Tests and changes for 7.0.0 (#80)

* testing

* versions

* seql

* cov

* release

* softdep

* testing for latest sklearn

* maybe mark

* copy

* copy

* copy

* more testing

* examples and bounds

* bad hints

Author: MatthewMiddlehurst

.github/workflows/periodic_tests.yml

@@ -12,27 +12,50 @@ concurrency:
 
 jobs:
   check-manifest:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - uses: pre-commit/[email protected]
         with:
           extra_args: check-manifest --hook-stage manual
 
+  test-no-soft-deps:
+    runs-on: ubuntu-24.04
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install
+        uses: nick-fields/retry@v3
+        with:
+          timeout_minutes: 30
+          max_attempts: 3
+          command: python -m pip install .[dev]
+
+      - name: Show dependencies
+        run: python -m pip list
+
+      - name: Run tests
+        run: python -m pytest -n logical
+
   pytest:
     runs-on: ${{ matrix.os }}
 
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-20.04, macos-14, windows-2022 ]
-        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
+        os: [ ubuntu-24.04, macos-14, windows-2022 ]
+        python-version: [ "3.9", "3.10", "3.11", "3.12", "3.13" ]
 
     steps:
       - uses: actions/checkout@v4
@@ -55,14 +78,14 @@ jobs:
         run: python -m pytest -n logical
 
   codecov:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Disable Numba JIT
         run: echo "NUMBA_DISABLE_JIT=1" >> $GITHUB_ENV

.github/workflows/pr_precommit.yml

@@ -14,14 +14,14 @@ concurrency:
 
 jobs:
   pre-commit:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - uses: tj-actions/changed-files@v46
         id: changed-files

.github/workflows/pr_pytest.yml

@@ -17,20 +17,45 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  test-no-soft-deps:
+    runs-on: ubuntu-24.04
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install
+        uses: nick-fields/retry@v3
+        with:
+          timeout_minutes: 30
+          max_attempts: 3
+          command: python -m pip install .[dev]
+
+      - name: Show dependencies
+        run: python -m pip list
+
+      - name: Run tests
+        run: python -m pytest -n logical
+
   pytest:
     runs-on: ${{ matrix.os }}
 
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-20.04, windows-2022 ]
-        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
+        os: [ ubuntu-24.04, windows-2022 ]
+        python-version: [ "3.9", "3.10", "3.11", "3.12", "3.13" ]
         # 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: "3.10"
+          - pr-testing: true
+            python-version: "3.12"
 
     steps:
       - uses: actions/checkout@v4
@@ -53,14 +78,14 @@ jobs:
         run: python -m pytest -n logical
 
   codecov:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Disable Numba JIT
         run: echo "NUMBA_DISABLE_JIT=1" >> $GITHUB_ENV
@@ -73,7 +98,7 @@ jobs:
           command: python -m pip install .[all_extras,dev,unstable_extras]
 
       - name: Tests
-        run: python -m pytest -n logical --cov=tsml_eval --cov-report=xml --timeout 1800
+        run: python -m pytest -n logical --cov=tsml --cov-report=xml --timeout 1800
 
       - uses: codecov/codecov-action@v5
         env:

.github/workflows/precommit_autoupdate.yml

@@ -8,14 +8,14 @@ on:
 
 jobs:
   pre-commit-auto-update:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - uses: browniebroke/pre-commit-autoupdate-action@v1
 

.github/workflows/release.yml

@@ -8,29 +8,29 @@ on:
 
 jobs:
   check-manifest:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - uses: pre-commit/[email protected]
         with:
           extra_args: check-manifest --hook-stage manual
 
   build-project:
     needs: check-manifest
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Build project
         run: |
@@ -51,7 +51,7 @@ jobs:
 
     strategy:
       matrix:
-        os: [ ubuntu-20.04, macos-14, windows-2022 ]
+        os: [ ubuntu-24.04, macos-14, windows-2022 ]
         python-version: [ "3.9", "3.10", "3.11", "3.12" ]
 
     steps:
@@ -93,7 +93,13 @@ jobs:
 
   upload-wheels:
     needs: test-wheels
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
+
+    environment:
+      name: release
+      url: https://pypi.org/p/tsml/
+    permissions:
+      id-token: write
 
     steps:
       - uses: actions/download-artifact@v4
@@ -103,5 +109,3 @@ jobs:
 
       - name: Publish package to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          password: ${{ secrets.PYPI_TOKEN }}

README.md

@@ -16,7 +16,7 @@ Please see [`tsml_eval`](https://github.com/time-series-machine-learning/tsml-ev
 is more of a sandbox for testing out new ideas and algorithms. It may contain some
 algorithms and implementations that are not available in the other toolkits.
 
-The current release of `tsml` is v0.6.1.
+The current release of `tsml` is v0.7.0.
 
 ## Installation
 

pyproject.toml

@@ -4,16 +4,16 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "tsml"
-version = "0.6.1"
-description = "A development sandbox for time series machine learning algorithms."
+version = "0.7.0"
+description = "A development sandbox for time series machine learning algorithms which dont fit into aeon."
 authors = [
     {name = "Matthew Middlehurst", email = "[email protected]"},
 ]
 maintainers = [
     {name = "Matthew Middlehurst", email = "[email protected]"},
 ]
 readme = "README.md"
-requires-python = ">=3.9,<3.13"
+requires-python = ">=3.9,<3.14"
 keywords = [
     "data-science",
     "machine-learning",
@@ -36,8 +36,10 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
+    "aeon>=1.0.0",
     "numba>=0.55.0",
     "numpy>=1.21.0",
     "scipy>=1.9.0",
@@ -49,7 +51,7 @@ dependencies = [
 [project.optional-dependencies]
 all_extras = [
     "grailts",
-    # "scikit-fda>=0.7.0",
+    "scikit-fda>=0.7.0; python_version > '3.9' and python_version < '3.13'",
     "statsmodels>=0.12.1",
     "wildboar",
 ]

tsml/__init__.py

@@ -1,3 +1,3 @@
 """tsml."""
 
-__version__ = "0.6.1"
+__version__ = "0.7.0"

tsml/base.py

@@ -115,7 +115,7 @@ def _convert_X(
         pad_unequal: bool = False,
         concatenate_channels: bool = False,
     ) -> Union[np.ndarray, List[np.ndarray]]:
-        dtypes = self._get_tags()["X_types"]
+        dtypes = _safe_tags(self)["X_types"]
 
         if isinstance(X, np.ndarray) and X.ndim == 3:
             if "3darray" in dtypes:
@@ -247,6 +247,9 @@ def _check_n_features(self, X: Union[np.ndarray, List[np.ndarray]], reset: bool)
                 f"is expecting {self.n_features_in_[1]} series length as input."
             )
 
+    def _get_tags(self) -> dict:
+        return _safe_tags(self)
+
     def _more_tags(self) -> dict:
         return _DEFAULT_TAGS
 

tsml/compose/_channel_ensemble.py

@@ -330,6 +330,7 @@ def predict_proba(self, X: Union[np.ndarray, List[np.ndarray]]) -> np.ndarray:
     def _more_tags(self) -> dict:
         return {
             "X_types": ["np_list", "3darray"],
+            "equal_length_only": False,
         }
 
     @classmethod
@@ -497,9 +498,7 @@ def predict(self, X: Union[np.ndarray, List[np.ndarray]]) -> np.ndarray:
         return np.average(preds, axis=0)
 
     def _more_tags(self) -> dict:
-        return {
-            "X_types": ["np_list", "3darray"],
-        }
+        return {"X_types": ["np_list", "3darray"], "equal_length_only": False}
 
     @classmethod
     def get_test_params(

tsml/dictionary_based/_mrseql.py

@@ -66,7 +66,9 @@ def fit(self, X: Union[np.ndarray, List[np.ndarray]], y: np.ndarray) -> object:
         self :
             Reference to self.
         """
-        X, y = self._validate_data(X=X, y=y, ensure_min_samples=2)
+        X, y = self._validate_data(
+            X=X, y=y, ensure_min_samples=2, ensure_equal_length=True
+        )
         X = self._convert_X(X)
 
         check_classification_targets(y)
@@ -115,7 +117,7 @@ def predict(self, X: Union[np.ndarray, List[np.ndarray]]) -> np.ndarray:
         if self.n_classes_ == 1:
             return np.repeat(list(self.class_dictionary_.keys()), X.shape[0], axis=0)
 
-        X = self._validate_data(X=X, reset=False)
+        X = self._validate_data(X=X, reset=False, ensure_equal_length=True)
         X = self._convert_X(X)
 
         return self.clf_.predict(_convert_data(X))
@@ -139,7 +141,7 @@ def predict_proba(self, X: Union[np.ndarray, List[np.ndarray]]) -> np.ndarray:
         if self.n_classes_ == 1:
             return np.repeat([[1]], X.shape[0], axis=0)
 
-        X = self._validate_data(X=X, reset=False)
+        X = self._validate_data(X=X, reset=False, ensure_equal_length=True)
         X = self._convert_X(X)
 
         return self.clf_.predict_proba(_convert_data(X))

tsml/dictionary_based/_mrsqm.py

@@ -100,7 +100,9 @@ def fit(self, X: Union[np.ndarray, List[np.ndarray]], y: np.ndarray) -> object:
         self :
             Reference to self.
         """
-        X, y = self._validate_data(X=X, y=y, ensure_min_samples=2)
+        X, y = self._validate_data(
+            X=X, y=y, ensure_min_samples=2, ensure_equal_length=True
+        )
         X = self._convert_X(X)
 
         check_classification_targets(y)
@@ -152,7 +154,7 @@ def predict(self, X: Union[np.ndarray, List[np.ndarray]]) -> np.ndarray:
         if self.n_classes_ == 1:
             return np.repeat(list(self.class_dictionary_.keys()), X.shape[0], axis=0)
 
-        X = self._validate_data(X=X, reset=False)
+        X = self._validate_data(X=X, reset=False, ensure_equal_length=True)
         X = self._convert_X(X)
 
         return self.clf_.predict(_convert_data(X))
@@ -176,7 +178,7 @@ def predict_proba(self, X: Union[np.ndarray, List[np.ndarray]]) -> np.ndarray:
         if self.n_classes_ == 1:
             return np.repeat([[1]], X.shape[0], axis=0)
 
-        X = self._validate_data(X=X, reset=False)
+        X = self._validate_data(X=X, reset=False, ensure_equal_length=True)
         X = self._convert_X(X)
 
         return self.clf_.predict_proba(_convert_data(X))