Refactor website to tidy up unused files and update README

Author: liamjberrisford

README.md

@@ -2,46 +2,45 @@
 
 Welcome to the repository for the Coding For Reproducible Research (CfRR) training program at the [University of Exeter](https://www.exeter.ac.uk/). This repository contains all the materials and modules used in the CfRR training program, presented on our [Jupyter Book website](https://coding-for-reproducible-research.github.io/CfRR_Courses/home_page.html).
 
-This training programme provides a series workshops to support researchers at the University of Exeter to expand their skillsets and position them to confidently perform their informatics research projects in an efficient and reproducible way. The programme covers not only training on specific languages, such as Python, R, and Unix/Linux, but additionally incorporates training relating to good practise and reproducible working methods that is designed to be agnostic of programming language. In this way we offer a holistic perspective as to how programming tasks should be approached, ultimately providing researchers with the tools and knowledge to feel confident in what they are doing. All workshops are open to any staff or student, from any college or department and are accessible from any campus.
+This training programme provides workshops to support researchers at the University of Exeter to expand their skillsets and position them to perform their informatics research projects efficiently and reproducibly confidently. The program covers training on specific coding languages, such as Python, R, and Unix/Linux, as well as training relating to good coding practice and reproducible working methods designed to be agnostic of programming language. In this way, we offer a holistic perspective on how programming tasks should be approached, ultimately providing researchers with the tools and knowledge to feel confident in their actions. All workshops are open to any staff or student from any college or department and are accessible from any campus.
 
 These workshops are brought to you by the [University of Exeter Research Software and Analytics Group](https://www.exeter.ac.uk/research/research-software-and-analytics/), [University of Exeter Researcher Development](https://www.exeter.ac.uk/research/doctoralcollege/researcherdevelopment/) and the [University of Exeter Doctoral College](https://www.exeter.ac.uk/research/doctoralcollege/).
 
 You can contact the CfRR team at the following email: [[email protected]](mailto:[email protected])
 
-## About the Repository
-
-This repository includes:
-- **Course Materials**: All the theoretical content, code examples, and exercises used in the training program.
-- **Interactive Quizzes**: Tools to help attendees assess their understanding and determine which courses to take.
-- **Course Delivery Dates**: Information on the schedule for course deliveries.
-- **Self Study Notes**: Comprehensive notes for each course module.
-- **Contributing Guidelines**: Instructions for those who wish to contribute to the CfRR program.
-
 ## Repository Structure
 
 The repository is organized into several directories:
-- **course_details_markdowns**: Markdown files containing detailed descriptions of each course.
+- **cfrr_program_details**: Several jupyter notebook files relate to general content concerning the CfRR training programme, including the code of conduct, feedback ages, how to use the website, etc.
+- **contributing**: Several jupyter notebook files that describe the process that is used to contribute to the the CfRR program and website. Broadly relate to the "Join Us!" section on the website. 
 - **course_homepages**: Homepage content for the individual courses.
-- **individual_modules**: The main content for each course module.
+- **data**: Contains several .csv files that are used with code throughout the website to generate HTML and markdown content to populate different parts of the website.
+    - **workshop_info.csv**: Used to generate the content on the "Workshop Schedule and Signup Page", generated via the Jupyter Notebook at "cfrr_program_details/courses_overview.ipynb". Within this notebook, markdown content on the upcoming workshops is generated alongside the MS Forms to sign up based on the data within workshop_info.csv.
+    - **previous_workshops.csv**: Used to generate the content on the "Workshop Schedule and Signup Page", generated via the Jupyter Notebook at "cfrr_program_details/courses_overview.ipynb". Within this notebook, HTML content on historical workshops is created that act as a record of individuals contributions to the CfRR program.
+    - **workshop_details.csv**: Used to generate the pathway content on the "How do these courses relate?" section of the website. The Jupyter notebook that creates the networks used within this section is "pathways/related_courses.ipynb".
+- **individual_modules**: The main content for each course module. These are all of the markdown and Jupyter notebook files used for the self study content on the website.
+    - **section_landing_pages**: A number of different markdown files that provide an overview of the different modules within the program. Including an overview of the course, objectives and pre-reqs, that act as heading splash page for each of the courses within the self-study notes section of the website.
 - **pathways**: Information on how the courses interrelate.
-- **supporting_scripts**: Additional scripts used to generate markdown content for the website.
-- **tutorial_directory**: The turoial directory is where example usage of the the jupyter book content is kept that can be used when contributing to the CfRR program.
+- **programme_information**: Detailed information on each of the courses that are offered. These files make up the content of the "Workshop Information" section of the website. 
 - **where_is_my_understanding**: Quizzes to help gauge understanding of course content.
 
-## How to Use This Repository
-
-1. **Explore the Courses**: Navigate through the directories to find the course materials that interest you.
-2. **Interactive Quizzes**: Use the quizzes to test your knowledge and determine which courses you should take next.
-3. **Self Study**: Follow the self-study notes for in-depth learning.
-4. **Contribute**: Follow the guidelines in the `CONTRIBUTING.md` file if you wish to contribute to the repository.
+There are also several files within the root directory; these include: 
+- **home_page.md**: This file is the main root page for the CfRR Jupyter Book website.
+- **_config.yml**: This file customizes the appearance and behaviour of the overall Jupyter Book. 
+- **_toc.yml**: This file organizes the structure and overall navigation of the content of the Jupyter Book that is built.
+- **CITATION.cff**: Provides citation information for the CfRR website, and the course content aggregated throughout the website. 
+- **Manifest.toml**: Specifies the dependencies and environment configuration for the Julia kernel used.
+- **Project.toml**: Records the exact versions of all Julia dependencies, ensuring reproducibility of the project environment. 
+- **references.bib**: Used to store bibliographic references throughout all of the content on the website. 
+- **requirements.txt**: A file that specifies the dependencies of the Python kernel used in the website.  
 
 ## Contributing
 
 We welcome contributions to improve and expand the CfRR training materials. Please visit the [contributing guidance](https://coding-for-reproducible-research.github.io/CfRR_Courses/contributing/contributing.html) on the CfRR website that explains the steps to take to contribute to this repo.
 
 ## License
 
-For more details, visit our [Jupyter Book website](https://coding-for-reproducible-research.github.io/CfRR_Courses/home_page.html).
+As this repository aggregates several courses, several different licenses apply depending on the content. The license is included in the course content's directory, and so will be in the subdirectory within "individual_modules". If you have any queries or concerns please reach out to us.
 
 ---
 

_config.yml

@@ -3,7 +3,7 @@
 
 title: Home Page
 author: Coding For Reproducible Research Community
-logo: exeter_logo.png
+logo: _static/exeter_logo.png
 copyright: "2024"
 
 # Define the name of the latex output file for PDF builds
@@ -46,7 +46,6 @@ exclude_patterns:
 execute:
   execute_notebooks: "force"
   exclude_patterns: 
-      - 'related_courses.ipynb'
       - 'individual_modules/introduction_to_r/basic_commands.ipynb'
       - 'individual_modules/introduction_to_r/data_types.ipynb'
       - 'individual_modules/introduction_to_r/load_data.ipynb'

exeter_logo.png renamed to _static/exeter_logo.png

@@ -257,7 +257,7 @@ parts:
                   - file: individual_modules/intermediate_version_control/github_workflows
                   - file: individual_modules/intermediate_version_control/rewriting_history
                   - file: individual_modules/intermediate_version_control/further_topics
-      - file: bibliography
+      - file: individual_modules/bibliography
 
   - caption: Join Us!
     chapters: 

_toc.yml

@@ -89,7 +89,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "id": "0a814add-f545-4663-8b06-39c40b636509",
    "metadata": {
     "editable": true,

cfrr_program_details/courses_overview.ipynb

@@ -1,13 +1,8 @@
---- 
-title: Home Page
----
-
 # Coding for Reproducible Research (CfRR) Training Programme Home Page
 This training programme provides a series of workshops to support researchers at the University of Exeter to expand their skillsets and position them to perform informatics research projects in an efficient and reproducible way. The programme covers not only training on specific languages, such as Python, R, and Unix/Linux, but additionally incorporates training relating to good practise and reproducible working methods that is designed to be agnostic of programming language. In this way we offer a holistic perspective as to how programming tasks should be approached, ultimately providing researchers with the tools and knowledge to feel confident in conducting their research. All workshops are open to any staff or student, from any college or department and are accessible from any campus.
 
 You can contact the CfRR team at the following email: [[email protected]](mailto:[email protected])
 
 Please register your interest in a particular course by completing the relevant form on the Workshop Schedule and Signup page available [here](cfrr_program_details/courses_overview.ipynb).
 
-
 For more details on the structure and use of this website, please go to ['How to use this website'](cfrr_program_details/how_to_use_CfRR.ipynb).