1148 Rework Data structure and Rename Mobility and Vaccination file

[HenrZu]

Changes and Information

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

• The name for the vaccination file was outdated in the epidata Package. Updated from all_county_ageinf_vacc to vacc_county_ageinf
• Remove default mobility matrix file.
• Extend function getSimulationData to really provide all files to execute the simulations.
• Remove Twitter data.
• Rework data structure, where the region are now the first instance.
• Data path for Model specific io function is now more concrete, allowing other data than germany via the input argument.
• clean_data cleans all created data via the pycode

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).

[codecov]

Codecov Report

Attention: Patch coverage is 92.85714% with 2 lines in your changes missing coverage. Please review.

Project coverage is 97.20%. Comparing base (a985af3) to head (358b49f).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
cpp/models/ode_secir/parameters_io.h	90.90%	1 Missing ⚠️
cpp/models/ode_secirvvs/parameters_io.h	85.71%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1150      +/-   ##
==========================================
- Coverage   97.21%   97.20%   -0.02%     
==========================================
  Files         154      154              
  Lines       14203    14193      -10     
==========================================
- Hits        13808    13796      -12     
- Misses        395      397       +2     

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

🚀 New features to boost your workflow:

• ❄ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[HenrZu]

To validate the changes, I ran the Simulation once in the current main and in this branch once in cpp and once in python while saving the graph and compared it then. The results are identical to the previous one.

[xsaschako]

Looks good to me. If you can answer the one question i'd be happy but i approve for now.

[xsaschako]

lgtm