From d1f4d1f794cd18163973a3c4735697a971a160de Mon Sep 17 00:00:00 2001 From: Jerome Kelleher Date: Wed, 4 Mar 2026 17:10:34 +0000 Subject: [PATCH] Revert back to zarr v2 --- pyproject.toml | 2 +- tests/test_cli.py | 2 +- tests/test_compression.py | 8 +- tszip/compression.py | 5 +- uv.lock | 182 +++++++++++++++++++++++--------------- 5 files changed, 118 insertions(+), 81 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 4c07c66..ccc360f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,7 +32,7 @@ dependencies = [ "numpy", "humanize", "tskit>=1.0.0", - "zarr>=3.1", + "zarr>=2.18,<3", ] dynamic = ["version"] diff --git a/tests/test_cli.py b/tests/test_cli.py index 1ffcaa4..0e01b78 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -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,) diff --git a/tests/test_compression.py b/tests/test_compression.py index 88c6441..6b43cd8 100644 --- a/tests/test_compression.py +++ b/tests/test_compression.py @@ -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 @@ -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, @@ -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): @@ -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,) diff --git a/tszip/compression.py b/tszip/compression.py index c344172..80bbf92 100644 --- a/tszip/compression.py +++ b/tszip/compression.py @@ -107,7 +107,7 @@ def compress(ts, destination, variants_only=False, *, 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