Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Warn when using defaults that aren't explict and not metadata #992

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Warn when using defaults that aren't explict and not metadata #992

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
43 changes: 31 additions & 12 deletions tests/test_variantdata.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -218,7 +218,11 @@ def test_variantdata_accessors_defaults(tmp_path, in_mem):
ds = data if in_mem else sgkit.load_dataset(data)

default_schema = tskit.MetadataSchema.permissive_json().schema
assert vdata.sequence_length == ts.sequence_length
with pytest.warns(
UserWarning,
match="`sequence_length` was not found as an attribute in the dataset",
):
assert vdata.sequence_length == ts.sequence_length
assert vdata.sites_metadata_schema == default_schema
assert vdata.sites_metadata == [{} for _ in range(ts.num_sites)]
for time in vdata.sites_time:
Expand All @@ -234,17 +238,32 @@ def test_variantdata_accessors_defaults(tmp_path, in_mem):
assert vdata.individuals_metadata == [
{"variant_data_sample_id": sample_id} for sample_id in ds.sample_id[:]
]
for time in vdata.individuals_time:
assert tskit.is_unknown_time(time)
assert np.array_equal(
vdata.individuals_location, np.array([[]] * ts.num_individuals, dtype=float)
)
assert np.array_equal(
vdata.individuals_population, np.full(ts.num_individuals, tskit.NULL)
)
assert np.array_equal(
vdata.individuals_flags, np.zeros(ts.num_individuals, dtype=int)
)
with pytest.warns(
UserWarning, match="`individuals_time` was not found as an array in the dataset"
):
for time in vdata.individuals_time:
assert tskit.is_unknown_time(time)
with pytest.warns(
UserWarning,
match="`individuals_location` was not found as an array in the dataset",
):
assert np.array_equal(
vdata.individuals_location, np.array([[]] * ts.num_individuals, dtype=float)
)
with pytest.warns(
UserWarning,
match="`individuals_population` was not found as an array in the dataset",
):
assert np.array_equal(
vdata.individuals_population, np.full(ts.num_individuals, tskit.NULL)
)
with pytest.warns(
UserWarning,
match="`individuals_flags` was not found as an array in the dataset",
):
assert np.array_equal(
vdata.individuals_flags, np.zeros(ts.num_individuals, dtype=int)
)


@pytest.mark.skipif(sys.platform == "win32", reason="No cyvcf2 on windows")
Expand Down
27 changes: 27 additions & 0 deletions tsinfer/formats.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2520,6 +2520,12 @@ def sequence_length(self):
try:
return self.data.attrs["sequence_length"]
except KeyError:
warnings.warn(
"`sequence_length` was not found as an attribute in the dataset, so"
" the largest position has been used. It can be set with"
" ds.attrs['sequence_length'] = 1337; ds.to_zarr('path/to/store',"
" mode='a')"
)
return int(np.max(self.data["variant_position"])) + 1

@property
Expand Down Expand Up @@ -2653,6 +2659,12 @@ def individuals_time(self):
try:
return self.data["individuals_time"][:][self.individuals_select]
except KeyError:
warnings.warn(
"`individuals_time` was not found as an array in the dataset, so "
"tskit.UNKNOWN_TIME has been used. It can be apppended to the dataset "
"with data_array.to_zarr('path/to/store', append_dim='samples', "
"mode='a')"
)
return np.full(self.num_individuals, tskit.UNKNOWN_TIME)

@functools.cached_property
Expand Down Expand Up @@ -2696,20 +2708,35 @@ def individuals_location(self):
try:
return self.data["individuals_location"][:][self.individuals_select]
except KeyError:
warnings.warn(
"`individuals_location` was not found as an array in the dataset, "
"so [] has been used. It can be apppended to the dataset with "
"data_array.to_zarr('path/to/store', append_dim='samples', mode='a')"
)
return np.array([[]] * self.num_individuals, dtype=float)

@functools.cached_property
def individuals_population(self):
try:
return self.data["individuals_population"][:][self.individuals_select]
except KeyError:
warnings.warn(
"`individuals_population` was not found as an array in the dataset, "
"so tskit.NULL has been used. It can be apppended to the dataset with "
"data_array.to_zarr('path/to/store', append_dim='samples', mode='a')"
)
return np.full((self.num_individuals), tskit.NULL, dtype=np.int32)

@functools.cached_property
def individuals_flags(self):
try:
return self.data["individuals_flags"][:][self.individuals_select]
except KeyError:
warnings.warn(
"`individuals_flags` was not found as an array in the dataset, so 0 "
"has been used. It can be apppended to the dataset with "
"data_array.to_zarr('path/to/store', append_dim='samples', mode='a')"
)
return np.full((self.num_individuals), 0, dtype=np.int32)

@staticmethod
Expand Down
Loading