Update tensorflow requirement from !=2.6.0,!=2.6.1,<2.15.0,>=2.0.0 to…

… >=2.0.0,!=2.6.0,!=2.6.1,<2.19.0 (#1023) * Update tensorflow requirement Updates the requirements on [tensorflow](https://github.com/tensorflow/tensorflow) to permit the latest version. - [Release notes](https://github.com/tensorflow/tensorflow/releases) - [Changelog](https://github.com/tensorflow/tensorflow/blob/master/RELEASE.md) - [Commits](tensorflow/tensorflow@v2.0.0...v2.18.0) --- updated-dependencies: - dependency-name: tensorflow dependency-type: direct:development ... Signed-off-by: dependabot[bot] <[email protected]> * Upperbound spacy * Upperbound tf to 2.16 because of keras 3 and transformers compatibility * Fixed PDP tests * Updated alibi-testing branch for testing purposes * Modified keras import * Revert "Modified keras import" This reverts commit b3641a8. * Included keras legacy * Fixed setup.py * Fixed IG tests * Fixed cfrl tests * Fixed cfrl saving * Replace tf.keras with legacy keras * Fixed cfproto tests * Refactored and fixed tf1 tests * Fixed flake8 issues * Fixed mypy issues * Removed python3.8 from ci * Fixed tf1 tests * Improved linting * Included test makefile entry * Included tf_legacy for doc examples * Temp trigger the test for notebooks on push * Removed python 3.8 from test_all_notebooks * Fixed test make command * Included tf_legacy to more notebooks * Removed legacy keras import * Fixed path dependent tree shap notebook * Reverted dev requirements and test notebooks workflow * Set lowerbound for tf --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Robert <[email protected]>
SeldonIO · Dec 5, 2024 · e04a354 · e04a354
1 parent 4cca971
commit e04a354
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -35,7 +35,7 @@ jobs:
     strategy:
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11']
         include: # Run windows tests on only one python version
           - os: windows-latest
             python-version: '3.11'
@@ -68,9 +68,7 @@ jobs:
           limit-access-to-actor: true
 
       - name: Test with pytest
-        run: |
-          pytest -m tf1 alibi
-          pytest -m "not tf1" alibi
+        run: make test
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4

diff --git a/Makefile b/Makefile
@@ -64,3 +64,8 @@ check_licenses:
 tox-env=default
 repl:
 	env COMMAND="python" tox -e $(tox-env)
+
+.PHONY: test
+test:
+	TF_USE_LEGACY_KERAS=1 pytest -m "tf1" alibi
+	pytest -m "not tf1" alibi
diff --git a/alibi/datasets/default.py b/alibi/datasets/default.py
@@ -141,7 +141,7 @@ def load_cats(target_size: tuple = (299, 299), return_X_y: bool = False) -> Unio
     for member in tar.getmembers():
         # data
         img = tar.extractfile(member).read()  # type: ignore[union-attr]
-        img = PIL.Image.open(BytesIO(img))
+        img = PIL.Image.open(BytesIO(img))  # type: ignore[attr-defined]
         img = np.array(img.resize(target_size))
         img = np.expand_dims(img, axis=0)
         images.append(img)

diff --git a/alibi/explainers/backends/tensorflow/cfrl_base.py b/alibi/explainers/backends/tensorflow/cfrl_base.py
@@ -89,6 +89,9 @@ def __len__(self) -> int:
         return self.X.shape[0] // self.batch_size
 
     def __getitem__(self, idx) -> Dict[str, np.ndarray]:
+        if idx >= self.__len__():
+            raise IndexError("Index out of bounds.")
+
         if hasattr(self, 'num_classes'):
             # Generate random targets for classification task.
             tgts = np.random.randint(low=0, high=self.num_classes, size=self.batch_size)

diff --git a/alibi/explainers/partial_dependence.py b/alibi/explainers/partial_dependence.py
@@ -368,7 +368,7 @@ def _partial_dependence(self,
                 'average': averaged_predictions,
                 'individual': predictions
             })
-        return pd
+        return pd  # type: ignore[return-value]
 
     @abstractmethod
     def _compute_pd(self,

diff --git a/alibi/explainers/permutation_importance.py b/alibi/explainers/permutation_importance.py
@@ -348,7 +348,7 @@ def explain(self,  # type: ignore[override]
                                    sample_weight=sample_weight)
 
         # build and return the explanation object
-        return self._build_explanation(feature_names=feature_names,  # type: ignore[arg-type]
+        return self._build_explanation(feature_names=feature_names,
                                        individual_feature_importance=individual_feature_importance)
 
     @staticmethod

diff --git a/alibi/explainers/tests/test_anchor_image.py b/alibi/explainers/tests/test_anchor_image.py
@@ -1,8 +1,8 @@
 import pytest
 from pytest_lazyfixture import lazy_fixture
+import torch
 import numpy as np
 import tensorflow as tf
-import torch
 
 from alibi.api.defaults import DEFAULT_META_ANCHOR, DEFAULT_DATA_ANCHOR_IMG
 from alibi.exceptions import PredictorCallError, PredictorReturnTypeError
@@ -44,7 +44,7 @@ def func(image: np.ndarray) -> np.ndarray:
 
 @pytest.mark.parametrize('predict_fn', [lazy_fixture('models'), ], indirect=True)
 @pytest.mark.parametrize('models',
-                         [("mnist-cnn-tf2.2.0",), ("mnist-cnn-tf1.15.2.h5",), ("mnist-cnn-pt1.9.1.pt",)],
+                         [("mnist-cnn-tf2.18.0.keras",), ("mnist-cnn-pt1.9.1.pt",)],
                          indirect=True,
                          ids='models={}'.format
                          )
@@ -99,7 +99,7 @@ def test_sampler(predict_fn, models, mnist_data):
 
 @pytest.mark.parametrize('predict_fn', [lazy_fixture('models'), ], indirect=True)
 @pytest.mark.parametrize('models',
-                         [("mnist-cnn-tf2.2.0",), ("mnist-cnn-tf1.15.2.h5",), ("mnist-cnn-pt1.9.1.pt",)],
+                         [("mnist-cnn-tf2.18.0.keras",), ("mnist-cnn-pt1.9.1.pt",)],
                          indirect=True,
                          ids='models={}'.format
                          )

diff --git a/alibi/explainers/tests/test_cfrl.py b/alibi/explainers/tests/test_cfrl.py
@@ -2,8 +2,10 @@
 
 import pytest
 from pytest_lazyfixture import lazy_fixture
+
 import numpy as np
 from numpy.testing import assert_allclose
+
 import tensorflow as tf
 import tensorflow.keras as keras
 
@@ -260,8 +262,8 @@ def tf_keras_iris_explainer(models, iris_data, rf_classifier):
     ])
 
     # need to define a wrapper for the decoder to return a list of tensors
-    class DecoderList(tf.keras.Model):
-        def __init__(self, decoder: tf.keras.Model, **kwargs):
+    class DecoderList(keras.Model):
+        def __init__(self, decoder: keras.Model, **kwargs):
             super().__init__(**kwargs)
             self.decoder = decoder
 
@@ -295,11 +297,20 @@ def call(self, input: Union[tf.Tensor, List[tf.Tensor]], **kwargs):
     return explainer
 
 
-@pytest.mark.parametrize('models', [('iris-ae-tf2.2.0', 'iris-enc-tf2.2.0')], ids='model={}'.format, indirect=True)
-@pytest.mark.parametrize('rf_classifier',
-                         [lazy_fixture('iris_data')],
-                         indirect=True,
-                         ids='clf=rf_{}'.format)
+@pytest.mark.parametrize(
+    'models',
+    [
+        ('iris-ae-tf2.18.0.keras', 'iris-enc-tf2.18.0.keras')
+    ],
+    ids='model={}'.format,
+    indirect=True
+)
+@pytest.mark.parametrize(
+    'rf_classifier',
+    [lazy_fixture('iris_data')],
+    indirect=True,
+    ids='clf=rf_{}'.format
+)
 def test_explainer(tf_keras_iris_explainer, iris_data):
     explainer = tf_keras_iris_explainer
 
@@ -317,7 +328,7 @@ def test_explainer(tf_keras_iris_explainer, iris_data):
     # Fit the explainer
     explainer.fit(X=iris_data["X_train"])
 
-    # Construct explanation object.
+    # # Construct explanation object.
     explainer.explain(X=iris_data["X_test"], Y_t=np.array([2]), C=None)
 
 

diff --git a/alibi/explainers/tests/test_integrated_gradients.py b/alibi/explainers/tests/test_integrated_gradients.py
@@ -1,10 +1,11 @@
 from functools import partial
 
-import numpy as np
 import pytest
-import tensorflow as tf
+import numpy as np
 from numpy.testing import assert_allclose
-from tensorflow.keras import Model
+
+import tensorflow as tf
+import tensorflow.keras as keras
 
 from alibi.api.interfaces import Explanation
 from alibi.explainers import IntegratedGradients
@@ -39,7 +40,7 @@
 
 # classification labels
 y_classification_ordinal = (X[:, 0] + X[:, 1] > 1).astype(int)
-y_classification_categorical = tf.keras.utils.to_categorical(y_classification_ordinal)
+y_classification_categorical = keras.utils.to_categorical(y_classification_ordinal)
 
 y_train_classification_ordinal = y_classification_ordinal[:N_TRAIN]
 y_train_classification_categorical = y_classification_categorical[:N_TRAIN, :]
@@ -59,13 +60,13 @@ def ffn_model(request):
     Simple feed-forward model with configurable data, loss function, output activation and dimension
     """
     config = request.param
-    inputs = tf.keras.Input(shape=config['X_train'].shape[1:])
-    x = tf.keras.layers.Dense(20, activation='relu')(inputs)
-    x = tf.keras.layers.Dense(20, activation='relu')(x)
-    outputs = tf.keras.layers.Dense(config['output_dim'], activation=config['activation'])(x)
+    inputs = keras.Input(shape=config['X_train'].shape[1:])
+    x = keras.layers.Dense(20, activation='relu')(inputs)
+    x = keras.layers.Dense(20, activation='relu')(x)
+    outputs = keras.layers.Dense(config['output_dim'], activation=config['activation'])(x)
     if config.get('squash_output', False):
-        outputs = tf.keras.layers.Reshape(())(outputs)
-    model = tf.keras.models.Model(inputs=inputs, outputs=outputs)
+        outputs = keras.layers.Reshape(())(outputs)
+    model = keras.models.Model(inputs=inputs, outputs=outputs)
     model.compile(loss=config['loss'],
                   optimizer='adam')
 
@@ -80,17 +81,17 @@ def ffn_model_multi_inputs(request):
     Simple multi-inputs feed-forward model with configurable data, loss function, output activation and dimension
     """
     config = request.param
-    input0 = tf.keras.Input(shape=config['X_train_multi_inputs'][0].shape[1:])
-    input1 = tf.keras.Input(shape=config['X_train_multi_inputs'][1].shape[1:])
+    input0 = keras.Input(shape=config['X_train_multi_inputs'][0].shape[1:])
+    input1 = keras.Input(shape=config['X_train_multi_inputs'][1].shape[1:])
 
-    x = tf.keras.layers.Flatten()(input0)
-    x = tf.keras.layers.Concatenate()([x, input1])
+    x = keras.layers.Flatten()(input0)
+    x = keras.layers.Concatenate()([x, input1])
 
-    x = tf.keras.layers.Dense(20, activation='relu')(x)
-    outputs = tf.keras.layers.Dense(config['output_dim'], activation=config['activation'])(x)
+    x = keras.layers.Dense(20, activation='relu')(x)
+    outputs = keras.layers.Dense(config['output_dim'], activation=config['activation'])(x)
     if config.get('squash_output', False):
-        outputs = tf.keras.layers.Reshape(())(outputs)
-    model = tf.keras.models.Model(inputs=[input0, input1], outputs=outputs)
+        outputs = keras.layers.Reshape(())(outputs)
+    model = keras.models.Model(inputs=[input0, input1], outputs=outputs)
     model.compile(loss=config['loss'],
                   optimizer='adam')
 
@@ -106,13 +107,13 @@ def ffn_model_subclass(request):
     """
     config = request.param
 
-    class Linear(Model):
+    class Linear(keras.Model):
 
         def __init__(self, output_dim, activation):
             super(Linear, self).__init__()
-            self.dense_1 = tf.keras.layers.Dense(20, activation='relu')
-            self.dense_2 = tf.keras.layers.Dense(20, activation='relu')
-            self.dense_3 = tf.keras.layers.Dense(output_dim, activation)
+            self.dense_1 = keras.layers.Dense(20, activation='relu')
+            self.dense_2 = keras.layers.Dense(20, activation='relu')
+            self.dense_3 = keras.layers.Dense(output_dim, activation)
 
         def call(self, inputs, mask=None):
             if mask is not None:
@@ -124,10 +125,10 @@ def call(self, inputs, mask=None):
             outputs = self.dense_3(x)
             return outputs
 
-    model = Linear(config['output_dim'], activation=config['activation'])
-    model.compile(loss=config['loss'],
-                  optimizer='adam')
-
+    model_input = keras.layers.Input(shape=config['X_train'].shape[1:])
+    model_output = Linear(config['output_dim'], activation=config['activation'])(model_input)
+    model = keras.Model(inputs=model_input, outputs=model_output)
+    model.compile(loss=config['loss'], optimizer='adam')
     model.fit(config['X_train'], config['y_train'], epochs=1, batch_size=256, verbose=1)
 
     return model
@@ -141,14 +142,15 @@ def ffn_model_subclass_list_input(request):
     """
     config = request.param
 
-    class Linear(Model):
+    class Linear(keras.Model):
 
         def __init__(self, output_dim, activation):
             super(Linear, self).__init__()
-            self.flat = tf.keras.layers.Flatten()
-            self.concat = tf.keras.layers.Concatenate()
-            self.dense_1 = tf.keras.layers.Dense(20, activation='relu')
-            self.dense_2 = tf.keras.layers.Dense(output_dim, activation)
+
+            self.flat = keras.layers.Flatten()
+            self.concat = keras.layers.Concatenate()
+            self.dense_1 = keras.layers.Dense(20, activation='relu')
+            self.dense_2 = keras.layers.Dense(output_dim, activation)
 
         def call(self, inputs):
             inp0 = self.flat(inputs[0])
@@ -158,12 +160,14 @@ def call(self, inputs):
             outputs = self.dense_2(x)
             return outputs
 
-    model = Linear(config['output_dim'], activation=config['activation'])
-    model.compile(loss=config['loss'],
-                  optimizer='adam')
-
+    inputs = [
+        keras.layers.Input(shape=config['X_train_multi_inputs'][0].shape[1:]),
+        keras.layers.Input(shape=config['X_train_multi_inputs'][1].shape[1:])
+    ]
+    output = Linear(config['output_dim'], activation=config['activation'])(inputs)
+    model = keras.Model(inputs=inputs, outputs=output)
+    model.compile(loss=config['loss'], optimizer='adam')
     model.fit(config['X_train_multi_inputs'], config['y_train'], epochs=1, batch_size=256, verbose=1)
-
     return model
 
 
@@ -174,18 +178,15 @@ def ffn_model_sequential(request):
     """
     config = request.param
     layers = [
-        tf.keras.layers.InputLayer(input_shape=config['X_train'].shape[1:]),
-        tf.keras.layers.Dense(20, activation='relu'),
-        tf.keras.layers.Dense(config['output_dim'], activation=config['activation'])
+        keras.layers.InputLayer(input_shape=config['X_train'].shape[1:]),
+        keras.layers.Dense(20, activation='relu'),
+        keras.layers.Dense(config['output_dim'], activation=config['activation'])
     ]
     if config.get('squash_output', False):
-        layers.append(tf.keras.layers.Reshape(()))
-    model = tf.keras.models.Sequential(layers)
-    model.compile(loss=config['loss'],
-                  optimizer='adam')
-
+        layers.append(keras.layers.Reshape(()))
+    model = keras.models.Sequential(layers)
+    model.compile(loss=config['loss'], optimizer='adam')
     model.fit(config['X_train'], config['y_train'], epochs=1, batch_size=256, verbose=1)
-
     return model
 
 
@@ -547,7 +548,7 @@ def test_integrated_gradients_binary_classification_layer_subclass(ffn_model_sub
                                                                    target):
     model = ffn_model_subclass
     if layer_nb is not None:
-        layer = model.layers[layer_nb]
+        layer = model.layers[1].layers[layer_nb]
     else:
         layer = None
 
@@ -614,14 +615,18 @@ def test_integrated_gradients_regression(ffn_model, method, baselines):
 def test_run_forward_from_layer(layer_nb,
                                 run_from_layer_inputs):
     # One layer ffn with all weights = 1.
-    inputs = tf.keras.Input(shape=(16,))
-    out = tf.keras.layers.Dense(8,
-                                kernel_initializer=tf.keras.initializers.Ones(),
-                                name='linear1')(inputs)
-    out = tf.keras.layers.Dense(1,
-                                kernel_initializer=tf.keras.initializers.Ones(),
-                                name='linear3')(out)
-    model = tf.keras.Model(inputs=inputs, outputs=out)
+    inputs = keras.Input(shape=(16,))
+    out = keras.layers.Dense(
+        8,
+        kernel_initializer=keras.initializers.Ones(),
+        name='linear1'
+    )(inputs)
+    out = keras.layers.Dense(
+        1,
+        kernel_initializer=keras.initializers.Ones(),
+        name='linear3'
+    )(out)
+    model = keras.Model(inputs=inputs, outputs=out)
 
     # Select layer
     layer = model.layers[layer_nb]
@@ -630,11 +635,11 @@ def test_run_forward_from_layer(layer_nb,
     dummy_input = np.zeros((1, 16))
 
     if run_from_layer_inputs:
-        x_layer = [tf.convert_to_tensor(np.ones((2,) + (layer.input_shape[1:])))]
+        x_layer = [tf.convert_to_tensor(np.ones((2,) + (layer.input.shape[1:])))]
         expected_shape = (2, 1)
         expected_values = 128
     else:
-        x_layer = tf.convert_to_tensor(np.ones((3,) + (layer.output_shape[1:])))
+        x_layer = tf.convert_to_tensor(np.ones((3,) + (layer.output.shape[1:])))
         expected_shape = (3, 1)
         expected_values = 8
 

diff --git a/alibi/explainers/tests/test_partial_dependence.py b/alibi/explainers/tests/test_partial_dependence.py
@@ -302,10 +302,10 @@ def test_grid_points_error(adult_data, use_int):
 def assert_feature_values_equal(exp_alibi: Explanation, exp_sklearn: Bunch):
     """ Compares feature values of `alibi` explanation and `sklearn` explanation. """
     if isinstance(exp_alibi.data['feature_names'][0], tuple):
-        for i in range(len(exp_sklearn['values'])):
-            assert np.allclose(exp_alibi.data['feature_values'][0][i], exp_sklearn['values'][i])
+        for i in range(len(exp_sklearn['grid_values'])):
+            assert np.allclose(exp_alibi.data['feature_values'][0][i], exp_sklearn['grid_values'][i])
     else:
-        assert np.allclose(exp_alibi.data['feature_values'][0], exp_sklearn['values'][0])
+        assert np.allclose(exp_alibi.data['feature_values'][0], exp_sklearn['grid_values'][0])
 
 
 def get_alibi_pd_explanation(predictor: BaseEstimator,