Skip to content

MIGRATION.md

Latest commit

 

History

History
149 lines (109 loc) · 3.7 KB

MIGRATION.md

File metadata and controls

149 lines (109 loc) · 3.7 KB

Migration Guide: v0.0.4 to v0.1.0

Breaking Changes

Version 0.1.0 introduces a thread-safe, instance-based configuration system. The previous static configuration pattern has been removed.

Configuration API Changes

v0.0.4 (Old)

from emodlib.malaria import IntrahostComponent

# Set params globally (affected all instances)
IntrahostComponent.set_params({'Run_Number': 42})
IntrahostComponent.update_params({'infection_params': {'Antigen_Switch_Rate': 1e-9}})

# Create instance (used global params)
ic = IntrahostComponent.create()

v0.1.0 (New)

from emodlib.malaria import IntrahostComponent, create_config

# Create config instance (thread-safe, independent)
config = create_config({'Run_Number': 42})

# Or with nested params
config = create_config({
    'Run_Number': 42,
    'infection_params': {'Antigen_Switch_Rate': 1e-9}
})

# Create instance with config
ic = IntrahostComponent.create(config)

Removed Functions

Removed Replacement
IntrahostComponent.set_params(params) config = create_config(params)
IntrahostComponent.update_params(params) config.update(params)
IntrahostComponent.params config.yaml or config properties

Incremental Updates with config.update()

The update() method provides the same incremental merge behavior as the old update_params():

# Create config with initial params
config = create_config({'Run_Number': 1, 'Max_Individual_Infections': 3})

# Later, update just one param (keeps Run_Number=1, Max_Individual_Infections=3)
config.update({'infection_params': {'Antigen_Switch_Rate': 1e-8}})

# Method chaining also works
config.update({'Run_Number': 2}).update({'infection_params': {'Antigen_Switch_Rate': 1e-9}})

Creating Susceptibility and Infection Objects

v0.0.4

from emodlib.malaria import Susceptibility, Infection

s = Susceptibility.create()
inf = Infection.create(susceptibility=s, hepatocytes=1)

v0.1.0

from emodlib.malaria import Susceptibility, Infection, create_config

config = create_config()
s = Susceptibility.create(config)
inf = Infection.create(susceptibility=s, config=config, hepatocytes=1)

Viewing Configuration

v0.0.4

print(IntrahostComponent.params.yaml)

v0.1.0

config = create_config()
print(config.yaml)

Multi-Simulation Workflows

v0.0.4 - Simulations with different parameters required careful sequencing:

IntrahostComponent.set_params({'Run_Number': 1})
ic1 = IntrahostComponent.create()

IntrahostComponent.set_params({'Run_Number': 2})  # Changed global state!
ic2 = IntrahostComponent.create()

v0.1.0 - Each config is independent (thread-safe):

config1 = create_config({'Run_Number': 1})
config2 = create_config({'Run_Number': 2})

ic1 = IntrahostComponent.create(config1)
ic2 = IntrahostComponent.create(config2)

# Can run in parallel without interference

Quick Migration Checklist

  1. Add create_config to imports:

    from emodlib.malaria import IntrahostComponent, create_config

  2. Replace set_params() with create_config():

    # Before
IntrahostComponent.set_params({'Run_Number': 42})

# After
config = create_config({'Run_Number': 42})

  3. Replace update_params() with config.update():

    # Before
IntrahostComponent.update_params({'infection_params': {'X': 1}})

# After
config.update({'infection_params': {'X': 1}})

  4. Pass config to create():

    # Before
ic = IntrahostComponent.create()

# After
ic = IntrahostComponent.create(config)

  5. For Susceptibility.create() and Infection.create(), add config parameter.