Update tensorflow requirement from !=2.6.0,!=2.6.1,<2.15.0,>=2.2.0 to >=2.2.0,!=2.6.0,!=2.6.1,<2.19.0 (#908)

* 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@v2.2.0...v2.18.0)

---
updated-dependencies:
- dependency-name: tensorflow
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <[email protected]>

* Updated upper and lower bound on tensorflow

* Fixed input shape for test_misc_tf

* Fixed activation serialization issue for test_saving_legacy.py

* Fixed preprocessor

* Fixed admd

* Fixed model cloning

* Fixed TFDataset index error

* Fixed trainable vars for spot the diff detector

* Fixed infer sigma flag in mmd

* Fixed classifier tf test

* Fixed kernes trainable variables

* Fixed llr tests

* Fixed saving and optimizer saving

* Included test entry in Makefile and updated ci

* Test all notebooks - to be reverted

* Removed python3.8 from ci

* Improved test command

* Fixed saving test models

* Fixed non-tensor inputs as positional arguments

* Fixed env variable in makefile

* Fixed optimizer tests, including legacy tests

* Fixed optional dependencies imports

* Fixed od_vae_adult.ipynb

* Fixed od_vae_cifar10.ipynb

* Fixed cd_model_unc_cifar10_wine.ipynb

* Fixed od_aegmm_kddcup.ipynb

* Fixed od_vae_kddcup.ipynb

* Fixed od_seq2seq_ecg.ipynb

* Fixed od_ae_cifar10.ipynb

* Fixed cd_distillation_cifar10.ipynb

* Fixed cd_ks_cifar10.ipynb

* Fixed cd_mmd_cifar10.ipynb

* Fixed od_llr_genome.ipynb

* Fixed od_llr_mnist.ipynb

* Fixed od_seq2seq_synth.ipynb

* Fixed cd_text_imdb.ipynb

* Fixed alibi_detect_deploy.ipynb

* Fixed ad_ae_cifar10.ipynb

* Reverted a few things in misc

* Fixed flake8 errors

* Reverted test all notebooks github actions

* Addressed PR comments

* Fixed flake8 error

---------

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]>

Author: dependabot[bot]

.github/workflows/ci.yml

@@ -34,7 +34,7 @@ jobs:
     strategy:
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11']
         pydantic-version: [ '1.10.15', '2.7.1' ]
         include: # Run windows tests on only one python version
           - os: windows-latest
@@ -71,10 +71,7 @@ jobs:
           limit-access-to-actor: true
 
       - name: Test with pytest
-        run: |
-          pytest --randomly-seed=0 alibi_detect
-          # Note: The pytest-randomly seed is fixed at 0 for now. Once the legacy np.random.seed(0)'s
-          # are removed from tests, this can be removed, allowing all tests to use random seeds.
+        run: make test
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3

Makefile

@@ -6,9 +6,12 @@ install-dev:
 install:
 	pip install -e .[all]
 
+# Note: The pytest-randomly seed is fixed at 0 for now. Once the legacy np.random.seed(0)'s
+# are removed from tests, this can be removed, allowing all tests to use random seeds.
 .PHONY: test
-test: ## Run all tests
-	python setup.py test
+test:
+	TF_USE_LEGACY_KERAS=1 pytest --randomly-seed=0 alibi_detect/utils/tests/test_saving_legacy.py
+	pytest --randomly-seed=0 --ignore=alibi_detect/utils/tests/test_saving_legacy.py alibi_detect
 
 .PHONY: lint
 lint: ## Check linting according to the flake8 configuration in setup.cfg
@@ -68,3 +71,4 @@ check_licenses:
 tox-env=default
 repl:
 	env COMMAND="python" tox -e $(tox-env)
+

alibi_detect/ad/tests/test_admd.py

@@ -42,7 +42,7 @@ def test_adv_md(adv_md_params):
     threshold, loss_type, threshold_perc, return_instance_score = adv_md_params
 
     # define ancillary model
-    layers = [tf.keras.layers.InputLayer(input_shape=(input_dim)),
+    layers = [tf.keras.layers.InputLayer(input_shape=(input_dim, )),
               tf.keras.layers.Dense(y.shape[1], activation=tf.nn.softmax)]
     distilled_model = tf.keras.Sequential(layers)
 

alibi_detect/cd/tensorflow/mmd.py

@@ -93,7 +93,7 @@ def __init__(
 
     def kernel_matrix(self, x: Union[np.ndarray, tf.Tensor], y: Union[np.ndarray, tf.Tensor]) -> tf.Tensor:
         """ Compute and return full kernel matrix between arrays x and y. """
-        k_xy = self.kernel(x, y, self.infer_sigma)
+        k_xy = self.kernel(x, y, infer_sigma=self.infer_sigma)
         k_xx = self.k_xx if self.k_xx is not None and self.update_x_ref is None else self.kernel(x, x)
         k_yy = self.kernel(y, y)
         kernel_mat = tf.concat([tf.concat([k_xx, k_xy], 1), tf.concat([tf.transpose(k_xy, (1, 0)), k_yy], 1)], 0)

alibi_detect/cd/tensorflow/preprocess.py

@@ -2,9 +2,11 @@
 
 import numpy as np
 import tensorflow as tf
+
 from alibi_detect.utils.tensorflow.prediction import (
-    predict_batch, predict_batch_transformer)
-from tensorflow.keras.layers import Dense, Flatten, Input, InputLayer
+    predict_batch, predict_batch_transformer, get_call_arg_mapping
+)
+from tensorflow.keras.layers import Dense, Flatten, Input, Lambda
 from tensorflow.keras.models import Model
 
 
@@ -34,7 +36,11 @@ def __init__(
                              'tf.keras.Sequential or tf.keras.Model `mlp`')
 
     def call(self, x: Union[np.ndarray, tf.Tensor, Dict[str, tf.Tensor]]) -> tf.Tensor:
-        x = self.input_layer(x)
+        if not isinstance(x, (np.ndarray, tf.Tensor)):
+            x = get_call_arg_mapping(self.input_layer, x)
+            x = self.input_layer(**x)
+        else:
+            x = self.input_layer(x)
         return self.mlp(x)
 
 
@@ -52,7 +58,7 @@ def __init__(
         if is_enc:
             self.encoder = encoder_net
         elif not is_enc and is_enc_dim:  # set default encoder
-            input_layer = InputLayer(input_shape=shape) if input_layer is None else input_layer
+            input_layer = Lambda(lambda x: x) if input_layer is None else input_layer
             input_dim = np.prod(shape)
             step_dim = int((input_dim - enc_dim) / 3)
             self.encoder = _Encoder(input_layer, enc_dim=enc_dim, step_dim=step_dim)
@@ -61,7 +67,11 @@ def __init__(
                              ' or tf.keras.Model `encoder_net`.')
 
     def call(self, x: Union[np.ndarray, tf.Tensor, Dict[str, tf.Tensor]]) -> tf.Tensor:
-        return self.encoder(x)
+        if not isinstance(x, (np.ndarray, tf.Tensor)):
+            x = get_call_arg_mapping(self.encoder, x)
+            return self.encoder(**x)
+        else:
+            return self.encoder(x)
 
 
 class HiddenOutput(tf.keras.Model):
@@ -73,7 +83,7 @@ def __init__(
             flatten: bool = False
     ) -> None:
         super().__init__()
-        if input_shape and not model.inputs:
+        if input_shape and not (hasattr(model, 'inputs') and model.inputs):
             inputs = Input(shape=input_shape)
             model.call(inputs)
         else:

alibi_detect/cd/tensorflow/spot_the_diff.py

@@ -170,9 +170,23 @@ def __init__(self, kernel: tf.keras.Model, x_ref: np.ndarray, initial_diffs: np.
             self.config = {'kernel': kernel, 'x_ref': x_ref, 'initial_diffs': initial_diffs}
             self.kernel = kernel
             self.mean = tf.convert_to_tensor(x_ref.mean(0))
-            self.diffs = tf.Variable(initial_diffs, dtype=np.float32)
-            self.bias = tf.Variable(tf.zeros((1,)))
-            self.coeffs = tf.Variable(tf.zeros((len(initial_diffs),)))
+
+            self.diffs = self.add_weight(
+                shape=initial_diffs.shape,
+                initializer=tf.keras.initializers.Constant(initial_diffs),
+                dtype=tf.float32,
+                trainable=True
+            )
+            self.bias = self.add_weight(
+                shape=(1,),
+                initializer="zeros",
+                trainable=True,
+            )
+            self.coeffs = self.add_weight(
+                shape=(len(initial_diffs),),
+                initializer="zeros",
+                trainable=True,
+            )
 
         def call(self, x: tf.Tensor) -> tf.Tensor:
             k_xtl = self.kernel(x, self.mean + self.diffs)

alibi_detect/cd/tensorflow/tests/test_classifier_tf.py

@@ -2,7 +2,7 @@
 import numpy as np
 import pytest
 import tensorflow as tf
-from tensorflow.keras.layers import Dense, Input
+from tensorflow.keras.layers import Dense, Input, Softmax
 from typing import Union
 from alibi_detect.cd.tensorflow.classifier import ClassifierDriftTF
 
@@ -14,7 +14,7 @@ def mymodel(shape, softmax: bool = True):
     x = Dense(20, activation=tf.nn.relu)(x_in)
     x = Dense(2)(x)
     if softmax:
-        x = tf.nn.softmax(x)
+        x = Softmax()(x)
     return tf.keras.models.Model(inputs=x_in, outputs=x)
 
 

alibi_detect/od/tests/test_llr.py

@@ -2,7 +2,7 @@
 import numpy as np
 import pytest
 import tensorflow as tf
-from tensorflow.keras.layers import Dense, Input, LSTM
+from tensorflow.keras.layers import Dense, Input, LSTM, CategoryEncoding
 from alibi_detect.od import LLR
 from alibi_detect.version import __version__
 
@@ -48,7 +48,7 @@ def test_llr(llr_params):
 
     # define model and detector
     inputs = Input(shape=(shape[-1] - 1,), dtype=tf.int32)
-    x = tf.one_hot(tf.cast(inputs, tf.int32), input_dim)
+    x = CategoryEncoding(num_tokens=input_dim, output_mode="one_hot")(inputs)
     x = LSTM(hidden_dim, return_sequences=True)(x)
     logits = Dense(input_dim, activation=None)(x)
     model = tf.keras.Model(inputs=inputs, outputs=logits)

alibi_detect/saving/_tensorflow/tests/test_saving_tf.py

@@ -15,26 +15,18 @@
 backend = param_fixture("backend", ['tensorflow'])
 
 
-# Note: The full save/load functionality of optimizers (inc. validation) is tested in test_save_classifierdrift.
-@pytest.mark.skipif(version.parse(tf.__version__) < version.parse('2.11.0'),
-                    reason="Skipping since tensorflow < 2.11.0")
-@parametrize('legacy', [True, False])
-def test_load_optimizer_object_tf2pt11(legacy, backend):
+def test_load_optimizer_object_tf2pt11(backend):
     """
-    Test the _load_optimizer_config with a tensorflow optimizer config. Only run if tensorflow>=2.11.
-
-    Here we test that "new" and legacy optimizers can be saved/laoded. We expect the returned optimizer to be an
-    instantiated `tf.keras.optimizers.Optimizer` object. Also test that the loaded optimizer can be saved.
+    Test the _load_optimizer_config with a tensorflow optimizer config. Only run if tensorflow>=2.16.
     """
     class_name = 'Adam'
-    class_str = class_name if legacy else 'Custom>' + class_name  # Note: see discussion in #739 re 'Custom>'
-    learning_rate = np.float32(0.01)  # Set as float32 since this is what _save_optimizer_config returns
-    epsilon = np.float32(1e-7)
+    learning_rate = 0.01
+    epsilon = 1e-7
     amsgrad = False
 
     # Load
     cfg_opt = {
-        'class_name': class_str,
+        'class_name': class_name,
         'config': {
             'name': class_name,
             'learning_rate': learning_rate,
@@ -45,10 +37,7 @@ def test_load_optimizer_object_tf2pt11(legacy, backend):
     optimizer = _load_optimizer_config(cfg_opt, backend=backend)
     # Check optimizer
     SupportedOptimizer.validate_optimizer(optimizer, {'backend': 'tensorflow'})
-    if legacy:
-        assert isinstance(optimizer, tf.keras.optimizers.legacy.Optimizer)
-    else:
-        assert isinstance(optimizer, tf.keras.optimizers.Optimizer)
+    assert isinstance(optimizer, tf.keras.optimizers.Optimizer)
     assert type(optimizer).__name__ == class_name
     assert optimizer.learning_rate == learning_rate
     assert optimizer.epsilon == epsilon
@@ -58,7 +47,10 @@ def test_load_optimizer_object_tf2pt11(legacy, backend):
     cfg_saved = _save_optimizer_config(optimizer)
     # Compare to original config
     for key, value in cfg_opt['config'].items():
-        assert value == cfg_saved['config'][key]
+        if isinstance(value, float):
+            assert np.isclose(value, cfg_saved['config'][key])
+        else:
+            assert value == cfg_saved['config'][key]
 
 
 @pytest.mark.skipif(version.parse(tf.__version__) >= version.parse('2.11.0'),

alibi_detect/saving/tests/models.py

@@ -3,6 +3,7 @@
 
 import numpy as np
 import tensorflow as tf
+from tensorflow.keras.activations import relu, softmax
 import torch
 import torch.nn as nn
 from sklearn.ensemble import RandomForestClassifier
@@ -46,7 +47,7 @@ def encoder_model(backend, current_cases):
         model = tf.keras.Sequential(
                [
                    tf.keras.layers.InputLayer(input_shape=(input_dim,)),
-                   tf.keras.layers.Dense(5, activation=tf.nn.relu),
+                   tf.keras.layers.Dense(5, activation=relu),
                    tf.keras.layers.Dense(LATENT_DIM, activation=None)
                ]
            )
@@ -73,7 +74,7 @@ def encoder_dropout_model(backend, current_cases):
         model = tf.keras.Sequential(
                [
                    tf.keras.layers.InputLayer(input_shape=(input_dim,)),
-                   tf.keras.layers.Dense(5, activation=tf.nn.relu),
+                   tf.keras.layers.Dense(5, activation=relu),
                    tf.keras.layers.Dropout(0.0),  # 0.0 to ensure determinism
                    tf.keras.layers.Dense(LATENT_DIM, activation=None)
                ]
@@ -191,7 +192,7 @@ def classifier_model(backend, current_cases):
         model = tf.keras.Sequential(
                [
                    tf.keras.layers.InputLayer(input_shape=(input_dim,)),
-                   tf.keras.layers.Dense(2, activation=tf.nn.softmax),
+                   tf.keras.layers.Dense(2, activation=softmax),
                ]
            )
     elif backend in ('pytorch', 'keops'):
@@ -240,7 +241,7 @@ def nlp_embedding_and_tokenizer(model_name, max_len, uae, backend):
         except (OSError, HTTPError):
             pytest.skip(f"Problem downloading {model_name} from huggingface.co")
         if uae:
-            x_emb = embedding(tokens)
+            x_emb = embedding(tokens=tokens)
             shape = (x_emb.shape[1],)
             embedding = UAE_tf(input_layer=embedding, shape=shape, enc_dim=enc_dim)
     elif backend == 'pt':

alibi_detect/utils/missing_optional_dependency.py

@@ -32,6 +32,7 @@
     "prophet": 'prophet',
     "tensorflow_probability": 'tensorflow',
     "tensorflow": 'tensorflow',
+    "keras": 'tensorflow',
     "torch": 'torch',
     "pytorch": 'torch',
     "keops": 'keops',

alibi_detect/utils/tensorflow/data.py

@@ -14,6 +14,9 @@ def __init__(
         self.shuffle = shuffle
 
     def __getitem__(self, idx: int) -> Union[Tuple[Indexable, ...], Indexable]:
+        if idx >= self.__len__():
+            raise IndexError("Index out of bounds.")
+
         istart, istop = idx * self.batch_size, (idx + 1) * self.batch_size
         output = tuple(indexable[istart:istop] for indexable in self.indexables)
         return output if len(output) > 1 else output[0]

alibi_detect/utils/tensorflow/kernels.py

@@ -1,5 +1,4 @@
 import tensorflow as tf
-import numpy as np
 from . import distance
 from typing import Optional, Union, Callable
 from scipy.special import logit
@@ -59,11 +58,19 @@ def __init__(
         init_sigma_fn = sigma_median if init_sigma_fn is None else init_sigma_fn
         self.config = {'sigma': sigma, 'trainable': trainable, 'init_sigma_fn': init_sigma_fn}
         if sigma is None:
-            self.log_sigma = tf.Variable(np.empty(1), dtype=tf.keras.backend.floatx(), trainable=trainable)
+            self.log_sigma = self.add_weight(
+                shape=(1,),
+                initializer='zeros',
+                trainable=trainable
+            )
             self.init_required = True
         else:
             sigma = tf.cast(tf.reshape(sigma, (-1,)), dtype=tf.keras.backend.floatx())  # [Ns,]
-            self.log_sigma = tf.Variable(tf.math.log(sigma), trainable=trainable)
+            self.log_sigma = self.add_weight(
+                shape=(sigma.shape[0],),
+                initializer=tf.keras.initializers.Constant(tf.math.log(sigma)),
+                trainable=trainable
+            )
             self.init_required = False
         self.init_sigma_fn = init_sigma_fn
         self.trainable = trainable

alibi_detect/utils/tensorflow/misc.py

@@ -1,4 +1,6 @@
+import keras
 import tensorflow as tf
+from tensorflow.keras.models import Sequential, Model
 
 
 def zero_diag(mat: tf.Tensor) -> tf.Tensor:
@@ -85,13 +87,19 @@ def subset_matrix(mat: tf.Tensor, inds_0: tf.Tensor, inds_1: tf.Tensor) -> tf.Te
     return subbed_rows_cols
 
 
-def clone_model(model: tf.keras.Model) -> tf.keras.Model:
+def clone_model(model: Model) -> Model:
     """ Clone a sequential, functional or subclassed tf.keras.Model. """
-    try:  # sequential or functional model
+    conditions = [
+        isinstance(model, Sequential),
+        isinstance(model, keras.src.models.functional.Functional)
+    ]
+
+    if any(conditions):
         return tf.keras.models.clone_model(model)
-    except ValueError:  # subclassed model
+    else:
         try:
             config = model.get_config()
         except NotImplementedError:
             config = {}
+
         return model.__class__.from_config(config)