944 streamline secir python code

[MaxBetzDLR]

Changes and Information

Please briefly list the changes (main added features, changed items, or corrected bugs) made:

• Change depreciated module name of secir model in python package
• Improve continuity of code structure and naming
• Update documentation
• Script to check missing/old license
• Check and update current examples

If need be, add additional information and what the reviewer should look out for in particular:

Merge Request - Guideline Checklist

Please check our git workflow. Use the draft feature if the Pull Request is not yet ready to review.

Checks by code author

• Every addressed issue is linked (use the "Closes #ISSUE" keyword below)
• New code adheres to coding guidelines
• No large data files have been added (files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
• Tests are added for new functionality and a local test run was successful (with and without OpenMP)
• Appropriate documentation for new functionality has been added (Doxygen in the code and Markdown files if necessary)
• Proper attention to licenses, especially no new third-party software with conflicting license has been added
• (For ABM development) Checked benchmark results and ran and posted a local test above from before and after development to ensure performance is monitored.

Checks by code reviewer(s)

• Corresponding issue(s) is/are linked and addressed
• Code is clean of development artifacts (no deactivated or commented code lines, no debugging printouts, etc.)
• Appropriate unit tests have been added, CI passes, code coverage and performance is acceptable (did not decrease)
• No large data files added in the whole history of commits(files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
• On merge, add 2-5 lines with the changes (main added features, changed items, or corrected bugs) to the merge-commit-message. This can be taken from the briefly-list-the-changes above (best case) or the separate commit messages (worst case).

Closes #944

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 96.23%. Comparing base (575a146) to head (307c401).

❗ Current head 307c401 differs from pull request most recent head 3443466

Please upload reports for the commit 3443466 to get more accurate results.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1041   +/-   ##
=======================================
  Coverage   96.23%   96.23%           
=======================================
  Files         128      128           
  Lines       10852    10852           
=======================================
  Hits        10443    10443           
  Misses        409      409           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[HenrZu]

Thank you for these changes :) Some comments and then it can be merged