Merge branch 'main' into msm-bug-fix

Author: chrisholder

.codecov.yml

@@ -25,6 +25,6 @@ github_checks:
 ignore:
   - ".github/"
   - ".binder/"
-  - "aeon/testing/expected_results/results_reproduction/"
+  - "aeon/testing/expected_results/_write_estimator_results.py"
   - "docs/"
   - "examples/"

.github/ISSUE_TEMPLATE/config.yml

@@ -3,7 +3,7 @@ contact_links:
     url: https://github.com/aeon-toolkit/aeon/discussions/new/choose
     about: If none of these options fit, your question or topic may be better suited to a discussion.
   - name: "\U0001F4AC Slack"
-    url: https://join.slack.com/t/aeon-toolkit/shared_invite/zt-36dlmbouu-vajTShUYAHopSXUUVtHGzw
+    url: https://join.slack.com/t/aeon-toolkit/shared_invite/zt-3ihx5vif8-SwFzy1unNNMeQueC84MXVA
     about: For all other questions and general chat, come chat with the aeon community on Slack!
   - name: "\u2709\uFE0F Email"
     url: https://mailxto.com/jbp3ave49x

.github/utilities/_commons.py

@@ -0,0 +1,12 @@
+label_options = [
+    ("full pre-commit", "Run `pre-commit` checks for all files"),
+    ("run typecheck test", "Run `mypy` typecheck tests"),
+    ("full pytest actions", "Run all `pytest` tests and configurations"),
+    ("full examples run", "Run all notebook example tests"),
+    ("codecov actions", "Run numba-disabled `codecov` tests"),
+    (
+        "stop pre-commit fixes",
+        "Stop automatic `pre-commit` fixes (always disabled for drafts)",
+    ),
+    ("no numba cache", "Disable numba cache loading"),
+]

.github/utilities/pr_open_commenter.py

@@ -98,7 +98,7 @@
 
 If our `pre-commit` code quality check fails, any trivial fixes will automatically be pushed to your PR unless it is a draft.
 
-Don't hesitate to ask questions on the `aeon` [Slack](https://join.slack.com/t/aeon-toolkit/shared_invite/zt-36dlmbouu-vajTShUYAHopSXUUVtHGzw) channel if you have any.
+Don't hesitate to ask questions on the `aeon` [Slack](https://join.slack.com/t/aeon-toolkit/shared_invite/zt-3ihx5vif8-SwFzy1unNNMeQueC84MXVA) channel if you have any.
 
 <details><summary>PR CI actions</summary>
 <p>
@@ -112,6 +112,7 @@
 - [ ] Run numba-disabled `codecov` tests
 - [ ] Stop automatic `pre-commit` fixes (always disabled for drafts)
 - [ ] Disable numba cache loading
+- [ ] Regenerate expected results for testing
 - [ ] Push an empty commit to re-run CI checks
 
 </p>

.github/utilities/pr_welcome_edited.py

@@ -1,9 +1,10 @@
-"""Labels PRs and process based on bot comment checkboxes."""
+"""Labels PRs based on bot comment checkboxes."""
 
 import json
 import os
 import sys
 
+from _commons import label_options
 from github import Github
 
 context_dict = json.loads(os.getenv("CONTEXT_GITHUB"))
@@ -17,62 +18,41 @@
 comment_user = context_dict["event"]["comment"]["user"]["login"]
 labels = [label.name for label in issue.get_labels()]
 
+
 if (
-    issue.pull_request is None
+    "[bot]" in context_dict["event"]["sender"]["login"]
+    or issue.pull_request is None
     or comment_user != "aeon-actions-bot[bot]"
     or "## Thank you for contributing to `aeon`" not in comment_body
 ):
     with open(os.environ["GITHUB_OUTPUT"], "a") as fh:
+        print("expected_results=false", file=fh)  # noqa: T201
         print("empty_commit=false", file=fh)  # noqa: T201
     sys.exit(0)
-pr = issue.as_pull_request()
-
-
-def check_label_option(label, option):
-    """Add or remove a label based on a checkbox in a comment."""
-    if f"- [x] {option}" in comment_body:
-        if label not in labels:
-            pr.add_to_labels(label)
-    elif f"- [ ] {option}" in comment_body:
-        if label in labels:
-            pr.remove_from_labels(label)
-
 
-label_options = [
-    ("full pre-commit", "Run `pre-commit` checks for all files"),
-    ("run typecheck test", "Run `mypy` typecheck tests"),
-    ("full pytest actions", "Run all `pytest` tests and configurations"),
-    ("full examples run", "Run all notebook example tests"),
-    ("codecov actions", "Run numba-disabled `codecov` tests"),
-    (
-        "stop pre-commit fixes",
-        "Stop automatic `pre-commit` fixes (always disabled for drafts)",
-    ),
-    ("no numba cache", "Disable numba cache loading"),
-]
+pr = issue.as_pull_request()
+comment = pr.get_issue_comment(context_dict["event"]["comment"]["id"])
 
 for option in label_options:
-    check_label_option(option[0], option[1])
+    if f"- [x] {option[1]}" in comment_body and option[0] not in labels:
+        pr.add_to_labels(option[0])
+    elif f"- [ ] {option[1]}" in comment_body and option[0] in labels:
+        pr.remove_from_labels(option[0])
 
 repo_name = pr.head.repo.full_name
 branch_name = pr.head.ref
 with open(os.environ["GITHUB_OUTPUT"], "a") as fh:
     print(f"repo={repo_name}", file=fh)  # noqa: T201
     print(f"branch={branch_name}", file=fh)  # noqa: T201
 
+if "- [x] Regenerate expected results for testing" in comment_body:
+    with open(os.environ["GITHUB_OUTPUT"], "a") as fh:
+        print("expected_results=true", file=fh)  # noqa: T201
+else:
+    with open(os.environ["GITHUB_OUTPUT"], "a") as fh:
+        print("expected_results=false", file=fh)  # noqa: T201
+
 if "- [x] Push an empty commit to re-run CI checks" in comment_body:
-    for comment in pr.get_comments():
-        if (
-            comment.user.login == comment_user
-            and "## Thank you for contributing to `aeon`" in comment.body
-        ):
-            comment.edit(
-                comment_body.replace(
-                    "- [x] Push an empty commit to re-run CI checks",
-                    "- [ ] Push an empty commit to re-run CI checks",
-                )
-            )
-            break
     with open(os.environ["GITHUB_OUTPUT"], "a") as fh:
         print("empty_commit=true", file=fh)  # noqa: T201
 else:

.github/utilities/pr_welcome_updater.py

@@ -0,0 +1,47 @@
+"""Labels PRs based on bot comment checkboxes."""
+
+import json
+import os
+import sys
+
+from _commons import label_options
+from github import Github
+
+context_dict = json.loads(os.getenv("CONTEXT_GITHUB"))
+
+repo = context_dict["repository"]
+g = Github(os.getenv("GITHUB_TOKEN"))
+repo = g.get_repo(repo)
+pr_number = context_dict["event"]["number"]
+pr = repo.get_pull(number=pr_number)
+labels = [label.name for label in pr.get_labels()]
+
+if "[bot]" in context_dict["event"]["sender"]["login"]:
+    sys.exit(0)
+
+comment = None
+for c in pr.get_issue_comments():
+    if (
+        c.user.login == "aeon-actions-bot[bot]"
+        and "## Thank you for contributing to `aeon-eval`" in c.body
+    ):
+        comment = c
+        break
+
+if comment is None:
+    sys.exit(0)
+
+comment_body = comment.body
+for option in label_options:
+    if f"- [x] {option[1]}" in comment_body and option[0] not in labels:
+        comment_body = comment_body.replace(
+            f"- [x] {option[1]}",
+            f"- [ ] {option[1]}",
+        )
+    elif f"- [ ] {option[1]}" in comment_body and option[0] in labels:
+        comment_body = comment_body.replace(
+            f"- [ ] {option[1]}",
+            f"- [x] {option[1]}",
+        )
+
+comment.edit(comment_body)

.github/utilities/uncheck_welcome_boxes.py

@@ -0,0 +1,45 @@
+"""Uncheck relevant boxes after running the comment edit workflow."""
+
+import json
+import os
+import sys
+
+from github import Github
+
+context_dict = json.loads(os.getenv("CONTEXT_GITHUB"))
+
+repo = context_dict["repository"]
+g = Github(os.getenv("GITHUB_TOKEN"))
+repo = g.get_repo(repo)
+issue_number = context_dict["event"]["issue"]["number"]
+issue = repo.get_issue(number=issue_number)
+comment_body = context_dict["event"]["comment"]["body"]
+comment_user = context_dict["event"]["comment"]["user"]["login"]
+
+if (
+    "[bot]" in context_dict["event"]["sender"]["login"]
+    or issue.pull_request is None
+    or comment_user != "aeon-actions-bot[bot]"
+    or "## Thank you for contributing to `aeon`" not in comment_body
+):
+    sys.exit(0)
+
+pr = issue.as_pull_request()
+comment = pr.get_issue_comment(context_dict["event"]["comment"]["id"])
+
+new_comment_body = comment_body
+
+if "- [x] Regenerate expected results for testing" in comment_body:
+    new_comment_body = new_comment_body.replace(
+        "- [x] Regenerate expected results for testing",
+        "- [ ] Regenerate expected results for testing",
+    )
+
+if "- [x] Push an empty commit to re-run CI checks" in comment_body:
+    new_comment_body = new_comment_body.replace(
+        "- [x] Push an empty commit to re-run CI checks",
+        "- [ ] Push an empty commit to re-run CI checks",
+    )
+
+if new_comment_body != comment_body:
+    comment.edit(new_comment_body)

.github/workflows/fast_release.yml

@@ -9,10 +9,10 @@ jobs:
     runs-on: ubuntu-24.04
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Setup Python 3.12
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.12"
 
@@ -22,7 +22,7 @@ jobs:
           python -m build
 
       - name: Store build files
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: dist
           path: dist/*
@@ -38,7 +38,7 @@ jobs:
       id-token: write
 
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v6
         with:
           name: dist
           path: dist

.github/workflows/issue_assigned.yml

@@ -21,12 +21,12 @@ jobs:
           private-key: ${{ secrets.PR_APP_KEY }}
 
       - name: Checkout main
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           sparse-checkout: .github/utilities
 
       - name: Setup Python 3.12
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.12"
 

.github/workflows/issue_comment_edited.yml

@@ -22,12 +22,12 @@ jobs:
           private-key: ${{ secrets.PR_APP_KEY }}
 
       - name: Checkout main
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           sparse-checkout: .github/utilities
 
       - name: Setup Python 3.12
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.12"
 
@@ -41,19 +41,36 @@ jobs:
           CONTEXT_GITHUB: ${{ toJson(github) }}
           GITHUB_TOKEN: ${{ steps.app-token.outputs.token }}
 
-      - if: ${{ steps.label_out.outputs.empty_commit == 'true' }}
+      - if: ${{ steps.label_out.outputs.expected_results == 'true' || steps.label_out.outputs.empty_commit == 'true' }}
         name: Checkout head
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           repository: ${{ steps.label_out.outputs.repo }}
           ref: ${{ steps.label_out.outputs.branch }}
           token: ${{ steps.app-token.outputs.token }}
 
+      - if: ${{ steps.label_out.outputs.expected_results == 'true' }}
+        name: Regenerate expected results
+        run: python aeon/testing/expected_results/_write_estimator_results.py
+
+      - if: ${{ steps.label_out.outputs.expected_results == 'true' }}
+        name: Push expected results
+        uses: stefanzweifel/git-auto-commit-action@v7
+        with:
+          commit_message: Regenerated expected results for testing
+          commit_user_name: aeon-actions-bot[bot]
+
       - if: ${{ steps.label_out.outputs.empty_commit == 'true' }}
         name: Push empty commit
-        uses: stefanzweifel/git-auto-commit-action@v6
+        uses: stefanzweifel/git-auto-commit-action@v7
         with:
           commit_message: Empty commit for CI
           commit_user_name: aeon-actions-bot[bot]
           commit_options: --allow-empty
           skip_dirty_check: true
+
+      - name: Uncheck relevant boxes
+        run: python .github/utilities/uncheck_welcome_boxes.py
+        env:
+          CONTEXT_GITHUB: ${{ toJson(github) }}
+          GITHUB_TOKEN: ${{ steps.app-token.outputs.token }}