def git_info(filename=None, check=False, comments=None, old_info=None, die=False, indent=2, verbose=True, frame=2, **kwargs):
'''
Get current git information and optionally write it to disk. Simplest usage
is cv.git_info(__file__)
Args:
filename (str): name of the file to write to or read from
check (bool): whether or not to compare two git versions
comments (dict): additional comments to include in the file
old_info (dict): dictionary of information to check against
die (bool): whether or not to raise an exception if the check fails
indent (int): how many indents to use when writing the file to disk
verbose (bool): detail to print
frame (int): how many frames back to look for caller info
kwargs (dict): passed to sc.loadjson() (if check=True) or sc.savejson() (if check=False)
**Examples**::
cv.git_info() # Return information
cv.git_info(__file__) # Writes to disk
cv.git_info('covasim_version.gitinfo') # Writes to disk
cv.git_info('covasim_version.gitinfo', check=True) # Checks that current version matches saved file
'''
# Handle the case where __file__ is supplied as the argument
if isinstance(filename, str) and filename.endswith('.py'):
filename = filename.replace('.py', '.gitinfo')
# Get git info
calling_file = sc.makefilepath(sc.getcaller(frame=frame, tostring=False)['filename'])
cv_info = {'version':cvv.__version__}
cv_info.update(sc.gitinfo(__file__, verbose=False))
caller_info = sc.gitinfo(calling_file, verbose=False)
caller_info['filename'] = calling_file
info = {'covasim':cv_info, 'called_by':caller_info}
if comments:
info['comments'] = comments
# Just get information and optionally write to disk
if not check:
if filename is not None:
output = sc.savejson(filename, info, indent=indent, **kwargs)
else:
output = info
return output
# Check if versions match, and optionally raise an error
else:
if filename is not None:
old_info = sc.loadjson(filename, **kwargs)
string = ''
old_cv_info = old_info['covasim'] if 'covasim' in old_info else old_info
if cv_info != old_cv_info: # pragma: no cover
string = f'Git information differs: {cv_info} vs. {old_cv_info}'
if die:
raise ValueError(string)
elif verbose:
print(string)
return
def debuginfo(output=False):
import sciris as sc
outstr = '\nHealthPrior debugging info:\n'
outstr += ' Version: %s\n' % version
outstr += ' Branch: %s\n' % sc.gitinfo()['branch']
outstr += ' SHA: %s\n' % sc.gitinfo()['hash']
outstr += ' Date: %s\n' % sc.gitinfo()['date']
outstr += ' Path: %s\n' % HPpath()
if output:
return outstr
else:
print(outstr)
return None
def git_info(filename=None, check=False, old_info=None, die=False, verbose=True, **kwargs):
'''
Get current git information and optionally write it to disk.
Args:
filename (str): name of the file to write to or read from
check (bool): whether or not to compare two git versions
old_info (dict): dictionary of information to check against
die (bool): whether or not to raise an exception if the check fails
**Examples**::
cv.git_info('covasim_version.json') # Writes to disk
cv.git_info('covasim_version.json', check=True) # Checks that current version matches saved file
'''
info = sc.gitinfo(__file__)
if not check: # Just get information
if filename is not None:
output = sc.savejson(filename, info, **kwargs)
else:
output = info
else:
if filename is not None:
old_info = sc.loadjson(filename, **kwargs)
string = ''
if info != old_info:
string = f'Git information differs: {info} vs. {old_info}'
if die:
raise ValueError(string)
elif verbose:
print(string)
return output
def version_info():
print(
f'Loading SynthPops v{spv.__version__} ({spv.__versiondate__}) from {spd.settings.thisdir}'
)
print(f'Data folder: {spd.settings.datadir}')
try:
gitinfo = sc.gitinfo(__file__)
print(f'Git information:')
sc.pp(gitinfo)
except:
pass # Don't worry if git info isn't available
return
def get_version_info():
''' Return the information about the project. '''
gitinfo = sc.gitinfo(__file__)
version_info = {
'version': hp.version,
'date': hp.versiondate,
'gitbranch': gitinfo['branch'],
'githash': gitinfo['hash'],
'gitdate': gitinfo['date'],
'server': socket.gethostname(),
'cpu': '%0.1f%%' % psutil.cpu_percent(),
}
return version_info
def __init__(self,
name='Default',
burdenfile=None,
interventionsfile=None,
country=None,
makepackage=True,
verbose=2):
''' Initialize the project '''
## Define the structure sets
self.burdensets = sc.odict()
self.intervsets = sc.odict()
self.packagesets = sc.odict()
## Define other quantities
self.name = name
self.country = country
self.uid = sc.uuid()
self.created = sc.now()
self.modified = sc.now()
self.version = hp.version
self.gitinfo = sc.gitinfo(__file__)
self.filename = None # File path, only present if self.save() is used
## Load burden spreadsheet, if available
if burdenfile:
self.loadburden(filename=burdenfile, verbose=verbose)
## Load interventions spreadsheet, if available
if interventionsfile:
self.loadinterventions(filename=interventionsfile, verbose=verbose)
## Combine into health package, if available
if makepackage and burdenfile and interventionsfile:
self.makepackage()
return None
# This code is used to build the pars_* file containing parameter configuations and corresponding rand_seed values.
import os
import sciris as sc
import optuna as op
import numpy as np
import pandas as pd
import create_sim as cs
import covasim_schools as cvsch
import covasim as cv
import synthpops as sp
cv.check_save_version('1.7.6', folder='gitinfo', comments={'SynthPops':sc.gitinfo(sp.__file__)})
pop_size = 2.25e5
folder = 'v20201019'
children_equally_sus = False
alternate_symptomaticity = True
# This is the data we're trying to fit
to_fit = {
'cases_begin': 75, # per 100k over 2-weeks
'cases_end': 75, # per 100k over 2-weeks
're': 1.0,
'prevalence': 0.002,
'yield': 0.024, # 2.4% positive
'tests': 225, # per 100k (per day) - 225 is 5000 tests in 2.23M pop per day
}
# And here are the weights for each element
weight = {
'cases_begin': 1, # per 100k over 2-weeks
import os
import numpy as np
import covasim as cv
import create_sim as cs
import sciris as sc
import matplotlib.pyplot as plt
import covasim_schools as cvsch
import testing_scenarios as t_s
import synthpops as sp
from calibrate_model import evaluate_sim
from pathlib import Path
cv.check_save_version('1.7.6',
folder='gitinfo',
comments={'SynthPops': sc.gitinfo(sp.__file__)})
do_run = True
children_equally_sus = False
alternate_symptomaticity = True
assert (not children_equally_sus or not alternate_symptomaticity)
par_inds = (0, 30) # First and last parameters to run
pop_size = 2.25e5 # 1e5 2.25e4 2.25e5
batch_size = 30
folder = 'v20201019'
if children_equally_sus:
stem = f'calib_cheqsu_{par_inds[0]}-{par_inds[1]}'
calibfile = os.path.join(
folder,
def set_metadata(obj):
''' Set standard metadata for an object '''
obj.version = spv.__version__
obj.created = sc.now()
obj.git_info = sc.gitinfo(__file__, verbose=False)
return
average_teacher_teacher_degree=3,
average_student_all_staff_ratio=15,
average_additional_staff_degree=20,
)
if __name__ == '__main__':
T = sc.tic()
pop = sp.make_population(**pars)
elapsed = sc.toc(T, output=True)
for person in [6, 66, 666]:
print(f'\n\nPerson {person}')
sc.pp(pop[person])
print('\n\n')
print(sc.gitinfo(sp.__file__))
print(sp.version.__version__)
popkeys = list(pop.keys())
stridekeys = [popkeys[i] for i in range(0, len(pop), stride)]
subpop = {k: pop[k] for k in stridekeys}
if do_save:
sc.savejson(f'pop_v{sp.version.__version__}.json', subpop, indent=2)
print('\n\n')
pps = pars["n"] / elapsed
print(
f'Total time: {elapsed:0.3f} s for {pars["n"]} people ({pps:0.0f} people/second)'
)
