Merge branch 'main' into wnorm_add

Author: MatthewMiddlehurst

.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

.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:

.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:

.github/workflows/pr_precommit.yml

@@ -37,7 +37,7 @@ jobs:
           python-version: "3.10"
 
       - name: Get changed files
-        uses: tj-actions/changed-files@v45
+        uses: tj-actions/changed-files@v46.0.3
         id: changed-files
 
       - name: List changed files

.pre-commit-config.yaml

@@ -29,7 +29,7 @@ repos:
         args: [ "--create", "--python-folders", "aeon" ]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.10
+    rev: v0.11.2
     hooks:
       - id: ruff
         args: [ "--fix"]
@@ -48,7 +48,7 @@ repos:
         args: [ "--profile=black", "--multi-line=3" ]
 
   - repo: https://github.com/pycqa/flake8
-    rev: 7.1.2
+    rev: 7.2.0
     hooks:
       - id: flake8
         additional_dependencies: [ flake8-bugbear, flake8-print, Flake8-pyproject ]

aeon/base/_base.py

@@ -86,6 +86,11 @@ class and object methods, class attributes
         -------
         self : object
             Reference to self.
+
+        Raises
+        ------
+        TypeError
+            If 'keep' is not a string or a list of strings.
         """
         # retrieve parameters to copy them later
         params = self.get_params(deep=False)

aeon/benchmarking/metrics/anomaly_detection/__init__.py

@@ -14,6 +14,9 @@
     "range_pr_auc_score",
     "range_pr_vus_score",
     "range_roc_vus_score",
+    "ts_precision",
+    "ts_recall",
+    "ts_fscore",
 ]
 
 from aeon.benchmarking.metrics.anomaly_detection._binary import (
@@ -35,3 +38,8 @@
     range_roc_auc_score,
     range_roc_vus_score,
 )
+from aeon.benchmarking.metrics.anomaly_detection.range_metrics import (
+    ts_fscore,
+    ts_precision,
+    ts_recall,
+)

aeon/benchmarking/metrics/anomaly_detection/_binary.py

@@ -6,11 +6,19 @@
 import warnings
 
 import numpy as np
+from deprecated.sphinx import deprecated
 
 from aeon.benchmarking.metrics.anomaly_detection._util import check_y
 from aeon.utils.validation._dependencies import _check_soft_dependencies
 
 
+# TODO: Remove in v1.2.0
+@deprecated(
+    version="1.1.0",
+    reason="range_precision is deprecated and will be removed in v1.2.0. "
+    "Please use ts_precision from the range_metrics module instead.",
+    category=FutureWarning,
+)
 def range_precision(
     y_true: np.ndarray,
     y_pred: np.ndarray,
@@ -70,6 +78,13 @@ def range_precision(
     return ts_precision(y_true, y_pred, alpha=alpha, cardinality=cardinality, bias=bias)
 
 
+# TODO: Remove in v1.2.0
+@deprecated(
+    version="1.1.0",
+    reason="range_recall is deprecated and will be removed in v1.2.0. "
+    "Please use ts_recall from the range_metrics module instead.",
+    category=FutureWarning,
+)
 def range_recall(
     y_true: np.ndarray,
     y_pred: np.ndarray,
@@ -131,6 +146,13 @@ def range_recall(
     return ts_recall(y_true, y_pred, alpha=alpha, cardinality=cardinality, bias=bias)
 
 
+# TODO: Remove in v1.2.0
+@deprecated(
+    version="1.1.0",
+    reason="range_f_score is deprecated and will be removed in v1.2.0. "
+    "Please use ts_fscore from the range_metrics module instead.",
+    category=FutureWarning,
+)
 def range_f_score(
     y_true: np.ndarray,
     y_pred: np.ndarray,