Chores (#27)

CHANGELOG.rst

@@ -6,20 +6,30 @@
 Changelog
 =========
 
+0.6.2 (unreleased)
+------------------
+
+**Other changes**
+
+- Fixed various deprecation warnings
+
+
 0.6.1 (2024-07-12)
 ------------------
 
 **Bug fixes**
 
 - Division now complies more strictly with the Array API standard by returning a floating-point result regardless of input data types.
 
+
 0.6.0 (2024-07-11)
 ------------------
 
 **Other changes**
 
 - ``ndonnx.promote_nullable`` is now publicly exported.
 
+
 0.5.0 (2024-07-01)
 ------------------
 
@@ -31,6 +41,7 @@ Changelog
 
 - ``__array_namespace__`` now accepts the optional ``api_version`` argument to specify the version of the Array API to use.
 
+
 0.4.0 (2024-05-16)
 ------------------
 

ndonnx/_core/_impl.py

@@ -15,7 +15,6 @@
 import ndonnx._data_types as dtypes
 import ndonnx._opset_extensions as opx
 from ndonnx._utility import promote
-from ndonnx.additional import make_nullable
 
 from ._interface import OperationsBlock
 
@@ -311,7 +310,7 @@ def sign(self, x):
         if x_null is None:
             return out_values
         else:
-            return make_nullable(out_values, x_null)
+            return ndx.additional.make_nullable(out_values, x_null)
 
     def sin(self, x):
         return _unary_op(x, opx.sin, dtypes.float64)
@@ -549,7 +548,7 @@ def where_dtype_agnostic(a: ndx.Array, b: ndx.Array) -> ndx.Array:
         if condition.dtype == ndx.nbool:
             # propagate null if present
             if not isinstance(output.dtype, dtypes.Nullable):
-                output = make_nullable(output, condition.null)
+                output = ndx.additional.make_nullable(output, condition.null)
             else:
                 output.null = output.null | condition.null
         return output
@@ -889,9 +888,9 @@ def make_nullable(self, x, null):
         if null.dtype != dtypes.bool:
             raise TypeError("null must be a boolean array")
         if not isinstance(x.dtype, dtypes.CoreType):
-            raise TypeError("make_nullable does not accept nullable arrays")
+            raise TypeError("'make_nullable' does not accept nullable arrays")
         return ndx.Array._from_fields(
-            dtypes.promote_nullable(x.dtype),
+            dtypes.into_nullable(x.dtype),
             values=x.copy(),
             null=ndx.reshape(null, x.shape),
         )
@@ -939,7 +938,7 @@ def _variadic_op(
         values = _via_dtype(op, via_dtype, data, cast_return=cast_return)
 
     if (out_null := functools.reduce(_or_nulls, nulls)) is not None:
-        dtype = dtypes.promote_nullable(values.dtype)
+        dtype = dtypes.into_nullable(values.dtype)
         return ndx.Array._from_fields(dtype, values=values, null=out_null)
     else:
         return values
@@ -1002,7 +1001,7 @@ def _via_dtype(
 
     if out_null is not None:
         out_value = ndx.Array._from_fields(
-            dtypes.promote_nullable(out_value.dtype), values=out_value, null=out_null
+            dtypes.into_nullable(out_value.dtype), values=out_value, null=out_null
         )
     else:
         out_value = ndx.Array._from_fields(out_value.dtype, data=out_value._core())

ndonnx/_data_types/__init__.py

@@ -2,7 +2,7 @@
 # SPDX-License-Identifier: BSD-3-Clause
 
 from __future__ import annotations
-from warnings import warn
+from ndonnx._utility import deprecated
 
 from .aliases import (
     bool,
@@ -51,9 +51,8 @@
 from .structtype import StructType
 
 
-# TODO: to be removed
-def promote_nullable(dtype: StructType | CoreType) -> _NullableCore:
-    """Promotes a non-nullable type to its nullable counterpart, if present.
+def into_nullable(dtype: StructType | CoreType) -> _NullableCore:
+    """Return nullable counterpart, if present.
 
     Parameters
     ----------
@@ -70,13 +69,6 @@ def promote_nullable(dtype: StructType | CoreType) -> _NullableCore:
     ValueError
         If the input type is unknown to ``ndonnx``.
     """
-
-    warn(
-        "Function 'ndonnx.promote_nullable' will be deprecated in ndonnx 0.7. "
-        "To create nullable array, use 'ndonnx.additional.make_nullable' instead.",
-        DeprecationWarning,
-    )
-
     if dtype == bool:
         return nbool
     elif dtype == float32:
@@ -107,6 +99,14 @@ def promote_nullable(dtype: StructType | CoreType) -> _NullableCore:
         raise ValueError(f"Cannot promote {dtype} to nullable")
 
 
+@deprecated(
+    "Function 'ndonnx.promote_nullable' will be deprecated in ndonnx 0.7. "
+    "To create nullable array, use 'ndonnx.additional.make_nullable' instead."
+)
+def promote_nullable(dtype: StructType | CoreType) -> _NullableCore:
+    return into_nullable(dtype)
+
+
 __all__ = [
     "CoreType",
     "StructType",

ndonnx/_funcs.py

@@ -77,7 +77,7 @@ def asarray(
         if dtype is None:
             dtype = dtypes.from_numpy_dtype(arr.dtype)
             if isinstance(arr, np.ma.masked_array):
-                dtype = dtypes.promote_nullable(dtype)
+                dtype = dtypes.into_nullable(dtype)
 
         ret = Array._construct(
             shape=arr.shape, dtype=dtype, eager_values=dtype._parse_input(arr)
@@ -297,7 +297,7 @@ def result_type(
 
     ret_dtype = dtypes.from_numpy_dtype(np.result_type(*np_dtypes))
     if nullable:
-        return dtypes.promote_nullable(ret_dtype)
+        return dtypes.into_nullable(ret_dtype)
     else:
         return ret_dtype
 

ndonnx/_utility.py

@@ -3,7 +3,9 @@
 
 from __future__ import annotations
 
+from functools import wraps
 from typing import TYPE_CHECKING
+from warnings import warn
 
 import numpy as np
 import numpy.typing as npt
@@ -111,3 +113,17 @@ def unwrap_var(tensor: _CoreArray | Var) -> Var:
         return tensor
     else:
         return tensor.var
+
+
+def deprecated(msg: str):
+    """Decorates a function as deprecated and raises a warning when it is called."""
+
+    def _deprecated(fn):
+        @wraps(fn)
+        def inner(*args, **kwargs):
+            warn(msg, DeprecationWarning)
+            return fn(*args, **kwargs)
+
+        return inner
+
+    return _deprecated

pyproject.toml

@@ -87,10 +87,10 @@ module = ["onnxruntime"]
 ignore_missing_imports = true
 
 [tool.pytest.ini_options]
-pythonpath = "."
-addopts = "--import-mode=importlib --ignore=api-coverage-tests"
-testpaths = ["tests"]
-exclude = ["docs/"]
+addopts = "--ignore=api-coverage-tests"
+filterwarnings = [
+    "ignore:.*google.protobuf.pyext.*:DeprecationWarning",
+]
 
 [tool.typos.default]
 extend-ignore-identifiers-re = ["scatter_nd", "arange"]

tests/__init__.py

@@ -0,0 +1,2 @@
+# Copyright (c) QuantCo 2023-2024
+# SPDX-License-Identifier: BSD-3-Clause

tests/ndonnx/test_build_utils.py → tests/test_build_utils.py

@@ -28,7 +28,7 @@ def test_input_output_name_backwards_compatibility(dtype):
     model_proto = ndx.build({"input": a}, {"output": a})
     assert [node.name for node in model_proto.graph.input] == ["input"]
     assert [node.name for node in model_proto.graph.output] == ["output"]
-    a = ndx.array(shape=("N",), dtype=ndx._data_types.promote_nullable(dtype))
+    a = ndx.array(shape=("N",), dtype=ndx._data_types.into_nullable(dtype))
     model_proto = ndx.build({"input": a}, {"output": a})
     assert [node.name for node in model_proto.graph.input] == [
         "input_values",

tests/ndonnx/test_core.py → tests/test_core.py

@@ -19,7 +19,7 @@
 def numpy_to_graph_input(arr, eager=False):
     dtype: dtypes.CoreType | dtypes.StructType
     if isinstance(arr, np.ma.MaskedArray):
-        dtype = dtypes.promote_nullable(dtypes.from_numpy_dtype(arr.dtype))
+        dtype = dtypes.into_nullable(dtypes.from_numpy_dtype(arr.dtype))
     else:
         dtype = dtypes.from_numpy_dtype(arr.dtype)
     return (
@@ -601,3 +601,8 @@ def test_prod_no_implementation(dtype):
     x = ndx.asarray([2, 2]).astype(dtype)
     with pytest.raises(TypeError):
         ndx.prod(x)
+
+
+def test_promote_nullable():
+    with pytest.warns(DeprecationWarning):
+        assert ndx.promote_nullable(np.int64) == ndx.nint64

tests/ndonnx/test_masked.py → tests/test_masked.py

@@ -2,6 +2,7 @@
 # SPDX-License-Identifier: BSD-3-Clause
 
 import math
+import warnings
 
 import numpy as np
 import pytest
@@ -116,7 +117,11 @@ def test_unary_none_propagation(fn_name, args, kwargs):
     npx = get_numpy_array_api_namespace()
     np_fn = getattr(npx, fn_name)
     inp_a = npx.asarray(np.ma.filled(inp_a, np.nan))
-    expected_b = np_fn(inp_a, *args, **kwargs)
+
+    # Numpy might complain about invalid values
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore")
+        expected_b = np_fn(inp_a, *args, **kwargs)
     np.testing.assert_almost_equal(
         np.ma.masked_array(expected_b, mask=missing_a),
         ret_b,