Merge branch 'dev'

.github/workflows/pre-commit.yaml

@@ -7,5 +7,5 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
     - uses: pre-commit/action@v3.0.1

.github/workflows/release.yaml

@@ -12,7 +12,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.x
     - name: Install pypa/build
@@ -24,7 +24,7 @@ jobs:
     - name: Build a binary wheel and a source tarball
       run: python3 -m build
     - name: Store the distribution packages
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: python-package-distributions
         path: dist/
@@ -42,7 +42,7 @@ jobs:
       id-token: write  # IMPORTANT: mandatory for trusted publishing
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: python-package-distributions
         path: dist/
@@ -63,12 +63,12 @@ jobs:
 
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: python-package-distributions
         path: dist/
     - name: Sign the dists with Sigstore
-      uses: sigstore/gh-action-sigstore-python@v1.2.3
+      uses: sigstore/gh-action-sigstore-python@v3.0.0
       with:
         inputs: >-
           ./dist/*.tar.gz
@@ -107,7 +107,7 @@ jobs:
 
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: python-package-distributions
         path: dist/

.github/workflows/test.yaml

@@ -7,7 +7,7 @@ jobs:
 
     strategy:
       matrix:
-        platform: [ubuntu-latest, macos-latest, windows-latest]
+        platform: [ubuntu-latest, windows-latest]
         python-version: [3.7, 3.8, 3.9, '3.10', '3.11']
 
     runs-on: ${{ matrix.platform }}

CHANGELOG.md

@@ -1,3 +1,13 @@
+## v0.2.0 (2024-09-13)
+
+### Feat
+
+- allows to filter out patches containing NaN values
+
+### Fix
+
+- disable NaN filtering per default to ensure errors if they are unexpected
+
 ## v0.1.2 (2024-02-19)
 
 ## v0.1.1 (2024-02-19)

src/tensorflow_time_series_dataset/factory.py

@@ -4,7 +4,7 @@
 # author  : Marcel Arpogaus <marcel dot arpogaus at gmail dot com>
 #
 # created : 2022-01-07 09:02:38 (Marcel Arpogaus)
-# changed : 2024-02-19 12:57:42 (Marcel Arpogaus)
+# changed : 2024-09-12 16:21:24 (Marcel Arpogaus)
 # DESCRIPTION #################################################################
 # ...
 # LICENSE #####################################################################
@@ -53,6 +53,7 @@ class WindowedTimeSeriesDatasetFactory:
         "cycle_length": 1,
         "shuffle_buffer_size": 1000,
         "cache": True,
+        "filter_nans": False,
     }
 
     def __init__(

src/tensorflow_time_series_dataset/pipeline/patch_generator.py

@@ -4,7 +4,7 @@
 # author  : Marcel Arpogaus <marcel dot arpogaus at gmail dot com>
 #
 # created : 2022-01-07 09:02:38 (Marcel Arpogaus)
-# changed : 2024-02-19 12:52:06 (Marcel Arpogaus)
+# changed : 2024-09-12 15:52:32 (Marcel Arpogaus)
 # DESCRIPTION #################################################################
 # ...
 # LICENSE #####################################################################
@@ -35,20 +35,25 @@ class PatchGenerator:
         The size of each patch.
     shift : int
         The shift between patches.
+    filter_nans : int
+        Apply a filter function to drop patches containing NaN values.
 
     """
 
-    def __init__(self, window_size: int, shift: int) -> None:
+    def __init__(self, window_size: int, shift: int, filter_nans: bool) -> None:
         """Parameters
         ----------
         window_size : int
             The size of each patch.
         shift : int
             The shift between patches.
+        filter_nans : int
+            If True, apply a filter function to drop patches containing NaN values.
 
         """
         self.window_size: int = window_size
         self.shift: int = shift
+        self.filter_nans: bool = filter_nans
 
     def __call__(self, data: tf.Tensor) -> tf.data.Dataset:
         """Converts input data into patches of provided window size.
@@ -71,6 +76,18 @@ def __call__(self, data: tf.Tensor) -> tf.data.Dataset:
             size=self.window_size,
             shift=self.shift,
             drop_remainder=True,
-        ).flat_map(lambda sub: sub.batch(self.window_size, drop_remainder=True))
+        )
+
+        def sub_to_patch(sub):
+            return sub.batch(self.window_size, drop_remainder=True)
+
+        data_set = data_set.flat_map(sub_to_patch)
+
+        if self.filter_nans:
+
+            def filter_func(patch):
+                return tf.reduce_all(tf.logical_not(tf.math.is_nan(patch)))
+
+            data_set = data_set.filter(filter_func)
 
         return data_set

src/tensorflow_time_series_dataset/pipeline/windowed_time_series_pipeline.py

@@ -4,7 +4,7 @@
 # author  : Marcel Arpogaus <marcel dot arpogaus at gmail dot com>
 #
 # created : 2022-01-07 09:02:38 (Marcel Arpogaus)
-# changed : 2024-02-19 12:53:06 (Marcel Arpogaus)
+# changed : 2024-09-12 16:01:27 (Marcel Arpogaus)
 # DESCRIPTION #################################################################
 # ...
 # LICENSE #####################################################################
@@ -64,6 +64,8 @@ class WindowedTimeSeriesPipeline:
         Whether to cache the dataset in memory or to a specific file.
     drop_remainder : bool
         Whether to drop the remainder of batches that are not equal to the batch size.
+    filter_nans : int
+        Apply a filter function to drop patches containing NaN values.
 
     Raises
     ------
@@ -85,6 +87,7 @@ def __init__(
         shuffle_buffer_size: int,
         cache: Union[str, bool],
         drop_remainder: bool,
+        filter_nans: bool,
     ) -> None:
         assert (
             prediction_size > 0
@@ -101,6 +104,7 @@ def __init__(
         self.shuffle_buffer_size = shuffle_buffer_size
         self.cache = cache
         self.drop_remainder = drop_remainder
+        self.filter_nans = filter_nans
 
     def __call__(self, ds: Dataset) -> Dataset:
         """Applies the pipeline operations to the given dataset.
@@ -117,7 +121,7 @@ def __call__(self, ds: Dataset) -> Dataset:
 
         """
         ds = ds.interleave(
-            PatchGenerator(self.window_size, self.shift),
+            PatchGenerator(self.window_size, self.shift, self.filter_nans),
             cycle_length=self.cycle_length,
             num_parallel_calls=tf.data.experimental.AUTOTUNE,
         )

tests/test_pipleine.py

@@ -34,7 +34,7 @@ def patched_dataset(
 
     ds = tf.data.Dataset.from_tensors(df[sorted(used_cols)])
     ds = ds.interleave(
-        PatchGenerator(window_size=window_size, shift=shift),
+        PatchGenerator(window_size=window_size, shift=shift, filter_nans=False),
         num_parallel_calls=tf.data.experimental.AUTOTUNE,
     )
     return ds, df, window_size, shift
@@ -53,7 +53,7 @@ def test_patch_generator(time_series_df, window_size, shift):
 
     ds = tf.data.Dataset.from_tensors(df)
     ds_patched = ds.interleave(
-        PatchGenerator(window_size=window_size, shift=shift),
+        PatchGenerator(window_size=window_size, shift=shift, filter_nans=False),
         num_parallel_calls=tf.data.experimental.AUTOTUNE,
     )
     for i, patch in enumerate(ds_patched.as_numpy_iterator()):
@@ -65,6 +65,36 @@ def test_patch_generator(time_series_df, window_size, shift):
     assert i + 1 == patches, "Not enough patches"
 
 
+@pytest.mark.parametrize("window_size,shift", [(2 * 48, 48), (48 + 1, 1)])
+def test_patch_generator_filter_nans(time_series_df, window_size, shift):
+    df = time_series_df.set_index("date_time")
+    # randomly set 20% of elemnts in the dataset for nans
+
+    df = time_series_df.set_index("date_time")
+    nan_mask = np.random.default_rng(1).uniform(0, 1, df.shape) < 0.01
+    df[nan_mask] = np.nan
+
+    initial_size = window_size - shift
+    data_size = df.index.size - initial_size
+    patches = data_size // shift
+
+    expected_shape = (window_size, len(df.columns))
+
+    ds = tf.data.Dataset.from_tensors(df)
+    ds_patched = ds.interleave(
+        PatchGenerator(window_size=window_size, shift=shift, filter_nans=True),
+        num_parallel_calls=tf.data.experimental.AUTOTUNE,
+    )
+    for i, patch in enumerate(ds_patched.as_numpy_iterator()):
+        assert patch.shape == expected_shape, "Wrong shape"
+        x1 = patch[0, 0]
+        idx = int(x1 % 1e5)
+        expected_values = df.iloc[idx : idx + window_size]
+        assert np.all(patch == expected_values), "Patch contains wrong data"
+        assert not np.isnan(patch).any(), "Patch contains NaNs."
+    assert i + 1 < patches, "No patches have been dropped"
+
+
 @pytest.mark.parametrize("window_size,shift", [(2 * 48, 48), (48 + 1, 1)])
 def test_patch_generator_groupby(groupby_dataset, window_size, shift):
     ds, df = groupby_dataset
@@ -78,7 +108,7 @@ def test_patch_generator_groupby(groupby_dataset, window_size, shift):
     expected_shape = (window_size, len(columns))
 
     ds_patched = ds.interleave(
-        PatchGenerator(window_size=window_size, shift=shift),
+        PatchGenerator(window_size=window_size, shift=shift, filter_nans=True),
         num_parallel_calls=tf.data.experimental.AUTOTUNE,
     )
 
@@ -166,7 +196,9 @@ def test_windowed_time_series_pipeline(
         batch_size=batch_size,
         drop_remainder=True,
     )
-    pipeline_kwargs = dict(cycle_length=1, shuffle_buffer_size=100, cache=True)
+    pipeline_kwargs = dict(
+        cycle_length=1, shuffle_buffer_size=100, cache=True, filter_nans=False
+    )
 
     with validate_args(
         history_size=history_size,
@@ -209,7 +241,9 @@ def test_windowed_time_series_pipeline_groupby(
         batch_size=batch_size,
         drop_remainder=False,
     )
-    pipeline_kwargs = dict(cycle_length=len(ids), shuffle_buffer_size=1000, cache=True)
+    pipeline_kwargs = dict(
+        cycle_length=len(ids), shuffle_buffer_size=1000, cache=True, filter_nans=False
+    )
 
     with validate_args(
         history_size=history_size,