Fix Parquet emitter issues for colony simulations#390
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katha815 wants to merge 7 commits intoCovertLab:masterfrom
Open
Fix Parquet emitter issues for colony simulations#390katha815 wants to merge 7 commits intoCovertLab:masterfrom
katha815 wants to merge 7 commits intoCovertLab:masterfrom
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katha815
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thalassemia
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Feb 6, 2026
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Thanks for the PR! I left comments on all three changes. I'm very busy next week, but I'll try to get a PR up fixing issue 4 in the linked issue by next Friday.
katha815
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Feb 12, 2026
| import numpy as np | ||
| import orjson | ||
| import re | ||
| import ast |
katha815
commented
Feb 12, 2026
| metadata=metadata, | ||
| profile=config["profile"], | ||
| initial_global_time=config.get("start_time", 0.0), | ||
| emit_topology=config.get("emit_topology", True), |
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Added missing options with respect to vivarium-core Engine class. Default values also imported from Engine class initiation.
Change serialization to preserve original value type.
Serialize metadata using serialize_value as recommended.
katha815
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Feb 12, 2026
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Serialize metadata using default serializer.
thalassemia
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Mar 4, 2026
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Sorry for the delay! This looks good to me. Thanks!
| initial_global_time=config.get("start_time", 0.0), | ||
| emit_topology=config.get("emit_topology", True), | ||
| emit_processes=config.get("emit_processes", False), | ||
| emit_step=config.get("emit_step", 1), |
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Interesting, I did not know that the emit_step was configurable. Thanks for filling these in!
thalassemia
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Summary
Fixes several issues preventing Parquet emission when resuming colony simulations from saved JSON state files.
This PR is motivated by and discussed in detail in issue #389.
Changes
emit_configand other features of vivarium.core.engine will be included in engine process.Context
These issues occur when running
ecoli_engine_process.pywith"emitter": "parquet"under baseline colony simulations (no online emitter).