def test_all_tutorials():
# Get and run tests
filenames = sc.getfilelist(tex.examples_dir, pattern='t*.py', nopath=True)
for filename in filenames:
if filename[
1] in '0123456789': # Should have format e.g. t5_foo.py, not test_foo.py
sc.heading(f'Running {filename}...')
try:
tex.run_example(filename)
except (
pickle.PicklingError, NameError
): # Ignore these: issue with how the modules are loaded in the run_example function
pass
else:
print(f'[Skipping "{filename}" since does not match pattern]')
# Tidy up
testfiles = sc.getfilelist(tex.examples_dir, pattern='my-*.*')
sc.heading('Tidying...')
print(f'Deleting:')
for filename in testfiles:
print(f' {filename}')
print('in 3 seconds...')
sc.timedsleep(3)
for filename in testfiles:
os.remove(filename)
print(f' Deleted {filename}')
return
def test_progress_bar():
sc.heading('Progress bar')
n = 50
for i in range(n):
sc.progressbar(i + 1, n)
sc.timedsleep(1.0 / n, verbose=False)
return i
def run_sim(index,
scenpars=None,
label=None,
runinfo=None,
do_shrink=True,
from_cache=True,
verbose=True):
''' Load, modify, and run the simulation '''
if scenpars is None:
print('WARNING, loading default parameters!')
scenpars = sc.dcp(d_pars)
if label is None:
label = f'full_sim_trial{index}_nolabel'
# Run sim or load up until scenarios start
sim_loaded = 0
filename = f'./simcache/projection_trial{index}.sim'
if from_cache and os.path.exists(filename):
tries = 0
while not sim_loaded and tries < 3:
try:
print(f'run_sim(): Loading sim from cache ({filename})...')
sim = cv.load(filename)
assert isinstance(
sim, cv.Sim
) # Sometimes unpickling fails, but can reload locally
tn = sim.get_interventions('tn')
tn.subtarget = test_num_subtarg
sim_loaded = 1
except Exception as E:
print(f'Loading failed on try {tries}! {E}')
string = '\n\n'.join([
f'Index {index}', filename, f'Try {tries}',
str(E),
sc.traceback()
])
fn = f'simcache_exception_index{index}_try{tries}.err'
sc.savetext(fn, string)
tries += 1
sc.timedsleep(0.5)
if not sim_loaded:
print(f'run_sim(): Creating new sim (and saving to {filename})...')
sim = create_sim(index, verbose=verbose)
sim.run(until=sim.sceninfo.calib_end)
sim.save(filename, keep_people=True)
# Modify the sim with these scenario values
sim = modify_sim(sim, scenpars=scenpars, label=label, runinfo=runinfo)
# Rerun till the end and optionally shrink
sim.run(restore_pars=False) # So we can see the changes made
if do_shrink:
sim.shrink()
return sim
sc.toc(T)
def make_study(restart=False):
''' Make a study, deleting one if it already exists '''
try:
if restart:
print(f'About to delete {storage}:{name}, you have 5 seconds to intervene!')
sc.timedsleep(5.0)
op.delete_study(storage=storage, study_name=name)
except:
pass
output = op.create_study(storage=storage, study_name=name, load_if_exists=not(restart))
return output
if __name__ == '__main__':
T = sc.tic()
try:
sh.rmtree('./progress/', ignore_errors=True)
os.makedirs('./progress/', exist_ok=True)
except Exception as E:
print(f'Could not make progress folder: {E}')
if which == 'a':
sweeps = construct1dsweeps()
ntrials = len(sweeps)
sc.heading(f'Beginning run for type "{which}" for {ntrials} trials...')
sc.timedsleep(3)
sims = sc.parallelize(run_scenario,
iterarg=np.arange(ntrials),
ncpus=ncpus,
kwargs={'which': which})
msim = cv.MultiSim(sims)
msim.save(msimfile)
if doplot:
msim.plot(max_sims=8,
to_plot='overview',
fig_args={'figsize': (38, 19)})
print('Done.')
sc.toc(T)
n_scenarios = len(scenarios)
goodseeds = cv.load(f'{resfolder}/goodseeds.obj')[:max_seeds]
sims_file = f'{cachefolder}/all_sims.obj'
T = sc.tic()
# Optionally remove the cache folder
if do_load and os.path.exists(cachefolder):
response = input(
f'Do you want to delete the cache folder "{os.path.abspath(cachefolder)}" before starting? y/[n] '
)
if response in ['y', 'yes', 'Yes']:
print(f'Deleting "{cachefolder}"...')
shutil.rmtree(cachefolder)
else:
print(f'OK, not deleting "{cachefolder}" -- you were warned!')
sc.timedsleep(2) # Wait for a moment so messages can be seen
# Make sims
sc.heading('Making sims...')
if os.path.isfile(sims_file) and do_load: # Don't run, just load
sim_configs = cv.load(sims_file)
else:
n_sims = n_scenarios * sy_npts * tr_npts * max_seeds
count = 0
ikw = []
for i_sc, scenname in enumerate(scenarios):
for i_fst, future_symp_test in enumerate(symp_test_vals):
print(f'Creating arguments for sim {count} of {n_sims}...')
daily_test = np.round(1 - (1 - future_symp_test)**(1 / 10),
3) if future_symp_test < 1 else 0.4
for i_fte, future_t_eff in enumerate(trace_eff_vals):