def test_openfiles(prompt=None):
outdir = os.path.join(script_dir, "test_openfiles_output")
if os.path.exists(outdir):
OutputFiles.remove(outdir, prompt=prompt)
of = OutputFiles(outdir)
assert of.is_open()
assert not of.is_closed()
with pytest.raises(ValueError):
of.open("../test.txt")
with pytest.raises(ValueError):
of.open("/test.txt")
FILE = of.open("test.txt")
assert of.is_open()
FILE.write("hello\n")
of.close()
assert of.is_closed()
assert open(os.path.join(outdir, "test.txt")).readline() == "hello\n"
with pytest.raises(FileExistsError):
OutputFiles(outdir, prompt=None)
with OutputFiles(outdir, force_empty=True, prompt=None) as of:
FILE = of.open("test.txt")
assert of.is_open()
assert of.get_filename("test.txt").endswith("test.txt")
FILE.write("goodbye\n")
FILE = of.open("test2.txt", auto_bzip=True)
FILE.write("hello ")
assert of.get_filename("test2.txt").endswith("test2.txt.bz2")
FILE = of.open("test2.txt")
FILE.write("world\n")
assert open(os.path.join(outdir, "test.txt")).readline() == "goodbye\n"
import bz2
line = bz2.open(os.path.join(outdir, "test2.txt.bz2"), "rt").readline()
assert line == "hello world\n"
OutputFiles.remove(outdir, prompt=None)
def output_wards_i_serial(network: metawards.Network,
population: metawards.Population,
output_dir: metawards.OutputFiles,
workspace: metawards.Workspace, **kwargs):
if network.name is None:
name = ""
else:
name = "_" + network.name.replace(" ", "_")
d_vars = network.params.disease_params
u_vars = network.params.user_params
infect_file = output_dir.open(f"wards_trajectory{name}_I.csv")
rclass_file = output_dir.open(f"wards_trajectory{name}_R.csv")
# Just print the design parameters:
head_str = "beta[2],beta[3],progress[1],progress[2],progress[3],.scale_rate[1],.scale_rate[2]"
design_out = [
d_vars.beta[2], d_vars.beta[3], d_vars.progress[1], d_vars.progress[2],
d_vars.progress[3]
]
design_out += [u_vars["lock_1_restrict"], u_vars["lock_2_release"]]
if population.day == 0:
# Print header
ident: List[str] = ["day", "date"]
ident += [head_str]
ident += [
"ward[" + str(i) + "]" for i, _ in enumerate(workspace.I_in_wards)
]
header = ','.join(ident)
infect_file.write(header)
infect_file.write("\n")
rclass_file.write(header)
rclass_file.write("\n")
day = str(population.day) + ","
date = str(population.date) + ","
# NOTE: The standard extractors write .dat tables, but R doesn't load these properly (and pandas sometimes)
# Write a CSV instead
infect_file.write(day)
infect_file.write(date)
infect_file.write(",".join(str(x) for x in design_out))
infect_file.write(",")
infect_file.write(",".join([str(x) for x in workspace.I_in_wards]))
infect_file.write("\n")
# NOTE: The standard extractors write .dat tables, but R doesn't load these properly (and pandas sometimes)
# Write a CSV instead
rclass_file.write(day)
rclass_file.write(date)
rclass_file.write(",".join(str(x) for x in design_out))
rclass_file.write(",")
rclass_file.write(",".join([str(x) for x in workspace.R_in_wards]))
rclass_file.write("\n")