Vivarium

Latest version: v3.2.5

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3.0.1

- Create script to find matching dependency branches
- Add results category exclusion tests

3.0.0

Breaking changes:
- Remove the unnecessary metrics pipeline
- Refactor lookup table creation and allow configuration of lookup columns
- Refactor results manager to process results directly

Major changes:
- Move results controller and interface from managers to default plugins
- Add a get_configuration method and configuration attribute to Component
- Enable build_lookup_table to accept a list as input data
- Implement an Observation dataclass
- Remove --location/-l option from simulate run command
- Change the metrics/ folder to results/; refer to "results" instead of "metrics" throughout
- Implement multiple new interface functions for registering stratifications and observations
- Implement multiple new Observer types
- Implement simulation backups
- Implement excluding results categories via the configuration

Other changes:
- Use layered-config-tree package instead of local ConfigTree class
- Add a report emitter to the SimulationContext
- Check for and log unused stratifications and raise for missing required stratifications
- Move all steps of running a simulation into a run_simulation instance method
- Add simulate run e2e test
- Stop writing seed and draw columns to the results
- Install matching upstream branches in github builds
- Automatically run Jenkins builds on push or pull request
- Add type hints throughout results modules
- Various other minor updates

2.3.8

- Hotfix pin numpy below 2.0

2.3.7

- Add deprecation warning to import ConfigTree from the config_tree package

2.3.6

- Update population keys in testing utilities to be mmore descriptive

2.3.5

- Improves boids example and tutorial

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