[MNT] Update workflows (#229)

* update workflows

* back to 13

.github/actions/numba_cache/action.yml

@@ -0,0 +1,63 @@
+name: Numba cache setup
+description: "Tries to restore the numba cache and sets relevant environment variables for numba to use"
+
+inputs:
+  cache_name:
+    description: "The name of the cache"
+    required: true
+  runner_os:
+    description: "The runner os"
+    required: true
+  python_version:
+    description: "The python version"
+    required: true
+  restore_cache:
+    description: "Whether to restore the cache"
+    required: false
+    default: "true"
+
+runs:
+  using: "composite"
+  steps:
+    # Set the location for numba cache to exist
+    - name: Set numba cache env
+      run: echo "NUMBA_CACHE_DIR=${{ github.workspace }}/.numba_cache" >> $GITHUB_ENV
+      shell: bash
+
+    # Sets the cpu name for numba to use
+    - name: Set numba cpu env
+      run: echo "NUMBA_CPU_NAME=generic" >> $GITHUB_ENV
+      shell: bash
+
+    # Sets the cpu features for numba to use
+    - name: Set numba cpu features env
+      run: echo "NUMBA_CPU_FEATURES=+64bit +adx +aes +avx +avx2 -avx512bf16 -avx512bitalg -avx512bw -avx512cd -avx512dq -avx512er -avx512f -avx512ifma -avx512pf -avx512vbmi -avx512vbmi2 -avx512vl -avx512vnni -avx512vpopcntdq +bmi +bmi2 -cldemote -clflushopt -clwb -clzero +cmov +cx16 +cx8 -enqcmd +f16c +fma -fma4 +fsgsbase +fxsr -gfni +invpcid -lwp +lzcnt +mmx +movbe -movdir64b -movdiri -mwaitx +pclmul -pconfig -pku +popcnt -prefetchwt1 +prfchw -ptwrite -rdpid +rdrnd +rdseed +rtm +sahf -sgx -sha -shstk +sse +sse2 +sse3 +sse4.1 +sse4.2 -sse4a +ssse3 -tbm -vaes -vpclmulqdq -waitpkg -wbnoinvd -xop +xsave -xsavec +xsaveopt -xsaves" >> $GITHUB_ENV
+      shell: bash
+
+    # Set the CICD_RUNNING env so that numba knows it is running in a CI environment
+    - name: Set CICD_RUNNING env
+      run: echo "CICD_RUNNING=1" >> $GITHUB_ENV
+      shell: bash
+
+    # Get current date for cache restore
+    - name: Get Current Date
+      run: echo "CURRENT_DATE=$(date +'%d/%m/%Y')" >> $GITHUB_ENV
+      shell: bash
+
+      # GNU tar on windows runs much faster than the default BSD tar
+    - name: Use GNU tar instead BSD tar if Windows
+      if: ${{ inputs.runner_os == 'Windows' }}
+      shell: cmd
+      run: echo C:\Program Files\Git\usr\bin>>"%GITHUB_PATH%"
+
+    # Restore cache if restore_cache is true
+    - name: Restore cache
+      uses: actions/cache/restore@v4
+      if: ${{ inputs.restore_cache == 'true' }}
+      with:
+        path: ${{ github.workspace }}/.numba_cache
+        # Try restore using today's date
+        key: numba-${{ inputs.cache_name }}-${{ inputs.runner_os }}-${{ inputs.python_version }}-${{ env.CURRENT_DATE }}
+        # If cant restore with today's date try another cache (without date)
+        restore-keys: |
+          numba-${{ inputs.cache_name }}-${{ inputs.runner_os }}-${{ inputs.python_version }}-

.github/workflows/issue_comment_edited.yml

@@ -0,0 +1,33 @@
+name: Issue Comment Posted
+
+on:
+  issue_comment:
+    types: [edited]
+
+jobs:
+  check-pr-labels:
+    runs-on: ubuntu-20.04
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          sparse-checkout: build_tools
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install PyGithub
+        run: pip install -Uq PyGithub
+
+      - uses: actions/create-github-app-token@v1
+        id: app-token
+        with:
+          app-id: ${{ vars.PR_APP_ID }}
+          private-key: ${{ secrets.PR_APP_KEY }}
+
+      - name: Assign issue
+        run: python build_tools/comment_pr_labeler.py
+        env:
+          CONTEXT_GITHUB: ${{ toJson(github) }}
+          GITHUB_TOKEN: ${{ steps.app-token.outputs.token }}

.github/workflows/issue_comment_posted.yml

@@ -0,0 +1,33 @@
+name: Issue Comment Posted
+
+on:
+  issue_comment:
+    types: [created]
+
+jobs:
+  self-assign:
+    runs-on: ubuntu-20.04
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          sparse-checkout: build_tools
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install PyGithub
+        run: pip install -Uq PyGithub
+
+      - uses: actions/create-github-app-token@v1
+        id: app-token
+        with:
+          app-id: ${{ vars.PR_APP_ID }}
+          private-key: ${{ secrets.PR_APP_KEY }}
+
+      - name: Assign issue
+        run: python build_tools/issue_assign.py
+        env:
+          CONTEXT_GITHUB: ${{ toJson(github) }}
+          GITHUB_TOKEN: ${{ steps.app-token.outputs.token }}

.github/workflows/periodic_github_maintenace.yml

@@ -0,0 +1,34 @@
+name: GitHub Maintenance
+
+on:
+  schedule:
+    # Run on 1st and 15th of every month at 01:00 AM UTC
+    - cron:  "0 1 1,15 * * *"
+  workflow_dispatch:
+
+permissions:
+  issues: write
+  contents: write
+
+jobs:
+  stale_branches:
+    runs-on: ubuntu-20.04
+
+    steps:
+      - uses: actions/create-github-app-token@v1
+        id: app-token
+        with:
+          app-id: ${{ vars.PR_APP_ID }}
+          private-key: ${{ secrets.PR_APP_KEY }}
+
+      - name: Stale Branches
+        uses: crs-k/[email protected]
+        with:
+          repo-token: ${{ steps.app-token.outputs.token }}
+          days-before-stale: 365
+          days-before-delete: 99999
+          comment-updates: true
+          tag-committer: true
+          stale-branch-label: "stale branch"
+          compare-branches: "info"
+          pr-check: true

.github/workflows/periodic_tests.yml

@@ -49,6 +49,14 @@ jobs:
         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: "run-notebook-examples"
+          runner_os: ${{ runner.os }}
+          python_version: "3.10"
+          restore_cache: "false"
+
       - name: Install
         uses: nick-fields/retry@v3
         with:
@@ -60,13 +68,19 @@ jobs:
         run: build_tools/run_examples.sh
         shell: bash
 
+      - name: Save new cache
+        uses: actions/cache/save@v4
+        with:
+          path: ${{ github.workspace }}/.numba_cache
+          key: numba-run-notebook-examples-${{ runner.os }}-3.10-${{ env.CURRENT_DATE }}
+
   pytest:
     runs-on: ${{ matrix.os }}
 
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-20.04, macOS-13, windows-2022 ]
+        os: [ ubuntu-20.04, macos-13, windows-2022 ]
         python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12" ]
 
     steps:
@@ -76,6 +90,14 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Use numba cache to set env variables but not restore cache
+        uses: ./.github/actions/numba_cache
+        with:
+          cache_name: "pytest"
+          runner_os: ${{ runner.os }}
+          python_version: ${{ matrix.python-version }}
+          restore_cache: "false"
+
       - name: Install
         uses: nick-fields/retry@v3
         with:
@@ -89,6 +111,12 @@ jobs:
       - name: Tests
         run: python -m pytest
 
+      - name: Save new cache
+        uses: actions/cache/save@v4
+        with:
+          path: ${{ github.workspace }}/.numba_cache
+          key: numba-pytest-${{ runner.os }}-${{ matrix.python-version}}-${{ env.CURRENT_DATE }}
+
   codecov:
     runs-on: ubuntu-20.04
 
@@ -113,7 +141,7 @@ jobs:
         run: python -m pip list
 
       - name: Run tests
-        run: python -m pytest --cov=aeon --cov-report=xml
+        run: python -m pytest --cov=aeon --cov-report=xml --timeout 1800
 
       - uses: codecov/codecov-action@v4
         env:

.github/workflows/pr_examples.yml

@@ -28,6 +28,13 @@ jobs:
         with:
           python-version: "3.10"
 
+      - name: Restore numba cache
+        uses: ./.github/actions/numba_cache
+        with:
+            cache_name: "run-notebook-examples"
+            runner_os: ${{ runner.os }}
+            python_version: "3.10"
+
       - name: Install
         uses: nick-fields/retry@v3
         with:
@@ -36,5 +43,5 @@ jobs:
           command: python -m pip install .[all_extras,dev,binder,unstable_extras]
 
       - name: Run example notebooks
-        run: build_tools/run_examples.sh
+        run: build_tools/run_examples.sh ${{ github.event_name != 'pull_request' || !contains(github.event.pull_request.labels.*.name, 'full examples run') }}
         shell: bash

.github/workflows/pr_opened.yml

@@ -34,11 +34,17 @@ jobs:
 
       - name: Label pull request
         id: label-pr
-        run: python build_tools/pr_labeler.py ${{ steps.app-token.outputs.token }}
+        run: python build_tools/pr_labeler.py
         env:
           CONTEXT_GITHUB: ${{ toJson(github) }}
+          GITHUB_TOKEN: ${{ steps.app-token.outputs.token }}
 
       - name: Write pull request comment
-        run: python build_tools/pr_open_commenter.py ${{ steps.app-token.outputs.token }} ${{ steps.label-pr.outputs.title-labels }} ${{ steps.label-pr.outputs.title-labels-new }} ${{ steps.label-pr.outputs.content-labels }} ${{ steps.label-pr.outputs.content-labels-status }}
+        run: python build_tools/pr_open_commenter.py
         env:
           CONTEXT_GITHUB: ${{ toJson(github) }}
+          GITHUB_TOKEN: ${{ steps.app-token.outputs.token }}
+          TITLE_LABELS: ${{ steps.label-pr.outputs.title-labels }}
+          TITLE_LABELS_NEW: ${{ steps.label-pr.outputs.title-labels-new }}
+          CONTENT_LABELS: ${{ steps.label-pr.outputs.content-labels }}
+          CONTENT_LABELS_STATUS: ${{ steps.label-pr.outputs.content-labels-status }}

.github/workflows/pr_pre_commit.yml

@@ -17,13 +17,22 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
+      - uses: actions/create-github-app-token@v1
+        id: app-token
+        with:
+          app-id: ${{ vars.PR_APP_ID }}
+          private-key: ${{ secrets.PR_APP_KEY }}
+
       - uses: actions/checkout@v4
+        with:
+          ref: ${{ github.head_ref }}
+          token: ${{ steps.app-token.outputs.token }}
 
       - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
 
-      - uses: tj-actions/changed-files@v44.5.2
+      - uses: tj-actions/changed-files@v44
         id: changed-files
 
       - name: List changed files
@@ -40,5 +49,9 @@ jobs:
         with:
           extra_args: --files ${{ steps.changed-files.outputs.all_changed_files }}
 
-      - if: ${{ failure() && github.event_name == 'pull_request' && github.event.pull_request.draft == false }}
-        uses: pre-commit-ci/[email protected]
+      - if: ${{ failure() && github.event_name == 'pull_request' && github.event.pull_request.draft == false && !contains(github.event.pull_request.labels.*.name, 'stop pre-commit fixes')}}
+        name: Push pre-commit fixes
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          commit_message: Automatic `pre-commit` fixes
+          commit_user_name: tsml-actions-bot[bot]

.github/workflows/pr_pytest.yml

@@ -23,7 +23,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-20.04, macOS-13, windows-2022 ]
+        os: [ ubuntu-20.04, windows-2022 ]
         python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12" ]
 
     steps:
@@ -33,6 +33,13 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Restore numba cache
+        uses: ./.github/actions/numba_cache
+        with:
+          cache_name: "pytest"
+          runner_os: ${{ runner.os }}
+          python_version: ${{ matrix.python-version }}
+
       - name: Install
         uses: nick-fields/retry@v3
         with:
@@ -67,7 +74,7 @@ jobs:
           command: python -m pip install .[all_extras,dev,unstable_extras]
 
       - name: Tests
-        run: python -m pytest --cov=tsml_eval --cov-report=xml
+        run: python -m pytest --cov=tsml_eval --cov-report=xml --timeout 1800
 
       - uses: codecov/codecov-action@v4
         env:

.github/workflows/precommit_autoupdate.yml

@@ -17,7 +17,7 @@ jobs:
         with:
           python-version: "3.10"
 
-      - uses: browniebroke/pre-commit-autoupdate-action@v1.0.0
+      - uses: browniebroke/pre-commit-autoupdate-action@v1
 
       - if: always()
         uses: actions/create-github-app-token@v1

.github/workflows/release.yml

@@ -51,7 +51,7 @@ jobs:
 
     strategy:
       matrix:
-        os: [ ubuntu-20.04, macOS-13, windows-2022 ]
+        os: [ ubuntu-20.04, macos-13, windows-2022 ]
         python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12" ]
 
     steps: