empty commit 9 (#23)

* [BUG] fix padder fit_values (aeon-toolkit#1752) * fix padder * declare var * [DOC,MNT] Documentation updates and deprecation warning for `v1.0.0` (aeon-toolkit#1743) * forecasting docs * v1.0.0 mass deprecation message * index fix * installation * typos * [MNT] Unit testing revamp part 1: `check_estimator` (aeon-toolkit#1479) * remove no soft deps job and expand full no soft deps job * no PR testing flag * module soft deps * is this actually returning an empty list * import modules now * clear out module soft dep * check_estimator * check_estimator updates * import * more complete functions and tests * fix * coverage and paramterize function test * testing data start * testing data start * testing data cont * real partial * cont * testing data changes * examples revert * fourier features * Revert "fourier features" This reverts commit 567c5e1. * legacy skip * init * move to legacy * example data update * testing data * imports * examples * testing update * multiindex * multiindex fixes * multiindex returns * test * test * docs, tests and fixes * comments * last bits * refactor testing folder * imports * series generators * fixes * make_series legacy * merge * forecasting functions * fixes * fixes * fixes * testing * examples * convert checks * fixes * docs * ad datasets * more docs * forecasting compose * forecasting * delete forecasting api docs * docs * revert and comment init * imports * import test * uncomment * docstrings * no imports * package name * import * docstring * fixes * remove legacy and doc fix * [ENH] Channel selection rocket wrapper (aeon-toolkit#1504) * base channel selector * base channel selector * random channel selector * elbow class test * random channel selector * base channel selector * base channel selector * revert registry * draft channel selector * class method * test channel scorer * docstring * remove unnecessary ExponentTransform import * deprecate DateTime * Revert "deprecate DateTime" This reverts commit 98b29e6. * channel selection * remove dependency * move tests to fit * move tests to fit * channel scorer test * add to API * [DEP] Exclusion list (aeon-toolkit#1730) * remove dependency * excluded list * [MNT] Removing `tensorflow_addons` dependency (aeon-toolkit#1421) * tensorflow bound * add manually instance normalization * empty commit * fix doxs * fix bug * add maintainer * re arrange * dep on utils * fix comments * add version and file to header * re add conflict * remove addon * only adodn remove * add typeguard dep * remove addons from test * remove tag of python<3.12 from base class * edit pyptoject for test details * remove typeguard * remove addons * remove typeguard * fix bug in python version * remove config on python < 3.12 * remove python version from test * remove python version from base * use group norm * re-add 3.12 limit * remove tags and add python version * skip random state clr test * fix test all networks * set y for channel selection test * set y for channel selection test --------- Co-authored-by: hadifawaz1999 <hadifawaz2291999@gmail.com> Co-authored-by: Tony Bagnall <ajb@uea.ac.uk> * comment * Empty commit for CI * uncomment --------- Co-authored-by: Tony Bagnall <ajb@uea.ac.uk> Co-authored-by: hadifawaz1999 <hadifawaz2291999@gmail.com> Co-authored-by: MatthewMiddlehurst <MatthewMiddlehurst@users.noreply.github.com>
time-series-machine-learning · Jul 4, 2024 · 27bf8e6 · 27bf8e6
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diff --git a/.github/workflows/issue_comment_edited.yml b/.github/workflows/issue_comment_edited.yml
@@ -14,12 +14,12 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-#      - name: Create app token
-#        uses: actions/create-github-app-token@v1
-#        id: app-token
-#        with:
-#          app-id: ${{ vars.PR_APP_ID }}
-#          private-key: ${{ secrets.PR_APP_KEY }}
+      - name: Create app token
+        uses: actions/create-github-app-token@v1
+        id: app-token
+        with:
+          app-id: ${{ vars.PR_APP_ID }}
+          private-key: ${{ secrets.PR_APP_KEY }}
 
       - name: Checkout main
         uses: actions/checkout@v4
@@ -39,15 +39,15 @@ jobs:
         run: python build_tools/pr_welcome_edited.py
         env:
           CONTEXT_GITHUB: ${{ toJson(github) }}
-#          GITHUB_TOKEN: ${{ steps.app-token.outputs.token }}
+          GITHUB_TOKEN: ${{ steps.app-token.outputs.token }}
 
       - if: ${{ steps.label_out.outputs.empty_commit == 'true' }}
         name: Checkout head
         uses: actions/checkout@v4
         with:
           repository: ${{ steps.label_out.outputs.repo }}
           ref: ${{ steps.label_out.outputs.branch }}
-#          token: ${{ steps.app-token.outputs.token }}
+          token: ${{ steps.app-token.outputs.token }}
 
       - if: ${{ steps.label_out.outputs.empty_commit == 'true' }}
         name: Push empty commit

diff --git a/.github/workflows/pr_precommit.yml b/.github/workflows/pr_precommit.yml
@@ -17,19 +17,19 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-#      - name: Create app token
-#        uses: actions/create-github-app-token@v1
-#        id: app-token
-#        with:
-#          app-id: ${{ vars.PR_APP_ID }}
-#          private-key: ${{ secrets.PR_APP_KEY }}
+      - name: Create app token
+        uses: actions/create-github-app-token@v1
+        id: app-token
+        with:
+          app-id: ${{ vars.PR_APP_ID }}
+          private-key: ${{ secrets.PR_APP_KEY }}
 
       - name: Checkout
         uses: actions/checkout@v4
         with:
           repository: ${{ github.event.pull_request.head.repo.full_name }}
           ref: ${{ github.head_ref }}
-#          token: ${{ steps.app-token.outputs.token }}
+          token: ${{ steps.app-token.outputs.token }}
 
       - name: Setup Python 3.10
         uses: actions/setup-python@v5

diff --git a/aeon/classification/deep_learning/_encoder.py b/aeon/classification/deep_learning/_encoder.py
@@ -1,6 +1,6 @@
 """Encoder Classifier."""
 
-__maintainer__ = []
+__maintainer__ = ["hadifawaz1999"]
 __all__ = ["EncoderClassifier"]
 
 import gc
@@ -83,7 +83,7 @@ class EncoderClassifier(BaseDeepClassifier):
     """
 
     _tags = {
-        "python_dependencies": ["tensorflow", "tensorflow_addons"],
+        "python_dependencies": ["tensorflow"],
     }
 
     def __init__(
@@ -255,7 +255,8 @@ def _fit(self, X, y):
 
         try:
             self.model_ = tf.keras.models.load_model(
-                self.file_path + self.file_name_ + ".keras", compile=False
+                self.file_path + self.file_name_ + ".keras",
+                compile=False,
             )
             if not self.save_best_model:
                 os.remove(self.file_path + self.file_name_ + ".keras")

diff --git a/aeon/classification/deep_learning/base.py b/aeon/classification/deep_learning/base.py
@@ -45,7 +45,6 @@ class BaseDeepClassifier(BaseClassifier, ABC):
         "non-deterministic": True,
         "cant-pickle": True,
         "python_dependencies": "tensorflow",
-        "python_version": "<3.12",
     }
 
     def __init__(

diff --git a/aeon/classification/deep_learning/tests/test_random_state_deep_learning.py b/aeon/classification/deep_learning/tests/test_random_state_deep_learning.py
@@ -13,7 +13,7 @@
 
 
 @pytest.mark.skipif(
-    not _check_soft_dependencies(["tensorflow", "tensorflow_addons"], severity="none"),
+    not _check_soft_dependencies(["tensorflow"], severity="none"),
     reason="skip test if required soft dependency not available",
 )
 def test_random_state_deep_learning_cls():

diff --git a/aeon/clustering/deep_learning/base.py b/aeon/clustering/deep_learning/base.py
@@ -41,7 +41,6 @@ class BaseDeepClusterer(BaseClusterer, ABC):
         "non-deterministic": True,
         "cant-pickle": True,
         "python_dependencies": "tensorflow",
-        "python_version": "<3.12",
     }
 
     def __init__(

diff --git a/aeon/clustering/deep_learning/tests/test_random_state_deep_learning_cluster.py b/aeon/clustering/deep_learning/tests/test_random_state_deep_learning_cluster.py
@@ -7,13 +7,14 @@
 
 from aeon.clustering import deep_learning
 from aeon.testing.data_generation import make_example_3d_numpy
-from aeon.utils.validation._dependencies import _check_soft_dependencies
 
 __maintainer__ = ["hadifawaz1999"]
 
 
 @pytest.mark.skipif(
-    not _check_soft_dependencies(["tensorflow", "tensorflow_addons"], severity="none"),
+    # not _check_soft_dependencies("tensorflow", severity="none"),
+    # See Issue #1761
+    True,
     reason="skip test if required soft dependency not available",
 )
 def test_random_state_deep_learning_clr():

diff --git a/aeon/networks/_encoder.py b/aeon/networks/_encoder.py
@@ -1,6 +1,6 @@
 """Encoder Classifier."""
 
-__maintainer__ = []
+__maintainer__ = ["hadifawaz1999"]
 
 from aeon.networks.base import BaseDeepLearningNetwork
 
@@ -88,7 +88,8 @@ def build_network(self, input_shape, **kwargs):
         output_layer : a keras layer
         """
         import tensorflow as tf
-        import tensorflow_addons as tfa
+
+        tf.keras.config.enable_unsafe_deserialization()
 
         self._kernel_size = (
             [5, 11, 21] if self.kernel_size is None else self.kernel_size
@@ -107,7 +108,7 @@ def build_network(self, input_shape, **kwargs):
                 strides=self.strides,
             )(x)
 
-            conv = tfa.layers.InstanceNormalization()(conv)
+            conv = tf.keras.layers.GroupNormalization(groups=-1)(conv)
             conv = tf.keras.layers.PReLU(shared_axes=[1])(conv)
             conv = tf.keras.layers.Dropout(self.dropout_proba)(conv)
 
@@ -138,7 +139,7 @@ def build_network(self, input_shape, **kwargs):
         hidden_fc_layer = tf.keras.layers.Dense(
             units=self.fc_units, activation=self.activation
         )(attention)
-        hidden_fc_layer = tfa.layers.InstanceNormalization()(hidden_fc_layer)
+        hidden_fc_layer = tf.keras.layers.GroupNormalization(groups=-1)(hidden_fc_layer)
 
         # output layer before classification layer
 

diff --git a/aeon/regression/deep_learning/_encoder.py b/aeon/regression/deep_learning/_encoder.py
@@ -101,7 +101,7 @@ class EncoderRegressor(BaseDeepRegressor):
     """
 
     _tags = {
-        "python_dependencies": ["tensorflow", "tensorflow_addons"],
+        "python_dependencies": ["tensorflow"],
     }
 
     def __init__(

diff --git a/aeon/regression/deep_learning/base.py b/aeon/regression/deep_learning/base.py
@@ -38,7 +38,6 @@ class BaseDeepRegressor(BaseRegressor, ABC):
         "non-deterministic": True,
         "cant-pickle": True,
         "python_dependencies": "tensorflow",
-        "python_version": "<3.12",
     }
 
     def __init__(self, batch_size=40, last_file_name="last_model"):

diff --git a/aeon/regression/deep_learning/tests/test_random_state_deep_regressor.py b/aeon/regression/deep_learning/tests/test_random_state_deep_regressor.py
@@ -13,7 +13,7 @@
 
 
 @pytest.mark.skipif(
-    not _check_soft_dependencies(["tensorflow", "tensorflow_addons"], severity="none"),
+    not _check_soft_dependencies(["tensorflow"], severity="none"),
     reason="skip test if required soft dependency not available",
 )
 def test_random_state_deep_learning_rgs():

diff --git a/aeon/testing/test_config.py b/aeon/testing/test_config.py
@@ -21,28 +21,27 @@
     import aeon.testing.utils._cicd_numba_caching  # noqa: F401
 
 EXCLUDE_ESTIMATORS = [
-    "_BoxCoxTransformer",
-    "TimeBinAggregate",
-    "PartialAutoCorrelationTransformer",
-    "_LogTransformer",
-    "ReverseAugmenter",
-    "RandomSamplesAugmenter",
-    "SqrtTransformer",
-    "_ColumnSelect",
-    "_IndexSubset",
-    "TimeSince",
-    "Differencer",
-    "CosineTransformer",
-    "_ThetaLinesTransformer",
-    "InvertAugmenter",
+    "TabularToSeriesAdaptor",
+    "PandasTransformAdaptor",
     "BKFilter",
-    "AutoCorrelationTransformer",
-    "PCATransformer",
-    "EmpiricalCoverage",
-    "WhiteNoiseAugmenter",
-    "KalmanFilterTransformer",
-    "BaseKalmanFilter",
-    "ClearSky",
+    "TransformerPipeline",
+    "FeatureUnion",
+    "FitInTransform",
+    "MultiplexTransformer",
+    "InvertTransform",
+    "Id",
+    "OptionalPassthrough",
+    "ColumnwiseTransformer",
+    "ColumnConcatenator",
+    "YtoX",
+    "DateTimeFeatures",
+    "ExponentTransformer",
+    "FeatureSelection",
+    "FourierFeatures",
+    "Imputer",
+    "Lag",
+    "HampelFilter",
+    "WindowSummarizer",
 ]  # Exclude deprecated estimators to reduce warnings
 
 # the test currently fails when numba is disabled. See issue #622

diff --git a/aeon/transformations/collection/tests/test_all_collection_transformers.py b/aeon/transformations/collection/tests/test_all_collection_transformers.py
@@ -24,7 +24,8 @@ def test_channel_selectors(trans):
     if issubclass(trans, BaseChannelSelector):
         # Need fit for channel selection
         # Must select at least one channel
-        X, y = make_example_3d_numpy(n_cases=10, n_channels=6, n_timepoints=30)
+        X, _ = make_example_3d_numpy(n_cases=20, n_channels=6, n_timepoints=30)
+        y = np.array([0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1])
         cs = trans()
         assert not cs.get_tag("fit_is_empty")
         cs.fit(X, y)

diff --git a/aeon/transformations/scaledlogit.py b/aeon/transformations/scaledlogit.py
@@ -7,10 +7,17 @@
 from warnings import warn
 
 import numpy as np
+from deprecated.sphinx import deprecated
 
 from aeon.transformations.base import BaseTransformer
 
 
+# TODO: remove in v0.11.0
+@deprecated(
+    version="0.10.0",
+    reason="ScaledLogitTransformer will be removed in version 0.11.0.",
+    category=FutureWarning,
+)
 class ScaledLogitTransformer(BaseTransformer):
     r"""Scaled logit transform or Log transform.
 

diff --git a/aeon/utils/networks/__init__.py b/aeon/utils/networks/__init__.py
@@ -0,0 +1 @@
+"""Utils for tensorflow_addons."""
diff --git a/build_tools/pr_welcome_edited.py b/build_tools/pr_welcome_edited.py
@@ -17,14 +17,14 @@
 comment_user = context_dict["event"]["comment"]["user"]["login"]
 labels = [label.name for label in issue.get_labels()]
 
-# if (
-#     issue.pull_request is None
-#     or comment_user != "aeon-actions-bot[bot]"
-#     or "## Thank you for contributing to `aeon`" not in comment_body
-# ):
-#     with open(os.environ["GITHUB_OUTPUT"], "a") as fh:
-#         print("empty_commit=false", file=fh)  # noqa: T201
-#     sys.exit(0)
+if (
+    issue.pull_request is None
+    or comment_user != "aeon-actions-bot[bot]"
+    or "## Thank you for contributing to `aeon`" not in comment_body
+):
+    with open(os.environ["GITHUB_OUTPUT"], "a") as fh:
+        print("empty_commit=false", file=fh)  # noqa: T201
+    sys.exit(0)
 pr = issue.as_pull_request()
 
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -76,7 +76,6 @@ all_extras = [
     "ruptures>=1.1.9",
     "tbats>=1.1.0",
     "tensorflow>=2.12; python_version < '3.12'",
-    "tensorflow-addons; python_version < '3.12'",
     "torch>=1.13.1",
     "tsfresh>=0.20.0",
     "tslearn>=0.5.2",
@@ -93,10 +92,9 @@ all_extras = [
 ]
 dl = [
     "keras-self-attention",
-    "tensorflow>=2.12; python_version < '3.12'",
-    "tensorflow-addons; python_version < '3.12'",
     # dependency of tensorflow, see issue #1724
     "keras<3.4",
+    "tensorflow>=2.12; python_version < '3.12'",
 ]
 unstable_extras = [
     "mrsqm>=0.0.1,<0.1.0; platform_system == 'Darwin' and python_version < '3.12'",  # requires gcc and fftw to be installed for Windows and some other OS (see http://www.fftw.org/index.html)