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Revert back to zarr v2 #145

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jeromekelleher wants to merge 1 commit into from
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Revert back to zarr v2 #145

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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ dependencies = [
"numpy",
"humanize",
"tskit>=1.0.0",
"zarr>=3.1",
"zarr>=2.18,<3",
]
dynamic = ["version"]

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2 changes: 1 addition & 1 deletion tests/test_cli.py
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Expand Up @@ -266,7 +266,7 @@ def test_chunk_size(self):
ts = tszip.decompress(outpath)
assert ts.tables == self.ts.tables
store = zarr.storage.ZipStore(str(outpath), mode="r")
root = zarr.open_group(store=store, zarr_format=2, mode="r")
root = zarr.open_group(store=store, mode="r")
for _, g in root.groups():
for _, a in g.arrays():
assert a.chunks == (20,)
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8 changes: 4 additions & 4 deletions tests/test_compression.py
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Expand Up @@ -296,7 +296,7 @@ def test_format_written(self):
ts = msprime.simulate(10, random_seed=1)
tszip.compress(ts, self.path)
with zarr.storage.ZipStore(str(self.path), mode="r") as store:
root = zarr.open_group(store=store, zarr_format=2, mode="r")
root = zarr.open_group(store=store, mode="r")
assert root.attrs["format_name"] == compression.FORMAT_NAME
assert root.attrs["format_version"] == compression.FORMAT_VERSION

Expand All @@ -305,7 +305,7 @@ def test_provenance(self):
for variants_only in [True, False]:
tszip.compress(ts, self.path, variants_only=variants_only)
with zarr.storage.ZipStore(str(self.path), mode="r") as store:
root = zarr.open_group(store=store, zarr_format=2, mode="r")
root = zarr.open_group(store=store, mode="r")
assert root.attrs["provenance"] == provenance.get_provenance_dict(
{
"variants_only": variants_only,
Expand All @@ -315,7 +315,7 @@ def test_provenance(self):

def write_file(self, attrs, path):
with zarr.storage.ZipStore(str(path), mode="w") as store:
root = zarr.open_group(store=store, zarr_format=2, mode="a")
root = zarr.open_group(store=store, mode="a")
root.attrs.update(attrs)

def test_missing_format_keys(self):
Expand Down Expand Up @@ -539,7 +539,7 @@ def test_good_chunks(self, tmpdir, chunk_size):
assert ts1 == ts2

store = zarr.storage.ZipStore(str(path), mode="r")
root = zarr.open_group(store=store, zarr_format=2, mode="r")
root = zarr.open_group(store=store, mode="r")
for _, g in root.groups():
for _, a in g.arrays():
assert a.chunks == (chunk_size,)
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5 changes: 2 additions & 3 deletions tszip/compression.py
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Expand Up @@ -107,7 +107,7 @@ def compress(ts, destination, variants_only=False, *, chunk_size=None):
filename = pathlib.Path(tmpdir, "tmp.trees.tgz")
logging.debug(f"Writing to temporary file {filename}")
with ZipStore(filename, mode="w") as store:
root = zarr.open_group(store=store, zarr_format=2, mode="a")
root = zarr.open_group(store=store, mode="a")
compress_zarr(ts, root, variants_only=variants_only, chunk_size=chunk_size)
if is_path:
os.replace(filename, destination)
Expand Down Expand Up @@ -156,7 +156,6 @@ def compress(self, root, compressor):
shape=shape,
dtype=dtype,
chunks=self.chunks,
zarr_format=2,
filters=filters,
compressor=compressor,
)
Expand Down Expand Up @@ -297,7 +296,7 @@ def load_zarr(path):
path = str(path)
try:
store = ZipStore(path, mode="r")
root = zarr.open_group(store=store, zarr_format=2, mode="r")
root = zarr.open_group(store=store, mode="r")
except zipfile.BadZipFile as bzf:
raise exceptions.FileFormatError("File is not in tszip format") from bzf

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