Add backup writing to vivarium simulation Context #455
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
patricktnast
requested review from
albrja,
collijk,
hussain-jafari,
rmudambi and
stevebachmeier
as code owners
stevebachmeier
approved these changes
Aug 2, 2024
albrja
reviewed
Aug 5, 2024
albrja
approved these changes
Aug 5, 2024
rmudambi
reviewed
Aug 6, 2024
rmudambi
reviewed
Aug 6, 2024
hussain-jafari
approved these changes
Aug 8, 2024
stevebachmeier
pushed a commit
that referenced
this pull request
Aug 13, 2024
* add feature and test * remove unused import * add skipped test * lint * lint * add test and adjust sim.run() * lint * change protocol * add logging statement * Update test_engine.py add ticket * add self.current_time * Revert "add self.current_time" This reverts commit 322fd19. * use current time but do it right instead of wrong
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Add backup writing to vivarium simulation Context
Description
Changes and notes
This is a prerequisite for the simulation backups in psimulate. I elected to make the SimulationContext pickle itself, and also make a new public "past stop time" method that we can use from VCT.
For mysterious reasons, we can't pickle the sim object within a pytest context unless I globally disable cap logging with "pytest -s". Pickling works just fine in normal use, and trying to disable caplog or capsys etc. per-test hasn't worked so far. this appears to be something wrong on
dill's end, cfuqfoundation/dill#663
pytest-dev/pytest#10845
pytest-dev/pytest#12448
For now I've put in a skipped test.
Testing