaded as a module.
• Use argparse to handle command-line arguments in standard ways.
• Use short options for common controls and long options for less common or more complicated ones.
• Use docstrings to document functions and scripts.
• Place functions that are used across multiple scripts in a separate file that those scripts can import.