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Extend documentation and fix typos and bugs in documentation#1531

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mknaranja wants to merge 16 commits intomainfrom
2026_03_doc
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Extend documentation and fix typos and bugs in documentation#1531
mknaranja wants to merge 16 commits intomainfrom
2026_03_doc

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@mknaranja mknaranja commented Apr 2, 2026

Changes and Information

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

  • Extensive additions with references to tutorials in getting started
  • Updated figures (added to getting started and in general start)
  • Some small typo corrections and changes to the documentation
  • Extended MEmilio developer's list

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

  • Two figures have been updated on my webspace (not explicitly visible in the changes)

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 within the code (Doxygen) for new functionality has been added in the code.
  • Appropriate external documentation (ReadTheDocs) for new functionality has been added to the online documentation and checked in the preview.
  • 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).

@mknaranja mknaranja requested review from HenrZu and kilianvolmer April 4, 2026 10:34
@mknaranja mknaranja marked this pull request as ready for review April 4, 2026 10:40
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codecov bot commented Apr 4, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.38%. Comparing base (cd10687) to head (fbd474a).
⚠️ Report is 10 commits behind head on main.

Additional details and impacted files
@@           Coverage Diff           @@
##             main    #1531   +/-   ##
=======================================
  Coverage   97.38%   97.38%           
=======================================
  Files         188      188           
  Lines       16536    16621   +85     
=======================================
+ Hits        16103    16186   +83     
- Misses        433      435    +2     

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@kilianvolmer kilianvolmer left a comment

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Thank you for updating the literature and adding links to the tutorials, that is a great addition!
However, I am not happy with the changes regarding flow model -> FlowModel and infection states -> InfectionStates. The latter is not changed in all locations and we now have a combination of InfectionStates, InfectionStates and InfectionStates. This should be unified.
FInally, I would like to remind you that we now build a preview for the documentation on every PR. You can access this one at https://memilio--1531.org.readthedocs.build/en/1531/index.html and check that all links are working.

Comment thread docs/source/cpp/aggregated_models.rst
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Comment thread docs/source/team.rst Outdated
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Comment thread docs/source/getting_started.rst Outdated
Comment thread docs/source/getting_started.rst Outdated
Co-authored-by: Kilian Volmer <[email protected]>
Co-authored-by: Carlotta Gerstein <[email protected]>
Comment thread cpp/memilio/compartments/flow_model.h
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5 participants