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Source  : aef59db
Branch  : main
Author  : Joe Heffer <60133133+Joe-Heffer-Shef@users.noreply.github.com>
Time    : 2024-09-12 12:33:26 +0000
Message : Merge pull request #42 from Joe-Heffer-Shef/todos

resolve some TODOs

contributors.md

@@ -54,10 +54,12 @@ On code hosting platforms such as GitHub, the contribution guide will be created
 
 :::: challenge
 
-TODO 
-
 Create a new file called `CONTRIBUTING.md` and populate it with a few sentences.
 
+- What are the most important things for a new contributor to know?
+- What should a user do if they encounter a bug?
+- What are the common questions that a new developer might have when they work on this research software?
+
 ::::
 
 ## Software project governance

docstrings.md

@@ -129,7 +129,20 @@ Use the `help()` function to view the documentation string for a function.
 
 ::::::::::::::::: solution
 
-TODO
+Let's view the help text for an in-built [function `abs()`](https://docs.python.org/3/library/functions.html#abs) that finds the absolute value of a number.
+
+```python
+help(abs)
+```
+
+The following text will be printed to the screen@
+
+```output
+Help on built-in function abs in module builtins:
+
+abs(x, /)
+    Return the absolute value of the argument.
+```
 
 ::::::::::::::::::::::::::
 

md5sum.txt

@@ -7,10 +7,10 @@
 "links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2024-05-20"
 "episodes/introduction.md" "123579b22c95b6dcb57401b057235db5" "site/built/introduction.md" "2024-08-16"
 "episodes/readmes.md" "7f814493f5072a579424de3222583ebb" "site/built/readmes.md" "2024-07-22"
-"episodes/docstrings.md" "28d95c6f87a20ecb3ece5010a999f8b9" "site/built/docstrings.md" "2024-08-16"
+"episodes/docstrings.md" "144c97b797a8bdeafbaf8a9fae4d2099" "site/built/docstrings.md" "2024-09-12"
 "episodes/readable.md" "1f80fef3634faac146f4d6d324a92a3b" "site/built/readable.md" "2024-08-16"
-"episodes/sites.md" "65aa4c45daf0fd4749034d961dd511c6" "site/built/sites.md" "2024-06-10"
-"episodes/contributors.md" "1ee5921b02ebee9da030e06f06d52d08" "site/built/contributors.md" "2024-08-05"
+"episodes/sites.md" "84cbf67bb259144ed1083711614f8f2a" "site/built/sites.md" "2024-09-12"
+"episodes/contributors.md" "1e5a2cae9d5ef5fb6949ebd0abdbfb1d" "site/built/contributors.md" "2024-09-12"
 "episodes/cli.md" "605efa02a00db1bb673591623c31b632" "site/built/cli.md" "2024-06-21"
 "instructors/instructor-notes.md" "cae72b6712578d74a49fea7513099f8c" "site/built/instructor-notes.md" "2024-05-20"
 "learners/acknowledgements.md" "a751175e5c52ccbf05f8291162bc2cea" "site/built/acknowledgements.md" "2024-08-16"

sites.md

@@ -6,16 +6,16 @@ exercises: 2
 
 :::::::::::::::::::::::::::::::::::::: questions 
 
-- What is a documentation website for research software?
+- How do I present **comprehensive information** to users of my research software?
 - How do I generate a website containing a user guide to my code?
-- What should my documentation site contain?
+- What should a good documentation website contain?
 - How do I publish my software documentation on the internet?
 
 ::::::::::::::::::::::::::::::::::::::::::::::::
 
 ::::::::::::::::::::::::::::::::::::: objectives
 
-- Learn about documentation websites for software packages.
+- Learn about **documentation websites** for software packages.
 - Gain basic familiarity with some common website generation tools.
 - Understand the basics of structuring a documentation website.
 - Be able to set up a static site deployment workflow.
@@ -106,6 +106,13 @@ For more information about the wiki feature on GitHub, see [Documenting your pro
 
 :::
 
+
+### Documentation sites for R packages
+
+It's also possible to generate a documentation site to accompany R packages that you create. 
+For more information about this, please refer to the book *R Packages* by Hadley Wickham, which
+has a chapter on [documentation websites](https://r-pkgs.org/website.html).
+
 ### Sphinx
 
 [Sphinx](https://www.sphinx-doc.org/) is a tool for building documentation websites that is commonly used amongst developers of Python packages, although it's also compatible with other programming languages. It doesn't currently support packages written using the R statistical language.
@@ -124,12 +131,32 @@ Let's use Sphinx to create a documentation site for our Python code.
 
 ##### Installing Sphinx
 
-Navigate to the root folder of your code project. Create a virtual environment using [venv](https://docs.python.org/3/library/venv.html) which is a separate area in which to install the Sphinx package.
+Navigate to the root folder of your code project.
+Create a virtual environment using [venv](https://docs.python.org/3/library/venv.html) which is a separate area in which to install the Sphinx package.
+This command will create a virtual environment in a directory called `.venv/`
+
+::: group-tab
+
+### Windows
+
+```bash
+python -m venv .venv
+```
+
+### Linux
+
+```bash
+python3 -m venv .venv
+```
+
+### macOS
 
 ```bash
 python -m venv .venv
 ```
 
+:::
+
 This will create a subdirectory that contains the packages we'll need to complete the exercises in this section.
 
 Run the activation script to enable the virtual environment. The specific command needed to activate the virtual environment depends on the operating system you are using.
@@ -154,14 +181,14 @@ source .venv/bin/activate
 source .venv/bin/activate
 ```
 
+:::
+
 Use the Python package manager [pip](https://pip.pypa.io/en/stable/) to [install Sphinx](https://www.sphinx-doc.org/en/master/usage/installation.html).
 
 ```bash
 pip install sphinx
 ```
 
-:::
-
 ##### Start a new Sphinx project
 
 Sphinx includes a command to set up a new project called [sphinx-quickstart](https://www.sphinx-doc.org/en/master/man/sphinx-quickstart.html). Navigate to your project's root folder and run the following command. 
@@ -178,15 +205,19 @@ This will initialise the configuration files for a new Sphinx site in a subdirec
 
 ::: callout
 
-To find out more about the Sphinx configuration files, please read their guide to [defining document structure](https://www.sphinx-doc.org/en/master/usage/quickstart.html#defining-document-structure) on the Sphinx documentation.
+### Sphinx options
+
+To find out more about the Sphinx configuration files,
+please read their guide to [defining document structure](https://www.sphinx-doc.org/en/master/usage/quickstart.html#defining-document-structure) on the Sphinx documentation.
 
 :::
 
 #### Building the site
 
-In this context, building means taking our collection of Sphinx files and converting them into the source code files that define a website. Sphinx will create HyperText Markup Language (HTML) files, which is the markup language for pages that display in a web browser commonly used on the internet.
+In this context, _building_ means taking our collection of Sphinx files and converting them into the source code files that define a website.
+Sphinx will create _HyperText Markup Language_ (HTML) files, which is the markup language for pages that display in a web browser commonly used on the internet.
 
-To build our site, we run the [sphinx-build](https://www.sphinx-doc.org/en/master/man/sphinx-build.html) command using the `-M` option to select HTML syntax as the output format.
+To build our site, we run the [sphinx-build](https://www.sphinx-doc.org/en/master/man/sphinx-build.html) command using the `-M` option to select <abbr title="HyperText Markup Language">HTML</abbr> syntax as the output format.
 
 ```bash
 sphinx-build -M html docs docs/_build
@@ -205,10 +236,9 @@ It can be useful to automatically populate our documentation sites by converting
 ##### Configuring Autodoc
 
 Let's set up the options for `autodoc`.
+(If you struggle with these steps, please refer to the [template project](https://github.com/Joe-Heffer-Shef/oddsong).)
 
-If you struggle with these steps, please refer to the [template project](https://github.com/Joe-Heffer-Shef/oddsong).
-
-Add the following lines to `docs/conf.py`
+Add the following lines to `docs/conf.py` which 
 
 ```python
 # Our Python code may be imported from the parent directory
@@ -217,15 +247,42 @@ import sys
 sys.path.insert(0, os.path.abspath('..'))
 ```
 
-This ensures that Sphinx can access our Python code.
+This ensures that Sphinx can access our Python code by pointing at the root directory of our project.
+The `..` syntax means "one folder up", which means `autodoc` will search in the root directory for code to import.
+
+:::: spoiler
+
+### What does this code mean?
+
+The Python code uses [`sys.path`](https://docs.python.org/3/library/sys.html#sys.path), a list of locations to search for code.
+By modifying the Python _module search path_, we allow `autodoc` to locate and import our code modules from a specific directory that is not in the default search path.
 
-Next, edit `docs/index.rst` and add the following lines:
+This is often necessary when working with project structures that involve multiple directories, helping the interpreter to find code that isn't installed in the standard library location.
+
+::::
+
+Next, edit `docs/index.rst` and add the following lines to instruct Sphinx to automatically generation documentation for our Python module.
 
 ```rst
 .. automodule:: oddsong.song
     :members:
 ```
 
+:::: spoiler
+
+### What does this code mean?
+
+This [reStructuredText (reST)](https://docutils.sourceforge.io/rst.html) markup language has the following elements:
+
+- `..` indicates a _directive_ within a <abbr title="reStructuredText">reST</abbr> document that is used to configure Sphinx.
+- `automodule::` indicates a specific directive to use `autodoc` to automatically generate documentation for a module.
+- `oddsong.song` is the path to our Python module, for which documentation will be created.
+- `:members:` is an optional argument for the automodule directive that instructs Sphinx to include documentation for all members (functions, classes, variables) defined within the specified module.
+
+For more information about <abbr title="reStructuredText">reST</abbr>, please read the [Introduction to reStructuredText](https://www.writethedocs.org/guide/writing/reStructuredText/) by _Write The Docs_.
+
+::::
+
 Now, when we build our site, Sphinx will scan the contents of the `oddsong` Python module and automatically generate a useful reference guide to our functions.
 
 ```bash
@@ -238,23 +295,14 @@ The result looks something like this:
 
 ::::::::::::::::::::::::::::::::::::: challenge
 
-## Automatically generated content
-
-Try using `autodoc`.
+## Automatically generate content
 
-:::::::::::::::: solution
+Try using `autodoc` to analyise your own code and build a documentation site by following the steps above.
 
-TODO
+After the `sphinx-build` command has completed successfully, browse the contents of the `docs/_build/html` folder and discuss what you find.
 
-:::::::::::::::::::::::::
 :::::::::::::::::::::::::::::::::::::::::::::::
 
-### Documentation sites for R packages
-
-It's also possible to generate a documentation site to accompany R packages that you create. 
-For more information about this, please refer to the book *R Packages* by Hadley Wickham, which
-has a chapter on [documentation websites](https://r-pkgs.org/website.html).
-
 ## Publishing
 
 Now that you've started writing your documentation website, there are various ways to upload it to the internet so that others can read it.
@@ -271,3 +319,11 @@ The detailed of setting up the deployment of your site to these platforms is bey
 - Documentation websites may be deployed to a hosting platform.
 
 ::::::::::::::::::::::::::::::::::::::::::::::::
+
+## Further resources
+
+Please review the following material which provides more information about some of the topics covered in this episode.
+
+- Sphinx [Getting Started](https://www.sphinx-doc.org/en/master/usage/quickstart.html)
+- _Write the Docs_ [Introduction to reStructuredText](https://www.writethedocs.org/guide/writing/reStructuredText/)
+- GitHub documentation [About wikis](https://docs.github.com/en/communities/documenting-your-project-with-wikis/about-wikis)