Support Zarr 2 and 3 (again)

.github/workflows/zarr-v2-compat.yml

@@ -0,0 +1,24 @@
+name: zarr v2 compatibility
+
+on:
+  pull_request:
+  push:
+    branches: [main, test]
+
+jobs:
+  test:
+    name: zarr v2 / Python 3.11 / ubuntu
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: astral-sh/setup-uv@v5
+
+      - name: Install dependencies
+        run: uv sync --python 3.11 --group test
+
+      - name: Downgrade zarr to v2
+        run: uv pip install "zarr>=2.18,<3"
+
+      - name: Run tests
+        run: uv run pytest

pyproject.toml

@@ -32,7 +32,7 @@ dependencies = [
     "numpy",
     "humanize",
     "tskit>=1.0.0",
-    "zarr>=3.1",
+    "zarr>=2.18",
 ]
 dynamic = ["version"]
 

tests/test_cli.py

@@ -32,10 +32,10 @@
 import numpy as np
 import pytest
 import tskit
-import zarr
 
 import tszip
 import tszip.cli as cli
+from tszip import _zarr_compat
 
 
 def get_stdout_for_pytest():
@@ -265,8 +265,8 @@ def test_chunk_size(self):
         assert outpath.exists()
         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")
+        store = _zarr_compat.open_zip_store(outpath, mode="r")
+        root = _zarr_compat.open_group_for_read(store)
         for _, g in root.groups():
             for _, a in g.arrays():
                 assert a.chunks == (20,)

tests/test_compression.py

@@ -30,12 +30,12 @@
 import numpy as np
 import pytest
 import tskit
-import zarr
 
 import tszip
 import tszip.compression as compression
 import tszip.exceptions as exceptions
 import tszip.provenance as provenance
+from tszip import _zarr_compat
 
 
 class TestMinimalDtype:
@@ -295,17 +295,17 @@ def setup(self, tmp_path):
     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")
+        with _zarr_compat.open_zip_store(self.path, mode="r") as store:
+            root = _zarr_compat.open_group_for_read(store)
             assert root.attrs["format_name"] == compression.FORMAT_NAME
             assert root.attrs["format_version"] == compression.FORMAT_VERSION
 
     def test_provenance(self):
         ts = msprime.simulate(10, random_seed=1)
         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")
+            with _zarr_compat.open_zip_store(self.path, mode="r") as store:
+                root = _zarr_compat.open_group_for_read(store)
                 assert root.attrs["provenance"] == provenance.get_provenance_dict(
                     {
                         "variants_only": variants_only,
@@ -314,8 +314,8 @@ 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")
+        with _zarr_compat.open_zip_store(path, mode="w") as store:
+            root = _zarr_compat.open_group_for_write(store)
             root.attrs.update(attrs)
 
     def test_missing_format_keys(self):
@@ -538,8 +538,8 @@ def test_good_chunks(self, tmpdir, chunk_size):
         ts2 = tszip.decompress(path)
         assert ts1 == ts2
 
-        store = zarr.storage.ZipStore(str(path), mode="r")
-        root = zarr.open_group(store=store, zarr_format=2, mode="r")
+        store = _zarr_compat.open_zip_store(path, mode="r")
+        root = _zarr_compat.open_group_for_read(store)
         for _, g in root.groups():
             for _, a in g.arrays():
                 assert a.chunks == (chunk_size,)

tszip/_zarr_compat.py

@@ -0,0 +1,47 @@
+import zarr
+
+_ZARR_V3 = int(zarr.__version__.split(".")[0]) >= 3
+
+
+def open_zip_store(path, mode):
+    """Open a ZipStore compatible with zarr v2 and v3."""
+    return zarr.storage.ZipStore(str(path), mode=mode)
+
+
+def open_group_for_read(store):
+    """Open a zarr group for reading in zarr v2 format."""
+    if _ZARR_V3:
+        return zarr.open_group(store=store, zarr_format=2, mode="r")
+    else:
+        return zarr.open_group(store=store, mode="r")
+
+
+def open_group_for_write(store):
+    """Open a zarr group for writing in zarr v2 format."""
+    if _ZARR_V3:
+        return zarr.open_group(store=store, zarr_format=2, mode="a")
+    else:
+        return zarr.open_group(store=store, mode="a")
+
+
+def empty_array(root, name, shape, dtype, chunks, filters, compressor):
+    """Create an empty zarr array in zarr v2 format."""
+    if _ZARR_V3:
+        return root.empty(
+            name=name,
+            shape=shape,
+            dtype=dtype,
+            chunks=chunks,
+            zarr_format=2,
+            filters=filters,
+            compressor=compressor,
+        )
+    else:
+        return root.empty(
+            name=name,
+            shape=shape,
+            dtype=dtype,
+            chunks=chunks,
+            filters=filters,
+            compressor=compressor,
+        )

tszip/compression.py

@@ -39,9 +39,8 @@
 import numpy as np
 import tskit
 import zarr
-from zarr.storage import ZipStore
 
-from . import exceptions, provenance
+from . import _zarr_compat, exceptions, provenance
 
 logger = logging.getLogger(__name__)
 
@@ -106,8 +105,8 @@ def compress(ts, destination, variants_only=False, *, chunk_size=None):
     with tempfile.TemporaryDirectory(dir=destdir, prefix=".tszip_work_") as tmpdir:
         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")
+        with _zarr_compat.open_zip_store(filename, mode="w") as store:
+            root = _zarr_compat.open_group_for_write(store)
             compress_zarr(ts, root, variants_only=variants_only, chunk_size=chunk_size)
         if is_path:
             os.replace(filename, destination)
@@ -151,12 +150,12 @@ def compress(self, root, compressor):
         filters = None
         if self.delta_filter:
             filters = [numcodecs.Delta(dtype=dtype)]
-        compressed_array = root.empty(
+        compressed_array = _zarr_compat.empty_array(
+            root,
             name=self.name,
             shape=shape,
             dtype=dtype,
             chunks=self.chunks,
-            zarr_format=2,
             filters=filters,
             compressor=compressor,
         )
@@ -296,8 +295,8 @@ def check_format(root):
 def load_zarr(path):
     path = str(path)
     try:
-        store = ZipStore(path, mode="r")
-        root = zarr.open_group(store=store, zarr_format=2, mode="r")
+        store = _zarr_compat.open_zip_store(path, mode="r")
+        root = _zarr_compat.open_group_for_read(store)
     except zipfile.BadZipFile as bzf:
         raise exceptions.FileFormatError("File is not in tszip format") from bzf