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Commit32ad385

Browse files
authored
Fixes Array API with onnxruntime (#3)
* Check Array API with onnxruntime* better error message* improvment* disable one test for older version of sklearn* add one more pipeline* fix pipeline* fix array api* remove unnecessary code* disable one test one the current scikit-learn version
1 parent062b6c1 commit32ad385

18 files changed

+265
-68
lines changed

‎CHANGELOGS.rst‎

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@@ -0,0 +1,7 @@
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Change Logs
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===========
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0.2.0
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+++++
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*:pr:`3`: fixes Array API with onnxruntime

‎_doc/conf.py‎

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@@ -57,6 +57,11 @@
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}
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epkg_dictionary= {
60+
"Array API":"https://data-apis.org/array-api/",
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"ArrayAPI": (
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"https://data-apis.org/array-api/",
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("2022.12/API_specification/generated/array_api.{0}.html",1),
64+
),
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"DOT":"https://graphviz.org/doc/info/lang.html",
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"JIT":"https://en.wikipedia.org/wiki/Just-in-time_compilation",
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"onnx":"https://onnx.ai/onnx/",
@@ -65,7 +70,7 @@
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"numpy":"https://numpy.org/",
6671
"numba":"https://numba.pydata.org/",
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"onnx-array-api": (
68-
"http://www.xavierdupre.fr/app/""onnx-array-api/helpsphinx/index.html"
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"http://www.xavierdupre.fr/app/onnx-array-api/helpsphinx/index.html"
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),
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"pyinstrument":"https://github.com/joerick/pyinstrument",
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"python":"https://www.python.org/",

‎_doc/index.rst‎

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@@ -34,6 +34,7 @@ well as to execute it.
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tutorial/index
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api/index
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auto_examples/index
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../CHANGELOGS
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Sources available on
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`github/onnx-array-api<https://github.com/sdpython/onnx-array-api>`_,

‎_unittests/ut_npx/test_sklearn_array_api.py‎

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Original file line numberDiff line numberDiff line change
@@ -1,7 +1,8 @@
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importunittest
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importnumpyasnp
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frompackaging.versionimportVersion
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fromonnx.defsimportonnx_opset_version
4-
fromsklearnimportconfig_context
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fromsklearnimportconfig_context,__version__assklearn_version
56
fromsklearn.discriminant_analysisimportLinearDiscriminantAnalysis
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fromonnx_array_api.ext_test_caseimportExtTestCase
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fromonnx_array_api.npx.npx_numpy_tensorsimportEagerNumpyTensor
@@ -10,23 +11,15 @@
1011
DEFAULT_OPSET=onnx_opset_version()
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1213

13-
deftake(self,X,indices,*,axis):
14-
# Overwritting method take as it is using iterators.
15-
# When array_api supports `take` we can use this directly
16-
# https://github.com/data-apis/array-api/issues/177
17-
X_np=self._namespace.take(X,indices,axis=axis)
18-
returnself._namespace.asarray(X_np)
19-
20-
2114
classTestSklearnArrayAPI(ExtTestCase):
15+
@unittest.skipIf(
16+
Version(sklearn_version)<=Version("1.2.2"),
17+
reason="reshape ArrayAPI not followed",
18+
)
2219
deftest_sklearn_array_api_linear_discriminant(self):
23-
fromsklearn.utils._array_apiimport_ArrayAPIWrapper
24-
25-
_ArrayAPIWrapper.take=take
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X=np.array([[-1,-1], [-2,-1], [-3,-2], [1,1], [2,1], [3,2]])
2721
y=np.array([1,1,1,2,2,2])
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ana=LinearDiscriminantAnalysis()
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ana=LinearDiscriminantAnalysis()
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ana.fit(X,y)
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expected=ana.predict(X)
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importunittest
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importnumpyasnp
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frompackaging.versionimportVersion
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fromonnx.defsimportonnx_opset_version
5+
fromsklearnimportconfig_context,__version__assklearn_version
6+
fromsklearn.discriminant_analysisimportLinearDiscriminantAnalysis
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fromonnx_array_api.ext_test_caseimportExtTestCase
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fromonnx_array_api.ort.ort_tensorsimportEagerOrtTensor,OrtTensor
9+
10+
11+
DEFAULT_OPSET=onnx_opset_version()
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13+
14+
classTestSklearnArrayAPIOrt(ExtTestCase):
15+
@unittest.skipIf(
16+
Version(sklearn_version)<=Version("1.2.2"),
17+
reason="reshape ArrayAPI not followed",
18+
)
19+
deftest_sklearn_array_api_linear_discriminant(self):
20+
X=np.array([[-1,-1], [-2,-1], [-3,-2], [1,1], [2,1], [3,2]])
21+
y=np.array([1,1,1,2,2,2])
22+
ana=LinearDiscriminantAnalysis()
23+
ana.fit(X,y)
24+
expected=ana.predict(X)
25+
26+
new_x=EagerOrtTensor(OrtTensor.from_array(X))
27+
self.assertEqual(new_x.device_name,"Cpu")
28+
self.assertStartsWith(
29+
"EagerOrtTensor(OrtTensor.from_array(array([[",repr(new_x)
30+
)
31+
withconfig_context(array_api_dispatch=True):
32+
got=ana.predict(new_x)
33+
self.assertEqualArray(expected,got.numpy())
34+
35+
36+
if__name__=="__main__":
37+
# import logging
38+
# logging.basicConfig(level=logging.DEBUG)
39+
unittest.main(verbosity=2)

‎azure-pipelines.yml‎

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@@ -43,6 +43,53 @@ jobs:
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artifactName:'wheel-linux-wheel-$(python.version)'
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targetPath:'dist'
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-job:'TestLinuxNightly'
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pool:
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vmImage:'ubuntu-latest'
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strategy:
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matrix:
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Python310-Linux:
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python.version:'3.11'
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maxParallel:3
54+
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steps:
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-task:UsePythonVersion@0
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inputs:
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versionSpec:'$(python.version)'
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architecture:'x64'
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-script:sudo apt-get update
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displayName:'AptGet Update'
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-script:sudo apt-get install -y pandoc
63+
displayName:'Install Pandoc'
64+
-script:sudo apt-get install -y inkscape
65+
displayName:'Install Inkscape'
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-script:sudo apt-get install -y graphviz
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displayName:'Install Graphviz'
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-script:python -m pip install --upgrade pip setuptools wheel
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displayName:'Install tools'
70+
-script:pip install -r requirements.txt
71+
displayName:'Install Requirements'
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-script:pip install -r requirements-dev.txt
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displayName:'Install Requirements dev'
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-script:pip uninstall -y scikit-learn
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displayName:'Uninstall scikit-learn'
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-script:pip install --pre --extra-index https://pypi.anaconda.org/scipy-wheels-nightly/simple scikit-learn
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displayName:'Install scikit-learn nightly'
78+
-script:pip install onnxmltools --no-deps
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displayName:'Install onnxmltools'
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-script:|
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ruff .
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displayName: 'Ruff'
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-script:|
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rstcheck -r ./_doc ./onnx_array_api
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displayName: 'rstcheck'
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-script:|
87+
black --diff .
88+
displayName: 'Black'
89+
-script:|
90+
python -m pytest -v
91+
displayName: 'Runs Unit Tests'
92+
4693
-job:'TestLinux'
4794
pool:
4895
vmImage:'ubuntu-latest'

‎onnx_array_api/npx/npx_array_api.py‎

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@@ -1,22 +1,34 @@
1-
fromtypingimportAny
1+
fromtypingimportAny,Optional
22

33
importnumpyasnp
44

55
from .npx_typesimportOptParType,ParType,TupleType
66

77

8+
classArrayApiError(RuntimeError):
9+
"""
10+
Raised when a function is not supported by the :epkg:`Array API`.
11+
"""
12+
13+
pass
14+
15+
816
classArrayApi:
917
"""
1018
List of supported method by a tensor.
1119
"""
1220

13-
def__array_namespace__(self):
21+
def__array_namespace__(self,api_version:Optional[str]=None):
1422
"""
1523
Returns the module holding all the available functions.
1624
"""
17-
fromonnx_array_api.npximportnpx_functions
25+
ifapi_versionisNoneorapi_version=="2022.12":
26+
fromonnx_array_api.npximportnpx_functions
1827

19-
returnnpx_functions
28+
returnnpx_functions
29+
raiseValueError(
30+
f"Unable to return an implementation for api_version={api_version!r}."
31+
)
2032

2133
defgeneric_method(self,method_name,*args:Any,**kwargs:Any)->Any:
2234
raiseNotImplementedError(

‎onnx_array_api/npx/npx_core_api.py‎

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Original file line numberDiff line numberDiff line change
@@ -252,3 +252,10 @@ def npxapi_inline(fn):
252252
to call.
253253
"""
254254
return_xapi(fn,inline=True)
255+
256+
257+
defnpxapi_no_inline(fn):
258+
"""
259+
Functions decorated with this decorator are not converted into ONNX.
260+
"""
261+
returnfn

‎onnx_array_api/npx/npx_functions.py‎

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@@ -1,14 +1,16 @@
11
fromtypingimportAny,Optional,Tuple,Union
22

3+
importarray_api_compat.numpyasnp_array_api
34
importnumpyasnp
45
fromonnximportFunctionProto,ModelProto,NodeProto,TensorProto
56
fromonnx.helperimportnp_dtype_to_tensor_dtype
67
fromonnx.numpy_helperimportfrom_array
78

89
from .npx_constantsimportFUNCTION_DOMAIN
9-
from .npx_core_apiimportcst,make_tuple,npxapi_inline,var
10+
from .npx_core_apiimportcst,make_tuple,npxapi_inline,npxapi_no_inline,var
1011
from .npx_tensorsimportArrayApi
1112
from .npx_typesimport (
13+
DType,
1214
ElemType,
1315
OptParType,
1416
ParType,
@@ -397,6 +399,17 @@ def identity(n: ParType[int], dtype=None) -> TensorType[ElemType.numerics, "T"]:
397399
returnv
398400

399401

402+
@npxapi_no_inline
403+
defisdtype(
404+
dtype:DType,kind:Union[DType,str,Tuple[Union[DType,str], ...]]
405+
)->bool:
406+
"""
407+
See :epkg:`ArrayAPI:isdtype`.
408+
This function is not converted into an onnx graph.
409+
"""
410+
returnnp_array_api.isdtype(dtype,kind)
411+
412+
400413
@npxapi_inline
401414
defisnan(x:TensorType[ElemType.numerics,"T"])->TensorType[ElemType.bool_,"T"]:
402415
"See :func:`numpy.isnan`."
@@ -460,9 +473,23 @@ def relu(x: TensorType[ElemType.numerics, "T"]) -> TensorType[ElemType.numerics,
460473

461474
@npxapi_inline
462475
defreshape(
463-
x:TensorType[ElemType.numerics,"T"],shape:TensorType[ElemType.int64,"I"]
476+
x:TensorType[ElemType.numerics,"T"],
477+
shape:TensorType[ElemType.int64,"I", (None,)],
464478
)->TensorType[ElemType.numerics,"T"]:
465-
"See :func:`numpy.reshape`."
479+
"""
480+
See :func:`numpy.reshape`.
481+
482+
.. warning::
483+
484+
Numpy definition is tricky because onnxruntime does not handle well
485+
dimensions with an undefined number of dimensions.
486+
However the array API defines a more stricly signature for
487+
`reshape <https://data-apis.org/array-api/2022.12/
488+
API_specification/generated/array_api.reshape.html>`_.
489+
:epkg:`scikit-learn` updated its code to follow the Array API in
490+
`PR 26030 ENH Forces shape to be tuple when using Array API's reshape
491+
<https://github.com/scikit-learn/scikit-learn/pull/26030>`_.
492+
"""
466493
ifisinstance(shape,int):
467494
shape=cst(np.array([shape],dtype=np.int64))
468495
shape_reshaped=var(shape,cst(np.array([-1],dtype=np.int64)),op="Reshape")

‎onnx_array_api/npx/npx_graph_builder.py‎

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@@ -798,6 +798,23 @@ def to_onnx(
798798
node_inputs.append(input_name)
799799
continue
800800

801+
ifisinstance(i,tuple)andall(map(lambdax:isinstance(x,int),i)):
802+
ai=np.array(list(i),dtype=np.int64)
803+
c=Cst(ai)
804+
input_name=self._unique(var._prefix)
805+
self._id_vars[id(i),index]=input_name
806+
self._id_vars[id(c),index]=input_name
807+
self.make_node(
808+
"Constant",
809+
[],
810+
[input_name],
811+
value=from_array(ai),
812+
opset=self.target_opsets[""],
813+
)
814+
self.onnx_names_[input_name]=c
815+
node_inputs.append(input_name)
816+
continue
817+
801818
raiseNotImplementedError(
802819
f"Unexpected type{type(i)} for node={domop}."
803820
)

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