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Source  : 1dfe857
Branch  : main
Author  : Steve Crouch <s.crouch@software.ac.uk>
Time    : 2025-07-31 07:52:11 +0000
Message : Update CITATION.md

Author: actions-user

00-setting-the-scene.md

@@ -193,7 +193,7 @@ All exercises contain solutions but, wherever possible, try and work out a solut
 ## Outdated Screenshots
 
 Throughout this lesson we will make use and show content
-from Graphical User Interface (GUI) tools (PyCharm and GitHub).
+from Graphical User Interface (GUI) tools such as Integrated Development Environments (IDEs) and GitHub.
 These are evolving tools and platforms, always adding new features and new visual elements.
 Screenshots in the lesson may then become out-of-sync,
 refer to or show content that no longer exists or is different to what you see on your machine.

10-section1-intro.md

@@ -98,8 +98,7 @@ as this knowledge can be ported to other programming languages
 and command line tools you may use in the future
 (but is applicable to the integrated versions too).
 
-We will use [PyCharm](https://www.jetbrains.com/pycharm/) in this course -
-a free, open source IDE.
+You have a choice of using [PyCharm](https://www.jetbrains.com/pycharm/) or [Visual Studio Code (VS Code)](https://code.visualstudio.com/) in this course.
 
 ### Git \& GitHub
 

11-software-project.md

@@ -348,8 +348,7 @@ as we have seen already it contains several files with patients' daily inflammat
 We will revisit the software architecture and MVC topics once again in later episodes
 when we talk in more detail about [software architecture and design](32-software-architecture-design.md).
 We now proceed to set up our virtual development environment
-and start working with the code using a more convenient graphical tool -
-[IDE PyCharm](https://www.jetbrains.com/pycharm/).
+and start working with the code using a more convenient graphical tool - an Integrated Development Environment (IDE).
 
 
 

12-virtual-environments.md

@@ -26,8 +26,8 @@ We now want to run our code to see what it does -
 let us do that from the command line.
 For the most part of the course we will run our code
 and interact with Git from the command line.
-While we will develop and debug our code using the PyCharm IDE
-and it is possible to use Git from PyCharm too,
+While we will develop and debug our code using an IDE
+and it is possible to use Git from the IDE too,
 typing commands in the command line allows you to familiarise yourself and learn it well.
 A bonus is that this knowledge is transferable to running code in other programming languages
 and is independent from any IDE you may use in the future.
@@ -142,7 +142,7 @@ and it may be a matter of personal preference which one you go for.
 In this course, we will use `venv` to create and manage our virtual environment
 (which is the preferred way for Python 3.3+).
 The upside is that `venv` virtual environments created from the command line are
-also recognised and picked up automatically by PyCharm IDE,
+also recognised and picked up automatically by the IDEs we will use in this course,
 as we will see in the next episode.
 
 ### Managing External Packages
@@ -203,7 +203,7 @@ using `venv` and manage packages using `pip`.
 
 ::::::::::::::::::::::::::::::::::::::::::  prereq
 
-## Making Sure You Can Invoke Python
+### Making Sure You Can Invoke Python
 
 You can test your Python installation from the command line with:
 
@@ -494,20 +494,14 @@ Once again, we can use `pip` to install our local package:
 python3 -m pip install --editable .
 ```
 
-:::::::::::::::::::::::::::::::::::::::::  spoiler
-
-### This command fails for me
-
-If your `pip` installation is older than version 21.3, then this command will probably fail for you.
-This is because these older versions of `pip` do not support `pyproject.toml` as the package metadata.
-Given these versions of `pip` are now over 4 years old, we strongly recommend that you update `pip` if you can:
+If the above command fails for you - your `pip` installation is older than version 21.3.
+Such older versions of `pip` do not support `pyproject.toml` as the package metadata.
+Given these versions of `pip` are now over 4 years old, we strongly recommend that you update `pip` if you can with:
 
 ```bash
 python3 -m pip install --upgrade pip
 ```
 
-:::::::::::::::::::::::::::::::::::::::::
-
 This is similar syntax to above, with two important differences:
 
 1. The `--editable` or `-e` flag indicates that the package we are specifying should be an "editable" install.
@@ -517,7 +511,6 @@ This is similar syntax to above, with two important differences:
    The `pyproject.toml` file located in this directory then handles the rest.
 
 
-
 If we reissue the `pip list` command we should now see our local package with the name `python-intermediate-inflammation` in the output:
 
 ```output
@@ -646,8 +639,13 @@ In the above command, we tell the command line two things:
 As we can see, the Python interpreter ran our script, which threw an error -
 `inflammation-analysis.py: error: the following arguments are required: infiles`.
 It looks like the script expects a list of input files to process,
-so this is expected behaviour since we do not supply any.
-We will fix this error in a moment.
+so this is expected behaviour since we do not supply any. 
+
+We should run our code as follows, passing one (or more) data file(s) as input:
+
+```bash
+(venv) $ python3 inflammation-analysis.py data/inflammation-01.csv
+```
 
 ## Optional Exercises