11/26/25, 12:24 PM Writing and running Python code

Writing and running Python code

Contents
Python script files: the traditional way of writing code
Jupyter Notebooks: Code and documentation combined
Other coding environments
Footnotes

Python script files: the traditional way of writing code

The traditional approach to writing programs comprises writing the actual program in source code files which are normally
plain text files having the file extension .py (see Figure 1.8). To be able to run these script files, you need to execute them
separately via a terminal, or call the functionalities from Python interpreter. Documenting the code is done either as text
comments within the source code files or separately in a word processed document or a website. There is nothing inherently
wrong with this approach (it’s the approach that e.g. software engineers use), however there are drawbacks. First,
documentation in source code files relies on users being able to access and read the source code. This may be difficult for
non-programmers. Second, documenting the functionality of software outside of the source code requires programmers to
take an additional step to write documentation separately, and also to keep the documentation in sync with the code as its
functionality changes. Among natural scientists, this often means that the documentation simply never gets written,latest
or that it
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does not keep up with changes in the software, which may mean the documentation has little value. Clearly, a solution that
would combine documentation of the code with the code itself would be quite helpful! Computational notebooks offer a
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solution to this problem through combining text, code, results, graphics and much more all in one file. In this book, we will be
using Jupyter Notebooks - computational notebooks developed in the Project Jupyter [1].

Figure 1.8. An example of a Python script file.

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Jupyter Notebooks: Code and documentation combined

Jupyter Notebooks are an application that combines source code with rich-text documentation, equations, images, and plots
in the form of a single interactive document (Figure 1.9). The Jupyter Notebooks (having a filename extension .ipynb) are
divided into cells, where each cell contains part of the document intended for either source code or documentation. The most
common cell types for use in Jupyter Notebooks are “Code” cells and “Markdown” cells (Figure 1.10). The code cells support
several different programming languages, including Python. The Markdown cells are for creating nicely formatted text using
the Markdown markup language [2]. To interact with the notebooks, they must be hosted on a server either locally or
remotely, and accessed via a web browser.

Combining source code and documentation into a single document is an excellent solution to the problem of having these
two exist separately in the traditional way of programming, however there are other benefits to Jupyter Notebooks as well.
For example, data science workflows often use Jupyter Notebooks to provide complete descriptions of how the author loads,
processes, and otherwise interacts with data files or other data sources in their data analysis. In this way, Jupyter Notebooks
can be used to give step-by-step descriptions of a data processing workflow, including producing plots and other data
visualizations that are saved within the notebook. By including references to scientific articles and sources in the notebook,
you can basically have a self-contained, reproducible scientific document where anyone can easily see exactly how you have
done your analysis (and redo it themselves if they like). In terms of open science, this is a huge benefit.

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Figure 1.9. Features of a Jupyter Notebook.

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Figure 1.10. An example Jupyter Notebook.

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Other coding environments

The Python interpreter

One of the simplest options for coding in Python is to use the Python interpreter (Figure 1.11). The Python interpreter is an
interface where Python code can be typed and executed when you press Enter. In this way it is similar to a “Code” cell in a
Jupyter notebook. For very simple tasks and for testing short sections of Python programs, the Python interpreter can be the
fastest and easiest option. The history of commands may be recorded when using the Python interpreter, however
commands that have been entered in the interpreter are not saved to a file. Thus, you should use the Python interpreter only
as a temporary coding environment that can be useful for quickly testing some code.

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Figure 1.11. The IPython console, an enhanced Python interpreter.

Integrated development environments (IDEs)

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At the other end of the spectrum in terms of comprehensiveness and complexity (compared to Python interpreter) are
integrated development environments, or IDEs as they are typically called. IDEs, such as the one in Figure 1.12, are software

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applications that typically include a source code editor, debugging tools, a file browser, software version control tools, and a
linter that can be used to detect syntax errors in source code. The idea of an IDE is to assemble relevant software
development tools into a single application that can help users to develop better software more quickly and with fewer
errors. For new programmers, an IDE can be somewhat intimidating, but can also be helpful because many IDEs will indicate
syntax errors and suggest fixes in the source code. These include some errors that may be difficult to identify from runtime
errors that arise when the code is executed.

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Figure 1.12. The PyCharm IDE.

There are several excellent IDEs for Python software development, including JupyterLab, PyCharm, Visual Studio Code,
Spyder, and IDLE. We briefly describe some of the key attributes of each below.

JupyterLab is a browser-based IDE for working with Jupyter notebooks. It builds upon the earlier Jupyter notebook
application by making the layout of the file browser, interactive notebook panel, Python interpreter, and system terminal
flexible and viewable within the same window, like most IDEs. There is also a system for adding functionality to
JupyterLab with useful plugins for version control and other IDE features. We recommend using JupyterLab with the
Jupyter notebooks included with this textbook.
PyCharm is an advanced IDE designed specifically for use in Python programming (Figure 1.12). It is perhaps the most
comprehensive option of all in the list here, offering excellent integrated tools for developing well-formatted, clean
Python code. PyCharm also supports Jupyter notebooks and a free educational edition that includes all the tools
available in the Professional edition.
Visual Studio Code is another IDE, but not one designed specifically for Python. Instead, Visual Studio Code (or VSCode)
is a generic source code editor that can be expanded to function like an IDE through extensions, including those specific
to Python and Jupyter notebooks. VSCode is highly customizable, and may appeal to those wanting to use the same IDE
for programming in Python and other programming languages.
Spyder, the Scientific Python Development Environment, is yet another IDE designed specifically for programming in
Python. This free and open-source IDE excels in scientific applications and offers a number of excellent tools that are
useful in debugging programs. Specifically, Spyder’s variable explorer is a great way to check the values assigned to
variables and arrays and ensure your programs are functioning correctly.
IDLE, Python’s Integrated Development and Learning Environment, is a lightweight IDE that is included with many
Python distributions. It is not as feature rich as some of the other options listed above, but computers that have Python
installed may also already have IDLE available. This can be handy when you’re working on a machine where you’re not
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Footnotes
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[2] [Link]

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