differences for PR #452

Author: actions-user

12-virtual-environments.md

@@ -649,9 +649,13 @@ 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.
 
-## Optional Exercises
+## Optional exercises
+
+Checkout [this optional exercise](17-section1-optional-exercises.md)
+to try out different virtual environment managers.
+Or, [this exercise](17-section1-optional-exercises.md)
+to customize the command line.
 
-Have a look at [some optional exercises](17-section1-optional-exercises.md).
 
 
 :::::::::::::::::::::::::::::::::::::::: keypoints

14-collaboration-using-git.md

@@ -158,7 +158,7 @@ You do, however, want to share `requirements.txt` with your team
 as this file can be used to replicate the virtual environment on your collaborators' systems.
 
 To tell Git to intentionally ignore and not track certain files and directories,
-you need to specify them in the `.gitignore` text file. A common place to put this file is in the project root.
+you need to specify them in the `.gitignore` text file in the project root.
 Our project already has `.gitignore`,
 but in cases where you do not have it -
 you can simply create it yourself.
@@ -519,7 +519,7 @@ We still prefer to explicitly state this information in commands.
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
-Let us confirm that the new branch `develop` now exists remotely on GitHub too.
+Let us confirm that the new branch `develop` now exist remotely on GitHub too.
 From the `Code` tab in your repository in GitHub,
 click the branch dropdown menu (currently showing the default branch `main`).
 You should see your `develop` branch in the list too.

15-coding-conventions.md

@@ -138,33 +138,33 @@ or a hanging indent.
 ```python
 # Add an extra level of indentation (extra 4 spaces) to distinguish arguments from the rest of the code that follows
 def long_function_name(
-        var_one, var_two, var_three,
-        var_four):
-    print(var_one)
+       var_one, var_two, var_three,
+       var_four):
+   print(var_one)
 
 
 # Aligned with opening delimiter
 foo = long_function_name(var_one, var_two,
-                         var_three, var_four)
+                        var_three, var_four)
 
 # Use hanging indents to add an indentation level like paragraphs of text where all the lines in a paragraph are
 # indented except the first one
 foo = long_function_name(
-    var_one, var_two,
-    var_three, var_four)
+   var_one, var_two,
+   var_three, var_four)
 
 # Using hanging indent again, but closing bracket aligned with the first non-blank character of the previous line
 a_long_list = [
-    [[1, 2, 3], [4, 5, 6], [7, 8, 9]], [[0.33, 0.66, 1], [0.66, 0.83, 1], [0.77, 0.88, 1]]
-    ]
+   [[1, 2, 3], [4, 5, 6], [7, 8, 9]], [[0.33, 0.66, 1], [0.66, 0.83, 1], [0.77, 0.88, 1]]
+   ]
 
 # Using hanging indent again, but closing bracket aligned with the start of the multiline contruct
 a_long_list2 = [
-    1,
-    2,
-    3,
-    # ...
-    79
+   1,
+   2,
+   3,
+   # ...
+   79
 ]
 ```
 
@@ -189,11 +189,11 @@ to indicate line continuation (slightly less preferred method).
 ```python
 # Using delimiters ( ) to wrap a multi-line expression
 if (a == True and
-    b == False):
+   b == False):
 
 # Using a backslash (\) for line continuation
 if a == True and \
-    b == False:
+   b == False:
 ```
 
 ### Should a Line Break Before or After a Binary Operator?
@@ -608,7 +608,7 @@ or using triple quotes as a way to 'quickly' comment out an entire block of code
 is considered bad practice.
 
 In our example case, we used the
-[Sphinx/ReadTheDocs docstring style](https://sphinx-rtd-tutorial.readthedocs.io/en/latest/docstrings.html)
+[Sphynx/ReadTheDocs docstring style](https://sphinx-rtd-tutorial.readthedocs.io/en/latest/docstrings.html)
 formatting for the `param`, `raises` and `returns` - other docstring formats exist as well.
 
 :::::::::::::::::::::::::::::::::::::::::  callout

17-section1-optional-exercises.md

@@ -1,5 +1,5 @@
 ---
-title: 1.7 Optional Exercises
+title: 1.7 Optional Exercises for Section 1
 start: no
 teaching: 0
 exercises: 45
@@ -13,25 +13,23 @@ exercises: 45
 
 :::::::::::::::::::::::::::::::::::::::: questions
 
-- How can I further fine-tune my coding environment?
+- How can I further finetune my coding environment?
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
-This episode has some optional exercises for Section 1.
+This episode holds some optional exercises for section 1.
 The exercises have an explorative nature, so feel free to go off in any direction that interests you.
 You will be looking at some tools that either complement or are alternatives to those already introduced.
 Even if you find something that you really like,
-for the sake of following through with the course, we still recommend sticking with the tools that we introduced prior to this episode
-and then switching to something else afterwards.
+we still recommend sticking with the tools that were introduced prior to this episode when you move onto other sections of the course.
 
-:::::::::::::::::::::::::::::::::::::::  discussion
+:::::::::::::::::::::::::::::::::::::::  challenge
 
 ## Exercise: Apply to your own project(s)
 
 Apply what you learned in this section to your own project(s).
-This is the time to ask any questions of your instructors, helpers or fellow learners.
-Everyone has different preferences for tooling, so getting input from experienced developers is a great opportunity to learn new things
-or different perspectives.
+This is the time to ask any questions to your instructors or helpers.
+Everyone has different preferences for tooling, so getting the input of experienced developers is a great opportunity.
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
@@ -42,17 +40,17 @@ or different perspectives.
 Install different Integrated Development Environments (IDEs) and test them out.
 Which one do you like the most and why?
 
-Some suggestions to try:
+You can try:
 
 - [Visual Studio Code](https://code.visualstudio.com/), with setup instructions [in the Extras of this course](../learners/vscode.md)
 - [Atom](https://atom-editor.cc/)
 - [Sublime Text](https://www.sublimetext.com/)
 - [RStudio](https://posit.co/download/rstudio-desktop/)
 
-When compared to PyCharm, the IDEs listed above are advanced source code editors capable of functioning as IDEs.
-To function as an IDE, you have to manually install plugins for these tools to obtain more advanced features -
+Technically, compared to PyCharm, the 'IDEs' listed above are source code editors capable of functioning as an IDE
+(with RStudio as an example).
+To function as an IDE, you have to manually install plugins for more powerful features
 such as support for a specific programming language or unit testing.
-
 What do you prefer, a lot of tooling out of the box or a lightweight editor with optional extensions?
 
 If you want an even more lightweight setup you can try out these configurable source code editors:
@@ -64,27 +62,28 @@ If you want an even more lightweight setup you can try out these configurable so
 
 :::::::::::::::::::::::::::::::::::::::  challenge
 
-## Exercise: Customise the command line tool
+## Exercise: Customize the command line
 
-You can customise the command line tool or use alternatives to `bash`, such as:
+You can customize the command line or use alternatives to `bash` to make yourself more productive.
 
-- [Bash Prompt Generator](https://bash-prompt-generator.org/) - it lets you try out different prompts,
+- Try out [Bash Prompt Generator](https://bash-prompt-generator.org/), it lets you try out different prompts,
   depending on the information you want displayed.
-- [z, a simple tool to more quickly move around directories](https://github.com/rupa/z).
-- [Z shell (zsh)](https://zsh.sourceforge.io/), a shell designed for interactive use.
-- [Oh My ZSH](https://ohmyz.sh/), which is a theming and package manager of the `zsh` terminal.
-- [fish](https://fishshell.com/), a smart and user-friendly command line shell.
+- Try out [z, a simple tool to more quickly move around directories](https://github.com/rupa/z).
+- Try out [Z shell (zsh)](https://zsh.sourceforge.io/), a shell designed for interactive use.
+- Try out [Oh My ZSH](https://ohmyz.sh/), which is a theming and package manager of the `zsh` terminal.
+- Try out [fish](https://fishshell.com/), a smart and user-friendly command line shell.
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
 :::::::::::::::::::::::::::::::::::::::  challenge
 
 ## Exercise: Try out different virtual environment managers
 
-So far we have used `venv`, but there are other virtual environment managers for Python:
+So far we used `venv`, but there are other virtual environment managers for Python:
 
-- [Poetry](https://python-poetry.org/), which we will explore using in [Section 4](43-software-release.md).
-- `conda`, which is part of [Anaconda Distribution](https://www.anaconda.com/download).
+- [Poetry](https://python-poetry.org/), which we will explore using in
+  [Section 4](43-software-release.md).
+- conda, which is part of [Anaconda Distribution)](https://www.anaconda.com/download).
 
 Anaconda is widely used in academia, but the current license does not allow use for research in most circumstances.
 An open-source alternative is [mini-forge](https://github.com/conda-forge/miniforge).
@@ -93,11 +92,11 @@ An open-source alternative is [mini-forge](https://github.com/conda-forge/minifo
 
 :::::::::::::::::::::::::::::::::::::::  challenge
 
-## Exercise: Customise `pylint`
-
-Tell `pylint` to accept the maximum line length of 100 characters instead of the default 80.
+## Exercise: Customize `pylint`
 
-Hint: find out different ways in which you can configure `pylint` (e.g. via `pylint` command line interface or its configuration file).
+You decide to change the max line length of your project to 100 instead of the default 80.
+Find out how you can configure pylint. You can first try to use the pylint command line interface,
+but also play with adding a configuration file that pylint reads in.
 
 :::::::::::::::  solution
 
@@ -109,7 +108,7 @@ Specify the max line length as an argument: `pylint --max-line-length=100`
 
 ### Using a configuration file
 
-You can create a file `.pylintrc` in the root of your project folder to overwrite `pylint` settings:
+You can create a file `.pylintrc` in the root of your project folder to overwrite pylint settings:
 
 ```
 [FORMAT]

21-automatically-testing-software.md

@@ -90,7 +90,7 @@ There are three main types of automated tests:
   for example after making changes your code to add new functionality or fix a bug.
 
 For the purposes of this course, we will focus on unit tests.
-But the principles and practices we will talk about can be built on
+But the principles and practices we wll talk about can be built on
 and applied to the other types of tests too.
 
 ## Set Up a New Feature Branch for Writing Tests

23-continuous-integration-automated-testing.md

@@ -128,10 +128,10 @@ Let us say we want to add more detail to our list of initial ascenders:
 ...
 first_scaled_by:
 - name: Hans Meyer
-  date_of_birth: 1858-03-22
+  date_of_birth: 22-03-1858
   nationality: German
 - name: Ludwig Purtscheller
-  date_of_birth: 1858-03-22
+  date_of_birth: 22-03-1858
   nationality: Austrian
 ```
 

32-software-architecture-design.md

@@ -131,6 +131,8 @@ goal of having *maintainable* code, which is:
 Now that we know what goals we should aspire to, let us take a critical look at the code in our
 software project and try to identify ways in which it can be improved.
 
+## Designing a New Feature for Our Project
+
 Our software project contains a pre-existing branch `full-data-analysis` which contains code for a new feature of our
 inflammation analysis software, which we will consider as a contribution by another developer.
 Recall that you can see all your branches as follows:
@@ -154,7 +156,7 @@ This bit of functionality is handled by `inflammation-analysis.py` in the projec
 The new data analysis code is located in `compute_data.py` file within the `inflammation` directory
 in a function called `analyse_data()`.
 This function loads all the data files for a given a directory path, then
-calculates and compares standard deviation across all the data by day and finaly plots a graph.
+calculates and compares standard deviation across all the data by day and finally plots a graph.
 
 :::::::::::::::::::::::::::::::::::::::  challenge
 

34-code-refactoring.md

@@ -95,12 +95,12 @@ we refactor or change code in the future.
 Start from the skeleton test code below:
 
 ```python
+from inflammation.compute_data import analyse_data
+
 def test_analyse_data():
-    from inflammation.compute_data import analyse_data
-    path = Path.cwd() / "../data"
+    path = os.path.join( os.getcwd(), "../data")
     data_source = CSVDataSource(path)
     result = analyse_data(data_source)
-
     # TODO: add assert statement(s) to test the result value is as expected
 ```
 
@@ -115,7 +115,6 @@ When determining the correct return data result to use in tests, it may be helpf
 result equals some random made-up data, observe the test fail initially and then
 copy and paste the correct result into the test.
 
-
 :::::::::::::::::::::::::
 
 :::::::::::::::  solution
@@ -134,11 +133,10 @@ Putting this together, our test may look like:
 
 ```python
 import numpy.testing as npt
-from pathlib import Path
+from inflammation.compute_data import analyse_data
 
 def test_analyse_data():
-    from inflammation.compute_data import analyse_data
-    path = Path.cwd() / "../data"
+    path = os.path.join( os.getcwd(), "../data")
     data_source = CSVDataSource(path)
     result = analyse_data(data_source)
     expected_output = [0.,0.22510286,0.18157299,0.1264423,0.9495481,0.27118211,

common-issues.md

@@ -143,7 +143,7 @@ Git Bash uses its own SSH library by default, which may result in errors such as
 even after adding your SSH key correctly:
 
 ```
-$ git clone git@github.com:ukaea-rse-training/python-intermediate-inflammation
+$ git clone git@github.com:https://github.com/ukaea-rse-training/python-intermediate-inflammation
 Cloning into 'python-intermediate-inflammation'...
 git@github.com: Permission denied (publickey).
 fatal: Could not read from remote repository.