Merge remote-tracking branch 'origin/main' into predict_cmd

# Conflicts:
#	bioimageio/core/_resource_tests.py

bioimageio/core/_resource_tests.py

@@ -35,13 +35,18 @@ def test_model(
     source: Union[v0_5.ModelDescr, PermissiveFileSource],
     weight_format: Optional[WeightsFormat] = None,
     devices: Optional[List[str]] = None,
-    decimal: int = 4,
+    absolute_tolerance: float = 1.5e-4,
+    relative_tolerance: float = 1e-4,
+    decimal: Optional[int] = None,
 ) -> ValidationSummary:
     """Test model inference"""
+    # NOTE: `decimal` is a legacy argument and is handled in `_test_model_inference`
     return test_description(
         source,
         weight_format=weight_format,
         devices=devices,
+        absolute_tolerance=absolute_tolerance,
+        relative_tolerance=relative_tolerance,
         decimal=decimal,
         expected_type="model",
     )
@@ -53,15 +58,20 @@ def test_description(
     format_version: Union[Literal["discover", "latest"], str] = "discover",
     weight_format: Optional[WeightsFormat] = None,
     devices: Optional[Sequence[str]] = None,
-    decimal: int = 4,
+    absolute_tolerance: float = 1.5e-4,
+    relative_tolerance: float = 1e-4,
+    decimal: Optional[int] = None,
     expected_type: Optional[str] = None,
 ) -> ValidationSummary:
     """Test a bioimage.io resource dynamically, e.g. prediction of test tensors for models"""
+    # NOTE: `decimal` is a legacy argument and is handled in `_test_model_inference`
     rd = load_description_and_test(
         source,
         format_version=format_version,
         weight_format=weight_format,
         devices=devices,
+        absolute_tolerance=absolute_tolerance,
+        relative_tolerance=relative_tolerance,
         decimal=decimal,
         expected_type=expected_type,
     )
@@ -74,10 +84,13 @@ def load_description_and_test(
     format_version: Union[Literal["discover", "latest"], str] = "discover",
     weight_format: Optional[WeightsFormat] = None,
     devices: Optional[Sequence[str]] = None,
-    decimal: int = 4,
+    absolute_tolerance: float = 1.5e-4,
+    relative_tolerance: float = 1e-4,
+    decimal: Optional[int] = None,
     expected_type: Optional[str] = None,
 ) -> Union[ResourceDescr, InvalidDescr]:
     """Test RDF dynamically, e.g. model inference of test inputs"""
+    # NOTE: `decimal` is a legacy argument and is handled in `_test_model_inference`
     if (
         isinstance(source, ResourceDescrBase)
         and format_version != "discover"
@@ -110,7 +123,9 @@ def load_description_and_test(
         else:
             weight_formats = [weight_format]
         for w in weight_formats:
-            _test_model_inference(rd, w, devices, decimal)
+            _test_model_inference(
+                rd, w, devices, absolute_tolerance, relative_tolerance, decimal
+            )
             if not isinstance(rd, v0_4.ModelDescr):
                 _test_model_inference_parametrized(rd, w, devices)
 
@@ -124,12 +139,21 @@ def _test_model_inference(
     model: Union[v0_4.ModelDescr, v0_5.ModelDescr],
     weight_format: WeightsFormat,
     devices: Optional[Sequence[str]],
-    decimal: int,
+    absolute_tolerance: float,
+    relative_tolerance: float,
+    decimal: Optional[int],
 ) -> None:
     test_name = f"Reproduce test outputs from test inputs ({weight_format})"
     logger.info("starting '{}'", test_name)
     error: Optional[str] = None
     tb: List[str] = []
+
+    precision_args = _handle_legacy_precision_args(
+        absolute_tolerance=absolute_tolerance,
+        relative_tolerance=relative_tolerance,
+        decimal=decimal,
+    )
+
     try:
         inputs = get_test_inputs(model)
         expected = get_test_outputs(model)
@@ -149,8 +173,11 @@ def _test_model_inference(
                     error = "Output tensors for test case may not be None"
                     break
                 try:
-                    np.testing.assert_array_almost_equal(
-                        res.data, exp.data, decimal=decimal
+                    np.testing.assert_allclose(
+                        res.data,
+                        exp.data,
+                        rtol=precision_args["relative_tolerance"],
+                        atol=precision_args["absolute_tolerance"],
                     )
                 except AssertionError as e:
                     error = f"Output and expected output disagree:\n {e}"
@@ -361,6 +388,38 @@ def _test_expected_resource_type(
     )
 
 
+def _handle_legacy_precision_args(
+    absolute_tolerance: float, relative_tolerance: float, decimal: Optional[int]
+) -> Dict[str, float]:
+    """
+    Transform the precision arguments to conform with the current implementation.
+
+    If the deprecated `decimal` argument is used it overrides the new behaviour with
+    the old behaviour.
+    """
+    # Already conforms with current implementation
+    if decimal is None:
+        return {
+            "absolute_tolerance": absolute_tolerance,
+            "relative_tolerance": relative_tolerance,
+        }
+
+    warnings.warn(
+        "The argument `decimal` has been depricated in favour of "
+        + "`relative_tolerance` and `absolute_tolerance`, with different validation "
+        + "logic, using `numpy.testing.assert_allclose, see "
+        + "'https://numpy.org/doc/stable/reference/generated/"
+        + "numpy.testing.assert_allclose.html'. Passing a value for `decimal` will "
+        + "cause validation to revert to the old behaviour."
+    )
+    # decimal overrides new behaviour,
+    #   have to convert the params to emulate old behaviour
+    return {
+        "absolute_tolerance": 1.5 * 10 ** (-decimal),
+        "relative_tolerance": 0,
+    }
+
+
 # def debug_model(
 #     model_rdf: Union[RawResourceDescr, ResourceDescr, URI, Path, str],
 #     *,

dev/env.yaml

@@ -1,7 +1,6 @@
 name: core
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - bioimageio.spec>=0.5.3.2
   - black
@@ -11,6 +10,8 @@ dependencies:
   - imageio>=2.5
   - jupyter
   - jupyter-black
+  - ipykernel
+  - matplotlib
   - keras>=3.0
   - loguru
   - numpy