def test_misc():
sc.heading('Testing miscellaneous functions')
sim_path = 'test_misc.sim'
json_path = 'test_misc.json'
gitinfo_path = 'test_misc.gitinfo'
fig_path = 'test_misc.png'
fig_comments = 'Test comment'
# Data loading
cv.load_data(csv_file)
cv.load_data(xlsx_file)
with pytest.raises(NotImplementedError):
cv.load_data('example_data.unsupported_extension')
with pytest.raises(ValueError):
cv.load_data(xlsx_file, columns=['missing_column'])
# Dates
d1 = cv.date('2020-04-04')
d2 = cv.date(sc.readdate('2020-04-04'))
ds = cv.date('2020-04-04', d2)
assert d1 == d2
assert d2 == ds[0]
with pytest.raises(ValueError):
cv.date([(2020, 4, 4)]) # Raises a TypeError which raises a ValueError
with pytest.raises(ValueError):
cv.date('Not a date')
cv.daydiff('2020-04-04')
# Run sim for more investigations
sim = cv.Sim(pop_size=500, verbose=0)
sim.run()
sim.plot(do_show=False)
# Saving and loading
cv.savefig(fig_path, comments=fig_comments)
cv.save(filename=sim_path, obj=sim)
cv.load(filename=sim_path)
# Version checks
cv.check_version('0.0.0') # Nonsense version
print('↑ Should complain about version')
with pytest.raises(ValueError):
cv.check_version('0.0.0', die=True)
# Git checks
cv.git_info(json_path)
cv.git_info(json_path, check=True)
# Poisson tests
c1 = 5
c2 = 8
for alternative in ['two-sided', 'larger', 'smaller']:
cv.poisson_test(c1, c2, alternative=alternative)
for method in ['score', 'wald', 'sqrt', 'exact-cond']:
cv.poisson_test(c1, c2, method=method)
with pytest.raises(ValueError):
cv.poisson_test(c1, c2, method='not a method')
# Test locations
for location in [None, 'viet-nam']:
cv.data.show_locations(location)
# Test versions
with pytest.raises(ValueError):
cv.check_save_version('1.3.2', die=True)
cv.check_save_version(cv.__version__,
filename=gitinfo_path,
comments='Test')
# Test PNG
try:
metadata = cv.get_png_metadata(fig_path, output=True)
assert metadata['Covasim version'] == cv.__version__
assert metadata['Covasim comments'] == fig_comments
except ImportError as E:
print(
f'Cannot test PNG function since pillow not installed ({str(E)}), skipping'
)
# Tidy up
remove_files(sim_path, json_path, fig_path, gitinfo_path)
return
import sciris as sc
import covasim as cv
import covasim.base as cvb
import covasim.parameters as cvp
import pylab as pl
import numpy as np
import matplotlib as mplt
import utils_vac
########################################################################
# Settings and initialisation
########################################################################
# Check version
cv.check_version('3.0.2')
cv.git_info('covasim_version.json')
# Saving and plotting settings
do_plot = 1
do_save = 1
save_sim = 1
plot_hist = 0 # Whether to plot an age histogram
do_show = 0
verbose = 1
seed = 1
n_runs = 200
to_plot = sc.objdict({
'Cumulative tests': ['cum_tests'],
'Cumulative diagnoses': ['cum_diagnoses'],
'Cumulative hospitalisations': ['cum_severe'],
'Cumulative deaths': ['cum_deaths'],
'New infections': ['new_infections'],
def test_misc():
sc.heading('Testing miscellaneous functions')
sim_path = 'test_misc.sim'
json_path = 'test_misc.json'
# Data loading
cv.load_data(csv_file)
cv.load_data(xlsx_file)
with pytest.raises(NotImplementedError):
cv.load_data('example_data.unsupported_extension')
with pytest.raises(ValueError):
cv.load_data(xlsx_file, columns=['missing_column'])
# Dates
d1 = cv.date('2020-04-04')
d2 = cv.date(sc.readdate('2020-04-04'))
ds = cv.date('2020-04-04', d2)
assert d1 == d2
assert d2 == ds[0]
with pytest.raises(ValueError):
cv.date([(2020, 4, 4)]) # Raises a TypeError which raises a ValueError
with pytest.raises(ValueError):
cv.date('Not a date')
cv.daydiff('2020-04-04')
# Saving and loading
sim = cv.Sim()
cv.save(filename=sim_path, obj=sim)
cv.load(filename=sim_path)
# Version checks
cv.check_version('0.0.0') # Nonsense version
print('↑ Should complain about version')
with pytest.raises(ValueError):
cv.check_version('0.0.0', die=True)
# Git checks
cv.git_info(json_path)
cv.git_info(json_path, check=True)
# Poisson tests
c1 = 5
c2 = 8
for alternative in ['two-sided', 'larger', 'smaller']:
cv.poisson_test(c1, c2, alternative=alternative)
for method in ['score', 'wald', 'sqrt', 'exact-cond']:
cv.poisson_test(c1, c2, method=method)
with pytest.raises(ValueError):
cv.poisson_test(c1, c2, method='not a method')
# Tidy up
remove_files(sim_path, json_path)
return