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Csv writing #249

Merged
merged 90 commits into from
Jan 12, 2024
Merged

Csv writing #249

merged 90 commits into from
Jan 12, 2024

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abbie-evans
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@abbie-evans abbie-evans commented Nov 30, 2023

Summary

  • Created a writer to write a csv for infection history and a csv for infectiousness
  • Added demographic sweep to record demographic information of the population in a csv
  • Ran on a test simulation of 100 people

Checklist

  • All new functions have docstrings in the correct style

  • I've verified the complete docs build locally without errors

  • I've maintained 100% coverage (please mention any 'no cover' annotations explicitly)

  • I've unit-tested all new methods directly

  • Breaking change (fix or feature that would cause existing functionality to change)

  • I have read the CONTRIBUTING document.

  • My code follows the code style of this project.

  • I have updated the wiki with new parameters/model functionality

Closing issues

Closes #248.

mghosh00 and others added 30 commits November 22, 2023 13:13
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@KCGallagher KCGallagher left a comment

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Really great work here both - some of those bugs were not easy to isolate (though I am sorry we hadn't picked them up before), so very well identified! I am not sure why the tests are failing but will look into that now

pyEpiabm/pyEpiabm/sweep/update_place_sweep.py Show resolved Hide resolved
pyEpiabm/docs/source/sweeps.rst Outdated Show resolved Hide resolved
pyEpiabm/pyEpiabm/routine/simulation.py Outdated Show resolved Hide resolved
pyEpiabm/pyEpiabm/sweep/host_progression_sweep.py Outdated Show resolved Hide resolved
pyEpiabm/pyEpiabm/sweep/initial_demographics_sweep.py Outdated Show resolved Hide resolved
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@KCGallagher KCGallagher left a comment

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One minor suggestion for some logic I don't quite understand (nested if statements - there are two examples in the same file), but otherwise am happy with this. Afraid I want to postpone merging until we resolve the functional test issue, but I will look into this tonight/tomorrow and decide what to do here.

pyEpiabm/pyEpiabm/routine/simulation.py Outdated Show resolved Hide resolved
@KCGallagher KCGallagher self-requested a review January 11, 2024 23:21
@abbie-evans abbie-evans merged commit a2504d1 into main Jan 12, 2024
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Infection history data
3 participants