Merge pull request #112 from tlambert03/drop-zarr

build: make zarr dependency optional

Author: d-v-b

.github/workflows/test.yml

@@ -21,7 +21,7 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.11', '3.12', '3.13']
-        zarr-version: ['3.0.10', '3.1.0']
+        zarr-version: ['3.0.10', '3.1.0', 'none']
         os: ["ubuntu-latest"]
     runs-on: ${{ matrix.os }}
 
@@ -36,10 +36,16 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install hatch
-    - name: Run Tests
+    - name: Run Tests (with zarr)
+      if: matrix.zarr-version != 'none'
       run: |
         hatch run test.py${{ matrix.python-version }}-${{ matrix.zarr-version }}:list-env
         hatch run test.py${{ matrix.python-version }}-${{ matrix.zarr-version }}:test-cov
+    - name: Run Tests (without zarr)
+      if: matrix.zarr-version == 'none'
+      run: |
+        hatch run test-base.py${{ matrix.python-version }}:list-env
+        hatch run test-base.py${{ matrix.python-version }}:test-cov
     - name: Upload coverage
       uses: codecov/codecov-action@v5
       with:

README.md

@@ -6,7 +6,11 @@
 
 ## Installation
 
-`pip install -U pydantic-zarr`
+```sh
+pip install -U pydantic-zarr
+# or, with zarr i/o support
+pip install -U "pydantic-zarr[zarr]"
+```
 
 ## Getting help
 

pyproject.toml

@@ -20,16 +20,17 @@ classifiers = [
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: Implementation :: CPython",
 ]
-dependencies = ["zarr>=3", "pydantic>2.0.0"]
+dependencies = ["pydantic>2.0.0", "numpy>=1.24.0"]
 [project.urls]
 Documentation = "https://zarr.dev/pydantic-zarr/"
 Issues = "https://github.com/zarr-developers/pydantic-zarr/issues"
 Source = "https://github.com/zarr-developers/pydantic-zarr"
 
 [project.optional-dependencies]
+zarr = ["zarr>=3.0.0"]
 # pytest pin is due to https://github.com/pytest-dev/pytest-cov/issues/693
-test = ["coverage", "pytest<8.4", "pytest-cov", "pytest-examples"]
-
+test-base = ["coverage", "pytest<8.4", "pytest-cov", "pytest-examples"]
+test = ["pydantic-zarr[test-base,zarr]"]
 docs = [
     "mkdocs-material",
     "mkdocstrings[python]",
@@ -57,6 +58,17 @@ list-env = "pip list"
 python = ["3.11", "3.12", "3.13"]
 zarr = ["3.0.10", "3.1.0"]
 
+[tool.hatch.envs.test-base]
+features = ["test-base"]
+
+[tool.hatch.envs.test-base.scripts]
+test = "pytest tests/test_pydantic_zarr/"
+test-cov = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report html --cov=src tests/test_pydantic_zarr"
+list-env = "pip list"
+
+[[tool.hatch.envs.test-base.matrix]]
+python = ["3.11", "3.12", "3.13"]
+
 [tool.hatch.envs.docs]
 features = ['docs']
 

src/pydantic_zarr/core.py

@@ -13,9 +13,6 @@
 import numpy as np
 import numpy.typing as npt
 from pydantic import BaseModel, ConfigDict
-from zarr.core.sync import sync
-from zarr.core.sync_group import get_node
-from zarr.storage._common import make_store_path
 
 if TYPE_CHECKING:
     import zarr
@@ -130,6 +127,10 @@ def maybe_node(
     Return the array or group found at the store / path, if an array or group exists there.
     Otherwise return None.
     """
+    from zarr.core.sync import sync
+    from zarr.core.sync_group import get_node
+    from zarr.storage._common import make_store_path
+
     # convert the storelike store argument to a Zarr store
     spath = sync(make_store_path(store, path=path))
     try:

src/pydantic_zarr/v2.py

@@ -2,6 +2,7 @@
 
 import json
 import math
+import sys
 from collections.abc import Mapping
 from importlib.metadata import version
 from typing import (
@@ -21,16 +22,9 @@
 
 import numpy as np
 import numpy.typing as npt
-import zarr
-from numcodecs.abc import Codec
 from packaging.version import Version
 from pydantic import AfterValidator, BaseModel, field_validator, model_validator
 from pydantic.functional_validators import BeforeValidator
-from zarr.core.array import Array, AsyncArray
-from zarr.core.metadata import ArrayV2Metadata
-from zarr.core.sync import sync
-from zarr.errors import ContainsArrayError, ContainsGroupError
-from zarr.storage._common import make_store_path
 
 from pydantic_zarr.core import (
     IncEx,
@@ -42,6 +36,8 @@
 )
 
 if TYPE_CHECKING:
+    import zarr
+    from numcodecs.abc import Codec
     from zarr.abc.store import Store
     from zarr.core.array_spec import ArrayConfigParams
 
@@ -90,7 +86,8 @@ def dictify_codec(value: dict[str, Any] | Codec) -> dict[str, Any]:
         object is returned. This should be a dict with string keys. All other values pass
         through unaltered.
     """
-    if isinstance(value, Codec):
+
+    if (numcodecs := sys.modules.get("numcodecs")) and isinstance(value, numcodecs.abc.Codec):
         return value.get_config()
     return value
 
@@ -334,6 +331,11 @@ def from_zarr(cls, array: zarr.Array) -> Self:
         ArraySpec(zarr_format=2, attributes={}, shape=(10, 10), chunks=(10, 10), dtype='<f8', fill_value=0.0, order='C', filters=None, dimension_separator='.', compressor={'id': 'blosc', 'cname': 'lz4', 'clevel': 5, 'shuffle': 1, 'blocksize': 0})
 
         """
+        try:
+            from zarr.core.metadata import ArrayV2Metadata
+        except ImportError as e:
+            raise ImportError("zarr must be installed to use from_zarr") from e
+
         if not isinstance(array.metadata, ArrayV2Metadata):
             msg = "Array is not a Zarr format 2 array"
             raise TypeError(msg)
@@ -378,6 +380,16 @@ def to_zarr(
         zarr.Array
             A Zarr array that is structurally identical to `self`.
         """
+        try:
+            import zarr
+            from zarr.core.array import Array, AsyncArray
+            from zarr.core.metadata import ArrayV2Metadata
+            from zarr.core.sync import sync
+            from zarr.errors import ContainsArrayError, ContainsGroupError
+            from zarr.storage._common import make_store_path
+        except ImportError as e:
+            raise ImportError("zarr must be installed to use to_zarr") from e
+
         store_path = sync(make_store_path(store, path=path))
 
         extant_node = maybe_node(store, path, zarr_format=2)
@@ -449,10 +461,10 @@ def like(
         """
 
         other_parsed: ArraySpec
-        if isinstance(other, zarr.Array):
+        if (zarr := sys.modules.get("zarr")) and isinstance(other, zarr.Array):
             other_parsed = ArraySpec.from_zarr(other)
         else:
-            other_parsed = other
+            other_parsed = other  # type: ignore[assignment]
 
         return model_like(self, other_parsed, include=include, exclude=exclude)
 
@@ -505,6 +517,10 @@ def from_zarr(cls, group: zarr.Group, *, depth: int = -1) -> Self:
         -------
         An instance of GroupSpec that represents the structure of the Zarr hierarchy.
         """
+        try:
+            import zarr
+        except ImportError as e:
+            raise ImportError("zarr must be installed to use from_zarr") from e
 
         result: GroupSpec[TAttr, TItem]
         attributes = group.attrs.asdict()
@@ -563,6 +579,12 @@ def to_zarr(
             A zarr group that is structurally identical to `self`.
 
         """
+        try:
+            import zarr
+            from zarr.errors import ContainsArrayError, ContainsGroupError
+        except ImportError as e:
+            raise ImportError("zarr must be installed to use to_zarr") from e
+
         spec_dict = self.model_dump(exclude={"members": True})
         attrs = spec_dict.pop("attributes")
         extant_node = maybe_node(store, path, zarr_format=2)
@@ -660,10 +682,10 @@ def like(
         """
 
         other_parsed: GroupSpec
-        if isinstance(other, zarr.Group):
+        if (zarr := sys.modules.get("zarr")) and isinstance(other, zarr.Group):
             other_parsed = GroupSpec.from_zarr(other)
         else:
-            other_parsed = other
+            other_parsed = other  # type: ignore[assignment]
 
         return model_like(self, other_parsed, include=include, exclude=exclude)
 
@@ -764,6 +786,7 @@ def from_zarr(element: zarr.Array | zarr.Group, depth: int = -1) -> AnyArraySpec
         An instance of `GroupSpec` or `ArraySpec` that models the structure of the input Zarr group
         or array.
     """
+    import zarr
 
     if isinstance(element, zarr.Array):
         return ArraySpec.from_zarr(element)

src/pydantic_zarr/v3.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import json
+import sys
 from collections.abc import Callable, Mapping
 from importlib.metadata import version
 from typing import (
@@ -20,11 +21,9 @@
 
 import numpy as np
 import numpy.typing as npt
-import zarr
 from packaging.version import Version
 from pydantic import AfterValidator, BaseModel, BeforeValidator
 from typing_extensions import TypedDict
-from zarr.errors import ContainsArrayError, ContainsGroupError
 
 from pydantic_zarr.core import (
     IncEx,
@@ -40,6 +39,7 @@
     from collections.abc import Sequence
 
     import numpy.typing as npt
+    import zarr  # noqa: TC004
     from zarr.abc.store import Store
     from zarr.core.array_spec import ArrayConfigParams
 
@@ -280,7 +280,7 @@ def from_array(
 
         """
         if attributes == "auto":
-            attributes_actual = cast(TAttr, auto_attributes(array))
+            attributes_actual = cast("TAttr", auto_attributes(array))
         else:
             attributes_actual = attributes
 
@@ -352,8 +352,12 @@ def from_zarr(cls, array: zarr.Array) -> Self:
         ArraySpec(zarr_format=2, attributes={}, shape=(10, 10), chunks=(10, 10), dtype='<f8', fill_value=0.0, order='C', filters=None, dimension_separator='.', compressor={'id': 'blosc', 'cname': 'lz4', 'clevel': 5, 'shuffle': 1, 'blocksize': 0})
 
         """
+        try:
+            from zarr.core.metadata import ArrayV3Metadata
+        except ImportError as e:
+            raise ImportError("zarr must be installed to use from_zarr") from e
+
         meta_json: Mapping[str, object]
-        from zarr.core.metadata import ArrayV3Metadata
 
         if not isinstance(array.metadata, ArrayV3Metadata):
             raise ValueError("Only zarr v3 arrays are supported")  # noqa: TRY004
@@ -407,10 +411,15 @@ def to_zarr(
         A zarr array that is structurally identical to the ArraySpec.
         This operation will create metadata documents in the store.
         """
-        from zarr.core.array import Array, AsyncArray
-        from zarr.core.metadata.v3 import ArrayV3Metadata
-        from zarr.core.sync import sync
-        from zarr.storage._common import make_store_path
+        try:
+            import zarr
+            from zarr.core.array import Array, AsyncArray
+            from zarr.core.metadata.v3 import ArrayV3Metadata
+            from zarr.core.sync import sync
+            from zarr.errors import ContainsArrayError, ContainsGroupError
+            from zarr.storage._common import make_store_path
+        except ImportError as e:
+            raise ImportError("zarr must be installed to use to_zarr") from e
 
         store_path = sync(make_store_path(store, path=path))
         extant_node = maybe_node(store, path, zarr_format=3)
@@ -620,6 +629,10 @@ def from_zarr(cls, group: zarr.Group, *, depth: int = -1) -> Self:
         -------
         An instance of GroupSpec that represents the structure of the zarr hierarchy.
         """
+        try:
+            import zarr
+        except ImportError as e:
+            raise ImportError("zarr must be installed to use from_zarr") from e
 
         result: GroupSpec[TAttr, TItem]
         attributes = group.attrs.asdict()
@@ -675,6 +688,11 @@ def to_zarr(
         A zarr group that is structurally identical to the GroupSpec.
         This operation will create metadata documents in the store.
         """
+        try:
+            import zarr
+            from zarr.errors import ContainsArrayError, ContainsGroupError
+        except ImportError as e:
+            raise ImportError("zarr must be installed to use to_zarr") from e
 
         spec_dict = self.model_dump(exclude={"members": True})
         attrs = spec_dict.pop("attributes")
@@ -776,10 +794,10 @@ def like(
         """
 
         other_parsed: GroupSpec[Any, Any]
-        if isinstance(other, zarr.Group):
+        if (zarr := sys.modules.get("zarr")) and isinstance(other, zarr.Group):
             other_parsed = GroupSpec.from_zarr(other)
         else:
-            other_parsed = other
+            other_parsed = other  # type: ignore[assignment]
 
         return model_like(self, other_parsed, include=include, exclude=exclude)
 

tests/test_docs/test_docs.py

@@ -15,4 +15,6 @@ def test_docstrings(example: CodeExample, eval_example: EvalExample) -> None:
 
 @pytest.mark.parametrize("example", find_examples("docs"), ids=str)
 def test_docs_examples(example: CodeExample, eval_example: EvalExample) -> None:
+    pytest.importorskip("zarr")
+
     eval_example.run_print_check(example)

tests/test_pydantic_zarr/conftest.py

@@ -2,11 +2,15 @@
 
 import warnings
 from dataclasses import dataclass
-from importlib.metadata import version
+from importlib.metadata import PackageNotFoundError, version
 
 from packaging.version import Version
 
-ZARR_PYTHON_VERSION = Version(version("zarr"))
+try:
+    ZARR_PYTHON_VERSION = Version(version("zarr"))
+except PackageNotFoundError:
+    ZARR_PYTHON_VERSION = Version("0.0.0")
+
 DTYPE_EXAMPLES_V2: tuple[DTypeExample, ...]
 DTYPE_EXAMPLES_V3: tuple[DTypeExample, ...]