debugtools

debugtools

Utilities to help with debugging Starsim runs

Classes

Name	Description
Debugger	Step through one or more sims and pause or raise an exception when a condition is met
Profile	Class to profile the performance of a simulation

Debugger

debugtools.Debugger(*args, func, skip=None, verbose=True, die=True, run=False)

Step through one or more sims and pause or raise an exception when a condition is met

Parameters

Name	Type	Description	Default
args	list	the sim or sims to step through	()
func	func / str	the function to run on the sims (or can use a built-in one, e.g. ‘equal’)	required
skip	list	if provided, additional object names/types to skip (not check)	None
verbose	bool	whether to print progress during the run	True
die	bool	whether to raise an exception if the condition is met; alternatively ‘pause’ will pause execution, and False will just print	True
run	bool	whether to run immediately	False

Examples:

## Example 1: Identical sims are identical
import starsim as ss

s1 = ss.Sim(pars=dict(diseases='sis', networks='random'), n_agents=250)
s2 = s1.copy()
s3 = s1.copy()
db = ss.Debugger(s1, s2, s3, func='equal')
db.run()

## Example 2: Pause when sim results diverge
import sciris as sc
import starsim as ss

# Set up the sims
pars = dict(networks='random', n_agents=1000, verbose=0)
sis1 = ss.SIS(beta=0.050)
sis2 = ss.SIS(beta=0.051) # Very slightly more
s1 = ss.Sim(pars, diseases=sis1)
s2 = ss.Sim(pars, diseases=sis2)

# Run the debugger
db = ss.Debugger(s1, s2, func='equal_results', die='pause')
db.run()

# Show non-matching results
sc.heading('Differing results')
df = db.results[-1].df
df = df[~df['equal']]
df.disp()

Methods

Name	Description
equal	Run all other tests
equal_check	Check if equality is false, and print a message or die
equal_dists	Check if the dists are equal
equal_pars	Check if SimPars are equal
equal_people	Check if people are equal

equal

debugtools.Debugger.equal(*sims)

Run all other tests

equal_check

debugtools.Debugger.equal_check(e, which)

Check if equality is false, and print a message or die

equal_dists

debugtools.Debugger.equal_dists(*sims)

Check if the dists are equal

equal_pars

debugtools.Debugger.equal_pars(*sims, skip='label')

Check if SimPars are equal

equal_people

debugtools.Debugger.equal_people(*sims)

Check if people are equal

Profile

debugtools.Profile(
    sim,
    follow=None,
    do_run=True,
    plot=True,
    verbose=True,
    **kwargs,
)

Class to profile the performance of a simulation

Typically invoked via sim.profile().

Parameters

Name	Type	Description	Default
sim	ss.Sim	the sim to profile	required
follow	func / list	a list of functions/methods to follow in detail	None
do_run	bool	whether to immediately run the sim	True
plot	bool	whether to plot time spent per module step	True
**kwargs	dict	passed to sc.profile()	{}

Example:

import starsim as ss

net = ss.RandomNet()
sis = ss.SIS()
sim = ss.Sim(networks=net, diseases=sis)
prof = sim.profile(follow=[net.add_pairs, sis.infect])
prof.disp()

Methods

Name	Description
disp	Same as sc.profile.disp(), but skip the run function by default
plot_cpu	Shortcut to sim.loop.plot_cpu()
profile_init	Handle sim init – both run it and profile it
run	Profile the performance of the simulation

disp

debugtools.Profile.disp(bytime=1, maxentries=10, skiprun=True)

Same as sc.profile.disp(), but skip the run function by default

plot_cpu

debugtools.Profile.plot_cpu()

Shortcut to sim.loop.plot_cpu()

profile_init

debugtools.Profile.profile_init()

Handle sim init – both run it and profile it

run

debugtools.Profile.run()

Profile the performance of the simulation

Functions

Name	Description
check_requires	Check that the module’s requirements (of other modules) are met
check_version	Check the expected Starsim version with the one actually installed. The expected
metadata	Store metadata; like sc.metadata(), but optimized for speed
mock_module	Create a minimal mock “Module” object
mock_people	Create a minimal mock “People” object
mock_sim	Create a minimal mock “Sim” object to initialize objects that require it
mock_time	Create a minimal mock “Time” object

check_requires

debugtools.check_requires(sim, requires, *args)

Check that the module’s requirements (of other modules) are met

check_version

debugtools.check_version(expected, die=False, warn=True)

Check the expected Starsim version with the one actually installed. The expected version string may optionally start with ‘>=’ or ‘<=’ (== is implied otherwise), but other operators (e.g. ~=) are not supported. Note that ‘>’ and ‘<’ are interpreted to mean ‘>=’ and ‘<=’; ‘>’ and ‘<’ are not supported.

Parameters

Name	Type	Description	Default
expected	str	expected version information	required
die	bool	whether or not to raise an exception if the check fails	False
warn	bool	whether to raise a warning if the check fails	True

Example:

ss.check_version('>=3.0.0', die=True) # Will raise an exception if an older version is used

metadata

debugtools.metadata(comments=None)

Store metadata; like sc.metadata(), but optimized for speed

mock_module

debugtools.mock_module(dur=10, **kwargs)

Create a minimal mock “Module” object

mock_people

debugtools.mock_people(n_agents=100)

Create a minimal mock “People” object

mock_sim

debugtools.mock_sim(n_agents=100, **kwargs)

Create a minimal mock “Sim” object to initialize objects that require it

Parameters

Name	Type	Description	Default
n_agents	int	the number of agents to create	100
**kwargs	dict	passed to ss.mock_time()	{}

mock_time

debugtools.mock_time(dt=1.0, dur=10, start=2000)

Create a minimal mock “Time” object