Merge branch 'main' into adds_class_weights

.all-contributorsrc

@@ -3,9 +3,11 @@
   "projectOwner": "aeon-toolkit",
   "repoType": "github",
   "repoHost": "https://github.com",
-  "files": ["CONTRIBUTORS.md"],
+  "files": [
+    "CONTRIBUTORS.md"
+  ],
   "imageSize": 80,
-  "commit": "false"
+  "commit": "false",
   "commitConvention": "atom",
   "contributorsPerLine": 8,
   "contributorsSortAlphabetically": true,
@@ -2349,7 +2351,7 @@
         "code",
         "doc",
         "research",
-        "tests",
+        "test",
         "review",
         "data"
       ]
@@ -2436,5 +2438,5 @@
         "doc"
       ]
     }
-  ],
+  ]
 }

.github/workflows/issue_comment_edited.yml

@@ -1,15 +1,27 @@
-name: Issue Comment Posted
+name: Issue Comment Edited
 
 on:
   issue_comment:
     types: [edited]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.comment.id }}
+  cancel-in-progress: true
+
 jobs:
-  check-pr-labels:
+  pr-welcome-edited:
+    if: ${{ github.event.issue.pull_request }}
     runs-on: ubuntu-20.04
 
     steps:
-      - name: Checkout
+      - 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
@@ -22,15 +34,27 @@ jobs:
       - name: Install PyGithub
         run: pip install -Uq PyGithub
 
-      - 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: Assign issue
-        run: python build_tools/comment_pr_labeler.py
+      - 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

.github/workflows/periodic_github_maintenace.yml

@@ -23,7 +23,7 @@ jobs:
           private-key: ${{ secrets.PR_APP_KEY }}
 
       - name: Stale Branches
-        uses: crs-k/stale-branches@v5
+        uses: crs-k/stale-branches@v5.0.1
         with:
           repo-token: ${{ steps.app-token.outputs.token }}
           days-before-stale: 140

.github/workflows/pr_precommit.yml

@@ -1,6 +1,9 @@
 name: PR pre-commit
 
 on:
+  push:
+    branches:
+      - main
   pull_request_target:
     branches:
       - main
@@ -24,7 +27,8 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
         with:
-          ref: ${{ github.event.pull_request.head.sha }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          ref: ${{ github.head_ref }}
           token: ${{ steps.app-token.outputs.token }}
 
       - name: Setup Python 3.10
@@ -50,9 +54,10 @@ jobs:
         with:
           extra_args: --files ${{ steps.changed-files.outputs.all_changed_files }}
 
-      - if: ${{ failure() && github.event_name == 'pull_request_target' && github.event.pull_request.draft == false && !contains(github.event.pull_request.labels.*.name, 'stop pre-commit fixes')}}
+      - 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: stefanzweifel/git-auto-commit-action@v5
         with:
           commit_message: Automatic `pre-commit` fixes
           commit_user_name: aeon-actions-bot[bot]
+          create_branch: false

.github/workflows/precommit_autoupdate.yml

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

.pre-commit-config.yaml

@@ -29,7 +29,7 @@ repos:
         args: [ "--create", "--python-folders", "aeon" ]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.8
+    rev: v0.5.1
     hooks:
       - id: ruff
         args: [ "--fix"]
@@ -48,7 +48,7 @@ repos:
         args: [ "--profile=black", "--multi-line=3" ]
 
   - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
+    rev: 7.1.0
     hooks:
       - id: flake8
         additional_dependencies: [ flake8-bugbear, flake8-print, Flake8-pyproject ]

CODEOWNERS

@@ -44,6 +44,8 @@ aeon/transformations/theta.py @GuzalBulatova
 
 aeon/utils/numba/ @baraline @MatthewMiddlehurst
 
+aeon/visualisation/ @baraline
+
 .github/ @aeon-toolkit/aeon-infrastructure-workgroup
 build_tools/ @aeon-toolkit/aeon-infrastructure-workgroup
 

CONTRIBUTORS.md

@@ -229,7 +229,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
       <td align="center" valign="top" width="12.5%"><a href="https://github.com/dasgupsa"><img src="https://avatars2.githubusercontent.com/u/10398956?v=4?s=80" width="80px;" alt="Saurabh Dasgupta"/><br /><sub><b>Saurabh Dasgupta</b></sub></a><br /><a href="https://github.com/aeon-toolkit/aeon/commits?author=dasgupsa" title="Code">💻</a></td>
       <td align="center" valign="top" width="12.5%"><a href="https://github.com/SebasKoel"><img src="https://avatars3.githubusercontent.com/u/66252156?v=4?s=80" width="80px;" alt="Sebastiaan Koel"/><br /><sub><b>Sebastiaan Koel</b></sub></a><br /><a href="https://github.com/aeon-toolkit/aeon/commits?author=SebasKoel" title="Code">💻</a> <a href="https://github.com/aeon-toolkit/aeon/commits?author=SebasKoel" title="Documentation">📖</a></td>
       <td align="center" valign="top" width="12.5%"><a href="https://github.com/shagn"><img src="https://avatars.githubusercontent.com/u/16029092?v=4?s=80" width="80px;" alt="Sebastian Hagn"/><br /><sub><b>Sebastian Hagn</b></sub></a><br /><a href="https://github.com/aeon-toolkit/aeon/commits?author=shagn" title="Documentation">📖</a></td>
-      <td align="center" valign="top" width="12.5%"><a href="https://github.com/codelionx"><img src="https://avatars.githubusercontent.com/u/10573700?v=4?s=80" width="80px;" alt="Sebastian Schmidl"/><br /><sub><b>Sebastian Schmidl</b></sub></a><br /><a href="https://github.com/aeon-toolkit/aeon/issues?q=author%3Acodelionx" title="Bug reports">🐛</a> <a href="https://github.com/aeon-toolkit/aeon/commits?author=codelionx" title="Code">💻</a> <a href="https://github.com/aeon-toolkit/aeon/commits?author=codelionx" title="Documentation">📖</a> <a href="#research-codelionx" title="Research">🔬</a></td>
+      <td align="center" valign="top" width="12.5%"><a href="https://github.com/codelionx"><img src="https://avatars.githubusercontent.com/u/10573700?v=4?s=80" width="80px;" alt="Sebastian Schmidl"/><br /><sub><b>Sebastian Schmidl</b></sub></a><br /><a href="https://github.com/aeon-toolkit/aeon/issues?q=author%3Acodelionx" title="Bug reports">🐛</a> <a href="https://github.com/aeon-toolkit/aeon/commits?author=codelionx" title="Code">💻</a> <a href="https://github.com/aeon-toolkit/aeon/commits?author=codelionx" title="Documentation">📖</a> <a href="#research-codelionx" title="Research">🔬</a> <a href="https://github.com/aeon-toolkit/aeon/commits?author=codelionx" title="Tests">⚠️</a> <a href="https://github.com/aeon-toolkit/aeon/pulls?q=is%3Apr+reviewed-by%3Acodelionx" title="Reviewed Pull Requests">👀</a> <a href="#data-codelionx" title="Data">🔣</a></td>
       <td align="center" valign="top" width="12.5%"><a href="https://github.com/AurumnPegasus"><img src="https://avatars.githubusercontent.com/u/54315149?v=4?s=80" width="80px;" alt="Shivansh Subramanian"/><br /><sub><b>Shivansh Subramanian</b></sub></a><br /><a href="https://github.com/aeon-toolkit/aeon/commits?author=AurumnPegasus" title="Documentation">📖</a> <a href="https://github.com/aeon-toolkit/aeon/commits?author=AurumnPegasus" title="Code">💻</a></td>
       <td align="center" valign="top" width="12.5%"><a href="https://www.linkedin.com/in/solomon-botchway-a1383821b/"><img src="https://avatars.githubusercontent.com/u/62394255?v=4?s=80" width="80px;" alt="Solomon Botchway"/><br /><sub><b>Solomon Botchway</b></sub></a><br /><a href="#maintenance-snnbotchway" title="Maintenance">🚧</a></td>
     </tr>

aeon/classification/shapelet_based/_rdst.py

@@ -60,6 +60,9 @@ class RDSTClassifier(BaseClassifier):
         If True, restrict the value of the shapelet dilation parameter to be prime
         values. This can greatly speed-up the algorithm for long time series and/or
         short shapelet length, possibly at the cost of some accuracy.
+    distance: str="manhattan"
+        Name of the distance function to be used. By default this is the
+        manhattan distance. Other distances from the aeon distance modules can be used.
     estimator : BaseEstimator or None, default=None
         Base estimator for the ensemble, can be supplied a sklearn `BaseEstimator`. If
         `None` a default `RidgeClassifierCV` classifier is used with standard scalling.
@@ -147,6 +150,7 @@ def __init__(
         estimator=None,
         save_transformed_data: bool = False,
         class_weight=None,
+        distance: str = "manhattan",
         n_jobs: int = 1,
         random_state: Union[int, Type[np.random.RandomState], None] = None,
     ) -> None:
@@ -157,7 +161,7 @@ def __init__(
         self.alpha_similarity = alpha_similarity
         self.use_prime_dilations = use_prime_dilations
         self.class_weight = class_weight
-
+        self.distance = distance
         self.estimator = estimator
         self.save_transformed_data = save_transformed_data
         self.random_state = random_state
@@ -198,6 +202,7 @@ def _fit(self, X, y):
             use_prime_dilations=self.use_prime_dilations,
             n_jobs=self.n_jobs,
             random_state=self.random_state,
+            distance=self.distance,
         )
         if self.estimator is None:
             self._estimator = make_pipeline(

aeon/transformations/collection/convolution_based/_hydra.py

@@ -68,7 +68,6 @@ class HydraTransformer(BaseCollectionTransformer):
         "output_data_type": "Tabular",
         "algorithm_type": "convolution",
         "python_dependencies": "torch",
-        "fit_is_empty": True,
     }
 
     def __init__(
@@ -82,7 +81,7 @@ def __init__(
 
         super().__init__()
 
-    def _transform(self, X, y=None):
+    def _fit(self, X, y=None):
         import torch
 
         if isinstance(self.random_state, int):
@@ -91,14 +90,16 @@ def _transform(self, X, y=None):
         n_jobs = check_n_jobs(self.n_jobs)
         torch.set_num_threads(n_jobs)
 
-        self.hydra = _HydraInternal(
+        self._hydra = _HydraInternal(
             X.shape[2],
             X.shape[1],
             k=self.n_kernels,
             g=self.n_groups,
             max_num_channels=self.max_num_channels,
         )
-        return self.hydra(torch.tensor(X).float())
+
+    def _transform(self, X, y=None):
+        return self._hydra(torch.tensor(X).float())
 
 
 if _check_soft_dependencies("torch", severity="none"):