def test_reasons_for_engine_citations(self):
for engine in stdpopsim.all_engines():
for citation in engine.citations:
assert len(citation.reasons) > 0, (
f"No reason given for '{citation.author}' citation "
f"in engine {engine.id}"
)
def test_required_params(self):
species = stdpopsim.get_species("HomSap")
model = species.get_demographic_model("AshkSub_7G19")
contig = (species.get_contig("chr1"), )
for engine in stdpopsim.all_engines():
with self.assertRaises(TypeError):
engine.simulate(model, contig)
def test_reasons_for_engine_citations(self):
for engine in stdpopsim.all_engines():
for citation in engine.citations:
self.assertGreater(
len(citation.reasons), 0,
msg=f"No reason given for '{citation.author}' citation "
f"in engine {engine.id}")
def test_zigzag_produces_warning(self):
species = stdpopsim.get_species("HomSap")
model = species.get_demographic_model("Zigzag_1S14")
contig = species.get_contig("chr22")
samples = model.get_samples(10)
for engine in stdpopsim.all_engines():
with self.assertWarnsRegex(UserWarning, "Zigzag_1S14"):
engine.simulate(model, contig, samples, dry_run=True)
def test_zigzag_produces_warning(self):
species = stdpopsim.get_species("HomSap")
model = species.get_demographic_model("Zigzag_1S14")
contig = species.get_contig("chr22")
samples = model.get_samples(10)
for engine in stdpopsim.all_engines():
with pytest.warns(UserWarning, match="Zigzag_1S14 model.*sizes 5x lower"):
engine.simulate(model, contig, samples, dry_run=True)
def test_mutation_rate_warning(self):
species = stdpopsim.get_species("HomSap")
model = copy.deepcopy(species.get_demographic_model("OutOfAfrica_3G09"))
contig = species.get_contig("chr22")
samples = model.get_samples(10, 10, 10)
for engine in stdpopsim.all_engines():
with pytest.warns(
UserWarning, match="model has mutation rate.*but this simulation used"
):
engine.simulate(model, contig, samples, dry_run=True)
def test_mutation_rate_warning(self):
species = stdpopsim.get_species("HomSap")
model = copy.deepcopy(species.get_demographic_model("OutOfAfrica_3G09"))
###
# unneeded after mutation rates are included in catalog!!
model.mutation_rate = 2.35e-8
###
contig = species.get_contig("chr22")
samples = model.get_samples(10, 10, 10)
for engine in stdpopsim.all_engines():
with self.assertWarnsRegex(UserWarning, "mutation"):
engine.simulate(model, contig, samples, dry_run=True)
def test_simulate_nonexistent_param(self):
species = stdpopsim.get_species("HomSap")
model = species.get_demographic_model("AshkSub_7G19")
good_kwargs = dict(
demographic_model=model,
contig=species.get_contig("chr1"),
samples=model.get_samples(10, 10, 10),
dry_run=True,
)
bad_kwargs = good_kwargs.copy().update(nonexistent_param=None)
for engine in stdpopsim.all_engines():
engine.simulate(**good_kwargs)
with self.assertRaises(TypeError):
engine.simulate(**bad_kwargs)
def test_mutation_rate_match(self):
species = stdpopsim.get_species("HomSap")
model = copy.deepcopy(species.get_demographic_model("OutOfAfrica_3G09"))
contig = species.get_contig("chr22")
assert model.mutation_rate != contig.mutation_rate
contig = species.get_contig("chr22", mutation_rate=model.mutation_rate)
assert model.mutation_rate == contig.mutation_rate
contig = species.get_contig(length=100)
assert model.mutation_rate != contig.mutation_rate
contig = species.get_contig(length=100, mutation_rate=model.mutation_rate)
assert model.mutation_rate == contig.mutation_rate
samples = model.get_samples(10, 10, 10)
for engine in stdpopsim.all_engines():
engine.simulate(model, contig, samples, dry_run=True)
def test_all_engines(self):
for engine in stdpopsim.all_engines():
self._test_engine(engine)
def test_engine_available(self):
all_engines = [engine.id for engine in stdpopsim.all_engines()]
self.assertEqual(IS_WINDOWS, "slim" not in all_engines)
def stdpopsim_cli_parser():
# TODO the CLI defined by this hierarchical and clumsy, but it's the best
# I could figure out. It can definitely be improved!
top_parser = argparse.ArgumentParser(
description="Command line interface for stdpopsim.")
top_parser.add_argument("-V",
"--version",
action='version',
version='%(prog)s {}'.format(
stdpopsim.__version__))
top_parser.add_argument("-v",
"--verbosity",
action='count',
default=0,
help="Increase the verbosity")
top_parser.add_argument(
"-c",
"--cache-dir",
type=str,
default=None,
help=("Set the cache directory to the specified value. "
"Note that this can also be set using the environment variable "
"STDPOPSIM_CACHE. If both the environment variable and this "
"option are set, the option takes precedence. "
f"Default: {stdpopsim.get_cache_dir()}"))
top_parser.add_argument("-e",
"--engine",
default=stdpopsim.get_default_engine().id,
choices=[e.id for e in stdpopsim.all_engines()],
help="Specify a simulation engine.")
for engine in stdpopsim.all_engines():
group = top_parser.add_argument_group(
f"{engine.id} specific parameters")
engine.add_arguments(group)
subparsers = top_parser.add_subparsers(dest="subcommand")
subparsers.required = True
for species in stdpopsim.all_species():
add_simulate_species_parser(subparsers, species)
download_maps_parser = subparsers.add_parser(
"download-genetic-maps",
help="Download genetic maps",
description=(
"Download genetic maps and store them in the cache directory. "
"Maps are downloaded regardless of whether they are already "
"in the cache or not. Please use the --cache-dir option to "
"download maps to a specific directory. "))
download_maps_parser.add_argument(
"species",
nargs="?",
help=("Download genetic maps for this species. If not specified "
"download all known genetic maps."))
download_maps_parser.add_argument(
"genetic_maps",
type=str,
nargs="*",
help=("If specified, download these genetic maps. If no maps "
"are provided, download all maps for this species."))
download_maps_parser.set_defaults(runner=run_download_genetic_maps)
return top_parser
def stdpopsim_cli_parser():
# TODO the CLI defined by this hierarchical and clumsy, but it's the best
# I could figure out. It can definitely be improved!
top_parser = argparse.ArgumentParser(
description="Command line interface for stdpopsim.")
top_parser.add_argument("-V",
"--version",
action='version',
version='%(prog)s {}'.format(
stdpopsim.__version__))
top_parser.add_argument("-v",
"--verbosity",
action='count',
default=1,
help="Increase the verbosity")
top_parser.add_argument(
"-c",
"--cache-dir",
type=str,
default=None,
help=("Set the cache directory to the specified value. "
"Note that this can also be set using the environment variable "
"STDPOPSIM_CACHE. If both the environment variable and this "
"option are set, the option takes precedence. "
f"Default: {stdpopsim.get_cache_dir()}"))
top_parser.add_argument("-e",
"--engine",
default=stdpopsim.get_default_engine().id,
choices=[e.id for e in stdpopsim.all_engines()],
help="Specify a simulation engine.")
supported_models = stdpopsim.get_engine("msprime").supported_models
msprime_parser = top_parser.add_argument_group(
"msprime specific parameters")
msprime_parser.add_argument(
"--msprime-model",
default=supported_models[0],
choices=supported_models,
help="Specify the simulation model used by msprime. "
"See msprime API documentation for details.")
def time_or_model(arg, _arg_is_time=[
True,
], parser=top_parser):
if _arg_is_time[0]:
try:
arg = float(arg)
except ValueError:
parser.error(f"`{arg}' is not a number")
else:
if arg not in supported_models:
parser.error(f"`{arg}' is not a supported model")
_arg_is_time[0] = not _arg_is_time[0]
return arg
msprime_parser.add_argument(
"--msprime-change-model",
metavar=("T", "MODEL"),
type=time_or_model,
default=[],
action="append",
nargs=2,
help="Change to the specified simulation MODEL at generation T. "
"This option may provided multiple times.")
# SLiM is not available for windows.
if not IS_WINDOWS:
def slim_exec(path):
# Hack to set the SLIM environment variable at parse time,
# before get_version() can be called.
os.environ["SLIM"] = path
return path
slim_parser = top_parser.add_argument_group("SLiM specific parameters")
slim_parser.add_argument("--slim-path",
metavar="PATH",
type=slim_exec,
default=None,
help="Full path to `slim' executable.")
slim_parser.add_argument(
"--slim-script",
action="store_true",
default=False,
help="Write script to stdout and exit without running SLiM.")
slim_parser.add_argument(
"--slim-scaling-factor",
metavar="Q",
default=1,
type=float,
help="Rescale model parameters by Q to speed up simulation. "
"See SLiM manual: `5.5 Rescaling population sizes to "
"improve simulation performance`. "
"[default=%(default)s].")
slim_parser.add_argument(
"--slim-burn-in",
metavar="X",
default=10,
type=float,
help="Length of the burn-in phase, in units of N generations "
"[default=%(default)s].")
subparsers = top_parser.add_subparsers(dest="subcommand")
subparsers.required = True
for species in stdpopsim.all_species():
add_simulate_species_parser(subparsers, species)
download_maps_parser = subparsers.add_parser(
"download-genetic-maps",
help="Download genetic maps",
description=(
"Download genetic maps and store them in the cache directory. "
"Maps are downloaded regardless of whether they are already "
"in the cache or not. Please use the --cache-dir option to "
"download maps to a specific directory. "))
download_maps_parser.add_argument(
"species",
nargs="?",
help=("Download genetic maps for this species. If not specified "
"download all known genetic maps."))
download_maps_parser.add_argument(
"genetic_maps",
type=str,
nargs="*",
help=("If specified, download these genetic maps. If no maps "
"are provided, download all maps for this species."))
download_maps_parser.set_defaults(runner=run_download_genetic_maps)
return top_parser
