merge main

.github/utilities/run_examples.sh

@@ -7,7 +7,6 @@ CMD="jupyter nbconvert --to notebook --inplace --execute --ExecutePreprocessor.t
 
 excluded=(
   "tsml_eval/publications/y2023/distance_based_clustering/package_distance_timing.ipynb"
-  "examples/regression_experiments.ipynb"
 )
 if [ "$1" = true ]; then
   excluded+=()

.github/workflows/issue_comment_edited.yml

@@ -11,7 +11,7 @@ concurrency:
 jobs:
   pr-welcome-edited:
     if: ${{ github.event.issue.pull_request }}
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/create-github-app-token@v1

.github/workflows/issue_comment_posted.yml

@@ -6,7 +6,7 @@ on:
 
 jobs:
   self-assign:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/periodic_github_maintenace.yml

@@ -6,13 +6,17 @@ on:
     - cron:  "0 1 1,15 * *"
   workflow_dispatch:
 
-permissions:
-  issues: write
-  contents: write
+concurrency:
+  group: ${{ github.workflow }}
+  cancel-in-progress: true
 
 jobs:
   stale_branches:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
+
+    permissions:
+      issues: write
+      contents: write
 
     steps:
       - uses: actions/create-github-app-token@v1
@@ -22,7 +26,7 @@ jobs:
           private-key: ${{ secrets.PR_APP_KEY }}
 
       - name: Stale Branches
-        uses: crs-k/stale-branches@v6.0.2
+        uses: crs-k/stale-branches@v7.0.0
         with:
           repo-token: ${{ steps.app-token.outputs.token }}
           days-before-stale: 365
@@ -32,3 +36,58 @@ jobs:
           stale-branch-label: "stale branch"
           compare-branches: "info"
           pr-check: true
+
+  pre-commit-auto-update:
+    runs-on: ubuntu-24.04
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - uses: browniebroke/pre-commit-autoupdate-action@v1.0.0
+
+      - if: always()
+        uses: actions/create-github-app-token@v1
+        id: app-token
+        with:
+          app-id: ${{ vars.PR_APP_ID }}
+          private-key: ${{ secrets.PR_APP_KEY }}
+
+      - if: always()
+        uses: peter-evans/create-pull-request@v7
+        with:
+          token: ${{ steps.app-token.outputs.token }}
+          commit-message: "Automated `pre-commit` hook update"
+          branch: pre-commit-hooks-update
+          title: "[MNT] Automated `pre-commit` hook update"
+          body: "Automated weekly update to `.pre-commit-config.yaml` hook versions."
+          labels: maintenance, full pre-commit
+
+  github-security-scorecard:
+    runs-on: ubuntu-24.04
+
+    permissions:
+      security-events: write
+      id-token: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: ossf/scorecard-action@v2.4.1
+        with:
+          results_file: results.sarif
+          results_format: sarif
+          publish_results: true
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: SARIF file
+          path: results.sarif
+          retention-days: 5
+
+      - uses: github/codeql-action/upload-sarif@v3
+        with:
+          sarif_file: results.sarif

.github/workflows/periodic_tests.yml

@@ -12,7 +12,7 @@ concurrency:
 
 jobs:
   check-manifest:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4
@@ -26,7 +26,7 @@ jobs:
           extra_args: check-manifest --hook-stage manual
 
   pre-commit:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4
@@ -65,7 +65,7 @@ jobs:
         run: mypy tsml_eval/
 
   run-notebook-examples:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4
@@ -99,13 +99,74 @@ jobs:
           path: ${{ github.workspace }}/.numba_cache
           key: numba-run-notebook-examples-${{ runner.os }}-3.10-${{ env.CURRENT_DATE }}
 
+  test-no-soft-deps:
+    runs-on: ubuntu-24.04
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - 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"
+          restore_cache: "false"
+
+      - name: Install
+        uses: nick-fields/retry@v3
+        with:
+          timeout_minutes: 30
+          max_attempts: 3
+          command: python -m pip install .[dev]
+
+      - name: Show dependencies
+        run: python -m pip list
+
+      - name: Run tests
+        run: python -m pytest -n logical
+
+      - name: Save new cache
+        uses: actions/cache/save@v4
+        with:
+          path: ${{ github.workspace }}/.numba_cache
+          # Save cache with the current date (ENV set in numba_cache action)
+          key: numba-test-no-soft-deps-${{ runner.os }}-3.10-${{ env.CURRENT_DATE }}
+
+  test-core-imports:
+    runs-on: ubuntu-24.04
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install
+        uses: nick-fields/retry@v3
+        with:
+          timeout_minutes: 30
+          max_attempts: 3
+          command: python -m pip install .
+
+      - name: Show dependencies
+        run: python -m pip list
+
+      - name: Run import test
+        run: python tsml_eval/testing/tests/test_core_imports.py
+
   pytest:
     runs-on: ${{ matrix.os }}
 
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-20.04, macos-14, windows-2022 ]
+        os: [ ubuntu-24.04, macos-14, windows-2022 ]
         python-version: [ "3.9", "3.10", "3.11", "3.12" ]
 
     steps:
@@ -143,7 +204,7 @@ jobs:
           key: numba-pytest-${{ runner.os }}-${{ matrix.python-version}}-${{ env.CURRENT_DATE }}
 
   codecov:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4
@@ -168,6 +229,6 @@ jobs:
       - name: Run tests
         run: python -m pytest -n logical --cov=aeon --cov-report=xml --timeout 1800
 
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/pr_examples.yml

@@ -19,7 +19,7 @@ concurrency:
 
 jobs:
   run-notebook-examples:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/pr_opened.yml

@@ -12,7 +12,7 @@ permissions:
 jobs:
   # based on the scikit-learn 1.3.1 PR labelers
   labeler:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/pr_precommit.yml

@@ -14,7 +14,7 @@ concurrency:
 
 jobs:
   pre-commit:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/create-github-app-token@v1

.github/workflows/pr_pytest.yml

@@ -17,13 +17,66 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  test-no-soft-deps:
+    runs-on: ubuntu-24.04
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Restore numba cache
+        uses: ./.github/actions/numba_cache
+        with:
+          cache_name: "test-no-soft-deps"
+          runner_os: ${{ runner.os }}
+          python_version: "3.10"
+
+      - name: Install
+        uses: nick-fields/retry@v3
+        with:
+          timeout_minutes: 30
+          max_attempts: 3
+          command: python -m pip install .[dev]
+
+      - name: Show dependencies
+        run: python -m pip list
+
+      - name: Run tests
+        run: python -m pytest -n logical
+
+  test-core-imports:
+    runs-on: ubuntu-24.04
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install
+        uses: nick-fields/retry@v3
+        with:
+          timeout_minutes: 30
+          max_attempts: 3
+          command: python -m pip install .
+
+      - name: Show dependencies
+        run: python -m pip list
+
+      - name: Run import test
+        run: python tsml_eval/testing/tests/test_core_imports.py
+
   pytest:
     runs-on: ${{ matrix.os }}
 
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-20.04, windows-2022 ]
+        os: [ ubuntu-24.04, windows-2022 ]
         python-version: [ "3.9", "3.10", "3.11", "3.12" ]
         # skip python versions unless the PR has the 'full pytest actions' label
         pr-testing:
@@ -60,7 +113,7 @@ jobs:
         run: python -m pytest -n logical
 
   codecov:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4
@@ -82,6 +135,6 @@ jobs:
       - name: Tests
         run: python -m pytest -n logical --cov=tsml_eval --cov-report=xml --timeout 1800
 
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/pr_typecheck.yml

@@ -9,6 +9,7 @@ on:
       - main
     paths:
       - "tsml_eval/**"
+      - "pyproject.toml"
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}