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Add event logging#208

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allison-li-1016 wants to merge 8 commits intomainfrom
allison/add-event-logging
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Add event logging#208
allison-li-1016 wants to merge 8 commits intomainfrom
allison/add-event-logging

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@allison-li-1016 allison-li-1016 commented Nov 12, 2025

Estimated time to review: small

Addresses #191

Description of changes:

  • added CLI option for logging events
  • added an 'EVENTS' output file logging events that occur at given tick intervals
  • added logging information to cytotoxic module to track lysis events & proliferation module to track division events and cycle length
  • edit tests to include new mocks for event logging

Discussion:

  • We can consider logging division as an event as a proxy for cell cycle durations
  • I am concerned about the events queue object getting exponentially larger if we start tracking frequent events, we should discuss clearing the queue once the events are logged

@allison-li-1016 allison-li-1016 marked this pull request as draft November 12, 2025 22:08
@allison-li-1016 allison-li-1016 marked this pull request as ready for review November 13, 2025 00:42
@allison-li-1016 allison-li-1016 requested review from a team, Jannetty, cainja, daniellevahdat, jacob-evarts, jessicasyu, kristaphommatha and pohaoc2 and removed request for a team November 13, 2025 00:42
@Jannetty
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Recording that we spoke about making sure to clear the events queue object each time it writes to file

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@kristaphommatha kristaphommatha left a comment

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LGTM!

@allison-li-1016
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@allison-li-1016 consider adding eventLog object in the Utils class to enforce logs to be of a certain format....

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3 participants