Update CI with latext onnxruntime, xgboost (#602)

* Update CI with latext onnxruntime, xgboost Signed-off-by: xadupre <xadupre@microsoft.com> * add one unit test for issue 601 Signed-off-by: xadupre <xadupre@microsoft.com> * fix iterable Signed-off-by: xadupre <xadupre@microsoft.com> * fix .str_ Signed-off-by: xadupre <xadupre@microsoft.com> * hinge Signed-off-by: xadupre <xadupre@microsoft.com> * fix hinge Signed-off-by: xadupre <xadupre@microsoft.com> * fix str Signed-off-by: xadupre <xadupre@microsoft.com> * update CI Signed-off-by: xadupre <xadupre@microsoft.com> * fix yml Signed-off-by: xadupre <xadupre@microsoft.com> * fix coreml issue Signed-off-by: xadupre <xadupre@microsoft.com> * update CI Signed-off-by: xadupre <xadupre@microsoft.com> * update CI Signed-off-by: xadupre <xadupre@microsoft.com> * fix CI Signed-off-by: xadupre <xadupre@microsoft.com> * fix CI Signed-off-by: xadupre <xadupre@microsoft.com> * update CI Signed-off-by: xadupre <xadupre@microsoft.com> * update CI Signed-off-by: xadupre <xadupre@microsoft.com> * update CI Signed-off-by: xadupre <xadupre@microsoft.com> * update CI Signed-off-by: xadupre <xadupre@microsoft.com> Signed-off-by: xadupre <xadupre@microsoft.com>
onnx · Jan 18, 2023 · cfb2cc0 · cfb2cc0
1 parent d9a6108
commit cfb2cc0
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diff --git a/.azure-pipelines/linux-conda-CI.yml b/.azure-pipelines/linux-conda-CI.yml
@@ -14,53 +14,68 @@ jobs:
     vmImage: 'ubuntu-latest'
   strategy:
     matrix:
+      Python310-1130-RT1131-xgb173:
+        python.version: '3.10'
+        ONNX_PATH: 'onnx==1.13.0' #'-i https://test.pypi.org/simple/ onnx==1.12.0rc4'
+        ONNXRT_PATH: onnxruntime==1.13.1 #'-i https://test.pypi.org/simple/ ort-nightly==1.11.0.dev20220311003'
+        COREML_PATH: NONE
+        xgboost.version: '>=1.7.3'
+        numpy.version: ''
       Python310-1120-RT1121-xgb161:
-        python.version: '3.9'
+        python.version: '3.10'
         ONNX_PATH: 'onnx==1.12.0' #'-i https://test.pypi.org/simple/ onnx==1.12.0rc4'
         ONNXRT_PATH: onnxruntime==1.12.1 #'-i https://test.pypi.org/simple/ ort-nightly==1.11.0.dev20220311003'
-        COREML_PATH: git+https://github.com/apple/coremltools@3.1
-        xgboost.version: '>=1.6.1'
+        COREML_PATH: NONE
+        xgboost.version: '==1.6.1'
+        numpy.version: ''
       Python39-1120-RT1110-xgb161:
         python.version: '3.9'
         ONNX_PATH: 'onnx==1.12.0' #'-i https://test.pypi.org/simple/ onnx==1.12.0rc4'
         ONNXRT_PATH: onnxruntime==1.11.0 #'-i https://test.pypi.org/simple/ ort-nightly==1.11.0.dev20220311003'
         COREML_PATH: git+https://github.com/apple/coremltools@3.1
         xgboost.version: '>=1.6.1'
+        numpy.version: ''
       Python39-1120-RT1110-xgb142:
         python.version: '3.9'
         ONNX_PATH: 'onnx==1.12.0' #'-i https://test.pypi.org/simple/ onnx==1.12.0rc4'
         ONNXRT_PATH: onnxruntime==1.11.0 #'-i https://test.pypi.org/simple/ ort-nightly==1.11.0.dev20220311003'
         COREML_PATH: git+https://github.com/apple/coremltools@3.1
         xgboost.version: '==1.4.2'
+        numpy.version: ''
       Python39-1110-RT1110:
         python.version: '3.9'
         ONNX_PATH: onnx==1.11.0  # '-i https://test.pypi.org/simple/ onnx==1.9.101'
         ONNXRT_PATH: onnxruntime==1.11.0 #'-i https://test.pypi.org/simple/ ort-nightly==1.11.0.dev20220311003'
         COREML_PATH: git+https://github.com/apple/coremltools@3.1
+        numpy.version: ''
       Python39-1110-RT1100:
         python.version: '3.9'
         ONNX_PATH: onnx==1.11.0  # '-i https://test.pypi.org/simple/ onnx==1.9.101'
         ONNXRT_PATH: onnxruntime==1.10.0
         COREML_PATH: git+https://github.com/apple/coremltools@3.1
         xgboost.version: '>=1.2'
+        numpy.version: ''
       Python39-1101-RT190:
         python.version: '3.9'
         ONNX_PATH: onnx==1.10.1
         ONNXRT_PATH: onnxruntime==1.9.0
         COREML_PATH: git+https://github.com/apple/coremltools@3.1
         xgboost.version: '>=1.2'
+        numpy.version: '<=1.23.5'
       Python39-190-RT180-xgb11:
         python.version: '3.9'
         ONNX_PATH: onnx==1.9.0
         ONNXRT_PATH: onnxruntime==1.8.0
         COREML_PATH: git+https://github.com/apple/coremltools@3.1
         xgboost.version: '>=1.2'
+        numpy.version: '<=1.23.5'
       Python38-181-RT170-xgb11:
         python.version: '3.8'
         ONNX_PATH: onnx==1.8.1
         ONNXRT_PATH: onnxruntime==1.7.0
         COREML_PATH: git+https://github.com/apple/coremltools@3.1
         xgboost.version: '>=1.2'
+        numpy.version: '<=1.23.5'
 
     maxParallel: 3
 
@@ -85,7 +100,7 @@ jobs:
       pip install xgboost$(xgboost.version)
       pip install $(ONNX_PATH)
       pip install $(ONNXRT_PATH)
-      pip install $(COREML_PATH)
+      pip install "numpy$(numpy.version)"
     displayName: 'Install xgboost, onnxruntime'
 
   - script: |
@@ -149,7 +164,7 @@ jobs:
     displayName: 'pytest - h2o'
 
   - script: |
-      pip install torch==1.8.1+cpu torchvision==0.9.1+cpu torchaudio==0.8.1 -f https://download.pytorch.org/whl/torch_stable.html
+      pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
       pip install hummingbird-ml --no-deps
     displayName: 'Install hummingbird-ml'
 
@@ -159,9 +174,16 @@ jobs:
     displayName: 'pytest - hummingbirdml'
 
   - script: |
-      export PYTHONPATH=.
-      pytest tests/coreml --durations=0
-    displayName: 'pytest - coreml'
+      if [ '$(COREML_PATH)' == 'NONE' ]
+      then
+        echo "required version of coremltools does not work on python 3.10"
+      else
+        export PYTHONPATH=.
+        pip install $(COREML_PATH)
+        pytest tests/coreml --durations=0
+      fi
+    displayName: 'pytest - coreml [$(COREML_PATH)]'
+    # condition: ne('$(COREML_PATH)', 'NONE')
 
   - task: PublishTestResults@2
     inputs:

diff --git a/.azure-pipelines/win32-conda-CI.yml b/.azure-pipelines/win32-conda-CI.yml
@@ -15,47 +15,61 @@ jobs:
   strategy:
     matrix:
 
+      Python310-1130-RT1131:
+        python.version: '3.10'
+        ONNX_PATH: 'onnx==1.13.0' # '-i https://test.pypi.org/simple/ onnx==1.12.0rc4'
+        ONNXRT_PATH: onnxruntime==1.13.1 #'-i https://test.pypi.org/simple/ ort-nightly==1.11.0.dev20220311003'
+        COREML_PATH: NONE
+        numpy.version: ''
+
       Python39-1120-RT1110:
         python.version: '3.9'
         ONNX_PATH: 'onnx==1.12.0' # '-i https://test.pypi.org/simple/ onnx==1.12.0rc4'
         ONNXRT_PATH: onnxruntime==1.11.0 #'-i https://test.pypi.org/simple/ ort-nightly==1.11.0.dev20220311003'
         COREML_PATH: git+https://github.com/apple/coremltools@3.1
+        numpy.version: ''
 
       Python39-1110-RT1110:
         python.version: '3.9'
         ONNX_PATH: onnx==1.11.0  # '-i https://test.pypi.org/simple/ onnx==1.9.101'
         ONNXRT_PATH: onnxruntime==1.11.0 #'-i https://test.pypi.org/simple/ ort-nightly==1.11.0.dev20220311003'
         COREML_PATH: git+https://github.com/apple/coremltools@3.1
+        numpy.version: ''
 
       Python39-1110-RT190:
         python.version: '3.9'
         ONNX_PATH: 'onnx==1.11.0'  # '-i https://test.pypi.org/simple/ onnx==1.9.101'
         ONNXRT_PATH: onnxruntime==1.10.0
         COREML_PATH: git+https://github.com/apple/coremltools@3.1
+        numpy.version: ''
 
       Python39-1102-RT190:
         python.version: '3.9'
         ONNX_PATH: 'onnx==1.10.2'  # '-i https://test.pypi.org/simple/ onnx==1.9.101'
         ONNXRT_PATH: onnxruntime==1.9.0
         COREML_PATH: git+https://github.com/apple/coremltools@3.1
+        numpy.version: '<=1.23.5'
 
       Python39-190-RT181:
         python.version: '3.9'
         ONNX_PATH: 'onnx==1.9.0'
         ONNXRT_PATH: onnxruntime==1.8.1
         COREML_PATH: git+https://github.com/apple/coremltools@3.1
+        numpy.version: '<=1.23.5'
 
       Python39-190-RT180:
         python.version: '3.9'
         ONNX_PATH: onnx==1.9.0
         ONNXRT_PATH: onnxruntime==1.8.0
         COREML_PATH: git+https://github.com/apple/coremltools@3.1
+        numpy.version: '<=1.23.5'
 
       Python38-181-RT170:
         python.version: '3.8'
         ONNX_PATH: onnx==1.8.1
         ONNXRT_PATH: onnxruntime==1.7.0
         COREML_PATH: git+https://github.com/apple/coremltools@3.1
+        numpy.version: '<=1.23.5'
 
     maxParallel: 3
 
@@ -83,15 +97,11 @@ jobs:
       python -m pip install --upgrade scikit-learn
     displayName: 'Install scikit-learn'
 
-  - script: |
-      call activate py$(python.version)
-      python -m pip install %COREML_PATH%
-    displayName: 'Install coremltools'
-
   - script: |
       call activate py$(python.version)
       python -m pip install %ONNX_PATH%
       python -m pip install %ONNXRT_PATH%
+      python -m pip install "numpy$(numpy.version)"
     displayName: 'Install onnxruntime'
 
   - script: |
@@ -124,9 +134,11 @@ jobs:
 
   - script: |
       call activate py$(python.version)
-      export PYTHONPATH=.
-      python -m pytest tests/coreml --durations=0
-    displayName: 'pytest coreml'
+      set PYTHONPATH=.
+      if "$(COREML_PATH)" neq "NONE" python -m pip install %COREML_PATH%
+      if "$(COREML_PATH)" neq "NONE" python -m pytest tests/coreml --durations=0
+    displayName: 'pytest coreml - [$(COREML_PATH)]'
+    #condition: ne('$(COREML_PATH)', 'NONE')
 
   - script: |
       call activate py$(python.version)
@@ -160,7 +172,7 @@ jobs:
 
   - script: |
       call activate py$(python.version)
-      python -m pip install torch==1.8.1+cpu torchvision==0.9.1+cpu torchaudio===0.8.1 -f https://download.pytorch.org/whl/torch_stable.html
+      python -m pip install torch
       python -m pip install hummingbird-ml --no-deps
     displayName: 'Install hummingbird-ml'
 

diff --git a/onnxmltools/convert/sparkml/operator_converters/aft_survival_regression.py b/onnxmltools/convert/sparkml/operator_converters/aft_survival_regression.py
@@ -15,7 +15,10 @@ def convert_aft_survival_regression(scope, operator, container):
     coefficients = op.coefficients.toArray().astype(float)
     coefficients_tensor = scope.get_unique_variable_name('coefficients_tensor')
     container.add_initializer(coefficients_tensor, onnx_proto.TensorProto.FLOAT, [1, len(coefficients)], coefficients)
-    intercepts = op.intercept.astype(float) if isinstance(op.intercept, collections.Iterable) else [float(op.intercept)]
+    intercepts = (
+        op.intercept.astype(float)
+        if isinstance(op.intercept, collections.abc.Iterable)
+        else [float(op.intercept)])
     intercepts_tensor = scope.get_unique_variable_name('intercepts_tensor')
     container.add_initializer(intercepts_tensor, onnx_proto.TensorProto.FLOAT, [len(intercepts)], intercepts)
 

diff --git a/onnxmltools/convert/sparkml/operator_converters/linear_regressor.py b/onnxmltools/convert/sparkml/operator_converters/linear_regressor.py
@@ -13,8 +13,10 @@ def convert_sparkml_linear_regressor(scope, operator, container):
     attrs = {
         'name': scope.get_unique_operator_name(op_type),
         'coefficients': op.coefficients.astype(float),
-        'intercepts': op.intercept.astype(float) if isinstance(op.intercept, collections.Iterable) else [
-                 float(op.intercept)]
+        'intercepts': (
+            op.intercept.astype(float)
+            if isinstance(op.intercept, collections.abc.Iterable)
+            else [float(op.intercept)])
     }
     container.add_node(op_type, operator.input_full_names, operator.output_full_names, op_domain='ai.onnx.ml', **attrs)
 

diff --git a/onnxmltools/convert/xgboost/convert.py b/onnxmltools/convert/xgboost/convert.py
@@ -41,4 +41,13 @@ def convert(model, name=None, initial_types=None, doc_string='', target_opset=No
     topology = parse_xgboost(model, initial_types, target_opset, custom_conversion_functions, custom_shape_calculators)
     topology.compile()
     onnx_model = convert_topology(topology, name, doc_string, target_opset, targeted_onnx)
+    opsets = {d.domain: d.version for d in onnx_model.opset_import}
+    if '' in opsets and opsets[''] < 9 and target_opset >= 9:
+        # a bug?
+        opsets[''] = 9
+        del onnx_model.opset_import[:]
+        for k, v in opsets.items():
+            opset = onnx_model.opset_import.add()
+            opset.domain = k
+            opset.version = v
     return onnx_model
diff --git a/onnxmltools/convert/xgboost/operator_converters/XGBoost.py b/onnxmltools/convert/xgboost/operator_converters/XGBoost.py
@@ -2,6 +2,7 @@
 
 import json
 import numpy as np
+from onnx import TensorProto
 from xgboost import XGBClassifier
 from ...common._registration import register_converter
 from ..common import get_xgb_params
@@ -241,14 +242,17 @@ def convert(scope, operator, container):
             raise RuntimeError("XGBoost model is empty.")
         if ncl <= 1:
             ncl = 2
-            # See https://github.com/dmlc/xgboost/blob/master/src/common/math.h#L23.
-            attr_pairs['post_transform'] = "LOGISTIC"
-            attr_pairs['class_ids'] = [0 for v in attr_pairs['class_treeids']]
-            if js_trees[0].get('leaf', None) == 0:
-                attr_pairs['base_values'] = [0.5]
-            elif base_score != 0.5:
-                cst = - np.log(1 / np.float32(base_score) - 1.)
-                attr_pairs['base_values'] = [cst]
+            if objective != 'binary:hinge':
+                # See https://github.com/dmlc/xgboost/blob/master/src/common/math.h#L23.
+                attr_pairs['post_transform'] = "LOGISTIC"
+                attr_pairs['class_ids'] = [0 for v in attr_pairs['class_treeids']]
+                if js_trees[0].get('leaf', None) == 0:
+                    attr_pairs['base_values'] = [0.5]
+                elif base_score != 0.5:
+                    cst = - np.log(1 / np.float32(base_score) - 1.)
+                    attr_pairs['base_values'] = [cst]
+            else:
+                attr_pairs['base_values'] = [base_score]
         else:
             # See https://github.com/dmlc/xgboost/blob/master/src/common/math.h#L35.
             attr_pairs['post_transform'] = "SOFTMAX"
@@ -264,13 +268,33 @@ def convert(scope, operator, container):
             attr_pairs['classlabels_strings'] = classes
 
         # add nodes
-        if objective == "binary:logistic":
+        if objective in ("binary:logistic", "binary:hinge"):
             ncl = 2
-            container.add_node('TreeEnsembleClassifier', operator.input_full_names,
-                               operator.output_full_names,
+            if objective == "binary:hinge":
+                attr_pairs['post_transform'] = 'NONE'
+                output_names = [operator.output_full_names[0],
+                                scope.get_unique_variable_name("output_prob")]
+            else:
+                output_names = operator.output_full_names
+            container.add_node('TreeEnsembleClassifier',
+                               operator.input_full_names,
+                               output_names,
                                op_domain='ai.onnx.ml',
                                name=scope.get_unique_operator_name('TreeEnsembleClassifier'),
                                **attr_pairs)
+            if objective == "binary:hinge":
+                if container.target_opset < 9:
+                    raise RuntimeError(
+                        f"hinge function cannot be implemented because "
+                        f"opset={container.target_opset}<9.")
+                zero = scope.get_unique_variable_name("zero")
+                one = scope.get_unique_variable_name("one")
+                container.add_initializer(zero, TensorProto.FLOAT, [1], [0.])
+                container.add_initializer(one, TensorProto.FLOAT, [1], [1.])
+                greater = scope.get_unique_variable_name("output_prob")
+                container.add_node("Greater", [output_names[1], zero], [greater])
+                container.add_node('Where', [greater, one, zero], 
+                                   operator.output_full_names[1])
         elif objective in ("multi:softprob", "multi:softmax"):
             ncl = len(js_trees) // params['n_estimators']
             if objective == 'multi:softmax':

diff --git a/onnxmltools/proto/__init__.py b/onnxmltools/proto/__init__.py
@@ -21,7 +21,7 @@ def _check_onnx_version():
 _check_onnx_version()
 
 
-def _make_tensor_fixed(name, data_type, dims, vals, raw=False):
+def make_tensor_fixed(name, data_type, dims, vals, raw=False):
     '''
     Make a TensorProto with specified arguments.  If raw is False, this
     function will choose the corresponding proto field to store the
@@ -45,6 +45,3 @@ def _make_tensor_fixed(name, data_type, dims, vals, raw=False):
 
     tensor.dims.extend(dims)
     return tensor
-
-
-helper.make_tensor = _make_tensor_fixed
diff --git a/onnxmltools/utils/utils_backend_onnxruntime.py b/onnxmltools/utils/utils_backend_onnxruntime.py
@@ -52,7 +52,7 @@ def compare_runtime(test, decimal=5, options=None, verbose=False, context=None):
         return
 
     try:
-        sess = onnxruntime.InferenceSession(onx)
+        sess = onnxruntime.InferenceSession(onx, providers=["CPUExecutionProvider"])
     except ExpectedAssertionError as expe:
         raise expe
     except Exception as e:
@@ -312,7 +312,7 @@ def run_with_runtime(inputs, model_path):
     '''
     try:
         import onnxruntime
-        session = onnxruntime.InferenceSession(model_path)
+        session = onnxruntime.InferenceSession(model_path, providers=["CPUExecutionProvider"])
         output = session.run(None, inputs)
         return (output, session)
     except Exception as e:

diff --git a/tests/baseline/test_convert_baseline.py b/tests/baseline/test_convert_baseline.py
@@ -9,7 +9,10 @@
 from onnx.defs import onnx_opset_version
 from onnxmltools.convert import convert_coreml
 from onnxconverter_common.onnx_ex import DEFAULT_OPSET_NUMBER
-import coremltools
+try:
+    import coremltools
+except ImportError:
+    coremltools = None
 
 
 TARGET_OPSET = min(DEFAULT_OPSET_NUMBER, onnx_opset_version())
@@ -24,6 +27,8 @@ def check_baseline(self, input_file, ref_file):
     def get_diff(self, input_file, ref_file):
         this = os.path.dirname(__file__)
         coreml_file = os.path.join(this, "models", input_file)
+        if coremltools is None:
+            return  []
         cml = coremltools.utils.load_spec(coreml_file)
         onnx_model = convert_coreml(cml, target_opset=TARGET_OPSET)
         output_dir = os.path.join(this, "outmodels")

diff --git a/tests/h2o/test_h2o_converters.py b/tests/h2o/test_h2o_converters.py
@@ -91,7 +91,7 @@ def _prepare_one_hot(file, y, exclude_cols=None):
 
 
 def _train_test_split_as_frames(x, y, is_str=False, is_classifier=False):
-    y = y.astype(np.str) if is_str else y.astype(np.int64)
+    y = y.astype(np.str_) if is_str else y.astype(np.int64)
     x_train, x_test, y_train, _ = train_test_split(x, y, test_size=0.3, random_state=42)
     f_train_x = H2OFrame(x_train)
     f_train_y = H2OFrame(y_train)
@@ -138,7 +138,7 @@ def predict_with_probabilities(self, data):
             return [preds.to_numpy()]
         else:
             return [
-                preds.iloc[:, 0].to_numpy().astype(np.str),
+                preds.iloc[:, 0].to_numpy().astype(np.str_),
                 preds.iloc[:, 1:].to_numpy()
             ]