Merge remote-tracking branch 'origin/main' into pm/time_point_ROCKAD_refactor

# Conflicts:
#	aeon/anomaly_detection/collection/_classification.py
#	aeon/anomaly_detection/collection/_outlier_detection.py
#	aeon/anomaly_detection/collection/base.py
#	aeon/anomaly_detection/series/base.py
#	aeon/anomaly_detection/series/distance_based/__init__.py
#	aeon/anomaly_detection/series/outlier_detection/__init__.py
#	aeon/anomaly_detection/series/outlier_detection/tests/test_one_class_svm.py
#	aeon/testing/estimator_checking/_yield_collection_anomaly_detection_checks.py
#	aeon/testing/estimator_checking/_yield_estimator_checks.py
#	aeon/testing/testing_data.py
#	aeon/utils/base/_identifier.py
#	aeon/utils/base/_register.py
#	aeon/utils/tags/_tags.py
#	docs/api_reference/anomaly_detection.rst

Author: MatthewMiddlehurst

.all-contributorsrc

@@ -2701,6 +2701,52 @@
       "contributions": [
         "code"
       ]
+    },
+    {
+      "login": "SomtoOnyekwelu",
+      "name": "Somtochukwu Benedict Onyekwelu",
+      "avatar_url": "https://avatars.githubusercontent.com/u/117727947?v=4",
+      "profile": "https://github.com/SomtoOnyekwelu",
+      "contributions": [
+        "doc"
+      ]
+    },
+    {
+      "login": "TinaJin0228",
+      "name": "Tina Jin",
+      "avatar_url": "https://avatars.githubusercontent.com/TinaJin0228",
+      "profile": "https://github.com/TinaJin0228",
+      "contributions": [
+        "code",
+        "doc"
+      ]
+    },
+    {
+      "login": "lucifer4073",
+      "name": "Balgopal Moharana",
+      "avatar_url": "https://avatars.githubusercontent.com/u/99070111?v=4",
+      "profile": "https://github.com/lucifer4073",
+      "contributions": [
+        "code"
+      ]
+    },
+    {
+      "login": "Ahmed-Zahran02",
+      "name": "Ahmed Zahran",
+      "avatar_url": "https://avatars.githubusercontent.com/u/136983104?v=4",
+      "profile": "https://github.com/Ahmed-Zahran02",
+      "contributions": [
+        "doc"
+      ]
+    },
+    {
+      "login": "AnaghDeshpande",
+      "name": "Anagh.B.Deshpande",
+      "avatar_url": "https://avatars.githubusercontent.com/u/125550290?v=4",
+      "profile": "https://github.com/AnaghDeshpande",
+      "contributions": [
+        "doc"
+      ]
     }
   ],
   "commitType": "docs"

.github/ISSUE_TEMPLATE/config.yml

@@ -3,11 +3,11 @@ 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-22vwvut29-HDpCu~7VBUozyfL_8j3dLA
+    url: https://join.slack.com/t/aeon-toolkit/shared_invite/zt-36dlmbouu-vajTShUYAHopSXUUVtHGzw
     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
     about: Send an email to the aeon developers at contact@aeon-toolkit.org. Checked periodically.
   - name: "\u2709\uFE0F CoC Report"
-    url: https://www.aeon-toolkit.org/en/latest/code_of_conduct.html
-    about: Report an incident to the Code of Conduct Workgroup.
+    url: https://www.aeon-toolkit.org/en/stable/code_of_conduct.html
+    about: Report an incident to the Code of Conduct Moderators.

.github/actions/cpu_all_extras/action.yml

@@ -5,7 +5,7 @@ inputs:
   python_version:
     description: "Python version used"
     required: false
-    default: "3.11"
+    default: "3.12"
   additional_extras:
     description: "Comma-separated list of additional extras to install"
     required: false
@@ -15,7 +15,7 @@ runs:
   using: "composite"
   steps:
     - name: Install CPU TensorFlow
-      if: ${{ runner.os == 'Linux' && inputs.python_version != '3.13' }}
+      if: ${{ runner.os == 'Linux' && inputs.python_version != '3.13.5' }}
       uses: nick-fields/retry@v3
       with:
         timeout_minutes: 30

.github/utilities/generate_developer_tables.py

@@ -11,6 +11,7 @@
 generate_authors_table.py
 """
 
+import os
 import sys
 import time
 from os import path
@@ -19,7 +20,7 @@
 import requests
 
 LOGO_URL = "https://avatars2.githubusercontent.com/u/78909809"
-REPO_FOLDER = Path(path.abspath(__file__)).parent.parent
+REPO_FOLDER = Path(path.abspath(__file__)).parent.parent.parent
 
 
 def get(url, auth):
@@ -41,8 +42,8 @@ def get(url, auth):
 
 def get_contributors(auth):
     """Get the list of contributor profiles. Require admin rights."""
-    cocw = []
-    cocw_slug = "aeon-code-of-conduct-workgroup"
+    cocm = []
+    cocm_slug = "aeon-code-of-conduct-moderators"
     cw = []
     cw_slug = "aeon-communications-workgroup"
     cd = []
@@ -53,51 +54,54 @@ def get_contributors(auth):
     iw_slug = "aeon-infrastructure-workgroup"
     rmw = []
     rmw_slug = "aeon-release-management-workgroup"
+    sd = []
+    sd_slug = "aeon-supporting-developers"
 
     entry_point = "https://api.github.com/orgs/aeon-toolkit/"
 
     for team_slug, lst in zip(
-        (cocw_slug, cw_slug, cd_slug, fw_slug, iw_slug, rmw_slug),
-        (cocw, cw, cd, fw, iw, rmw),
+        (cocm_slug, cw_slug, cd_slug, fw_slug, iw_slug, rmw_slug, sd_slug),
+        (cocm, cw, cd, fw, iw, rmw, sd),
     ):
         for page in range(5):  # 5 pages, 30 per page
             reply = get(f"{entry_point}teams/{team_slug}/members?page={page}", auth)
             lst.extend(reply.json())
 
     # keep only the logins
-    cocw = {c["login"] for c in cocw}
+    cocm = {c["login"] for c in cocm}
     cw = {c["login"] for c in cw}
     cd = {c["login"] for c in cd}
     fw = {c["login"] for c in fw}
     iw = {c["login"] for c in iw}
     rmw = {c["login"] for c in rmw}
-
-    # add missing contributors with GitHub accounts
-    cocw |= {"KatieBuc"}
+    sd = {c["login"] for c in sd}
 
     # get profiles from GitHub
-    cocw = [get_profile(login, auth) for login in cocw]
+    cocm = [get_profile(login, auth) for login in cocm]
     cw = [get_profile(login, auth) for login in cw]
     cd = [get_profile(login, auth) for login in cd]
     fw = [get_profile(login, auth) for login in fw]
     iw = [get_profile(login, auth) for login in iw]
     rmw = [get_profile(login, auth) for login in rmw]
+    sd = [get_profile(login, auth) for login in sd]
 
     # sort by last name
-    cocw = sorted(cocw, key=key)
+    cocm = sorted(cocm, key=key)
     cw = sorted(cw, key=key)
     cd = sorted(cd, key=key)
     fw = sorted(fw, key=key)
     iw = sorted(iw, key=key)
     rmw = sorted(rmw, key=key)
+    sd = sorted(sd, key=key)
 
     return (
-        cocw,
+        cocm,
         cw,
         cd,
         fw,
         iw,
         rmw,
+        sd,
     )
 
 
@@ -112,13 +116,6 @@ def get_profile(login, auth):
     if profile["name"] is None:
         profile["name"] = profile["login"]
 
-    # fix missing names
-    missing_names = {
-        "KatieBuc": "Katie Buchhorn",
-    }
-    if profile["name"] in missing_names:
-        profile["name"] = missing_names[profile["name"]]
-
     return profile
 
 
@@ -150,25 +147,28 @@ def generate_table(contributors):
 
 
 if __name__ == "__main__":
-    print("access token:", file=sys.stderr)  # noqa: T201
-    token = input()
-    auth = ("user", token)
+    auth = os.getenv("GITHUB_TOKEN")
+    if auth is None:
+        print("access token:", file=sys.stderr)  # noqa: T201
+        token = input()
+        auth = ("user", token)
 
     (
-        cocw,
+        cocm,
         cw,
         cd,
         fw,
         iw,
         rmw,
+        sd,
     ) = get_contributors(auth)
 
     with open(
-        REPO_FOLDER / "docs" / "about" / "code_of_conduct_workgroup.md",
+        REPO_FOLDER / "docs" / "about" / "code_of_conduct_moderators.md",
         "w+",
         encoding="utf-8",
     ) as rst_file:
-        rst_file.write(generate_table(cocw))
+        rst_file.write(generate_table(cocm))
 
     with open(
         REPO_FOLDER / "docs" / "about" / "communications_workgroup.md",
@@ -200,3 +200,10 @@ def generate_table(contributors):
         encoding="utf-8",
     ) as rst_file:
         rst_file.write(generate_table(rmw))
+
+    with open(
+        REPO_FOLDER / "docs" / "about" / "supporting_developers.md",
+        "w+",
+        encoding="utf-8",
+    ) as rst_file:
+        rst_file.write(generate_table(sd))

.github/utilities/pr_open_commenter.py

@@ -34,22 +34,10 @@
         if label == cur_label:
             content_labels[i] = new_label
 
-labels = [(label.name, label.color) for label in repo.get_labels()]
-title_labels = [
-    f"$\\color{{#{color}}}{{\\textsf{{{label}}}}}$"
-    for label, color in labels
-    if label in title_labels
-]
-title_labels_new = [
-    f"$\\color{{#{color}}}{{\\textsf{{{label}}}}}$"
-    for label, color in labels
-    if label in title_labels_new
-]
-content_labels = [
-    f"$\\color{{#{color}}}{{\\textsf{{{label}}}}}$"
-    for label, color in labels
-    if label in content_labels
-]
+labels = [label.name for label in repo.get_labels()]
+title_labels = [f"**{label}**" for label in labels if label in title_labels]
+title_labels_new = [f"**{label}**" for label in labels if label in title_labels_new]
+content_labels = [f"**{label}**" for label in labels if label in content_labels]
 
 title_labels_str = ""
 if len(title_labels) == 0:
@@ -62,30 +50,28 @@
     arr_str = str(title_labels_new).strip("[]").replace("'", "")
     title_labels_str = (
         "I have added the following labels to this PR based on the title: "
-        f"**[ {arr_str} ]**."
+        f"[ {arr_str} ]."
     )
     if len(title_labels) != len(title_labels_new):
         arr_str = (
             str(set(title_labels) - set(title_labels_new)).strip("[]").replace("'", "")
         )
-        title_labels_str += (
-            f" The following labels were already present: **[ {arr_str} ]**"
-        )
+        title_labels_str += f" The following labels were already present: [ {arr_str} ]"
 
 content_labels_str = ""
 if len(content_labels) != 0:
     if content_labels_status == "used":
         arr_str = str(content_labels).strip("[]").replace("'", "")
         content_labels_str = (
             "I have added the following labels to this PR based on "
-            f"the changes made: **[ {arr_str} ]**. Feel free "
+            f"the changes made: [ {arr_str} ]. Feel free "
             "to change these if they do not properly represent the PR."
         )
     elif content_labels_status == "ignored":
         arr_str = str(content_labels).strip("[]").replace("'", "")
         content_labels_str = (
             "I would have added the following labels to this PR "
-            f"based on the changes made: **[ {arr_str} ]**, "
+            f"based on the changes made: [ {arr_str} ], "
             "however some package labels are already present."
         )
     elif content_labels_status == "large":
@@ -112,9 +98,10 @@
 
 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-22vwvut29-HDpCu~7VBUozyfL_8j3dLA) 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-36dlmbouu-vajTShUYAHopSXUUVtHGzw) channel if you have any.
 
-### PR CI actions
+<details><summary>PR CI actions</summary>
+<p>
 
 These checkboxes will add labels to enable/disable CI functionality for this PR. This may not take effect immediately, and a new commit may be required to run the new configuration.
 
@@ -126,5 +113,8 @@
 - [ ] Stop automatic `pre-commit` fixes (always disabled for drafts)
 - [ ] Disable numba cache loading
 - [ ] Push an empty commit to re-run CI checks
+
+</p>
+</details>
     """  # noqa
 )

.github/workflows/fast_release.yml

@@ -11,10 +11,10 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Setup Python 3.11
+      - name: Setup Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Build project
         run: |

.github/workflows/issue_assigned.yml

@@ -25,10 +25,10 @@ jobs:
         with:
           sparse-checkout: .github/utilities
 
-      - name: Setup Python 3.11
+      - name: Setup Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - 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 3.11
+      - name: Setup Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Install PyGithub
         run: pip install -Uq PyGithub
@@ -51,10 +51,9 @@ jobs:
 
       - if: ${{ steps.label_out.outputs.empty_commit == 'true' }}
         name: Push empty commit
-        uses: stefanzweifel/git-auto-commit-action@v5
+        uses: stefanzweifel/git-auto-commit-action@v6
         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

.github/workflows/issue_comment_posted.yml

@@ -14,10 +14,10 @@ jobs:
         with:
           sparse-checkout: .github/utilities
 
-      - name: Setup Python 3.11
+      - name: Setup Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Install PyGithub
         run: pip install -Uq PyGithub