Lint, fix olde array compression test

.github/workflows/tests.yml

@@ -33,6 +33,8 @@ jobs:
 
   lint:
     runs-on: ubuntu-latest
+    continue-on-error: true
     steps:
       - uses: actions/checkout@v3
+      - uses: chartboost/ruff-action@v1
       - uses: psf/black@stable

pyproject.toml

@@ -66,7 +66,7 @@ testpaths = [
 
 [tool.ruff]
 target-version = "py311"
-include = ["numpydantic/**/*.py", "pyproject.toml"]
+include = ["src/numpydantic/**/*.py", "pyproject.toml"]
 exclude = ["tests"]
 
 [tool.ruff.lint]

src/numpydantic/__init__.py

@@ -1,6 +1,7 @@
 # ruff: noqa: E402
 # ruff: noqa: F401
 # ruff: noqa: I001
+# ruff: noqa: D104
 from numpydantic.monkeypatch import apply_patches
 
 apply_patches()

src/numpydantic/exceptions.py

@@ -1,3 +1,8 @@
+"""
+Exceptions used within numpydantic
+"""
+
+
 class DtypeError(TypeError):
     """Exception raised for invalid dtypes"""
 

src/numpydantic/interface/__init__.py

@@ -1,3 +1,7 @@
+"""
+Interfaces between nptyping types and array backends
+"""
+
 from numpydantic.interface.dask import DaskInterface
 from numpydantic.interface.hdf5 import H5Interface
 from numpydantic.interface.interface import Interface

src/numpydantic/interface/dask.py

@@ -1,5 +1,11 @@
+"""
+Interface for Dask arrays
+"""
+
 from typing import Any
+
 import numpy as np
+
 from numpydantic.interface.interface import Interface
 
 try:

src/numpydantic/interface/hdf5.py

@@ -1,6 +1,9 @@
-import pdb
+"""
+Interfaces for HDF5 Datasets
+"""
+
 from pathlib import Path
-from typing import Any, NamedTuple, Tuple, Union, TypeAlias
+from typing import Any, NamedTuple, Tuple, TypeAlias, Union
 
 import numpy as np
 
@@ -28,15 +31,15 @@ class H5Proxy:
     """
     Proxy class to mimic numpy-like array behavior with an HDF5 array
 
-    The attribute and item access methods only open the file for the duration of the method,
+    The attribute and item access methods only open the file for the duration of the
-    making it less perilous to share this object between threads and processes.
+    method, making it less perilous to share this object between threads and processes.
 
     This class attempts to be a passthrough class to a :class:`h5py.Dataset` object,
     including its attributes and item getters/setters.
 
     When using read-only methods, no locking is attempted (beyond the HDF5 defaults),
-    but when using the write methods (setting an array value), try and use the ``locking``
+    but when using the write methods (setting an array value), try and use the
-    methods of :class:`h5py.File` .
+    ``locking`` methods of :class:`h5py.File` .
 
     Args:
         file (pathlib.Path | str): Location of hdf5 file on filesystem
@@ -74,7 +77,7 @@ class H5Proxy:
             obj = h5f.get(self.path)
             obj[key] = value
 
-    def open(self, mode: str = "r"):
+    def open(self, mode: str = "r") -> "h5py.Dataset":
         """
         Return the opened :class:`h5py.Dataset` object
 
@@ -84,7 +87,7 @@ class H5Proxy:
             self._h5f = h5py.File(self.file, mode)
         return self._h5f.get(self.path)
 
-    def close(self):
+    def close(self) -> None:
         """
         Close the :class:`h5py.File` object left open when returning the dataset with
         :meth:`.open`
@@ -116,7 +119,10 @@ class H5Interface(Interface):
 
     @classmethod
     def check(cls, array: Union[H5ArrayPath, Tuple[Union[Path, str], str]]) -> bool:
-        """Check that the given array is a :class:`.H5ArrayPath` or something that resembles one."""
+        """
+        Check that the given array is a :class:`.H5ArrayPath` or something that
+        resembles one.
+        """
         if isinstance(array, H5ArrayPath):
             return True
 
@@ -152,7 +158,8 @@ class H5Interface(Interface):
             array = H5Proxy(file=array[0], path=array[1])
         else:
             raise ValueError(
-                "Need to specify a file and a path within an HDF5 file to use the HDF5 Interface"
+                "Need to specify a file and a path within an HDF5 file to use the HDF5 "
+                "Interface"
             )
 
         if not array.array_exists():
@@ -165,6 +172,14 @@ class H5Interface(Interface):
 
     @classmethod
     def to_json(cls, array: H5Proxy) -> dict:
+        """
+        Dump to a dictionary containing
+
+        * ``file``: :attr:`.file`
+        * ``path``: :attr:`.path`
+        * ``attrs``: Any HDF5 attributes on the dataset
+        * ``array``: The array as a list of lists
+        """
         try:
             dset = array.open()
             meta = {

src/numpydantic/interface/interface.py

@@ -1,3 +1,7 @@
+"""
+Base Interface metaclass
+"""
+
 from abc import ABC, abstractmethod
 from operator import attrgetter
 from typing import Any, Generic, Tuple, Type, TypeVar, Union
@@ -67,13 +71,15 @@ class Interface(ABC, Generic[T]):
             return array
         if not check_shape(array.shape, self.shape):
             raise ShapeError(
-                f"Invalid shape! expected shape {self.shape.prepared_args}, got shape {array.shape}"
+                f"Invalid shape! expected shape {self.shape.prepared_args}, "
+                f"got shape {array.shape}"
             )
         return array
 
     def after_validation(self, array: NDArrayType) -> T:
         """
-        Optional step post-validation that coerces the intermediate array type into the return type
+        Optional step post-validation that coerces the intermediate array type into the
+        return type
 
         Default method is a no-op
         """
@@ -90,13 +96,15 @@ class Interface(ABC, Generic[T]):
     @abstractmethod
     def enabled(cls) -> bool:
         """
-        Check whether this array interface can be used (eg. its dependent packages are installed, etc.)
+        Check whether this array interface can be used (eg. its dependent packages are
+        installed, etc.)
         """
 
     @classmethod
     def to_json(cls, array: Type[T]) -> Union[list, dict]:
         """
-        Convert an array of :attr:`.return_type` to a JSON-compatible format using base python types
+        Convert an array of :attr:`.return_type` to a JSON-compatible format using
+        base python types
         """
         if not isinstance(array, np.ndarray):
             array = np.array(array)

src/numpydantic/interface/numpy.py

@@ -1,3 +1,7 @@
+"""
+Interface to numpy arrays
+"""
+
 from typing import Any
 
 from numpydantic.interface.interface import Interface
@@ -22,7 +26,10 @@ class NumpyInterface(Interface):
 
     @classmethod
     def check(cls, array: Any) -> bool:
-        """Check that this is in fact a numpy ndarray or something that can be coerced to one"""
+        """
+        Check that this is in fact a numpy ndarray or something that can be
+        coerced to one
+        """
         if isinstance(array, ndarray):
             return True
         else:
@@ -34,7 +41,8 @@ class NumpyInterface(Interface):
 
     def before_validation(self, array: Any) -> ndarray:
         """
-        Coerce to an ndarray. We have already checked if coercion is possible in :meth:`.check`
+        Coerce to an ndarray. We have already checked if coercion is possible
+        in :meth:`.check`
         """
         if not isinstance(array, ndarray):
             array = ndarray(array)

src/numpydantic/interface/xarray.py

@@ -0,0 +1,5 @@
+"""
+Interface to xarray
+
+(Not implemented)
+"""

src/numpydantic/interface/zarr.py

@@ -0,0 +1,5 @@
+"""
+Interface to zarr arrays
+
+(Not Implemented)
+"""

src/numpydantic/maps.py

@@ -1,8 +1,12 @@
+"""
+Maps from one value system to another
+"""
+
 from datetime import datetime
 from typing import Any
 
 import numpy as np
-from nptyping import Float, Int, String, Bool
+from nptyping import Bool, Float, Int, String
 
 np_to_python = {
     Any: Any,
@@ -43,6 +47,7 @@ np_to_python = {
     },
     **{n: str for n in (np.character, np.str_, np.string_, np.unicode_)},
 }
+"""Map from python types to numpy"""
 
 
 flat_to_nptyping = {
@@ -75,5 +80,7 @@ flat_to_nptyping = {
     "AnyType": "Any",
     "object": "Object",
 }
+"""Map from NWB-style flat dtypes to nptyping types"""
 
 python_to_nptyping = {float: Float, str: String, int: Int, bool: Bool}
+"""Map from python types to nptyping types"""

src/numpydantic/monkeypatch.py

@@ -1,3 +1,10 @@
+"""
+Functions to monkeypatch dependent packages - most notably nptyping
+"""
+
+# ruff: noqa: ANN001
+
+
 def patch_npytyping_perf() -> None:
     """
     npytyping makes an expensive call to inspect.stack()
@@ -14,6 +21,7 @@ def patch_npytyping_perf() -> None:
     from nptyping.pandas_ import dataframe
 
     # make a new __module__ methods for the affected classes
+
     def new_module_ndarray(cls) -> str:
         return cls._get_module(inspect.currentframe(), "nptyping.ndarray")
 

src/numpydantic/ndarray.py

@@ -5,7 +5,7 @@ Extension of nptyping NDArray for pydantic that allows for JSON-Schema serializa
 """
 
 from collections.abc import Callable
-from typing import Any, Tuple, Union
+from typing import TYPE_CHECKING, Any, Tuple, Union
 
 import nptyping.structure
 import numpy as np
@@ -21,6 +21,9 @@ from numpydantic.maps import np_to_python
 # from numpydantic.proxy import NDArrayProxy
 from numpydantic.types import DtypeType, NDArrayType, ShapeType
 
+if TYPE_CHECKING:
+    from pydantic import ValidationInfo
+
 COMPRESSION_THRESHOLD = 16 * 1024
 """
 Arrays larger than this size (in bytes) will be compressed and b64 encoded when 
@@ -62,10 +65,11 @@ def list_of_lists_schema(shape: Shape, array_type_handler: dict) -> ListSchema:
 
 def _get_validate_interface(shape: ShapeType, dtype: DtypeType) -> Callable:
     """
-    Validate using a matching :class:`.Interface` class using its :meth:`.Interface.validate` method
+    Validate using a matching :class:`.Interface` class using its
+    :meth:`.Interface.validate` method
     """
 
-    def validate_interface(value: Any, info) -> NDArrayType:
+    def validate_interface(value: Any, info: "ValidationInfo") -> NDArrayType:
         interface_cls = Interface.match(value)
         interface = interface_cls(shape, dtype)
         value = interface.validate(value)
@@ -99,7 +103,8 @@ class NDArrayMeta(_NDArrayMeta, implementation="NDArray"):
 
 class NDArray(NPTypingType, metaclass=NDArrayMeta):
     """
-    Constrained array type allowing npytyping syntax for dtype and shape validation and serialization.
+    Constrained array type allowing npytyping syntax for dtype and shape validation
+    and serialization.
 
     Integrates with pydantic such that
     - JSON schema for list of list encoding

src/numpydantic/types.py

@@ -4,6 +4,8 @@ Types for numpydantic
 Note that these are types as in python typing types, not classes.
 """
 
+# ruff: noqa: D102
+
 from typing import Any, Protocol, Tuple, runtime_checkable
 
 import numpy as np
@@ -15,6 +17,7 @@ DtypeType = np.dtype | str | type | Any | DType
 
 @runtime_checkable
 class NDArrayType(Protocol):
+    """A protocol for describing types that should be considered ndarrays"""
 
     @property
     def dtype(self) -> DtypeType: ...

tests/test_ndarray.py

@@ -83,24 +83,18 @@ def test_ndarray_coercion():
 
 def test_ndarray_serialize():
     """
-    Large arrays should get compressed with blosc, otherwise just to list
+    Arrays should be dumped to a list when using json, but kept as ndarray otherwise
     """
 
     class Model(BaseModel):
-        large_array: NDArray[Any, Number]
+        array: NDArray[Any, Number]
-        small_array: NDArray[Any, Number]
 
-    mod = Model(
+    mod = Model(array=np.random.random((3, 3)))
-        large_array=np.random.random((1024, 1024)), small_array=np.random.random((3, 3))
-    )
     mod_str = mod.model_dump_json()
     mod_json = json.loads(mod_str)
-    for a in ("array", "shape", "dtype", "unpack_fns"):
+    assert isinstance(mod_json["array"], list)
-        assert a in mod_json["large_array"].keys()
-    assert isinstance(mod_json["large_array"]["array"], str)
-    assert isinstance(mod_json["small_array"], list)
 
-    # but when we just dump to a dict we don't compress
+    # but when we just dump to a dict we don't coerce
     mod_dict = mod.model_dump()
     assert isinstance(mod_dict["large_array"], np.ndarray)