def test_one_chrom_from_each_map(self):
for gm in stdpopsim.all_genetic_maps():
species = gm.species
if gm.id in ("NaterPA_PonAbe2", "NaterPP_PonAbe2"):
# XXX: these maps are currently broken:
# ValueError: The last entry in the 'rate' column must be zero
continue
# Just load the first chromosome in the list.
# There's no requirement that any given chromosome is actually
# in the map, and we don't have a direct way to check
# for its presence. But if this chromsome is *not* in the
# map, we will recieve a warning (and then fail the test below).
chrom = species.genome.chromosomes[0]
with pytest.warns(None) as record:
gm.get_chromosome_map(chrom.id)
# Fail the test if we get any warnings matching the message below.
# There doesn't seem to be a way to simply check for the absense
# of a specific warning using pytest, so we record all warnings
# and check manually.
record = [
r for r in record if re.match(r"Recombination map not found",
str(r.message)) is not None
]
assert len(record) == 0, f"{species.id} / {gm.id}"
def test_reason_for_genetic_map_citations(self):
for genetic_map in stdpopsim.all_genetic_maps():
for citation in genetic_map.citations:
assert len(citation.reasons) > 0, (
f"No reason given for '{citation.author}' citation "
f"in genetic map "
f"{genetic_map.species.id}/{genetic_map.id}"
)
def setUpModule():
destination = pathlib.Path("_test_cache/tarballs")
for genetic_map in stdpopsim.all_genetic_maps():
key = genetic_map.id
local_file = destination / (key + ".tar.gz")
if not local_file.exists():
cache_dir = local_file.parent
cache_dir.mkdir(exist_ok=True, parents=True)
# print("Downloading", genetic_map.url)
urllib.request.urlretrieve(genetic_map.url, local_file)
saved_urls[key] = genetic_map.url
genetic_map.url = local_file.resolve().as_uri()
def test_multiple_threads_downloading(self):
gm = next(stdpopsim.all_genetic_maps())
gm.download()
saved = gm.is_cached
try:
# Trick the download code into thinking there's several happening
# concurrently
gm.is_cached = lambda: False
with self.assertWarns(UserWarning):
gm.download()
finally:
gm.is_cached = saved
def test_one_chrom_from_each_map(self):
for gm in stdpopsim.all_genetic_maps():
species = gm.species
if gm.id in ("NaterPA_PonAbe2", "NaterPP_PonAbe2"):
# XXX: these maps are currently broken:
# ValueError: The last entry in the 'rate' column must be zero
continue
# Just load the first chromosome in the list.
# There's no requirement that any given chromosome is actually
# in the map, and we don't have a direct way to check
# for its presence. But if this chromsome is *not* in the
# map, we will recieve a warning (which is treated as an error
# using the warnings filter).
chrom = species.genome.chromosomes[0]
gm.get_chromosome_map(chrom.id)
def setUpModule():
destination = pathlib.Path("_test_cache/tarballs")
for genetic_map in stdpopsim.all_genetic_maps():
key = genetic_map.id
local_file = destination / (key + ".tar.gz")
if not local_file.exists():
cache_dir = local_file.parent
cache_dir.mkdir(exist_ok=True, parents=True)
print("Downloading", genetic_map.url)
utils.download(genetic_map.url, local_file)
# This assertion could fail if we update a file on AWS,
# or a developer creates a new genetic map with the wrong checksum
# (in the latter case, this should at least be caught during CI tests).
assert utils.sha256(local_file) == genetic_map.sha256, (
f"SHA256 for {local_file} doesn't match the SHA256 for "
f"{genetic_map.id}. If you didn't add this SHA256 yourself, "
f"try deleting {local_file} and restarting the tests.")
saved_urls[key] = genetic_map.url
genetic_map.url = local_file.resolve().as_uri()
genetic_map._cache.url = genetic_map.url
def tearDownModule():
for genetic_map in stdpopsim.all_genetic_maps():
genetic_map.url = saved_urls[genetic_map.id]
def test_ids(self):
for gm in stdpopsim.all_genetic_maps():
self.assertIsInstance(gm.id, str)
self.assertTrue(utils.is_valid_genetic_map_id(gm.id))
def test_types(self):
for gm in stdpopsim.all_genetic_maps():
self.assertIsInstance(gm, genetic_maps.GeneticMap)
def test_non_empty(self):
self.assertGreater(len(list(stdpopsim.all_genetic_maps())), 0)
def test_download_over_cache(self):
for gm in stdpopsim.all_genetic_maps():
gm.download()
self.assertTrue(gm.is_cached())
gm.download()
self.assertTrue(gm.is_cached())
def teardown_module():
for genetic_map in stdpopsim.all_genetic_maps():
genetic_map.url = saved_urls[genetic_map.id]
genetic_map._cache.url = genetic_map.url
def test_ids(self):
for gm in stdpopsim.all_genetic_maps():
assert isinstance(gm.id, str)
assert utils.is_valid_genetic_map_id(gm.id)
def test_types(self):
for gm in stdpopsim.all_genetic_maps():
assert isinstance(gm, stdpopsim.GeneticMap)
def test_non_empty(self):
assert len(list(stdpopsim.all_genetic_maps())) > 0
