Repository: aeon-toolkit/aeon (python)

Issue:
[MNT] Use MacOS for `examples/` workflow
### Describe the issue

MacOS is generally faster for our CI, we should try running our examples workflow using it and see if there is a speed up.

### Suggest a potential alternative/fix

Swap over to MacOS runners in the example CI. Evaluate whether this is faster than the current Linux runner.

### Additional context

See https://github.com/aeon-toolkit/aeon/pull/2390, these are the three files that will have to change (at least)

Pull request:
[MNT] Use MacOS for examples/ workflow
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#### Reference Issues/PRs
Fixes #2665
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#### What does this implement/fix? Explain your changes.
- Changed the os in the workflows for `pr_examples` and `periodic_tests` to `macos-latest`.
- Changed the workflow to install `bash 5.x` before running `run_examples.sh`
as lastpipe isnt available in `bash 3.2` which is in the github runner image for `macos-latest` (https://github.com/actions/runner-images/blob/main/images/macos/macos-15-arm64-Readme.md).
- Also added a step to install `boost` and `esig` before the `run_examples.sh` as `esig` is not installed on Darwin since its excluded in `pyproject.toml`.


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#### Does your contribution introduce a new dependency? If yes, which one?
No
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Patch:
diff --git a/.github/utilities/run_examples.sh b/.github/utilities/run_examples.sh
index fd7376c0..fdbcdb90 100755
--- a/.github/utilities/run_examples.sh
+++ b/.github/utilities/run_examples.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/opt/homebrew/bin/bash
 
 # Script to run all example notebooks.
 set -euxo pipefail
@@ -23,6 +23,7 @@ if [ "$1" = true ]; then
     "examples/classification/shapelet_based.ipynb"
     "examples/classification/convolution_based.ipynb"
     "examples/similarity_search/code_speed.ipynb"
+    "examples/transformations/signature_method.ipynb"
 
   )
 fi
@@ -32,7 +33,7 @@ notebooks=()
 runtimes=()
 
 # Loop over all notebooks in the examples directory.
-find "examples/" -name "*.ipynb" -print0 |
+find "examples" -name "*.ipynb" -print0 |
   while IFS= read -r -d "" notebook; do
     # Skip notebooks in the excluded list.
     if printf "%s\0" "${excluded[@]}" | grep -Fxqz -- "$notebook"; then
diff --git a/.github/workflows/pr_examples.yml b/.github/workflows/pr_examples.yml
index adc26631..2d7ea6f1 100644
--- a/.github/workflows/pr_examples.yml
+++ b/.github/workflows/pr_examples.yml
@@ -19,12 +19,17 @@ concurrency:
 
 jobs:
   run-notebook-examples:
-    runs-on: ubuntu-24.04
+    runs-on: macos-14
 
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
+      - name: Install latest version of bash
+        run: |
+          brew install bash
+          /opt/homebrew/bin/bash --version
+
       - name: Setup Python 3.10
         uses: actions/setup-python@v5
         with:
diff --git a/.github/workflows/pr_precommit.yml b/.github/workflows/pr_precommit.yml
index a74e8b12..809803fe 100644
--- a/.github/workflows/pr_precommit.yml
+++ b/.github/workflows/pr_precommit.yml
@@ -37,7 +37,7 @@ jobs:
           python-version: "3.10"
 
       - name: Get changed files
-        uses: tj-actions/changed-files@v46.0.1
+        uses: tj-actions/changed-files@v46.0.3
         id: changed-files
 
       - name: List changed files
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 854da8df..b09f5f22 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -29,7 +29,7 @@ repos:
         args: [ "--create", "--python-folders", "aeon" ]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.0
+    rev: v0.11.2
     hooks:
       - id: ruff
         args: [ "--fix"]
diff --git a/aeon/classification/feature_based/_catch22.py b/aeon/classification/feature_based/_catch22.py
index bec5deff..26a56d0a 100644
--- a/aeon/classification/feature_based/_catch22.py
+++ b/aeon/classification/feature_based/_catch22.py
@@ -43,8 +43,11 @@ class Catch22Classifier(BaseClassifier):
         true. If a List of specific features to extract is provided, "Mean" and/or
         "StandardDeviation" must be added to the List to extract these features.
     outlier_norm : bool, optional, default=False
-        Normalise each series during the two outlier Catch22 features, which can take a
-        while to process for large values.
+        If True, each time series is normalized during the computation of the two
+        outlier Catch22 features, which can take a while to process for large values
+        as it depends on the max value in the timseries. Note that this parameter
+        did not exist in the original publication/implementation as they used time
+        series that were already normalized.
     replace_nans : bool, default=True
         Replace NaN or inf values from the Catch22 transform with 0.
     use_pycatch22 : bool, default=False
@@ -136,7 +139,7 @@ class Catch22Classifier(BaseClassifier):
         self,
         features="all",
         catch24=True,
-        outlier_norm=False,
+        outlier_norm=True,
         replace_nans=True,
         use_pycatch22=False,
         estimator=None,
diff --git a/aeon/clustering/feature_based/_catch22.py b/aeon/clustering/feature_based/_catch22.py
index 33f0b79b..30fad7ff 100644
--- a/aeon/clustering/feature_based/_catch22.py
+++ b/aeon/clustering/feature_based/_catch22.py
@@ -42,9 +42,12 @@ class Catch22Clusterer(BaseClusterer):
         Extract the mean and standard deviation as well as the 22 Catch22 features if
         true. If a List of specific features to extract is provided, "Mean" and/or
         "StandardDeviation" must be added to the List to extract these features.
-    outlier_norm : bool, optional, default=False
-        Normalise each series during the two outlier Catch22 features, which can take a
-        while to process for large values.
+        outlier_norm : bool, optional, default=False
+            If True, each time series is normalized during the computation of the two
+            outlier Catch22 features, which can take a while to process for large values
+            as it depends on the max value in the timseries. Note that this parameter
+            did not exist in the original publication/implementation as they used
+            time series that were already normalized.
     replace_nans : bool, default=True
         Replace NaN or inf values from the Catch22 transform with 0.
     use_pycatch22 : bool, default=False
@@ -103,7 +106,7 @@ class Catch22Clusterer(BaseClusterer):
         self,
         features="all",
         catch24=True,
-        outlier_norm=False,
+        outlier_norm=True,
         replace_nans=True,
         use_pycatch22=False,
         estimator=None,
diff --git a/aeon/regression/feature_based/_catch22.py b/aeon/regression/feature_based/_catch22.py
index f669cbe8..1ab04ee6 100644
--- a/aeon/regression/feature_based/_catch22.py
+++ b/aeon/regression/feature_based/_catch22.py
@@ -43,8 +43,11 @@ class Catch22Regressor(BaseRegressor):
         True. If a List of specific features to extract is provided, "Mean" and/or
         "StandardDeviation" must be added to the List to extract these features.
     outlier_norm : bool, optional, default=False
-        Normalise each series during the two outlier Catch22 features, which can take a
-        while to process for large values.
+        If True, each time series is normalized during the computation of the two
+        outlier Catch22 features, which can take a while to process for large values
+        as it depends on the max value in the timseries. Note that this parameter
+        did not exist in the original publication/implementation as they used time
+        series that were already normalized.
     replace_nans : bool, optional, default=True
         Replace NaN or inf values from the Catch22 transform with 0.
     use_pycatch22 : bool, optional, default=False
@@ -110,7 +113,7 @@ class Catch22Regressor(BaseRegressor):
         self,
         features="all",
         catch24=True,
-        outlier_norm=False,
+        outlier_norm=True,
         replace_nans=True,
         use_pycatch22=False,
         estimator=None,
diff --git a/aeon/transformations/collection/base.py b/aeon/transformations/collection/base.py
index 013001d8..a3664eb4 100644
--- a/aeon/transformations/collection/base.py
+++ b/aeon/transformations/collection/base.py
@@ -64,8 +64,8 @@ class BaseCollectionTransformer(BaseCollectionEstimator, BaseTransformer):
         X : np.ndarray or list
             Data to fit transform to, of valid collection type. Input data,
             any number of channels, equal length series of shape ``(
-            n_cases, n_channels, n_timepoints)`` or list of numpy arrays (any number
-            of channels, unequal length series) of shape ``[n_cases]``, 2D np.array
+            n_cases, n_channels, n_timepoints)`` or list of numpy arrays (number
+            of channels, series length) of shape ``[n_cases]``, 2D np.array
             ``(n_channels, n_timepoints_i)``, where ``n_timepoints_i`` is length of
             series ``i``. Other types are allowed and converted into one of the above.
 
@@ -118,8 +118,8 @@ class BaseCollectionTransformer(BaseCollectionEstimator, BaseTransformer):
         X : np.ndarray or list
             Data to fit transform to, of valid collection type. Input data,
             any number of channels, equal length series of shape ``(
-            n_cases, n_channels, n_timepoints)`` or list of numpy arrays (any number
-            of channels, unequal length series) of shape ``[n_cases]``, 2D np.array
+            n_cases, n_channels, n_timepoints)`` or list of numpy arrays (number
+            of channels, series length) of shape ``[n_cases]``, 2D np.array
             ``(n_channels, n_timepoints_i)``, where ``n_timepoints_i`` is length of
             series ``i``. Other types are allowed and converted into one of the above.
 
@@ -171,10 +171,10 @@ class BaseCollectionTransformer(BaseCollectionEstimator, BaseTransformer):
         ----------
         X : np.ndarray or list
             Data to fit transform to, of valid collection type. Input data,
-            any number of channels, equal length series of shape ``(n_cases,
-            n_channels, n_timepoints)`` or list of numpy arrays (any number of
-            channels, unequal length series) of shape ``[n_cases]``, 2D np.array ``(
-            n_channels, n_timepoints_i)``, where ``n_timepoints_i`` is length of
+            any number of channels, equal length series of shape ``(
+            n_cases, n_channels, n_timepoints)`` or list of numpy arrays (number
+            of channels, series length) of shape ``[n_cases]``, 2D np.array
+            ``(n_channels, n_timepoints_i)``, where ``n_timepoints_i`` is length of
             series ``i``. Other types are allowed and converted into one of the above.
 
             Different estimators have different capabilities to handle different
@@ -222,8 +222,8 @@ class BaseCollectionTransformer(BaseCollectionEstimator, BaseTransformer):
         X : np.ndarray or list
             Data to fit transform to, of valid collection type. Input data,
             any number of channels, equal length series of shape ``(
-            n_cases, n_channels, n_timepoints)`` or list of numpy arrays (any number
-            of channels, unequal length series)  of shape ``[n_cases]``, 2D np.array
+            n_cases, n_channels, n_timepoints)`` or list of numpy arrays (number
+            of channels, series length) of shape ``[n_cases]``, 2D np.array
             ``(n_channels, n_timepoints_i)``, where ``n_timepoints_i`` is length of
             series ``i``. Other types are allowed and converted into one of the above.
 
diff --git a/aeon/transformations/collection/feature_based/_catch22.py b/aeon/transformations/collection/feature_based/_catch22.py
index daae46f5..0431da8d 100644
--- a/aeon/transformations/collection/feature_based/_catch22.py
+++ b/aeon/transformations/collection/feature_based/_catch22.py
@@ -111,8 +111,11 @@ class Catch22(BaseCollectionTransformer):
         true. If a List of specific features to extract is provided, "Mean" and/or
         "StandardDeviation" must be added to the List to extract these features.
     outlier_norm : bool, optional, default=False
-        Normalise each series during the two outlier Catch22 features, which can take a
-        while to process for large values.
+        If True, each time series is normalized during the computation of the two
+        outlier Catch22 features, which can take a while to process for large values
+        as it depends on the max value in the timseries. Note that this parameter
+        did not exist in the original publication/implementation as they used time
+        series that were already normalized.
     replace_nans : bool, default=False
         Replace NaN or inf values from the Catch22 transform with 0.
     use_pycatch22 : bool, optional, default=False
@@ -163,7 +166,7 @@ class Catch22(BaseCollectionTransformer):
     [1.15639531e+00 1.31700577e+00 5.66227710e-01 2.00000000e+00
      3.89048349e-01 2.33853577e-01 1.00000000e+00 3.00000000e+00
      8.23045267e-03 0.00000000e+00 1.70859420e-01 2.00000000e+00
-     1.00000000e+00 2.00000000e-01 0.00000000e+00 1.10933565e-32
+     1.00000000e+00 7.00000000e-01 2.00000000e-01 1.10933565e-32
      4.00000000e+00 2.04319187e+00 0.00000000e+00 0.00000000e+00
      1.96349541e+00 5.51667002e-01]
     """
@@ -181,7 +184,7 @@ class Catch22(BaseCollectionTransformer):
         self,
         features="all",
         catch24=False,
-        outlier_norm=False,
+        outlier_norm=True,
         replace_nans=False,
         use_pycatch22=False,
         n_jobs=1,


Test patch:
diff --git a/.github/workflows/periodic_tests.yml b/.github/workflows/periodic_tests.yml
index 64e297d6..15289595 100644
--- a/.github/workflows/periodic_tests.yml
+++ b/.github/workflows/periodic_tests.yml
@@ -46,12 +46,17 @@ jobs:
           extra_args: --all-files
 
   run-notebook-examples:
-    runs-on: ubuntu-24.04
+    runs-on: macos-14
 
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
+      - name: Install latest version of bash
+        run: |
+          brew install bash
+          /opt/homebrew/bin/bash --version
+
       - name: Setup Python 3.10
         uses: actions/setup-python@v5
         with:
diff --git a/aeon/transformations/collection/feature_based/tests/test_catch22.py b/aeon/transformations/collection/feature_based/tests/test_catch22.py
index 5b5bc289..9ebc6786 100644
--- a/aeon/transformations/collection/feature_based/tests/test_catch22.py
+++ b/aeon/transformations/collection/feature_based/tests/test_catch22.py
@@ -120,7 +120,7 @@ catch22_basic_motions_data = np.array(
             0.0616,
             1.0,
             0.5,
-            -0.2,
+            -0.2799,
             0.04,
             0.4158,
             4.0,
@@ -231,7 +231,7 @@ catch22_basic_motions_data = np.array(
             2.0,
             1.0,
             -0.11,
-            -0.72,
+            -0.81,
             1.7181,
             8.0,
             1.8142,
@@ -255,7 +255,7 @@ catch22_basic_motions_data = np.array(
             4.0,
             0.3333,
             -0.15,
-            0.03,
+            0.01,
             32.285,
             8.0,
             1.9501,
@@ -298,8 +298,8 @@ catch22_basic_motions_data = np.array(
             0.1303,
             3.0,
             0.3333,
-            -0.23,
-            -0.04,
+            -0.2299,
+            0.06,
             14.3938,
             5.0,
             2.0059,
@@ -320,8 +320,8 @@ catch22_basic_motions_data = np.array(
             0.1047,
             2.0,
             0.3333,
-            0.15,
-            -0.18,
+            0.06,
+            -0.235,
             7.1407,
             6.0,
             2.0097,
@@ -342,7 +342,7 @@ catch22_basic_motions_data = np.array(
             0.064,
             1.0,
             0.3333,
-            0.18,
+            0.20,
             0.3,
             1.6007,
             5.0,
@@ -365,7 +365,7 @@ catch22_basic_motions_data = np.array(
             2.0,
             0.3333,
             -0.14,
-            0.1,
+            -0.0399,
             7.3076,
             5.0,
             1.9736,
@@ -389,7 +389,7 @@ catch22_basic_motions_data = np.array(
             2.0,
             0.3333,
             -0.13,
-            0.02,
+            -0.3399,
             0.0081,
             5.0,
             2.133,
@@ -410,8 +410,8 @@ catch22_basic_motions_data = np.array(
             0.5715,
             2.0,
             1.0,
-            -0.12,
-            -0.02,
+            -0.1399,
+            -0.0099,
             0.1288,
             7.0,
             1.9505,
@@ -476,8 +476,8 @@ catch22_basic_motions_data = np.array(
             6.8497,
             2.0,
             0.3333,
-            -0.06,
-            0.05,
+            -0.0799,
+            0.03,
             0.0013,
             7.0,
             2.039,
@@ -498,8 +498,8 @@ catch22_basic_motions_data = np.array(
             3.1416,
             2.0,
             1.0,
-            -0.155,
-            0.125,
+            -0.1999,
+            0.1200,
             0.0212,
             7.0,
             1.8706,
@@ -522,7 +522,7 @@ catch22_basic_motions_data = np.array(
             0.1723,
             1.0,
             1.0,
-            -0.01,
+            -0.0799,
             -0.17,
             8.3186,
             5.0,
@@ -544,8 +544,8 @@ catch22_basic_motions_data = np.array(
             0.1222,
             1.0,
             1.0,
-            0.09,
-            0.01,
+            0.08,
+            -0.0099,
             5.3016,
             4.0,
             2.0075,
@@ -566,8 +566,8 @@ catch22_basic_motions_data = np.array(
             0.0841,
             2.0,
             0.5,
-            0.13,
-            -0.08,
+            -0.0199,
+            -0.1199,
             1.7627,
             5.0,
             2.1476,
@@ -611,7 +611,7 @@ catch22_basic_motions_data = np.array(
             1.0,
             0.5,
             -0.05,
-            -0.11,
+            -0.0999,
             0.2086,
             6.0,
             2.0597,
@@ -656,8 +656,8 @@ catch22_basic_motions_data = np.array(
             0.0718,
             1.0,
             0.3333,
-            0.03,
-            0.13,
+            0.025,
+            -0.1399,
             0.501,
             6.0,
             2.0492,
@@ -701,7 +701,7 @@ catch22_basic_motions_data = np.array(
             2.0,
             0.5,
             -0.13,
-            0.19,
+            0.29,
             0.3096,
             6.0,
             1.8881,
@@ -745,7 +745,7 @@ catch22_basic_motions_data = np.array(
             3.0,
             1.0,
             0.11,
-            0.35,
+            0.285,
             0.2719,
             7.0,
             1.7647,