Merge branch 'main' into julia_session_3

Author: liamjberrisford

_config.yml

@@ -40,6 +40,9 @@ exclude_patterns:
   - README.md
   - individual_modules/python_for_data_analysis/data-analysis-task-solutions.ipynb
 
+parse:
+  myst_enable_extensions:  # default extensions to enable in the myst parser. See https://myst
+    - strikethrough
 
 # Execute all notebooks by default. 
 # The R notebooks are excluded from running during the building of the book due to the formatting issues. When ran wen building the output for each of the cells will create a new code block for each space due to the R magic command.
@@ -94,3 +97,11 @@ execute:
       - 'individual_modules/improve_your_r_code/data_table.ipynb'
       - 'individual_modules/improve_your_r_code/parallelisation.ipynb'
       - 'individual_modules/improve_your_r_code/rcpp.ipynb'
+      - 'individual_modules/Introduction_to_Markdown_in_R/Background_to_Markdown.md'
+      - 'individual_modules/Introduction_to_Markdown_in_R/Course_Outro.md'
+      - 'individual_modules/Introduction_to_Markdown_in_R/Getting_Started_with_Markdown_in_R.md'
+      - 'individual_modules/Introduction_to_Markdown_in_R/Processing_RMarkdown_Files.md'
+      - 'individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_Embedded_Code.md'
+      - 'individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_Formatted_Text.md'
+      - 'individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_Visual_Prelude.md'
+      - 'individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_YAML_Header.md'

_static/multiple_regression_hyperplane.html

@@ -282,7 +282,7 @@ <h1></h1>
 
 
                   // parsing and collecting nodes and edges from the python
-                  nodes = new vis.DataSet([{"color": "#FFD700", "id": "Introduction to HPC", "label": "Introduction to HPC", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to HPC\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Parallel Computing"}, {"color": "#FFD700", "id": "Parallel Computing", "label": "Parallel Computing", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Parallel Computing\nCourse Pre-reqs: Introduction to HPC\nSubsequent Courses: None"}, {"color": "#FFD700", "id": "Introduction to Unix", "label": "Introduction to Unix", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Unix\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to HPC, Introduction to Version Control with Git and GitHub"}, {"color": "#FFD700", "id": "Introduction to Version Control with Git and GitHub", "label": "Introduction to Version Control with Git and GitHub", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Version Control with Git and GitHub\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Intermediate Version Control"}, {"color": "#FFD700", "id": "Intermediate Version Control", "label": "Intermediate Version Control", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Intermediate Version Control\nCourse Pre-reqs: Introduction to Version Control with Git and GitHub\nSubsequent Courses: None"}, {"color": "#FFD700", "id": "Introduction to Python", "label": "Introduction to Python", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Python\nCourse Pre-reqs: None\nSubsequent Courses: None"}]);
+                  nodes = new vis.DataSet([{"color": "#4682B4", "id": "Introduction to HPC", "label": "Introduction to HPC", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to HPC\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Parallel Computing"}, {"color": "#4682B4", "id": "Parallel Computing", "label": "Parallel Computing", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Parallel Computing\nCourse Pre-reqs: Introduction to HPC\nSubsequent Courses: None"}, {"color": "#4682B4", "id": "Introduction to Unix", "label": "Introduction to Unix", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Unix\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to HPC, Introduction to Version Control with Git and GitHub"}, {"color": "#4682B4", "id": "Introduction to Version Control with Git and GitHub", "label": "Introduction to Version Control with Git and GitHub", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Version Control with Git and GitHub\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Intermediate Version Control"}, {"color": "#4682B4", "id": "Intermediate Version Control", "label": "Intermediate Version Control", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Intermediate Version Control\nCourse Pre-reqs: Introduction to Version Control with Git and GitHub\nSubsequent Courses: None"}, {"color": "#4682B4", "id": "Introduction to Python", "label": "Introduction to Python", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Python\nCourse Pre-reqs: None\nSubsequent Courses: None"}]);
                   edges = new vis.DataSet([{"arrows": "to", "from": "Introduction to HPC", "to": "Parallel Computing", "width": 1}, {"arrows": "to", "from": "Introduction to Unix", "to": "Introduction to HPC", "width": 1}, {"arrows": "to", "from": "Introduction to Unix", "to": "Introduction to Version Control with Git and GitHub", "width": 1}, {"arrows": "to", "from": "Introduction to Version Control with Git and GitHub", "to": "Intermediate Version Control", "width": 1}]);
 
                   nodeColors = {};

_static/multiple_regression_hyperplane_2.html

@@ -282,7 +282,7 @@ <h1></h1>
 
 
                   // parsing and collecting nodes and edges from the python
-                  nodes = new vis.DataSet([{"color": "#4682B4", "id": "Introduction to Version Control with Git and GitHub", "label": "Introduction to Version Control with Git and GitHub", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Version Control with Git and GitHub\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Intermediate Version Control"}, {"color": "#4682B4", "id": "Intermediate Version Control", "label": "Intermediate Version Control", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Intermediate Version Control\nCourse Pre-reqs: Introduction to Version Control with Git and GitHub\nSubsequent Courses: None"}, {"color": "#4682B4", "id": "Introduction to Unix", "label": "Introduction to Unix", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Unix\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to Version Control with Git and GitHub"}, {"color": "#4682B4", "id": "Introduction to Python", "label": "Introduction to Python", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Python\nCourse Pre-reqs: None\nSubsequent Courses: Python for Data Analysis"}, {"color": "#4682B4", "id": "Python for Data Analysis", "label": "Python for Data Analysis", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Python for Data Analysis\nCourse Pre-reqs: Introduction to Python\nSubsequent Courses: Introduction to Machine Learning"}, {"color": "#4682B4", "id": "Introduction to Machine Learning", "label": "Introduction to Machine Learning", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Machine Learning\nCourse Pre-reqs: Python for Data Analysis\nSubsequent Courses: None"}]);
+                  nodes = new vis.DataSet([{"color": "#FF6347", "id": "Introduction to Version Control with Git and GitHub", "label": "Introduction to Version Control with Git and GitHub", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Version Control with Git and GitHub\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Intermediate Version Control"}, {"color": "#FF6347", "id": "Intermediate Version Control", "label": "Intermediate Version Control", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Intermediate Version Control\nCourse Pre-reqs: Introduction to Version Control with Git and GitHub\nSubsequent Courses: None"}, {"color": "#FF6347", "id": "Introduction to Unix", "label": "Introduction to Unix", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Unix\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to Version Control with Git and GitHub"}, {"color": "#FF6347", "id": "Introduction to Python", "label": "Introduction to Python", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Python\nCourse Pre-reqs: None\nSubsequent Courses: Python for Data Analysis"}, {"color": "#FF6347", "id": "Python for Data Analysis", "label": "Python for Data Analysis", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Python for Data Analysis\nCourse Pre-reqs: Introduction to Python\nSubsequent Courses: Introduction to Machine Learning"}, {"color": "#FF6347", "id": "Introduction to Machine Learning", "label": "Introduction to Machine Learning", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Machine Learning\nCourse Pre-reqs: Python for Data Analysis\nSubsequent Courses: None"}]);
                   edges = new vis.DataSet([{"arrows": "to", "from": "Introduction to Version Control with Git and GitHub", "to": "Intermediate Version Control", "width": 1}, {"arrows": "to", "from": "Introduction to Unix", "to": "Introduction to Version Control with Git and GitHub", "width": 1}, {"arrows": "to", "from": "Introduction to Python", "to": "Python for Data Analysis", "width": 1}, {"arrows": "to", "from": "Python for Data Analysis", "to": "Introduction to Machine Learning", "width": 1}]);
 
                   nodeColors = {};

_static/workshops_network_hpc.html

@@ -282,7 +282,7 @@ <h1></h1>
 
 
                   // parsing and collecting nodes and edges from the python
-                  nodes = new vis.DataSet([{"color": "#FF6347", "id": "Introduction to R", "label": "Introduction to R", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to R\nCourse Pre-reqs: None\nSubsequent Courses: Regression analysis with R, Working With Data In R"}, {"color": "#FF6347", "id": "Regression analysis with R", "label": "Regression analysis with R", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Regression analysis with R\nCourse Pre-reqs: Introduction to R\nSubsequent Courses: Advanced Regression Analysis With R "}, {"color": "#FF6347", "id": "Working With Data In R", "label": "Working With Data In R", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Working With Data In R\nCourse Pre-reqs: Introduction to R\nSubsequent Courses: None"}, {"color": "#FF6347", "id": "Advanced Regression Analysis With R ", "label": "Advanced Regression Analysis With R ", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Advanced Regression Analysis With R \nCourse Pre-reqs: Regression analysis with R\nSubsequent Courses: None"}, {"color": "#FF6347", "id": "Introduction to Version Control with Git and GitHub", "label": "Introduction to Version Control with Git and GitHub", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Version Control with Git and GitHub\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Intermediate Version Control"}, {"color": "#FF6347", "id": "Intermediate Version Control", "label": "Intermediate Version Control", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Intermediate Version Control\nCourse Pre-reqs: Introduction to Version Control with Git and GitHub\nSubsequent Courses: None"}, {"color": "#FF6347", "id": "Introduction to Unix", "label": "Introduction to Unix", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Unix\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to Version Control with Git and GitHub"}]);
+                  nodes = new vis.DataSet([{"color": "#FFD700", "id": "Introduction to R", "label": "Introduction to R", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to R\nCourse Pre-reqs: None\nSubsequent Courses: Regression analysis with R, Working With Data In R"}, {"color": "#FFD700", "id": "Regression analysis with R", "label": "Regression analysis with R", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Regression analysis with R\nCourse Pre-reqs: Introduction to R\nSubsequent Courses: Advanced Regression Analysis With R "}, {"color": "#FFD700", "id": "Working With Data In R", "label": "Working With Data In R", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Working With Data In R\nCourse Pre-reqs: Introduction to R\nSubsequent Courses: None"}, {"color": "#FFD700", "id": "Advanced Regression Analysis With R ", "label": "Advanced Regression Analysis With R ", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Advanced Regression Analysis With R \nCourse Pre-reqs: Regression analysis with R\nSubsequent Courses: None"}, {"color": "#FFD700", "id": "Introduction to Version Control with Git and GitHub", "label": "Introduction to Version Control with Git and GitHub", "level": 2, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Version Control with Git and GitHub\nCourse Pre-reqs: Introduction to Unix\nSubsequent Courses: Intermediate Version Control"}, {"color": "#FFD700", "id": "Intermediate Version Control", "label": "Intermediate Version Control", "level": 3, "shape": "dot", "size": 10, "title": "Course Name: Intermediate Version Control\nCourse Pre-reqs: Introduction to Version Control with Git and GitHub\nSubsequent Courses: None"}, {"color": "#FFD700", "id": "Introduction to Unix", "label": "Introduction to Unix", "level": 1, "shape": "dot", "size": 10, "title": "Course Name: Introduction to Unix\nCourse Pre-reqs: None\nSubsequent Courses: Introduction to Version Control with Git and GitHub"}]);
                   edges = new vis.DataSet([{"arrows": "to", "from": "Introduction to R", "to": "Regression analysis with R", "width": 1}, {"arrows": "to", "from": "Introduction to R", "to": "Working With Data In R", "width": 1}, {"arrows": "to", "from": "Regression analysis with R", "to": "Advanced Regression Analysis With R ", "width": 1}, {"arrows": "to", "from": "Introduction to Version Control with Git and GitHub", "to": "Intermediate Version Control", "width": 1}, {"arrows": "to", "from": "Introduction to Unix", "to": "Introduction to Version Control with Git and GitHub", "width": 1}]);
 
                   nodeColors = {};

_static/workshops_network_python_ds.html

@@ -24,6 +24,7 @@ parts:
                   - file: programme_information/intro_to_python
                   - file: programme_information/python_for_data_analysis
                   - file: programme_information/introduction_to_machine_learning
+                  - file: programme_information/markdown_with_python
               - file: programme_information/R
                 sections:
                   - file: programme_information/intro_to_r
@@ -32,6 +33,7 @@ parts:
                   - file: programme_information/advanced_regression_analysis_with_r
                   - file: programme_information/working_with_data_in_r
                   - file: programme_information/improve_your_r_code
+                  - file: programme_information/Introduction_to_Markdown_in_R
               - file: programme_information/unix
                 sections:
                   - file: programme_information/intro_to_unix
@@ -150,6 +152,15 @@ parts:
                   - file: individual_modules/introduction_to_machine_learning/2_model_selection
                   - file: individual_modules/introduction_to_machine_learning/3_pipeline_task
                   - file: individual_modules/introduction_to_machine_learning/4_unsupervised_learning
+              - file: individual_modules/section_landing_pages/markdown_with_python
+                sections:
+                  - file: individual_modules/markdown_with_python/2-Motivation-and-Background
+                  - file: individual_modules/markdown_with_python/3-Markdown-Fundamentals
+                  - file: individual_modules/markdown_with_python/4-Markdown-Task-1
+                  - file: individual_modules/markdown_with_python/5-How-to-embed-Python-Code-in-Markdown
+                  - file: individual_modules/markdown_with_python/6-Export-the-Document
+                  - file: individual_modules/markdown_with_python/7-Markdown-Task-2
+                  - file: individual_modules/markdown_with_python/8-Further-Knowledge
           - file: course_homepages/R
             sections:
               - file: individual_modules/section_landing_pages/introduction_to_r
@@ -196,6 +207,16 @@ parts:
                   - file: individual_modules/improve_your_r_code/data_table
                   - file: individual_modules/improve_your_r_code/parallelisation
                   - file: individual_modules/improve_your_r_code/rcpp
+              - file: individual_modules/section_landing_pages/Introduction_to_Markdown_in_R
+                sections:
+                  - file: individual_modules/Introduction_to_Markdown_in_R/Background_to_Markdown
+                  - file: individual_modules/Introduction_to_Markdown_in_R/Getting_Started_with_Markdown_in_R
+                  - file: individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_Visual_Prelude
+                  - file: individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_YAML_Header
+                  - file: individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_Formatted_Text
+                  - file: individual_modules/Introduction_to_Markdown_in_R/RMarkdown_Components_Embedded_Code
+                  - file: individual_modules/Introduction_to_Markdown_in_R/Processing_RMarkdown_Files
+                  - file: individual_modules/Introduction_to_Markdown_in_R/Course_Outro
           - file: course_homepages/unix
             sections:
               - file: individual_modules/section_landing_pages/introduction_to_unix
@@ -235,10 +256,13 @@ parts:
                   - file: individual_modules/introduction_to_hpc/exploiting_slurm
               - file: individual_modules/section_landing_pages/parallel_computing
                 sections:
-                  - file: individual_modules/parallel_computing/hello_world
-                  - file: individual_modules/parallel_computing/simple_communication
-                  - file: individual_modules/parallel_computing/collective_comms
-                  - file: individual_modules/parallel_computing/parallel_fractal
+                  - file: individual_modules/parallel_computing/architecture_and_concurrency
+                  - file: individual_modules/parallel_computing/multithreading_io
+                  - file: individual_modules/parallel_computing/multiprocessing_fractal
+                  - file: individual_modules/parallel_computing/mpi_hello_world
+                  - file: individual_modules/parallel_computing/mpi_simple_communication
+                  - file: individual_modules/parallel_computing/mpi_collective_comms
+                  - file: individual_modules/parallel_computing/mpi_parallel_fractal
           - file: course_homepages/software_development
             sections:
               - file: individual_modules/section_landing_pages/software_development_best_practice
@@ -292,6 +316,7 @@ parts:
 
   - caption: Join Us!
     chapters: 
+      - file: contributing/community
       - file: contributing/contributing
       - file: contributing/roles
       - file: contributing/contributing_guidelines