[MNT,ENH] Update to allow Python 3.13

.github/actions/cpu_all_extras/action.yml

@@ -2,6 +2,10 @@ name: Pip install all_extras with CPU versions
 description: "For CI testing install the CPU version of dependencies with all extras if on ubuntu"
 
 inputs:
+  python_version:
+    description: "Python version used"
+    required: false
+    default: "3.11"
   additional_extras:
     description: "Comma-separated list of additional extras to install"
     required: false
@@ -11,7 +15,7 @@ runs:
   using: "composite"
   steps:
     - name: Install CPU TensorFlow
-      if: runner.os == 'Linux'
+      if: ${{ runner.os == 'Linux' && inputs.python_version != '3.13' }}
       uses: nick-fields/retry@v3
       with:
         timeout_minutes: 30

.github/utilities/run_examples.sh

@@ -6,7 +6,8 @@ set -euxo pipefail
 CMD="jupyter nbconvert --to notebook --inplace --execute --ExecutePreprocessor.timeout=600"
 
 excluded=(
-    "examples/transformations/signature_method.ipynb"
+  # try removing when 3.9 is dropped
+  "examples/transformations/signature_method.ipynb"
 )
 if [ "$1" = true ]; then
   excluded+=(

.github/workflows/fast_release.yml

@@ -11,9 +11,10 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v5
+      - name: Setup Python 3.11
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Build project
         run: |

.github/workflows/issue_assigned.yml

@@ -25,10 +25,10 @@ jobs:
         with:
           sparse-checkout: .github/utilities
 
-      - name: Setup Python 3.10
+      - name: Setup Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install PyGithub
         run: pip install -Uq PyGithub

.github/workflows/issue_comment_edited.yml

@@ -26,10 +26,10 @@ jobs:
         with:
           sparse-checkout: .github/utilities
 
-      - name: Setup Python 3.10
+      - name: Setup Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install PyGithub
         run: pip install -Uq PyGithub

.github/workflows/issue_comment_posted.yml

@@ -14,10 +14,10 @@ jobs:
         with:
           sparse-checkout: .github/utilities
 
-      - name: Setup Python 3.10
+      - name: Setup Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install PyGithub
         run: pip install -Uq PyGithub

.github/workflows/periodic_tests.yml

@@ -18,10 +18,10 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Setup Python 3.10
+      - name: Setup Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Run check-manifest
         uses: pre-commit/action@v3.0.1
@@ -35,10 +35,10 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Setup Python 3.10
+      - name: Setup Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Run pre-commit
         uses: pre-commit/action@v3.0.1
@@ -57,17 +57,17 @@ jobs:
           brew install bash
           /opt/homebrew/bin/bash --version
 
-      - name: Setup Python 3.10
+      - name: Setup Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Use numba cache to set env variables but not restore cache
         uses: ./.github/actions/numba_cache
         with:
           cache_name: "run-notebook-examples"
           runner_os: ${{ runner.os }}
-          python_version: "3.10"
+          python_version: "3.11"
           restore_cache: "false"
 
       - uses: ./.github/actions/cpu_all_extras
@@ -92,10 +92,10 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Setup Python 3.10
+      - name: Setup Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install aeon and dependencies
         uses: nick-fields/retry@v3
@@ -117,17 +117,17 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Setup Python 3.10
+      - name: Setup Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Use numba cache to set env variables but not restore cache
         uses: ./.github/actions/numba_cache
         with:
           cache_name: "test-no-soft-deps"
           runner_os: ${{ runner.os }}
-          python_version: "3.10"
+          python_version: "3.11"
           restore_cache: "false"
 
       - name: Install aeon and dependencies
@@ -157,7 +157,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-24.04, macOS-14, windows-2022 ]
-        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
+        python-version: [ "3.9", "3.10", "3.11", "3.12", "3.13" ]
 
     steps:
       - name: Checkout
@@ -184,6 +184,7 @@ jobs:
 
       - uses: ./.github/actions/cpu_all_extras
         with:
+          python_version: ${{ matrix.python-version }}
           additional_extras: "dev"
 
       - name: Show dependencies
@@ -206,10 +207,10 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Setup Python 3.10
+      - name: Setup Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Disable Numba JIT
         run: echo "NUMBA_DISABLE_JIT=1" >> $GITHUB_ENV

.github/workflows/pr_core_dep_import.yml

@@ -24,10 +24,10 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Setup Python 3.10
+      - name: Setup Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install aeon and dependencies
         uses: nick-fields/retry@v3

.github/workflows/pr_examples.yml

@@ -30,18 +30,18 @@ jobs:
           brew install bash
           /opt/homebrew/bin/bash --version
 
-      - name: Setup Python 3.10
+      - name: Setup Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - if: ${{ github.event_name != 'pull_request' || !contains(github.event.pull_request.labels.*.name, 'no numba cache') }}
         name: Restore numba cache
         uses: ./.github/actions/numba_cache
         with:
           cache_name: "run-notebook-examples"
           runner_os: ${{ runner.os }}
-          python_version: "3.10"
+          python_version: "3.11"
 
       - uses: ./.github/actions/cpu_all_extras
         with:

.github/workflows/pr_opened.yml

@@ -20,10 +20,10 @@ jobs:
         with:
           sparse-checkout: .github/utilities
 
-      - name: Setup Python 3.10
+      - name: Setup Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install PyGithub
         run: pip install -Uq PyGithub

.github/workflows/pr_precommit.yml

@@ -31,10 +31,10 @@ jobs:
           ref: ${{ github.head_ref }}
           token: ${{ steps.app-token.outputs.token }}
 
-      - name: Setup Python 3.10
+      - name: Setup Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Get changed files
         uses: tj-actions/changed-files@v46.0.4

.github/workflows/pr_pytest.yml

@@ -24,18 +24,18 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Setup Python 3.10
+      - name: Setup Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - if: ${{ github.event_name != 'pull_request' || !contains(github.event.pull_request.labels.*.name, 'no numba cache') }}
         name: Restore numba cache
         uses: ./.github/actions/numba_cache
         with:
           cache_name: "test-no-soft-deps"
           runner_os: ${{ runner.os }}
-          python_version: "3.10"
+          python_version: "3.11"
 
       - name: Install aeon and dependencies
         uses: nick-fields/retry@v3
@@ -57,13 +57,15 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-24.04, macOS-14, windows-2022 ]
-        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
+        python-version: [ "3.9", "3.10", "3.11", "3.12", "3.13" ]
         # skip python versions unless the PR has the 'full pytest actions' label
         pr-testing:
           - ${{ (github.event_name == 'pull_request' && !contains(github.event.pull_request.labels.*.name, 'full pytest actions')) }}
         exclude:
           - pr-testing: true
             python-version: "3.10"
+          - pr-testing: true
+            python-version: "3.12"
 
     steps:
       - name: Checkout
@@ -90,6 +92,7 @@ jobs:
 
       - uses: ./.github/actions/cpu_all_extras
         with:
+          python_version: ${{ matrix.python-version }}
           additional_extras: "dev"
 
       - name: Show dependencies
@@ -109,10 +112,10 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Setup Python 3.10
+      - name: Setup Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Disable Numba JIT
         run: echo "NUMBA_DISABLE_JIT=1" >> $GITHUB_ENV

.github/workflows/pr_typecheck.yml

@@ -24,10 +24,10 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Setup Python 3.10
+      - name: Setup Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install aeon, dependencies and mypy
         uses: nick-fields/retry@v3

.github/workflows/precommit_autoupdate.yml

@@ -13,9 +13,10 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v5
+      - name: Setup Python 3.11
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - uses: browniebroke/pre-commit-autoupdate-action@v1.0.0
 

.github/workflows/release.yml

@@ -13,9 +13,10 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v5
+      - name: Setup Python 3.11
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - uses: pre-commit/action@v3.0.1
         with:
@@ -28,9 +29,10 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v5
+      - name: Setup Python 3.11
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Build project
         run: |
@@ -52,7 +54,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-24.04, macOS-14, windows-2022 ]
-        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
+        python-version: [ "3.9", "3.10", "3.11", "3.12", "3.13" ]
 
     steps:
       - uses: actions/checkout@v4

aeon/anomaly_detection/tests/test_cblof.py

@@ -21,7 +21,7 @@ def test_cblof_default():
     pred = cblof.fit_predict(series, axis=0)
 
     assert pred.shape == (80,)
-    assert pred.dtype == np.float_
+    assert np.issubdtype(pred.dtype, np.floating)
     assert 50 <= np.argmax(pred) <= 60
 
 

aeon/anomaly_detection/tests/test_copod.py

@@ -21,7 +21,7 @@ def test_copod_default():
     pred = copod.fit_predict(series, axis=0)
 
     assert pred.shape == (80,)
-    assert pred.dtype == np.float_
+    assert np.issubdtype(pred.dtype, np.floating)
     assert 50 <= np.argmax(pred) <= 60