Make python code that adds itself to the report.

[a-t-0]

Write a code that scans all the code files and adds them all automatically as separate appendices to the code.

Make it opinionated by first looking for __main__.py and putting that in the first (new) appendix, and then searching for main.py and putting that 2nd.

Add the remainder on alphabetic order.

Add tests after the main code.

[create-issue-branch[bot]]

Branch issue-3-Make_python_code_that_adds_itself_to_the_report created!

[a-t-0]

• [x] Generalize to also include the pdfs of jupyiter notebooks instead of only python coder
• [ ] Unit test code (ETD: 180 mins)
• [x] Specify order in which appendices should be added
• [x] Ensure appendices are added in specified order (ETD: 60 mins)
• [ ] Include the reproducability instructions in the same appendix that has __main__.py (ETD: 20 mins)

[a-t-0]

First find the amount of appendices that do not include code and only add appendices after that position. The order for python files should be:

__main__.py
main.py
<alphabetic order>

If some files are already included: They either follow the order or not. a. If yes: a.1 They either have other appendices in between or not. ____a.1.a If yes: find the last code appendix that is already included and add the remaining code appendices in the specified (alphabetic) order ____a.1.b If no: Integrate the remaining appendices in between there in the specified (alphabetic) order

b. If no: b.1 They either have other appendices in between or not. ____b.1.a.1 If yes: find the last code appendix that is already included and add the remaining code appendices in the specified (alphabetic) order. ____b.1.b.1 If no: find the last code appendix that is already included and add the remaining code appendices in the specified (alphabetic) order.

[a-t-0]

• [ ] write a method that comments out appendices that will not be found to ensure compilation (ETD: 60 mins)
• [x] Write a method that removes appendix duplicates when present (ETD: 20 mins)
• [x] Write a method that fixes the appendix session based on the appendices that are present (preferably without disturbing the non-code appendices that are included). (ETD: 120 mins)
• [ ] clean up code (ETD: 40 mins)
• [ ] comment code (ETD: 30 mins) 180 mins+60+270 mins = 180+330 mins=3+5.5 hrs = 8.5 hrs.

[a-t-0]

Change of order specification: write a separate method that classifies and restructures the appendices.

• [x] Identify the appendices without code without notebooks
• [x] Identify the appendices with code
• [x] Identify the appendices with notebooks
• [x] Identify the code files missing in the appendices
• [x] Identify the notebook files missing in the appendices
• [x] get the order in which these appendices are included in main.

Then always restructure according to the following order:

0. First include the appendices without code in the order they were included.
1. Include code in order: __main__.py,main.py,a-z
2. Include notebooks in order: __main__.py,main.py,a-z

[a-t-0]

• [x] Remove unused methods
• [x] Rename variable to sensible variable names.
• [x] Sort method arguments on alphabetic order
• [x] Pyment generate the docstring templates
• [x] write documentation
• [x] Structure code (spacing and newlines)
• [x] Make code more readable
• [ ] Simplify code

[a-t-0]

Completed in pull request #4 .