Merge branch 'main' into attbgru

aeon-toolkit · Jul 13, 2024 · e364e5b · e364e5b
2 parents b0edeee + 3a01b53
commit e364e5b
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diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -3,15 +3,17 @@
   "projectOwner": "aeon-toolkit",
   "repoType": "github",
   "repoHost": "https://github.com",
-  "commitConvention": "none",
   "files": [
     "CONTRIBUTORS.md"
   ],
   "imageSize": 80,
+  "commit": "false",
+  "commitConvention": "atom",
   "contributorsPerLine": 8,
   "contributorsSortAlphabetically": true,
-  "linkToUsage": true,
   "badgeTemplate": "[![All Contributors](https://img.shields.io/badge/all_contributors-<%= contributors.length %>-orange.svg)](#contributors)",
+  "linkToUsage": true,
+  "skipCi": true,
   "contributors": [
     {
       "login": "fkiraly",
@@ -2349,7 +2351,7 @@
         "code",
         "doc",
         "research",
-        "tests",
+        "test",
         "review",
         "data"
       ]
@@ -2436,6 +2438,5 @@
         "doc"
       ]
     }
-  ],
-  "commitType": "docs"
+  ]
 }
diff --git a/.github/workflows/issue_comment_edited.yml b/.github/workflows/issue_comment_edited.yml
@@ -0,0 +1,60 @@
+name: Issue Comment Edited
+
+on:
+  issue_comment:
+    types: [edited]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.comment.id }}
+  cancel-in-progress: true
+
+jobs:
+  pr-welcome-edited:
+    if: ${{ github.event.issue.pull_request }}
+    runs-on: ubuntu-20.04
+
+    steps:
+      - name: Create app token
+        uses: actions/create-github-app-token@v1
+        id: app-token
+        with:
+          app-id: ${{ vars.PR_APP_ID }}
+          private-key: ${{ secrets.PR_APP_KEY }}
+
+      - name: Checkout main
+        uses: actions/checkout@v4
+        with:
+          sparse-checkout: build_tools
+
+      - name: Setup Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install PyGithub
+        run: pip install -Uq PyGithub
+
+      - name: Process comment edit
+        id: label_out
+        run: python build_tools/pr_welcome_edited.py
+        env:
+          CONTEXT_GITHUB: ${{ toJson(github) }}
+          GITHUB_TOKEN: ${{ steps.app-token.outputs.token }}
+
+      - if: ${{ steps.label_out.outputs.empty_commit == 'true' }}
+        name: Checkout head
+        uses: actions/checkout@v4
+        with:
+          repository: ${{ steps.label_out.outputs.repo }}
+          ref: ${{ steps.label_out.outputs.branch }}
+          token: ${{ steps.app-token.outputs.token }}
+
+      - if: ${{ steps.label_out.outputs.empty_commit == 'true' }}
+        name: Push empty commit
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          commit_message: Empty commit for CI
+          commit_user_name: aeon-actions-bot[bot]
+          commit_options: --allow-empty
+          create_branch: false
+          skip_dirty_check: true
diff --git a/.github/workflows/issue_comment_posted.yml b/.github/workflows/issue_comment_posted.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-      - name: Checkout main
+      - name: Checkout
         uses: actions/checkout@v4
         with:
           sparse-checkout: build_tools

diff --git a/.github/workflows/periodic_github_maintenace.yml b/.github/workflows/periodic_github_maintenace.yml
@@ -23,13 +23,13 @@ jobs:
           private-key: ${{ secrets.PR_APP_KEY }}
 
       - name: Stale Branches
-        uses: crs-k/stale-branches@v5.0.0
+        uses: crs-k/stale-branches@v5.0.1
         with:
           repo-token: ${{ steps.app-token.outputs.token }}
           days-before-stale: 140
           days-before-delete: 175
           comment-updates: true
           tag-committer: true
           stale-branch-label: "stale branch"
-          compare-branches: 'info'
+          compare-branches: "info"
           pr-check: true
diff --git a/.github/workflows/periodic_tests.yml b/.github/workflows/periodic_tests.yml
@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-      - name: Checkout main
+      - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python 3.10
@@ -32,7 +32,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-      - name: Checkout main
+      - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python 3.10
@@ -49,7 +49,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-      - name: Checkout main
+      - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python 3.10
@@ -87,7 +87,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-      - name: Checkout main
+      - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python 3.10
@@ -114,7 +114,7 @@ jobs:
         run: python -m pip list
 
       - name: Run tests
-        run: python -m pytest
+        run: python -m pytest -n logical
 
       - name: Save new cache
         uses: actions/cache/save@v4
@@ -129,11 +129,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-20.04, macOS-13, windows-2022 ]
-        python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12" ]
+        os: [ ubuntu-20.04, macOS-14, windows-2022 ]
+        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
 
     steps:
-      - name: Checkout main
+      - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python
@@ -160,7 +160,7 @@ jobs:
         run: python -m pip list
 
       - name: Run tests
-        run: python -m pytest
+        run: python -m pytest -n logical
 
       - name: Save new cache
         uses: actions/cache/save@v4
@@ -173,7 +173,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-      - name: Checkout main
+      - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python 3.10
@@ -195,7 +195,7 @@ jobs:
         run: python -m pip list
 
       - name: Run tests
-        run: python -m pytest --cov=aeon --cov-report=xml --timeout 1800
+        run: python -m pytest -n logical --cov=aeon --cov-report=xml --timeout 1800
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4

diff --git a/.github/workflows/pr_examples.yml b/.github/workflows/pr_examples.yml
@@ -22,15 +22,15 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-      - name: Checkout main
+      - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python 3.10
         uses: actions/setup-python@v5
         with:
           python-version: "3.10"
 
-      - name: Use numba cache to set env variables but not restore cache
+      - name: Restore numba cache
         uses: ./.github/actions/numba_cache
         with:
           cache_name: "run-notebook-examples"

diff --git a/.github/workflows/pr_opened.yml b/.github/workflows/pr_opened.yml
@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-      - name: Checkout main
+      - name: Checkout
         uses: actions/checkout@v4
         with:
           sparse-checkout: build_tools

diff --git a/.github/workflows/pr_precommit.yml b/.github/workflows/pr_precommit.yml
@@ -4,7 +4,7 @@ on:
   push:
     branches:
       - main
-  pull_request:
+  pull_request_target:
     branches:
       - main
 
@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-      - name: Checkout main
+      - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python 3.10
@@ -26,23 +26,45 @@ jobs:
           python-version: "3.10"
 
       - name: Get changed files
-        uses: tj-actions/changed-files@v44.5.2
+        uses: tj-actions/changed-files@v44
         id: changed-files
 
       - name: List changed files
         run: echo '${{ steps.changed-files.outputs.all_changed_files }}'
 
-      - if: ${{ github.event_name == 'pull_request' && contains(github.event.pull_request.labels.*.name, 'full pre-commit') }}
+      # only check the full repository if PR and correctly labelled
+      - if: ${{ github.event_name == 'pull_request_target' && contains(github.event.pull_request.labels.*.name, 'full pre-commit') }}
         name: Full pre-commit
         uses: pre-commit/action@v3.0.1
         with:
           extra_args: --all-files
-      - if: ${{ github.event_name != 'pull_request' || !contains(github.event.pull_request.labels.*.name, 'full pre-commit') }}
+      - if: ${{ github.event_name != 'pull_request_target' || !contains(github.event.pull_request.labels.*.name, 'full pre-commit') }}
         name: Local pre-commit
         uses: pre-commit/action@v3.0.1
         with:
           extra_args: --files ${{ steps.changed-files.outputs.all_changed_files }}
 
-      - if: ${{ failure() && github.event_name == 'pull_request' && github.event.pull_request.draft == false }}
+      # push fixes if pre-commit fails and PR is eligible
+      - if: ${{ failure() && github.event_name == 'pull_request_target' && !github.event.pull_request.draft && !contains(github.event.pull_request.labels.*.name, 'stop pre-commit fixes') }}
+        name: Create app token
+        uses: actions/create-github-app-token@v1
+        id: app-token
+        with:
+          app-id: ${{ vars.PR_APP_ID }}
+          private-key: ${{ secrets.PR_APP_KEY }}
+
+      - if: ${{ failure() && github.event_name == 'pull_request_target' && !github.event.pull_request.draft && !contains(github.event.pull_request.labels.*.name, 'stop pre-commit fixes') }}
+        name: Checkout
+        uses: actions/checkout@v4
+        with:
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          ref: ${{ github.head_ref }}
+          token: ${{ steps.app-token.outputs.token }}
+
+      - if: ${{ failure() && github.event_name == 'pull_request_target' && !github.event.pull_request.draft && !contains(github.event.pull_request.labels.*.name, 'stop pre-commit fixes') }}
         name: Push pre-commit fixes
-        uses: pre-commit-ci/lite-action@v1.0.2
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          commit_message: Automatic `pre-commit` fixes
+          commit_user_name: aeon-actions-bot[bot]
+          create_branch: false
diff --git a/.github/workflows/pr_pytest.yml b/.github/workflows/pr_pytest.yml
@@ -21,15 +21,15 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-      - name: Checkout main
+      - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python 3.10
         uses: actions/setup-python@v5
         with:
           python-version: "3.10"
 
-      - name: Use numba cache to set env variables and restore cache
+      - name: Restore numba cache
         uses: ./.github/actions/numba_cache
         with:
           cache_name: "test-no-soft-deps"
@@ -47,35 +47,33 @@ jobs:
         run: python -m pip list
 
       - name: Run tests
-        run: python -m pytest -k 'not TestAll'
+        run: python -m pytest -n logical -k 'not TestAll'
 
   pytest:
     runs-on: ${{ matrix.os }}
 
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-20.04, macOS-13, windows-2022 ]
-        python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12" ]
+        os: [ ubuntu-20.04, macOS-14, 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:
           - ${{ (github.event_name != 'pull_request' || !contains(github.event.pull_request.labels.*.name, 'full pytest actions')) }}
         exclude:
           - pr-testing: true
-            python-version: "3.9"
-          - pr-testing: true
-            python-version: "3.11"
+            python-version: "3.10"
 
     steps:
-      - name: Checkout main
+      - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Use numba cache to set env variables and restore cache
+      - name: Restore numba cache
         uses: ./.github/actions/numba_cache
         with:
           cache_name: "pytest"
@@ -94,7 +92,7 @@ jobs:
 
       - name: Run tests
         # run the full test suit if a PR has the 'full pytest actions' label
-        run: python -m pytest --prtesting ${{ github.event_name != 'pull_request' || !contains(github.event.pull_request.labels.*.name, 'full pytest actions') }}
+        run: python -m pytest -n logical --prtesting ${{ github.event_name != 'pull_request' || !contains(github.event.pull_request.labels.*.name, 'full pytest actions') }}
 
   codecov:
     # run the code coverage job if a PR has the 'codecov actions' label
@@ -103,7 +101,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-      - name: Checkout main
+      - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python 3.10
@@ -125,7 +123,7 @@ jobs:
         run: python -m pip list
 
       - name: Run tests
-        run: python -m pytest --cov=aeon --cov-report=xml --timeout 1800
+        run: python -m pytest -n logical --cov=aeon --cov-report=xml --timeout 1800
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4