[MNT] Automated `pre-commit` hook update by aeon-actions-bot[bot] · Pull Request #2820 · aeon-toolkit/aeon

aeon-actions-bot · 2025-05-19T00:47:24Z

Automated weekly update to .pre-commit-config.yaml hook versions.

Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com>

* add difference transformer to series transformations * add myself to .all-contributorsrc * small modification * modify according to reviews * [ENH] add informational tags back to estimator docs (#2652) * feat: add new tags information for anomaly detection * feat: add tag information in given anomaly modles * fix: add new anomaly detector tags in mock anomaly detector class * fix: use anomaly-detector instead of estimator for new tags * update and add basic testing * fixes --------- Co-authored-by: MatthewMiddlehurst <pfm15hbu@gmail.com> * [DOC] Documentation improvement of BaseSeriesEstimator and BaseAeonEstimator (#2612) * Added the docs for base series and base classes * Updated documentation for base classes --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [ENH] HydraTransformer Output changed (#2656) * output type added * hydra wflow modified * hydra test file added * pr_pytest reverted * soft dep check added * soft dep corrected * docstring corrected, enhanced test cases * [DOC] Improved Hidalgo Segmentation Notebook (#2616) * Improved Hidalgo Segmentation Notebook * Updated hidalgo notebook --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * new devs and workflow consolidation (#2797) * all branches (#2809) * Automated `pre-commit` hook update (#2820) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * [MNT] Bump crs-k/stale-branches in the github-actions group (#2821) Bumps the github-actions group with 1 update: [crs-k/stale-branches](https://github.com/crs-k/stale-branches). Updates `crs-k/stale-branches` from 7.0.1 to 8.1.1 - [Release notes](https://github.com/crs-k/stale-branches/releases) - [Commits](crs-k/stale-branches@v7.0.1...v8.1.1) --- updated-dependencies: - dependency-name: crs-k/stale-branches dependency-version: 8.1.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * fix: indexing in kdtw (#2826) * [ENH] Added test cases for feature based clustering (#2690) * Added test cases for feature based clustering * Automatic `pre-commit` fixes * added docstring * Automatic `pre-commit` fixes * added . * added . * updated tsfresh * Automatic `pre-commit` fixes * added pytest _check_soft_dependencies for tsfresh * Automatic `pre-commit` fixes * added more testing * Automatic `pre-commit` fixes * added docs * added docs * added pytest * Automatic `pre-commit` fixes * improved docs * Automatic `pre-commit` fixes * improved test cases * changes made as requested by moderators * changes made as requested by moderators * Automatic `pre-commit` fixes * changed "percentiles" to "quantiles" --------- Co-authored-by: Ramana-Raja <ramanarajakesavaraja@gamil.com> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> * [DOC] Fix inconsistent double backticks in updated similarity_search module docstrings (#2618) * delete some descriptions * modification to _maintainer_ --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> Co-authored-by: Adarsh Dubey <dubeyadarshmain@gmail.com> Co-authored-by: Kevin Shah <161136814+kevinzb56@users.noreply.github.com> Co-authored-by: Balgopal Moharana <99070111+lucifer4073@users.noreply.github.com> Co-authored-by: Kavya Rambhia <161142013+kavya-r30@users.noreply.github.com> Co-authored-by: aeon-actions-bot[bot] <148872591+aeon-actions-bot[bot]@users.noreply.github.com> Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Sebastian Schmidl <10573700+SebastianSchmidl@users.noreply.github.com> Co-authored-by: Ramana Raja <83065061+Ramana-Raja@users.noreply.github.com> Co-authored-by: Ramana-Raja <ramanarajakesavaraja@gamil.com> Co-authored-by: Ciph3r <142653450+adityagh006@users.noreply.github.com>

Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com>

* add difference transformer to series transformations * add myself to .all-contributorsrc * small modification * modify according to reviews * [ENH] add informational tags back to estimator docs (#2652) * feat: add new tags information for anomaly detection * feat: add tag information in given anomaly modles * fix: add new anomaly detector tags in mock anomaly detector class * fix: use anomaly-detector instead of estimator for new tags * update and add basic testing * fixes --------- Co-authored-by: MatthewMiddlehurst <pfm15hbu@gmail.com> * [DOC] Documentation improvement of BaseSeriesEstimator and BaseAeonEstimator (#2612) * Added the docs for base series and base classes * Updated documentation for base classes --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [ENH] HydraTransformer Output changed (#2656) * output type added * hydra wflow modified * hydra test file added * pr_pytest reverted * soft dep check added * soft dep corrected * docstring corrected, enhanced test cases * [DOC] Improved Hidalgo Segmentation Notebook (#2616) * Improved Hidalgo Segmentation Notebook * Updated hidalgo notebook --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * new devs and workflow consolidation (#2797) * all branches (#2809) * Automated `pre-commit` hook update (#2820) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * [MNT] Bump crs-k/stale-branches in the github-actions group (#2821) Bumps the github-actions group with 1 update: [crs-k/stale-branches](https://github.com/crs-k/stale-branches). Updates `crs-k/stale-branches` from 7.0.1 to 8.1.1 - [Release notes](https://github.com/crs-k/stale-branches/releases) - [Commits](crs-k/stale-branches@v7.0.1...v8.1.1) --- updated-dependencies: - dependency-name: crs-k/stale-branches dependency-version: 8.1.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * fix: indexing in kdtw (#2826) * [ENH] Added test cases for feature based clustering (#2690) * Added test cases for feature based clustering * Automatic `pre-commit` fixes * added docstring * Automatic `pre-commit` fixes * added . * added . * updated tsfresh * Automatic `pre-commit` fixes * added pytest _check_soft_dependencies for tsfresh * Automatic `pre-commit` fixes * added more testing * Automatic `pre-commit` fixes * added docs * added docs * added pytest * Automatic `pre-commit` fixes * improved docs * Automatic `pre-commit` fixes * improved test cases * changes made as requested by moderators * changes made as requested by moderators * Automatic `pre-commit` fixes * changed "percentiles" to "quantiles" --------- Co-authored-by: Ramana-Raja <ramanarajakesavaraja@gamil.com> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> * [DOC] Fix inconsistent double backticks in updated similarity_search module docstrings (#2618) * delete some descriptions * modification to _maintainer_ --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> Co-authored-by: Adarsh Dubey <dubeyadarshmain@gmail.com> Co-authored-by: Kevin Shah <161136814+kevinzb56@users.noreply.github.com> Co-authored-by: Balgopal Moharana <99070111+lucifer4073@users.noreply.github.com> Co-authored-by: Kavya Rambhia <161142013+kavya-r30@users.noreply.github.com> Co-authored-by: aeon-actions-bot[bot] <148872591+aeon-actions-bot[bot]@users.noreply.github.com> Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Sebastian Schmidl <10573700+SebastianSchmidl@users.noreply.github.com> Co-authored-by: Ramana Raja <83065061+Ramana-Raja@users.noreply.github.com> Co-authored-by: Ramana-Raja <ramanarajakesavaraja@gamil.com> Co-authored-by: Ciph3r <142653450+adityagh006@users.noreply.github.com>

* added numba prange to all pairwise distances * sfa update * changed warning * custom pairwise threaded * fixed * added threaded decorator * fix * fix * expanded threaded decorator to work with classes * fix * Automated `CONTRIBUTORS.md` update (#2614) Co-authored-by: chrisholder <4674372+chrisholder@users.noreply.github.com> * Updated Interval Based Notebook (#2620) * [DOC] Added Docstring for regression forecasting (#2564) * Added Docstring for Regression * Added Docstring for Regression * exog fix * GSoC announcement (#2629) * Automated `pre-commit` hook update (#2632) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [MNT] Bump tj-actions/changed-files from 45 to 46 in the github-actions group (#2637) * [MNT] Bump tj-actions/changed-files in the github-actions group Bumps the github-actions group with 1 update: [tj-actions/changed-files](https://github.com/tj-actions/changed-files). Updates `tj-actions/changed-files` from 45 to 46 - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v45...v46) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> * Update pr_precommit.yml --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [MNT] Update numpy requirement in the python-packages group (#2643) Updates the requirements on [numpy](https://github.com/numpy/numpy) to permit the latest version. Updates `numpy` to 2.2.4 - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](https://github.com/numpy/numpy/compare/v1.21.0...v2.2.4) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production dependency-group: python-packages ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MNT,DEP] _binary.py metrics deprecated (#2600) * functions deprecated * Empty-Commit * version changed * Support for unequal length timeseries in itakura parallelogram (#2647) * [ENH] Implement DTW with Global alignment (#2565) * Implements Dynamic Time Warping with Global Invariances * Adds Numba JIT compilation support * Adds docs and numba support for dtw_gi and test_distance fixed * Fixes doctests * Automatic `pre-commit` fixes * Minor changes * Minor changes * Remove dtw_gi function and combine with private method _dtw_gi * Adds parameter tests * Fixes doctests * Minor changes * [ENH] Adds kdtw kernel support for kernelkmeans (#2645) * Adds kdtw kernel support for kernelkmeans * Code refactor * Adds tests for kdtw clustering * minor changes * minor changes * [MNT] Skip some excected results tests when numba is disabled (#2639) * skip some numba tests * Empty commit for CI * Update testing_config.py --------- Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [MNT] Remove REDCOMETs from testing exclusion list (#2630) * remove excluded estimators * redcomets fix * [ENH] Replace `prts` metrics (#2400) * Pre-commit fixes * Position parameter in calculate_bias * Added recall metric * merged into into one file * test added * Changes in test and range_metrics * list of list running but error! * flattening lists, all cases passed * Empty-Commit * changes * Protected functions * Changes in documentation * Changed test cases into seperate functions * test cases added and added range recall * udf_gamma removed from precision * changes * more changes * recommended changes * changes * Added Parameters * removed udf_gamma from precision * Added binary to range * error fixing * test comparing prts and range_metrics * Beta parameter added in fscore * Added udf_gamma function * f-score failing when comparing against prts * fixed f-score output * alpha usage * Empty-Commit * added test case to use range-based input for metrics * soft dependency added * doc update --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: Sebastian Schmidl <10573700+SebastianSchmidl@users.noreply.github.com> * Clarify documentation regarding unequal length series limitation (#2589) Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * Automated `pre-commit` hook update (#2683) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [MNT] Bump tj-actions/changed-files in the github-actions group (#2686) Bumps the github-actions group with 1 update: [tj-actions/changed-files](https://github.com/tj-actions/changed-files). Updates `tj-actions/changed-files` from 46.0.1 to 46.0.3 - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v46.0.1...v46.0.3) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [ENH] Set `outlier_norm` default to True for Catch22 estimators (#2659) * sets outlier_norm=True by deafault * Minor changes * Docs improvement * [MNT] Use MacOS for examples/ workflow (#2668) * update bash to 5.x for lastpipe support * added esig installation * install boost before esig * fixed examples path issue for excluded notebooks * switched to fixed version of macos * added signature_method.ipynb to excluded list * removed symlink for /bin/bash * Update dependencies.md (#2717) Correct typo in dependencies.md * Automated `pre-commit` hook update (#2708) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [ENH] Test Coverage for Pairwise Distance (#2590) * Pairwise distance matrix test * Empty commit for CI --------- Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * re-running notebook for fixing cell output error (#2597) * Docstring (#2609) * [DOC] Add 'Raises' section to docstring #1766 (#2617) * [DOC] Add 'Raises' section to docstring #1766 * Automatic `pre-commit` fixes * Update _base.py * Automatic `pre-commit` fixes --------- Co-authored-by: ayushsingh9720 <199482418+ayushsingh9720@users.noreply.github.com> * [DOC] Contributor docs update (#2554) * contributing docs update * contributing docs update 2 * typos * Update contributing.md new section * Update testing.md testing update * Update contributing.md dont steal code * Automatic `pre-commit` fixes * Update contributing.md if --------- Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> Co-authored-by: Antoine Guillaume <antoine.guillaume45@gmail.com> * prevent assignment on PRs (#2703) * Update run_examples.sh (#2701) * [BUG] SevenNumberSummary bugfix and input rename (#2555) * summary bugfix * maintainer * test * readme (#2556) * remove MutilROCKETRegressor from alias mapping (#2623) Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * Automated `pre-commit` hook update (#2731) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [MNT] Bump the github-actions group with 2 updates (#2733) Bumps the github-actions group with 2 updates: [actions/create-github-app-token](https://github.com/actions/create-github-app-token) and [tj-actions/changed-files](https://github.com/tj-actions/changed-files). Updates `actions/create-github-app-token` from 1 to 2 - [Release notes](https://github.com/actions/create-github-app-token/releases) - [Commits](https://github.com/actions/create-github-app-token/compare/v1...v2) Updates `tj-actions/changed-files` from 46.0.3 to 46.0.4 - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v46.0.3...v46.0.4) --- updated-dependencies: - dependency-name: actions/create-github-app-token dependency-version: '2' dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions - dependency-name: tj-actions/changed-files dependency-version: 46.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Fixed a few spelling/grammar mistakes on TSC docs examples (#2738) * Fix docstring inconsistencies in benchmarking module (resolves #809) (#2735) * issue#809 Fix docstrings for benchmarking functions * Fixed docstrings in results_loaders.py * Fix docstring inconsistencies in benchmarking module - resolves #809 * Fix docstring inconsistencies in benchmarking module - resolves #809 * [ENH] `best_on_top` addition in `plot_pairwise_scatter` (#2655) * Empty-Commit * best_on_top parameter added * changes * [ENH] Add dummy clusterer tags (#2551) * dummy clusterer tags * len * [ENH] Collection conversion cleanup and `df-list` fix (#2654) * collection conversion cleanup * notebook * fixes --------- Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> * [MNT] Updated the release workflows (#2638) * edit release workflows to use trusted publishing * docs * [MNT,ENH] Update to allow Python 3.13 (#2608) * python 3.13 * tensorflow * esig * tensorflow * tensorflow * esig and matrix profile * signature notebook * remove prts * fix * remove annoying deps from all_extras * Update pyproject.toml * [ENH] Hard-Coded Tests for `test_metrics.py` (#2672) * Empty-Commit * hard-coded tests * changes * Changed single ticks to double (#2640) Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * 📝 Add HaroonAzamFiza as a contributor for doc (#2740) * 📝 Update CONTRIBUTORS.md [skip ci] * 📝 Update .all-contributorsrc [skip ci] --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> * [ENH,MNT] Assign Bot (assigned issues>2) (#2702) * Empty-Commit * point 2 working * changes * changes in comment message * [MNT,ENH] Assign-bot (Allow users to type alternative phrases for assingment) (#2704) * added extra features * added comments * optimized code * optimized code * made changes requested by moderators * fixed conflicts * fixed conflicts * fixed conflicts --------- Co-authored-by: Ramana-Raja <ramanarajakesavaraja@gamil.com> * 📝 Add Ramana-Raja as a contributor for code (#2741) * 📝 Update CONTRIBUTORS.md [skip ci] * 📝 Update .all-contributorsrc [skip ci] --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> * Release v1.1.0 (#2696) * v1.1.0 draft * finish * Automated `pre-commit` hook update (#2743) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [MNT] Bump the github-actions group with 2 updates (#2744) Bumps the github-actions group with 2 updates: [crs-k/stale-branches](https://github.com/crs-k/stale-branches) and [tj-actions/changed-files](https://github.com/tj-actions/changed-files). Updates `crs-k/stale-branches` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/crs-k/stale-branches/releases) - [Commits](https://github.com/crs-k/stale-branches/compare/v7.0.0...v7.0.1) Updates `tj-actions/changed-files` from 46.0.4 to 46.0.5 - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v46.0.4...v46.0.5) --- updated-dependencies: - dependency-name: crs-k/stale-branches dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions - dependency-name: tj-actions/changed-files dependency-version: 46.0.5 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [DOC] Add implementation references (#2748) * implementation references * better attribution * use gpu installs for periodic tests (#2747) * Use shape calculation in _fit to optimize QUANTTransformer (#2727) * [REF] Refactor Anomaly Detection Module into Submodules by Algorithm Family (#2694) * Refactor Anomaly Detection Module into Submodules by Algorithm Family * updated documentation and references * implemented suggested changes * minor changes * added headers for remaining algorithm family * removing tree-based header * Automated `pre-commit` hook update (#2756) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [ENH]Type hints/forecasting (#2737) * Type hints for primitive data types in base module * Type hints for primitive data types and strings in forecating module * type hints for primitives in foreacasting module * Revert "type hints for primitives in foreacasting module" This reverts commit 575122d14b28742140ef1e16a3a351dd5db5072b. * type hints for primitives in forecasting module * Automated `pre-commit` hook update (#2766) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [ENH] Implement `load_model` function for ensemble classifiers (#2631) * feat: implement `load_model` function for LITETimeClassifier Implement separate `load_model` function for LITETimeClassifier, which takes in `model_path` as list of strings and `classes` and loads all the models separately and stores them in `self.classifiers_` * feat: implement `load_model` function for InceptionTimeClassifier Implement separate `load_model` function for InceptionTimeClassifier, which takes in `model_path` as list of strings and `classes` and loads all the models separately and stores them in `self.classifiers_` * fix: typo in load model function * feat: convert load_model functions to classmethods * test: implement test for save load for LITETIME and Inception classification models * Automatic `pre-commit` fixes * refactor: move loading tests to separate files * Update _ae_abgru.py (#2771) * Automated `pre-commit` hook update (#2779) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [DOC] Fix Broken [Source] Link and Improve Documentation for suppress_output() (#2677) * Fix Broken [Source] Link and Improve Documentation for suppress_output() Function * modified docstring and added tests * modified docstring example * modifying docstring examples * modifying docstring examples * updating conf file * updated docstring * base transform tidy (#2773) * DOC: Add Raises section for invalid weights in KNeighborsTimeSeriesClassifier (#1766) (#2764) Document the ValueError raised during initialization when an unsupported value is passed to the 'weights' parameter. Clarifies expected exceptions for users and improves API documentation consistency. Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [ENH] Fixes Issue Improve `_check_params` method in `kmeans.py` and `kmedoids.py` (#2682) * Improves _check_params * removes function and adds a var * minor changes * minor changes * minor changes * line endings to LF * use variable instead of duplicating strings * weird file change * weird file change --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [ENH] Add type hints for deep learning regression classes (#2644) * type hints for cnn for regrssion * editing import modules Model & Optim * type hints for disjoint_cnn for regrssion * FIX type hints _get_test_params * ENH Change linie of importing typing * type hints for _encoder for regrssion * type hints for _fcn for regrssion * type hints for _inception_time for regrssion * type hints for _lite_time for regrssion * type hints for _mlp for regrssion * type hints for _resnet for regrssion * type hints for _base for regrssion * FIX: mypy errors in _disjoint_cnn.py file * FIX: mypy typing errors * Fix: Delete variable types, back old-verbose * FIX: add model._save in save_last_model_to_file function * FIX: Put TYPE_CHECKING downside * Fix: Put Any at the top * [DOC] Add RotationForest Classifier Notebook for Time Series Classification (#2592) * Add RotationForest Classifier Notebook for Time Series Classification * Added references and modified doc * minor modifications to notebook description * Update rotation_forest.ipynb --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * fix: Codeowners for benchmarking metrics AD (#2784) * [GOV] Supporting Developer role (#2775) * supporting dev role * pr req * Update governance.md * typo * Automatic `pre-commit` fixes * aeon --------- Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [MNT, ENH, DOC] Rework similarity search (#2473) * WIP remake module structure * Update _brute_force.py * Update test__commons.py * WIP mock and test * Add test for base subsequence * Fix subsequence_search tests * debug brute force mp * more debug of subsequence tests * more debug of subsequence tests * Add functional LSH neighbors * add notebook for sim search tasks * Updated series similarity search * Fix mistake addition in transformers and fix base classes * Fix registry and api reference * Update documentation and fix some leftover bugs * Update documentation and add default test params * Fix identifiers and test data shape for all_estimators tests * Fix missing params * Fix n_jobs params and tags, add some docs * Fix numba test bug and update testing data for sim search * Fix imports, testing data tests, and impose predict/_predict interface to all sim search estimators * Fix args * Fix extract test * update docs api and notebooks * remove notes * Patrick comments * Adress comments and clean index code * Fix Patrick comments * Fix variable suppression mistake * Divide base class into task specific * Fix typo in imports * Empty commit for CI * Fix typo again * Add check_inheritance exception for similarity search * Revert back to non per type base classes * Factor check index and typo in test --------- Co-authored-by: Patrick Schäfer <patrick.schaefer@hu-berlin.de> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: baraline <10759117+baraline@users.noreply.github.com> * [ENH] Adapt the DCNN Networks to use Weight Norm Wrappers (#2628) * adapt the dcnn networks to use weight norm wrappers and remove l2 regularization * Automatic `pre-commit` fixes * add custom object * Automatic `pre-commit` fixes * fix trial --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [GOV] Remove inactive developers (#2776) * inactive devs * logo fix * Automated `pre-commit` hook update (#2792) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * Add SomtoOnyekwelu to .all-contributorsrc (#2788) * Automated `CONTRIBUTORS.md` update (#2794) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [BUG] Fix a bug in ClaSP Series Transformer when using floatXX as Input (where XX != 64) (#2774) * Automatic conversion to float64. * remove print * [DOC] Changed SummaryClusterer's summary_stat from "percentiles" to "quantiles" (#2778) * changed summary_stats * changed summary_stats * changed summary_stats * changed summary_stats for regression and classification * [ENH] Test coverage for AEAttentionBiGRUNetwork Improved (#2540) * test file for ae_abgru added * soft depedency of tf resolved * aeabgru test file changed, bug resolved * aeabgru file reverted to original state * [BUG] Better error message for Rotation Forest with no usable attributes (#2798) * better error message for rotf failure * Update _rotation_forest_classifier.py * Update _rotation_forest_regressor.py * [DOC] Inconsistent double ticks in segmentation package, public docstring only (#2622) * double ticks EAggloSegmenter docstring * double ticks HMMSegmenter docstring * double ticks InformationGainSegmenter docstring * double ticks for other EAggloSegmenter docstring and removed extra whitespace --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * put lower bound keras (#2808) * [REF] Refactor smoothing transformers into a sub-package (#2783) * mockup * init * decorator * correct import and tag * base docs * wrappers * tests * docs and imports * test params * register * big refactor * smoothing refactor * ad stuff * fixes * fixes * no longer required * [ENH] Refactor range-based metrics to restore original behavior (#2781) * feat: refactor range-based metrics to be consistent with the other AD metrics and integrate them into the AD test harness * refactor: move new range metrics methods into their old place and remove the deprecation * refactor: factor out test execution from test fixtures * refactor: move tests to new methods * fix: copy'n'paste error * [ENH]Use n_jobs parameter in KNeighborsTimeSeriesClassifier. (#2687) * Use n_jobs parameter in KNeighborsTimeSeriesClassifier. * Don't convert proba dtype. * Remove is_fitted checks, update docstring. * Implement parallel backend param. * Correct keyword argument for Parallel. * Add check_n_jobs. --------- Co-authored-by: stijn <s.j.rotman@tilburguniversity.edu> * [ENH] add informational tags back to estimator docs (#2652) * feat: add new tags information for anomaly detection * feat: add tag information in given anomaly modles * fix: add new anomaly detector tags in mock anomaly detector class * fix: use anomaly-detector instead of estimator for new tags * update and add basic testing * fixes --------- Co-authored-by: MatthewMiddlehurst <pfm15hbu@gmail.com> * [DOC] Documentation improvement of BaseSeriesEstimator and BaseAeonEstimator (#2612) * Added the docs for base series and base classes * Updated documentation for base classes --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [ENH] HydraTransformer Output changed (#2656) * output type added * hydra wflow modified * hydra test file added * pr_pytest reverted * soft dep check added * soft dep corrected * docstring corrected, enhanced test cases * [DOC] Improved Hidalgo Segmentation Notebook (#2616) * Improved Hidalgo Segmentation Notebook * Updated hidalgo notebook --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * new devs and workflow consolidation (#2797) * all branches (#2809) * Automated `pre-commit` hook update (#2820) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * [MNT] Bump crs-k/stale-branches in the github-actions group (#2821) Bumps the github-actions group with 1 update: [crs-k/stale-branches](https://github.com/crs-k/stale-branches). Updates `crs-k/stale-branches` from 7.0.1 to 8.1.1 - [Release notes](https://github.com/crs-k/stale-branches/releases) - [Commits](https://github.com/crs-k/stale-branches/compare/v7.0.1...v8.1.1) --- updated-dependencies: - dependency-name: crs-k/stale-branches dependency-version: 8.1.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * fix: indexing in kdtw (#2826) * [ENH] Added test cases for feature based clustering (#2690) * Added test cases for feature based clustering * Automatic `pre-commit` fixes * added docstring * Automatic `pre-commit` fixes * added . * added . * updated tsfresh * Automatic `pre-commit` fixes * added pytest _check_soft_dependencies for tsfresh * Automatic `pre-commit` fixes * added more testing * Automatic `pre-commit` fixes * added docs * added docs * added pytest * Automatic `pre-commit` fixes * improved docs * Automatic `pre-commit` fixes * improved test cases * changes made as requested by moderators * changes made as requested by moderators * Automatic `pre-commit` fixes * changed "percentiles" to "quantiles" --------- Co-authored-by: Ramana-Raja <ramanarajakesavaraja@gamil.com> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> * [DOC] Fix inconsistent double backticks in updated similarity_search module docstrings (#2618) * [ENH] Update `_continuous.py` functions (#2822) * update continuous, has test failure * parameters back to original * alpha added into precision * removes p_alpha deprecation * changes * [MNT] stop segmenters changing state in predict (#2526) * remove stored variables in predict * IGTS * GGS * FLUSS * FLUSS * CLASP * CLASP * revert clasp * revert clasp * revert clasp * Update testing_config.py * Update _fluss.py * refactor dummy to naive (#2831) * [ENH] add a difference transformer to series transformations (#2729) * add difference transformer to series transformations * add myself to .all-contributorsrc * small modification * modify according to reviews * [ENH] add informational tags back to estimator docs (#2652) * feat: add new tags information for anomaly detection * feat: add tag information in given anomaly modles * fix: add new anomaly detector tags in mock anomaly detector class * fix: use anomaly-detector instead of estimator for new tags * update and add basic testing * fixes --------- Co-authored-by: MatthewMiddlehurst <pfm15hbu@gmail.com> * [DOC] Documentation improvement of BaseSeriesEstimator and BaseAeonEstimator (#2612) * Added the docs for base series and base classes * Updated documentation for base classes --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [ENH] HydraTransformer Output changed (#2656) * output type added * hydra wflow modified * hydra test file added * pr_pytest reverted * soft dep check added * soft dep corrected * docstring corrected, enhanced test cases * [DOC] Improved Hidalgo Segmentation Notebook (#2616) * Improved Hidalgo Segmentation Notebook * Updated hidalgo notebook --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * new devs and workflow consolidation (#2797) * all branches (#2809) * Automated `pre-commit` hook update (#2820) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * [MNT] Bump crs-k/stale-branches in the github-actions group (#2821) Bumps the github-actions group with 1 update: [crs-k/stale-branches](https://github.com/crs-k/stale-branches). Updates `crs-k/stale-branches` from 7.0.1 to 8.1.1 - [Release notes](https://github.com/crs-k/stale-branches/releases) - [Commits](https://github.com/crs-k/stale-branches/compare/v7.0.1...v8.1.1) --- updated-dependencies: - dependency-name: crs-k/stale-branches dependency-version: 8.1.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * fix: indexing in kdtw (#2826) * [ENH] Added test cases for feature based clustering (#2690) * Added test cases for feature based clustering * Automatic `pre-commit` fixes * added docstring * Automatic `pre-commit` fixes * added . * added . * updated tsfresh * Automatic `pre-commit` fixes * added pytest _check_soft_dependencies for tsfresh * Automatic `pre-commit` fixes * added more testing * Automatic `pre-commit` fixes * added docs * added docs * added pytest * Automatic `pre-commit` fixes * improved docs * Automatic `pre-commit` fixes * improved test cases * changes made as requested by moderators * changes made as requested by moderators * Automatic `pre-commit` fixes * changed "percentiles" to "quantiles" --------- Co-authored-by: Ramana-Raja <ramanarajakesavaraja@gamil.com> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> * [DOC] Fix inconsistent double backticks in updated similarity_search module docstrings (#2618) * delete some descriptions * modification to _maintainer_ --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> Co-authored-by: Adarsh Dubey <dubeyadarshmain@gmail.com> Co-authored-by: Kevin Shah <161136814+kevinzb56@users.noreply.github.com> Co-authored-by: Balgopal Moharana <99070111+lucifer4073@users.noreply.github.com> Co-authored-by: Kavya Rambhia <161142013+kavya-r30@users.noreply.github.com> Co-authored-by: aeon-actions-bot[bot] <148872591+aeon-actions-bot[bot]@users.noreply.github.com> Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Sebastian Schmidl <10573700+SebastianSchmidl@users.noreply.github.com> Co-authored-by: Ramana Raja <83065061+Ramana-Raja@users.noreply.github.com> Co-authored-by: Ramana-Raja <ramanarajakesavaraja@gamil.com> Co-authored-by: Ciph3r <142653450+adityagh006@users.noreply.github.com> * Automated `CONTRIBUTORS.md` update (#2832) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [BUG] Fix data loader (#2810) * Update _data_loaders.py * Update _data_loaders.py * stop deleting directories * Automated `pre-commit` hook update (#2841) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * 📝 Add lucifer4073 as a contributor for code (#2846) * 📝 Update CONTRIBUTORS.md [skip ci] * 📝 Update .all-contributorsrc [skip ci] --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> * [BUG] Adds test case for using csr_matrix with pickle - invalidates #2210 (#2843) * Extend test parameter set to validate if csx_matrix works with pickle. * Invalidates bug #2210 * [DOC] Docstring improved for dummy regressor (#2839) * Docstring improved for dummy regressor * convo resolved * remove numba typing (#2858) * [DOC] Regression forecaster docstring (#2837) * docstring * docstring * [ENH] Whole-series anomaly detection (#2326) * mockup * init * decorator * correct import and tag * base docs * wrappers * tests * docs and imports * test params * register * big refactor * smoothing refactor * Revert "smoothing refactor" This reverts commit c245ccbd0c1481b188a9094ccd7ff493613a89cd. * fixes * final bits and docs for refactor * fixes * testing fixes * Update aeon/anomaly_detection/collection/base.py Co-authored-by: Sebastian Schmidl <10573700+SebastianSchmidl@users.noreply.github.com> * Update docs/api_reference/anomaly_detection.rst Co-authored-by: Sebastian Schmidl <10573700+SebastianSchmidl@users.noreply.github.com> * Review changes * docs * import --------- Co-authored-by: Sebastian Schmidl <10573700+SebastianSchmidl@users.noreply.github.com> * [MNT] Bump the github-actions group across 1 directory with 2 updates (#2868) Bumps the github-actions group with 2 updates in the / directory: [ossf/scorecard-action](https://github.com/ossf/scorecard-action) and [crs-k/stale-branches](https://github.com/crs-k/stale-branches). Updates `ossf/scorecard-action` from 2.4.1 to 2.4.2 - [Release notes](https://github.com/ossf/scorecard-action/releases) - [Changelog](https://github.com/ossf/scorecard-action/blob/main/RELEASE.md) - [Commits](https://github.com/ossf/scorecard-action/compare/v2.4.1...v2.4.2) Updates `crs-k/stale-branches` from 8.1.1 to 8.2.0 - [Release notes](https://github.com/crs-k/stale-branches/releases) - [Commits](https://github.com/crs-k/stale-branches/compare/v8.1.1...v8.2.0) --- updated-dependencies: - dependency-name: ossf/scorecard-action dependency-version: 2.4.2 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions - dependency-name: crs-k/stale-branches dependency-version: 8.2.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Automated `pre-commit` hook update (#2867) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * [ENH] introduce revised version of ETS (#2834) * first version for correctness testing * timing * examples * new tests * refactor predict * final ETS * arima first * docstrings * docstrings * Convert error, trend and seasonality types to strings * Automatic `pre-commit` fixes * Add Type hints back in * Fix Type hints * Fix Linting issue * Automatic `pre-commit` fixes * Update test_ets to use strings for error, trend and seasonality types * Automatic `pre-commit` fixes * switch to fastmath * remove _arima, incorrectly introduced here * all int or str parameters * refactor variable name --------- Co-authored-by: alexbanwell1 <31886108+alexbanwell1@users.noreply.github.com> * [DOC] Update the projects lists (#2146) * remove Theta * projects * draft * add some papers * update papers * update projects * remove completed projects * remove poorly specified/out of date projects * remove merlin projects * restructure papers by year * papers using aeon * projects list and previous projects * update papers --------- Co-authored-by: MatthewMiddlehurst <pfm15hbu@gmail.com> * [DEP] Remove `prts` dependency (#2863) * remove prts from pyproject * docs * Update _continuous.py * Automatic `pre-commit` fixes --------- Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [ENH] Starting Self Supervised Model with first example (#2385) * add ssl module in transformations collection * add api * add test params * fix example * restart tests * test fix params * network none * revert * import inside function * try dummy * test repr * network repr * enhance testing * fix test * replace tcnn by lite * tony's comments * fix typing * fix znorm * z_norm in test * add exp module * Update repr.py * Update base.py * Automatic `pre-commit` fixes --------- Co-authored-by: MatthewMiddlehurst <pfm15hbu@gmail.com> Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * update slack link (#2877) * [BUG] Switch results loaders from http to https (#2883) * https * https in tests * [ENH] Correct broken source links for `set_params` and `get_params` in Aeon estimator docs (#2754) * Correct broken source links for `set_params` and `get_params` in Aeon estimator docs * made necessary changes * made necessary changes * modified linkcode_resolve * added comments * open PR comment changes (#2878) * [ENH] Implemented Tracking differentiator-based multiview dilated characteristics (TD-MVDC) Classifier (#2535) * Files and structure of tdmvdc class added * utility functions for tdmvdc applied * unecessary files removed * Initial implementation of TDMVDC added * accuracy improved to the required 81 per cent * test params added for tdmvdc * n_jobs temporarily disabled * n_jobs test params removed * Revert "n_jobs test params removed" This reverts commit 91539099f3cd3a201b7fe68bfea80a9ae5ebc706. * multithreading capability temporarily removed from tdmvdc * multithreading added * n_jobs removed from test_param * test added for tdmvdc * test added for tdmvdc * optimized comments * Made tdmvdc uniform across all feauture based classifiers * tdmvdc tested * check constructor test exlcuded for tdmvdc * changed * init file changed * check constructor corrected tdmvdc --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> * Automated `pre-commit` hook update (#2888) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * [MNT] Update pandas requirement in the python-packages group (#2889) Updates the requirements on [pandas](https://github.com/pandas-dev/pandas) to permit the latest version. Updates `pandas` to 2.3.0 - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Commits](https://github.com/pandas-dev/pandas/compare/v2.0.0...v2.3.0) --- updated-dependencies: - dependency-name: pandas dependency-version: 2.3.0 dependency-type: direct:production dependency-group: python-packages ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MNT] Drop Python 3.9 (#2845) * drop python 3.9 * fixes * readme * tag * test skip * [ENH] Series transformer pipeline and datatype list tidy (#2830) * series pipeline * fixes and docs * test fix * fix * [ENH] Multivariate and unequal PF, speed-ups and distance classifier tidy (#2872) * pass 1 * pf change fixes and derivative function merge * test * fixes * expected result * unequal and deprecations * [ENH] Add two forecasting tags (#2882) * add tags * correct exog * typo * [DOC] A fix to inconsistent double tick quote for the classification.distance_based module (#2627) * A fix to inconsistent double quotes * A fix to inconsistent double quotes * A fix to inconsistent double quotes * A fix to inconsistent double quotes * Revert "A fix to inconsistent double quotes" This reverts commit ff98c81a6c29b61d053e66c80f9f167b718172f5. * A fix to inconsistent double quotes * A fix to inconsistent double quotes * fix inconsistent double ticks * Automatic `pre-commit` fixes * Update _elastic_ensemble.py * Update _proximity_forest.py --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * 📝 Add Ahmed-Zahran02 as a contributor for doc (#2892) * 📝 Update CONTRIBUTORS.md [skip ci] * 📝 Update .all-contributorsrc [skip ci] --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> * [BUG] Forecasting regressor fix and notebook (#2885) * stop returning an array * notebook * Create window.png * fix test and typo * remove unfinished sentence * 📝 Add AnaghDeshpande as a contributor for doc (#2896) * 📝 Update CONTRIBUTORS.md [skip ci] * 📝 Update .all-contributorsrc [skip ci] --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> * [GOV] Use the NumFOCUS code of conduct and rename `aeon` workgroup (#2852) * code of conduct update and readmes * typo --------- Co-authored-by: Sebastian Schmidl <10573700+SebastianSchmidl@users.noreply.github.com> * [DOC] resolved the inconsistency of double ticks for the anomaly detection module #809 (#2546) * resolved the inconsistency of double quotes * resolved the inconsistency of double ticks * resolved the pre-commit errors occuring due to flake8 * Update _cblof.py made changes in line number 19 and 145. * Automatic `pre-commit` fixes * Update _copod.py made changes in line number 76 * Automatic `pre-commit` fixes * Update _iforest.py made changes in line number 19 * Automatic `pre-commit` fixes * Update _kmeans.py made changes in line number 178 * Automatic `pre-commit` fixes * Update _merlin.py made changes in line number 215 * Automatic `pre-commit` fixes * Update _one_class_svm.py made changes in line number 19 * Automatic `pre-commit` fixes * Update _pyodadapter.py made changes in line number 165 * Update _stomp.py made changes in line number 125 * Automatic `pre-commit` fixes * converted directives to single ticks * added double ticks to code ref * fixed link in cblof.py and some other minor changes * Update base.py --------- Co-authored-by: Patrick Schäfer <patrick.schaefer@hu-berlin.de> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [ENH] Forecasting testing (#2891) * call forecasting checks * basic cleanup * fix * add assert error messages * remove fit_is_empty check (see #2893) * remove extra argument to fit * remove extra argument to predict * correct forecast argument * Update _yield_forecasting_checks.py * add test for predict --------- Co-authored-by: Tony Bagnall <ajb@uea.ac.uk> * [MNT] Fixing CI issues and separate doctests from regular CI runners (#2902) * trying to fix CI stuff * use numba in codecov * try cov * no cov * doctest-plus * doctest-plus * addopts * dedicated doctest test * periodic * [BUG] Fixes a bug with SFAFast throwing an error when calling transform after fit (#2897) * Bugfix for SFA_Fast with transform called after fit * [MNT] Bump stefanzweifel/git-auto-commit-action from 5 to 6 in the github-actions group (#2906) * [MNT] Bump stefanzweifel/git-auto-commit-action Bumps the github-actions group with 1 update: [stefanzweifel/git-auto-commit-action](https://github.com/stefanzweifel/git-auto-commit-action). Updates `stefanzweifel/git-auto-commit-action` from 5 to 6 - [Release notes](https://github.com/stefanzweifel/git-auto-commit-action/releases) - [Changelog](https://github.com/stefanzweifel/git-auto-commit-action/blob/master/CHANGELOG.md) - [Commits](https://github.com/stefanzweifel/git-auto-commit-action/compare/v5...v6) --- updated-dependencies: - dependency-name: stefanzweifel/git-auto-commit-action dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> * Update issue_comment_edited.yml * Update pr_precommit.yml --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [ENH] Added RNN in networks (#2875) * RNN net architecture added * Fixed activation function for both str and list * RNN test mesage corrected * reverted workflow * reverted workflow * requested changes applied * convo resolved * Update README.md (#2908) * [ENH] Add recursive and direct methods to forecasting base class (#2899) * base class methods * direct * recursive * base * direct_forecasting * recursive_forecasting * recursive_forecasting * recursive_forecasting * direct notebook * direct notebook * direct notebook * switch to iterative * switch to iterative * iterative * iterative notebook * append change * append change * fix regression bug * comment * [ENH] remove horizon from ETS constructor, parametrize ETS tests (#2898) * remove horizon from ETS argument, parametrize tests * remove horizon from example * docstring * [ENH] Refactor example dataset for unequal length univariate (#2859) * deprecate PLAID * add pickup * deprecated * [ENH, REF]Refactored time-point based ROCKAD implementation (#2804) * mockup * init * decorator * correct import and tag * base docs * wrappers * tests * docs and imports * test params * register * big refactor * smoothing refactor * Revert "smoothing refactor" This reverts commit c245ccbd0c1481b188a9094ccd7ff493613a89cd. * fixes * final bits and docs for refactor * move predict_proba logic into inner_predict for code consistency * Added reference and example code, updated description * Adapted tests to be semi-supervised * Added semi-supervised labeling to description * moved Attributes above References and Examples, updated path of collection based rockad implementation * merge 2 * CI errors * maintainer * doctest --------- Co-authored-by: MatthewMiddlehurst <m.middlehurst@uea.ac.uk> Co-authored-by: MatthewMiddlehurst <pfm15hbu@gmail.com> * [ENH] enhance naive forecaster with new strategies (#2869) * naive forecaster with new strategies * few modifications according to reviews * made modifications and add documentation * modifications according to reviews * try to pass the test * delete one comment * modify 1)more test cases for seasonal_last 2)raise exception for y input in _predict, and related documentation * fix typo * take y * Update _naive.py --------- Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> Co-authored-by: MatthewMiddlehurst <pfm15hbu@gmail.com> * [ENH,REF] Unequal length collection transforms (#2903) * move and update unequal transforms * unequal transforms * comment * better sorting * extra transform test * changes for review * Release v1.2.0 (#2912) * release prep * changelog * Automated `pre-commit` hook update (#2914) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * [MNT] Comments on numba caching and release CI fix (#2916) * release CI jank * comment * swap * [ENH] Improves `create_multi_comparison_matrix` parameters and saving (#2657) * Empty-Commit * condensed parameters and showing output * test cases updated * changes * updated examples * point 2 working * [DOC] Clarify comments regarding issue assignment limits and user notifications * condensed parameters and showing output * test cases updated * changes * dir -> save_path * Reverted _mcm.py and its test to match main * requested changes done, pdf not showing yet * changes * changes * updated docstring * changes * requested changes * example file changes * changed formats default to None --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [MNT] Prevents assignment on Restricted Labels (#2706) * restricted labels * set * resolve conflicts * merge assign PRs and small change --------- Co-authored-by: MatthewMiddlehurst <pfm15hbu@gmail.com> * [MNT] Update scikit-learn requirement from <1.7.0,>=1.0.0 to >=1.0.0,<1.8.0 in the python-packages group (#2907) * [MNT] Update scikit-learn requirement in the python-packages group Updates the requirements on [scikit-learn](https://github.com/scikit-learn/scikit-learn) to permit the latest version. Updates `scikit-learn` to 1.7.0 - [Release notes](https://github.com/scikit-learn/scikit-learn/releases) - [Commits](https://github.com/scikit-learn/scikit-learn/compare/1.0...1.7.0) --- updated-dependencies: - dependency-name: scikit-learn dependency-version: 1.7.0 dependency-type: direct:production dependency-group: python-packages ... Signed-off-by: dependabot[bot] <support@github.com> * new validation * Update test_rockad.py * Update _rockad.py --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: MatthewMiddlehurst <pfm15hbu@gmail.com> * [MNT] issue-assign-bot - only users with write access should be able to assign others (#2739) * only admins can assign others * improve comment message * Automatic `pre-commit` fixes * fixes according to latest code * Automatic `pre-commit` fixes * changes according to latest code * resolve merge conflicts * Automatic `pre-commit` fixes * adjust according to latest code * merge --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [MNT] Created workflow for closing "AI Spam" pull requests (#2750) * added ai_spam * Automatic `pre-commit` fixes * fixed comment text * fixed comment text * updated to python 3.11 --------- Co-authored-by: Ramana-Raja <ramanarajakesavaraja@gamil.com> * [ENH] Use `np.argpartition` for efficient top-k selection instead of `np.argsort` (#2805) * use argpartition for efficient selection instead of argsort * made the required changes * [EHN] Allow exogenous variables in regression forecasters (#2915) * add exogenous variable feature to base and regression forecasters * delete self._check_X for exog --------- Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> * Automated `pre-commit` hook update (#2922) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * [MNT] Bump actions/create-github-app-token in the github-actions group (#2923) Bumps the github-actions group with 1 update: [actions/create-github-app-token](https://github.com/actions/create-github-app-token). Updates `actions/create-github-app-token` from 1 to 2 - [Release notes](https://github.com/actions/create-github-app-token/releases) - [Commits](https://github.com/actions/create-github-app-token/compare/v1...v2) --- updated-dependencies: - dependency-name: actions/create-github-app-token dependency-version: '2' dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [ENH] Added RecurrentRegressor for time series regression (#2894) * RNN net architecture added * Fixed activation function for both str and list * RNN test mesage corrected * RNN regressor added * init updated w rnn * reverted workflow * reverted workflow * requested changes applied * updated with latest recurrent network * merged with main * [MNT] Add testing workflow for multithreading and make threaded estimators use `check_n_jobs` (#2913) * multithreading test * njons and workflow fix * tde and base test * _n_jobs in testing * _n_jobs in testing * more test fixes * fixes * more n_jobs * more n_jobs * more n_jobs * more n_jobs * more n_jobs * test fix * test fix * test fix * test fix * hopefully last * hopefully last again * dont enumerate * periodic test * [DOC,MNT] Documentation configuration clean-up (#2911) * start * remove old parameter * numpydoc config * conf tidy * headers * exclude unused methods and update gsoc in about * changelog * binder button * myst config * remove extra bullet point * changelog * Automatic `pre-commit` fixes --------- Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [DOC] fix incorrect references of classes in getting started page (#2762) * fix: incorrect references of classes in getting started page * fix: typo in BaseSimilaritySearch --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * Automated `pre-commit` hook update (#2932) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * [DOC] Add RecurrentRegressor and RecurrentNetowork to api_reference (#2935) * Recurrent Regressor added to API doc * Recurrent network added to API doc * [ENH] Refactor to set forecast_ in fit and to require y in predict (#2927) * require y in predict * forecast_ * remove calls to predict * doc examples * regression forecaster rework * other tests * docstrings * refactor forecasting checks * test * test * regression notebook * test_ets * Revert "test_ets" This reverts commit 827a12a0a2fa3fec2d55d481a97aed62bd290059. * Revert "regression notebook" This reverts commit 27978022921c8c436d1ae458511ce5885d425c09. * ets * notebook * naive testing * [ENH] Clone estimator in direct forecast (#2936) * clone estimator * clone estimator * tests * test update * [ENH] Implement Time-Varying Parameter (TVP) regression forecaster using Kalman filter (#2920) * TVP * bug * refactor * test * test * add notebook * docstring * add an intercept * includes * squeeze predict * format * remove incomplete example * add test params * dummy test * dummy test * clone estimator * clone estimator * remove y is none * notebook * tests * tests * test update * remove pointless test * docstring update * [MNT] Add codespell support (config, workflow to detect/not fix) and make it fix a "few" typos (#2653) * Add github action to codespell main on push and PRs * Add rudimentary codespell config * Add pre-commit definition for codespell * Some skips for codespell -- lots of work todo * [DATALAD RUNCMD] run codespell throughout fixing typos automagically (but ignoring overall fail due to ambigous ones) === Do not change lines below === { "chain": [], "cmd": "codespell -w || :", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ * codespeed notebook and testing * incorrect typos and notebooks * more typos * config and fixes * Update similarity_search.ipynb fix notebook typos * update skip * temp typo and annotation workflow * annotations * fix typos --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: Antoine Guillaume <antoine.guillaume45@gmail.com> * typo (#2944) * correct checkout (#2945) * DOC: fix typos in MatrixProfileSeriesTransformer (#2940) (#2941) Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> * 📝 Add CodeFor2001 as a contributor for doc (#2946) * 📝 Update CONTRIBUTORS.md [skip ci] * 📝 Update .all-contributorsrc [skip ci] --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> * [ENH] Rework ETS Forecaster (#2939) * iterative * iterative ETS * notebook * Fix bug in seasonality calculation * Add example for ETS iterative forecasting * ets tests * holding notebook * example * Run Itertive notebook --------- Co-authored-by: Alex Banwell <arb1g19@soton.ac.uk> * [MNT] add n_jobs parameter for sax invertion (#2953) * add n_jobs * add tag * Automated `pre-commit` hook update (#2949) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * [DEP] Deprecate PLAID dataset (#2928) * remove PLAID * remove PLAID * [DOC] Classification notebook links (#2942) * fix links * fix links --------- Co-authored-by: Antoine Guillaume <antoine.guillaume45@gmail.com> * [ENH] Added TemporalConvolutionalNetwork in aeon/networks (#2933) * tcn network added * tcn_net pytest added * tcn_network updated with default params * tcn reshaped * tcn changed * tcn updated * doctest corrected * tcn rshaped * workflow corrected * [BUG] Improve signature docs (#2929) * signature docs * tests * typo * notebook * correct image * fix test * decalre in init * switch classifier to store SignatureTransformer * revert classifier * revert transformer * embed image rather than link * equation * equation * remove tests * maths * maths * add eq * add eq * remove example * line break --------- Co-authored-by: Antoine Guillaume <antoine.guillaume45@gmail.com> * [MNT] Workflow maintenance (#2919) * keep running doctests on fail * renames * remove 3.13.5 * [ENH] Add Basic ARIMA model (#2860) * arima first * move utils * make functions private * Modularise SARIMA model * Add ARIMA forecaster to forecasting package * Add example to ARIMA forecaster, this also tests the forecaster is producing the expected results * Basic ARIMA model * Convert ARIMA to numba version * Adjust parameters to allow modification in fit * Update example and return native python type * Fix examples for tests * Fix Nelder-Mead Optimisation Algorithm Example * Fix Nelder-Mead Optimisation Algorithm Example #2 * Remove Nelder-Mead Example due to issues with numba caching functions * Fix return type issue * Address PR Feedback * Ignore small tolerances in floating point value in output of example * Fix kpss_test example * Fix kpss_test example #2 * Update documentation for ARIMAForecaster, change constant_term to be bool, and fix bug with it not operating on differemced data * Modify ARIMA to allow predicting multiple values by updating the state without refitting the model * Fix bug using self.d rather than self.d_ * refactor ARIMA * docstring * find forecast_ in fit * remove optional y * add iterative * typo * typo * calculate forecast_ * use differenced * example * iterative * arima tests * revert to float * switch nelder_mead version * isolate loss function * isolate loss function * remove the utils version of nelder mead * set self.c_ correctly * numba optimise * numba optimise * numba optimise * Add missing _extract_paras file * initial residuals bug and proper differencing d>1 * loss function ignores zeroed start points * fix test * revert FLOAT_CMP * refactor into forecasting * remove example --------- Co-authored-by: Tony Bagnall <ajb@uea.ac.uk> Co-authored-by: Alex Banwell <arb1g19@soton.ac.uk> Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * Automated `pre-commit` hook update (#2959) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * clean space for swap CI to stop sporadic failue (#2965) * [MNT] Bump crs-k/stale-branches in the github-actions group (#2950) --- updated-dependencies: - dependency-name: crs-k/stale-branches dependency-version: 8.2.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [ENH] New experimental module: imbalance in collection transformers (#2498) * first draft * [ENH] wrapper for smote and adasyn of the imbalance module in collection transformers (#2501) * smote & adasyn in aeon.transformation.imbalance * smote & adasyn in aeon.transformation.imbalance * smote & adasyn in aeon.transformation.imbalance * smote & adasyn in aeon.transformation.imbalance * make experimental * inherit from SMOTE * test equivalence to imblearn * move tests * format * import * add test parameters * Ported OHIT (#2573) * Automatic `pre-commit` fixes * docstrings * remove import * remove incorrect test parameters * docstrings * examples * examples * refactor variable name * format comments and reference * typos --------- Co-authored-by: Chuanhang Qiu <80885865+LinGinQiu@users.noreply.github.com> Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * stop overwriting y (#2969) * [BUG] Fix redcomets bug when using only one sample (#2952) * Fix * fix exemples * Empty commit for CI * Rework examples and add test * Try fixing example indentation error * Fix examples --------- Co-authored-by: baraline <10759117+baraline@users.noreply.github.com> Co-authored-by: Patrick Schäfer <patrick.schaefer@hu-berlin.de> * [DEP] Remove deprecated transforms (#2961) * remove depcated transforms * fixes * updated dtw gi * debug * debug * debug * debug * fix * Empty commit for CI * change to get_num_threads * resolved comments * fix refactor * fix refactor * fixed regressor test * removed kwargs * added test to ensure n_jobs > 1 doesnt break * merged main and set test to only run on threaded runner --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Antoine Guillaume <antoine.guillaume45@gmail.com> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: aeon-actions-bot[bot] <148872591+aeon-actions-bot[bot]@users.noreply.github.com> Co-authored-by: chrisholder <4674372+chrisholder@users.noreply.github.com> Co-authored-by: Kavya Rambhia <161142013+kavya-r30@users.noreply.github.com> Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Aryan Pola <98093778+aryanpola@users.noreply.github.com> Co-authored-by: Tanish Yelgoe <143334319+tanishy7777@users.noreply.github.com> Co-authored-by: Sebastian Schmidl <10573700+SebastianSchmidl@users.noreply.github.com> Co-authored-by: Kaustubh <97254178+Kaustbh@users.noreply.github.com> Co-authored-by: Akash Kawle <128881349+shinymack@users.noreply.github.com> Co-authored-by: TinaJin0228 <60577222+TinaJin0228@users.noreply.github.com> Co-authored-by: Ayush Singh <rawatsinghayush9720@gmail.com> Co-authored-by: ayushsingh9720 <199482418+ayushsingh9720@users.noreply.github.com> Co-authored-by: HaroonAzamFiza <haroonazamfiza@gmail.com> Co-authored-by: adityagh006 <142653450+adityagh006@users.noreply.github.com> Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> Co-authored-by: V_26@ <valencia.saldanha26@gmail.com> Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Ramana Raja <83065061+Ramana-Raja@users.noreply.github.com> Co-authored-by: Ramana-Raja <ramanarajakesavaraja@gamil.com> Co-authored-by: Ahmed Zahran <136983104+Ahmed-Zahran02@users.noreply.github.com> Co-authored-by: Adarsh Dubey <dubeyadarshmain@gmail.com> Co-authored-by: Ali El Hadi ISMAIL FAWAZ <54309336+hadifawaz1999@users.noreply.github.com> Co-authored-by: Somto Onyekwelu <117727947+SomtoOnyekwelu@users.noreply.github.com> Co-authored-by: Saad Al-Tohamy <92796871+saadaltohamy@users.noreply.github.com> Co-authored-by: Patrick Schäfer <patrick.schaefer@hu-berlin.de> Co-authored-by: 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* added numba prange to all pairwise distances * sfa update * changed warning * thread kneighbors * fix test * custom pairwise threaded * fixed * added threaded decorator * merge changes and fixed call * fix * fix * fixed * expanded threaded decorator to work with classes * fixed * fix * merge * added test for kneighbors * added test for kneighbors * fix * Automated `CONTRIBUTORS.md` update (#2614) Co-authored-by: chrisholder <4674372+chrisholder@users.noreply.github.com> * Updated Interval Based Notebook (#2620) * [DOC] Added Docstring for regression forecasting (#2564) * Added Docstring for Regression * Added Docstring for Regression * exog fix * GSoC announcement (#2629) * Automated `pre-commit` hook update (#2632) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [MNT] Bump tj-actions/changed-files from 45 to 46 in the github-actions group (#2637) * [MNT] Bump tj-actions/changed-files in the github-actions group Bumps the github-actions group with 1 update: [tj-actions/changed-files](https://github.com/tj-actions/changed-files). Updates `tj-actions/changed-files` from 45 to 46 - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v45...v46) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> * Update pr_precommit.yml --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [MNT] Update numpy requirement in the python-packages group (#2643) Updates the requirements on [numpy](https://github.com/numpy/numpy) to permit the latest version. Updates `numpy` to 2.2.4 - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](https://github.com/numpy/numpy/compare/v1.21.0...v2.2.4) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production dependency-group: python-packages ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MNT,DEP] _binary.py metrics deprecated (#2600) * functions deprecated * Empty-Commit * version changed * Support for unequal length timeseries in itakura parallelogram (#2647) * [ENH] Implement DTW with Global alignment (#2565) * Implements Dynamic Time Warping with Global Invariances * Adds Numba JIT compilation support * Adds docs and numba support for dtw_gi and test_distance fixed * Fixes doctests * Automatic `pre-commit` fixes * Minor changes * Minor changes * Remove dtw_gi function and combine with private method _dtw_gi * Adds parameter tests * Fixes doctests * Minor changes * [ENH] Adds kdtw kernel support for kernelkmeans (#2645) * Adds kdtw kernel support for kernelkmeans * Code refactor * Adds tests for kdtw clustering * minor changes * minor changes * [MNT] Skip some excected results tests when numba is disabled (#2639) * skip some numba tests * Empty commit for CI * Update testing_config.py --------- Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [MNT] Remove REDCOMETs from testing exclusion list (#2630) * remove excluded estimators * redcomets fix * [ENH] Replace `prts` metrics (#2400) * Pre-commit fixes * Position parameter in calculate_bias * Added recall metric * merged into into one file * test added * Changes in test and range_metrics * list of list running but error! * flattening lists, all cases passed * Empty-Commit * changes * Protected functions * Changes in documentation * Changed test cases into seperate functions * test cases added and added range recall * udf_gamma removed from precision * changes * more changes * recommended changes * changes * Added Parameters * removed udf_gamma from precision * Added binary to range * error fixing * test comparing prts and range_metrics * Beta parameter added in fscore * Added udf_gamma function * f-score failing when comparing against prts * fixed f-score output * alpha usage * Empty-Commit * added test case to use range-based input for metrics * soft dependency added * doc update --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: Sebastian Schmidl <10573700+SebastianSchmidl@users.noreply.github.com> * Clarify documentation regarding unequal length series limitation (#2589) Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * Automated `pre-commit` hook update (#2683) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [MNT] Bump tj-actions/changed-files in the github-actions group (#2686) Bumps the github-actions group with 1 update: [tj-actions/changed-files](https://github.com/tj-actions/changed-files). Updates `tj-actions/changed-files` from 46.0.1 to 46.0.3 - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v46.0.1...v46.0.3) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [ENH] Set `outlier_norm` default to True for Catch22 estimators (#2659) * sets outlier_norm=True by deafault * Minor changes * Docs improvement * [MNT] Use MacOS for examples/ workflow (#2668) * update bash to 5.x for lastpipe support * added esig installation * install boost before esig * fixed examples path issue for excluded notebooks * switched to fixed version of macos * added signature_method.ipynb to excluded list * removed symlink for /bin/bash * Update dependencies.md (#2717) Correct typo in dependencies.md * Automated `pre-commit` hook update (#2708) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [ENH] Test Coverage for Pairwise Distance (#2590) * Pairwise distance matrix test * Empty commit for CI --------- Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * re-running notebook for fixing cell output error (#2597) * Docstring (#2609) * [DOC] Add 'Raises' section to docstring #1766 (#2617) * [DOC] Add 'Raises' section to docstring #1766 * Automatic `pre-commit` fixes * Update _base.py * Automatic `pre-commit` fixes --------- Co-authored-by: ayushsingh9720 <199482418+ayushsingh9720@users.noreply.github.com> * [DOC] Contributor docs update (#2554) * contributing docs update * contributing docs update 2 * typos * Update contributing.md new section * Update testing.md testing update * Update contributing.md dont steal code * Automatic `pre-commit` fixes * Update contributing.md if --------- Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> Co-authored-by: Antoine Guillaume <antoine.guillaume45@gmail.com> * prevent assignment on PRs (#2703) * Update run_examples.sh (#2701) * [BUG] SevenNumberSummary bugfix and input rename (#2555) * summary bugfix * maintainer * test * readme (#2556) * remove MutilROCKETRegressor from alias mapping (#2623) Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * Automated `pre-commit` hook update (#2731) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [MNT] Bump the github-actions group with 2 updates (#2733) Bumps the github-actions group with 2 updates: [actions/create-github-app-token](https://github.com/actions/create-github-app-token) and [tj-actions/changed-files](https://github.com/tj-actions/changed-files). Updates `actions/create-github-app-token` from 1 to 2 - [Release notes](https://github.com/actions/create-github-app-token/releases) - [Commits](https://github.com/actions/create-github-app-token/compare/v1...v2) Updates `tj-actions/changed-files` from 46.0.3 to 46.0.4 - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v46.0.3...v46.0.4) --- updated-dependencies: - dependency-name: actions/create-github-app-token dependency-version: '2' dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions - dependency-name: tj-actions/changed-files dependency-version: 46.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Fixed a few spelling/grammar mistakes on TSC docs examples (#2738) * Fix docstring inconsistencies in benchmarking module (resolves #809) (#2735) * issue#809 Fix docstrings for benchmarking functions * Fixed docstrings in results_loaders.py * Fix docstring inconsistencies in benchmarking module - resolves #809 * Fix docstring inconsistencies in benchmarking module - resolves #809 * [ENH] `best_on_top` addition in `plot_pairwise_scatter` (#2655) * Empty-Commit * best_on_top parameter added * changes * [ENH] Add dummy clusterer tags (#2551) * dummy clusterer tags * len * [ENH] Collection conversion cleanup and `df-list` fix (#2654) * collection conversion cleanup * notebook * fixes --------- Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> * [MNT] Updated the release workflows (#2638) * edit release workflows to use trusted publishing * docs * [MNT,ENH] Update to allow Python 3.13 (#2608) * python 3.13 * tensorflow * esig * tensorflow * tensorflow * esig and matrix profile * signature notebook * remove prts * fix * remove annoying deps from all_extras * Update pyproject.toml * [ENH] Hard-Coded Tests for `test_metrics.py` (#2672) * Empty-Commit * hard-coded tests * changes * Changed single ticks to double (#2640) Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * 📝 Add HaroonAzamFiza as a contributor for doc (#2740) * 📝 Update CONTRIBUTORS.md [skip ci] * 📝 Update .all-contributorsrc [skip ci] --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> * [ENH,MNT] Assign Bot (assigned issues>2) (#2702) * Empty-Commit * point 2 working * changes * changes in comment message * [MNT,ENH] Assign-bot (Allow users to type alternative phrases for assingment) (#2704) * added extra features * added comments * optimized code * optimized code * made changes requested by moderators * fixed conflicts * fixed conflicts * fixed conflicts --------- Co-authored-by: Ramana-Raja <ramanarajakesavaraja@gamil.com> * 📝 Add Ramana-Raja as a contributor for code (#2741) * 📝 Update CONTRIBUTORS.md [skip ci] * 📝 Update .all-contributorsrc [skip ci] --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> * Release v1.1.0 (#2696) * v1.1.0 draft * finish * Automated `pre-commit` hook update (#2743) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [MNT] Bump the github-actions group with 2 updates (#2744) Bumps the github-actions group with 2 updates: [crs-k/stale-branches](https://github.com/crs-k/stale-branches) and [tj-actions/changed-files](https://github.com/tj-actions/changed-files). Updates `crs-k/stale-branches` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/crs-k/stale-branches/releases) - [Commits](https://github.com/crs-k/stale-branches/compare/v7.0.0...v7.0.1) Updates `tj-actions/changed-files` from 46.0.4 to 46.0.5 - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v46.0.4...v46.0.5) --- updated-dependencies: - dependency-name: crs-k/stale-branches dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions - dependency-name: tj-actions/changed-files dependency-version: 46.0.5 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [DOC] Add implementation references (#2748) * implementation references * better attribution * use gpu installs for periodic tests (#2747) * Use shape calculation in _fit to optimize QUANTTransformer (#2727) * [REF] Refactor Anomaly Detection Module into Submodules by Algorithm Family (#2694) * Refactor Anomaly Detection Module into Submodules by Algorithm Family * updated documentation and references * implemented suggested changes * minor changes * added headers for remaining algorithm family * removing tree-based header * Automated `pre-commit` hook update (#2756) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [ENH]Type hints/forecasting (#2737) * Type hints for primitive data types in base module * Type hints for primitive data types and strings in forecating module * type hints for primitives in foreacasting module * Revert "type hints for primitives in foreacasting module" This reverts commit 575122d14b28742140ef1e16a3a351dd5db5072b. * type hints for primitives in forecasting module * Automated `pre-commit` hook update (#2766) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [ENH] Implement `load_model` function for ensemble classifiers (#2631) * feat: implement `load_model` function for LITETimeClassifier Implement separate `load_model` function for LITETimeClassifier, which takes in `model_path` as list of strings and `classes` and loads all the models separately and stores them in `self.classifiers_` * feat: implement `load_model` function for InceptionTimeClassifier Implement separate `load_model` function for InceptionTimeClassifier, which takes in `model_path` as list of strings and `classes` and loads all the models separately and stores them in `self.classifiers_` * fix: typo in load model function * feat: convert load_model functions to classmethods * test: implement test for save load for LITETIME and Inception classification models * Automatic `pre-commit` fixes * refactor: move loading tests to separate files * Update _ae_abgru.py (#2771) * Automated `pre-commit` hook update (#2779) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [DOC] Fix Broken [Source] Link and Improve Documentation for suppress_output() (#2677) * Fix Broken [Source] Link and Improve Documentation for suppress_output() Function * modified docstring and added tests * modified docstring example * modifying docstring examples * modifying docstring examples * updating conf file * updated docstring * base transform tidy (#2773) * DOC: Add Raises section for invalid weights in KNeighborsTimeSeriesClassifier (#1766) (#2764) Document the ValueError raised during initialization when an unsupported value is passed to the 'weights' parameter. Clarifies expected exceptions for users and improves API documentation consistency. Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [ENH] Fixes Issue Improve `_check_params` method in `kmeans.py` and `kmedoids.py` (#2682) * Improves _check_params * removes function and adds a var * minor changes * minor changes * minor changes * line endings to LF * use variable instead of duplicating strings * weird file change * weird file change --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [ENH] Add type hints for deep learning regression classes (#2644) * type hints for cnn for regrssion * editing import modules Model & Optim * type hints for disjoint_cnn for regrssion * FIX type hints _get_test_params * ENH Change linie of importing typing * type hints for _encoder for regrssion * type hints for _fcn for regrssion * type hints for _inception_time for regrssion * type hints for _lite_time for regrssion * type hints for _mlp for regrssion * type hints for _resnet for regrssion * type hints for _base for regrssion * FIX: mypy errors in _disjoint_cnn.py file * FIX: mypy typing errors * Fix: Delete variable types, back old-verbose * FIX: add model._save in save_last_model_to_file function * FIX: Put TYPE_CHECKING downside * Fix: Put Any at the top * [DOC] Add RotationForest Classifier Notebook for Time Series Classification (#2592) * Add RotationForest Classifier Notebook for Time Series Classification * Added references and modified doc * minor modifications to notebook description * Update rotation_forest.ipynb --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * fix: Codeowners for benchmarking metrics AD (#2784) * [GOV] Supporting Developer role (#2775) * supporting dev role * pr req * Update governance.md * typo * Automatic `pre-commit` fixes * aeon --------- Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [MNT, ENH, DOC] Rework similarity search (#2473) * WIP remake module structure * Update _brute_force.py * Update test__commons.py * WIP mock and test * Add test for base subsequence * Fix subsequence_search tests * debug brute force mp * more debug of subsequence tests * more debug of subsequence tests * Add functional LSH neighbors * add notebook for sim search tasks * Updated series similarity search * Fix mistake addition in transformers and fix base classes * Fix registry and api reference * Update documentation and fix some leftover bugs * Update documentation and add default test params * Fix identifiers and test data shape for all_estimators tests * Fix missing params * Fix n_jobs params and tags, add some docs * Fix numba test bug and update testing data for sim search * Fix imports, testing data tests, and impose predict/_predict interface to all sim search estimators * Fix args * Fix extract test * update docs api and notebooks * remove notes * Patrick comments * Adress comments and clean index code * Fix Patrick comments * Fix variable suppression mistake * Divide base class into task specific * Fix typo in imports * Empty commit for CI * Fix typo again * Add check_inheritance exception for similarity search * Revert back to non per type base classes * Factor check index and typo in test --------- Co-authored-by: Patrick Schäfer <patrick.schaefer@hu-berlin.de> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: baraline <10759117+baraline@users.noreply.github.com> * [ENH] Adapt the DCNN Networks to use Weight Norm Wrappers (#2628) * adapt the dcnn networks to use weight norm wrappers and remove l2 regularization * Automatic `pre-commit` fixes * add custom object * Automatic `pre-commit` fixes * fix trial --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [GOV] Remove inactive developers (#2776) * inactive devs * logo fix * Automated `pre-commit` hook update (#2792) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * Add SomtoOnyekwelu to .all-contributorsrc (#2788) * Automated `CONTRIBUTORS.md` update (#2794) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [BUG] Fix a bug in ClaSP Series Transformer when using floatXX as Input (where XX != 64) (#2774) * Automatic conversion to float64. * remove print * [DOC] Changed SummaryClusterer's summary_stat from "percentiles" to "quantiles" (#2778) * changed summary_stats * changed summary_stats * changed summary_stats * changed summary_stats for regression and classification * [ENH] Test coverage for AEAttentionBiGRUNetwork Improved (#2540) * test file for ae_abgru added * soft depedency of tf resolved * aeabgru test file changed, bug resolved * aeabgru file reverted to original state * [BUG] Better error message for Rotation Forest with no usable attributes (#2798) * better error message for rotf failure * Update _rotation_forest_classifier.py * Update _rotation_forest_regressor.py * [DOC] Inconsistent double ticks in segmentation package, public docstring only (#2622) * double ticks EAggloSegmenter docstring * double ticks HMMSegmenter docstring * double ticks InformationGainSegmenter docstring * double ticks for other EAggloSegmenter docstring and removed extra whitespace --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * put lower bound keras (#2808) * [REF] Refactor smoothing transformers into a sub-package (#2783) * mockup * init * decorator * correct import and tag * base docs * wrappers * tests * docs and imports * test params * register * big refactor * smoothing refactor * ad stuff * fixes * fixes * no longer required * [ENH] Refactor range-based metrics to restore original behavior (#2781) * feat: refactor range-based metrics to be consistent with the other AD metrics and integrate them into the AD test harness * refactor: move new range metrics methods into their old place and remove the deprecation * refactor: factor out test execution from test fixtures * refactor: move tests to new methods * fix: copy'n'paste error * [ENH]Use n_jobs parameter in KNeighborsTimeSeriesClassifier. (#2687) * Use n_jobs parameter in KNeighborsTimeSeriesClassifier. * Don't convert proba dtype. * Remove is_fitted checks, update docstring. * Implement parallel backend param. * Correct keyword argument for Parallel. * Add check_n_jobs. --------- Co-authored-by: stijn <s.j.rotman@tilburguniversity.edu> * [ENH] add informational tags back to estimator docs (#2652) * feat: add new tags information for anomaly detection * feat: add tag information in given anomaly modles * fix: add new anomaly detector tags in mock anomaly detector class * fix: use anomaly-detector instead of estimator for new tags * update and add basic testing * fixes --------- Co-authored-by: MatthewMiddlehurst <pfm15hbu@gmail.com> * [DOC] Documentation improvement of BaseSeriesEstimator and BaseAeonEstimator (#2612) * Added the docs for base series and base classes * Updated documentation for base classes --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [ENH] HydraTransformer Output changed (#2656) * output type added * hydra wflow modified * hydra test file added * pr_pytest reverted * soft dep check added * soft dep corrected * docstring corrected, enhanced test cases * [DOC] Improved Hidalgo Segmentation Notebook (#2616) * Improved Hidalgo Segmentation Notebook * Updated hidalgo notebook --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * new devs and workflow consolidation (#2797) * all branches (#2809) * Automated `pre-commit` hook update (#2820) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * [MNT] Bump crs-k/stale-branches in the github-actions group (#2821) Bumps the github-actions group with 1 update: [crs-k/stale-branches](https://github.com/crs-k/stale-branches). Updates `crs-k/stale-branches` from 7.0.1 to 8.1.1 - [Release notes](https://github.com/crs-k/stale-branches/releases) - [Commits](https://github.com/crs-k/stale-branches/compare/v7.0.1...v8.1.1) --- updated-dependencies: - dependency-name: crs-k/stale-branches dependency-version: 8.1.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * fix: indexing in kdtw (#2826) * [ENH] Added test cases for feature based clustering (#2690) * Added test cases for feature based clustering * Automatic `pre-commit` fixes * added docstring * Automatic `pre-commit` fixes * added . * added . * updated tsfresh * Automatic `pre-commit` fixes * added pytest _check_soft_dependencies for tsfresh * Automatic `pre-commit` fixes * added more testing * Automatic `pre-commit` fixes * added docs * added docs * added pytest * Automatic `pre-commit` fixes * improved docs * Automatic `pre-commit` fixes * improved test cases * changes made as requested by moderators * changes made as requested by moderators * Automatic `pre-commit` fixes * changed "percentiles" to "quantiles" --------- Co-authored-by: Ramana-Raja <ramanarajakesavaraja@gamil.com> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> * [DOC] Fix inconsistent double backticks in updated similarity_search module docstrings (#2618) * [ENH] Update `_continuous.py` functions (#2822) * update continuous, has test failure * parameters back to original * alpha added into precision * removes p_alpha deprecation * changes * [MNT] stop segmenters changing state in predict (#2526) * remove stored variables in predict * IGTS * GGS * FLUSS * FLUSS * CLASP * CLASP * revert clasp * revert clasp * revert clasp * Update testing_config.py * Update _fluss.py * refactor dummy to naive (#2831) * [ENH] add a difference transformer to series transformations (#2729) * add difference transformer to series transformations * add myself to .all-contributorsrc * small modification * modify according to reviews * [ENH] add informational tags back to estimator docs (#2652) * feat: add new tags information for anomaly detection * feat: add tag information in given anomaly modles * fix: add new anomaly detector tags in mock anomaly detector class * fix: use anomaly-detector instead of estimator for new tags * update and add basic testing * fixes --------- Co-authored-by: MatthewMiddlehurst <pfm15hbu@gmail.com> * [DOC] Documentation improvement of BaseSeriesEstimator and BaseAeonEstimator (#2612) * Added the docs for base series and base classes * Updated documentation for base classes --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [ENH] HydraTransformer Output changed (#2656) * output type added * hydra wflow modified * hydra test file added * pr_pytest reverted * soft dep check added * soft dep corrected * docstring corrected, enhanced test cases * [DOC] Improved Hidalgo Segmentation Notebook (#2616) * Improved Hidalgo Segmentation Notebook * Updated hidalgo notebook --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * new devs and workflow consolidation (#2797) * all branches (#2809) * Automated `pre-commit` hook update (#2820) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * [MNT] Bump crs-k/stale-branches in the github-actions group (#2821) Bumps the github-actions group with 1 update: [crs-k/stale-branches](https://github.com/crs-k/stale-branches). Updates `crs-k/stale-branches` from 7.0.1 to 8.1.1 - [Release notes](https://github.com/crs-k/stale-branches/releases) - [Commits](https://github.com/crs-k/stale-branches/compare/v7.0.1...v8.1.1) --- updated-dependencies: - dependency-name: crs-k/stale-branches dependency-version: 8.1.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * fix: indexing in kdtw (#2826) * [ENH] Added test cases for feature based clustering (#2690) * Added test cases for feature based clustering * Automatic `pre-commit` fixes * added docstring * Automatic `pre-commit` fixes * added . * added . * updated tsfresh * Automatic `pre-commit` fixes * added pytest _check_soft_dependencies for tsfresh * Automatic `pre-commit` fixes * added more testing * Automatic `pre-commit` fixes * added docs * added docs * added pytest * Automatic `pre-commit` fixes * improved docs * Automatic `pre-commit` fixes * improved test cases * changes made as requested by moderators * changes made as requested by moderators * Automatic `pre-commit` fixes * changed "percentiles" to "quantiles" --------- Co-authored-by: Ramana-Raja <ramanarajakesavaraja@gamil.com> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> * [DOC] Fix inconsistent double backticks in updated similarity_search module docstrings (#2618) * delete some descriptions * modification to _maintainer_ --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> Co-authored-by: Adarsh Dubey <dubeyadarshmain@gmail.com> Co-authored-by: Kevin Shah <161136814+kevinzb56@users.noreply.github.com> Co-authored-by: Balgopal Moharana <99070111+lucifer4073@users.noreply.github.com> Co-authored-by: Kavya Rambhia <161142013+kavya-r30@users.noreply.github.com> Co-authored-by: aeon-actions-bot[bot] <148872591+aeon-actions-bot[bot]@users.noreply.github.com> Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Sebastian Schmidl <10573700+SebastianSchmidl@users.noreply.github.com> Co-authored-by: Ramana Raja <83065061+Ramana-Raja@users.noreply.github.com> Co-authored-by: Ramana-Raja <ramanarajakesavaraja@gamil.com> Co-authored-by: Ciph3r <142653450+adityagh006@users.noreply.github.com> * Automated `CONTRIBUTORS.md` update (#2832) Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [BUG] Fix data loader (#2810) * Update _data_loaders.py * Update _data_loaders.py * stop deleting directories * Automated `pre-commit` hook update (#2841) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * 📝 Add lucifer4073 as a contributor for code (#2846) * 📝 Update CONTRIBUTORS.md [skip ci] * 📝 Update .all-contributorsrc [skip ci] --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> * [BUG] Adds test case for using csr_matrix with pickle - invalidates #2210 (#2843) * Extend test parameter set to validate if csx_matrix works with pickle. * Invalidates bug #2210 * [DOC] Docstring improved for dummy regressor (#2839) * Docstring improved for dummy regressor * convo resolved * remove numba typing (#2858) * [DOC] Regression forecaster docstring (#2837) * docstring * docstring * [ENH] Whole-series anomaly detection (#2326) * mockup * init * decorator * correct import and tag * base docs * wrappers * tests * docs and imports * test params * register * big refactor * smoothing refactor * Revert "smoothing refactor" This reverts commit c245ccbd0c1481b188a9094ccd7ff493613a89cd. * fixes * final bits and docs for refactor * fixes * testing fixes * Update aeon/anomaly_detection/collection/base.py Co-authored-by: Sebastian Schmidl <10573700+SebastianSchmidl@users.noreply.github.com> * Update docs/api_reference/anomaly_detection.rst Co-authored-by: Sebastian Schmidl <10573700+SebastianSchmidl@users.noreply.github.com> * Review changes * docs * import --------- Co-authored-by: Sebastian Schmidl <10573700+SebastianSchmidl@users.noreply.github.com> * [MNT] Bump the github-actions group across 1 directory with 2 updates (#2868) Bumps the github-actions group with 2 updates in the / directory: [ossf/scorecard-action](https://github.com/ossf/scorecard-action) and [crs-k/stale-branches](https://github.com/crs-k/stale-branches). Updates `ossf/scorecard-action` from 2.4.1 to 2.4.2 - [Release notes](https://github.com/ossf/scorecard-action/releases) - [Changelog](https://github.com/ossf/scorecard-action/blob/main/RELEASE.md) - [Commits](https://github.com/ossf/scorecard-action/compare/v2.4.1...v2.4.2) Updates `crs-k/stale-branches` from 8.1.1 to 8.2.0 - [Release notes](https://github.com/crs-k/stale-branches/releases) - [Commits](https://github.com/crs-k/stale-branches/compare/v8.1.1...v8.2.0) --- updated-dependencies: - dependency-name: ossf/scorecard-action dependency-version: 2.4.2 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions - dependency-name: crs-k/stale-branches dependency-version: 8.2.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Automated `pre-commit` hook update (#2867) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * [ENH] introduce revised version of ETS (#2834) * first version for correctness testing * timing * examples * new tests * refactor predict * final ETS * arima first * docstrings * docstrings * Convert error, trend and seasonality types to strings * Automatic `pre-commit` fixes * Add Type hints back in * Fix Type hints * Fix Linting issue * Automatic `pre-commit` fixes * Update test_ets to use strings for error, trend and seasonality types * Automatic `pre-commit` fixes * switch to fastmath * remove _arima, incorrectly introduced here * all int or str parameters * refactor variable name --------- Co-authored-by: alexbanwell1 <31886108+alexbanwell1@users.noreply.github.com> * [DOC] Update the projects lists (#2146) * remove Theta * projects * draft * add some papers * update papers * update projects * remove completed projects * remove poorly specified/out of date projects * remove merlin projects * restructure papers by year * papers using aeon * projects list and previous projects * update papers --------- Co-authored-by: MatthewMiddlehurst <pfm15hbu@gmail.com> * [DEP] Remove `prts` dependency (#2863) * remove prts from pyproject * docs * Update _continuous.py * Automatic `pre-commit` fixes --------- Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [ENH] Starting Self Supervised Model with first example (#2385) * add ssl module in transformations collection * add api * add test params * fix example * restart tests * test fix params * network none * revert * import inside function * try dummy * test repr * network repr * enhance testing * fix test * replace tcnn by lite * tony's comments * fix typing * fix znorm * z_norm in test * add exp module * Update repr.py * Update base.py * Automatic `pre-commit` fixes --------- Co-authored-by: MatthewMiddlehurst <pfm15hbu@gmail.com> Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * update slack link (#2877) * [BUG] Switch results loaders from http to https (#2883) * https * https in tests * [ENH] Correct broken source links for `set_params` and `get_params` in Aeon estimator docs (#2754) * Correct broken source links for `set_params` and `get_params` in Aeon estimator docs * made necessary changes * made necessary changes * modified linkcode_resolve * added comments * open PR comment changes (#2878) * [ENH] Implemented Tracking differentiator-based multiview dilated characteristics (TD-MVDC) Classifier (#2535) * Files and structure of tdmvdc class added * utility functions for tdmvdc applied * unecessary files removed * Initial implementation of TDMVDC added * accuracy improved to the required 81 per cent * test params added for tdmvdc * n_jobs temporarily disabled * n_jobs test params removed * Revert "n_jobs test params removed" This reverts commit 91539099f3cd3a201b7fe68bfea80a9ae5ebc706. * multithreading capability temporarily removed from tdmvdc * multithreading added * n_jobs removed from test_param * test added for tdmvdc * test added for tdmvdc * optimized comments * Made tdmvdc uniform across all feauture based classifiers * tdmvdc tested * check constructor test exlcuded for tdmvdc * changed * init file changed * check constructor corrected tdmvdc --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> * Automated `pre-commit` hook update (#2888) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * [MNT] Update pandas requirement in the python-packages group (#2889) Updates the requirements on [pandas](https://github.com/pandas-dev/pandas) to permit the latest version. Updates `pandas` to 2.3.0 - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Commits](https://github.com/pandas-dev/pandas/compare/v2.0.0...v2.3.0) --- updated-dependencies: - dependency-name: pandas dependency-version: 2.3.0 dependency-type: direct:production dependency-group: python-packages ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MNT] Drop Python 3.9 (#2845) * drop python 3.9 * fixes * readme * tag * test skip * [ENH] Series transformer pipeline and datatype list tidy (#2830) * series pipeline * fixes and docs * test fix * fix * [ENH] Multivariate and unequal PF, speed-ups and distance classifier tidy (#2872) * pass 1 * pf change fixes and derivative function merge * test * fixes * expected result * unequal and deprecations * [ENH] Add two forecasting tags (#2882) * add tags * correct exog * typo * [DOC] A fix to inconsistent double tick quote for the classification.distance_based module (#2627) * A fix to inconsistent double quotes * A fix to inconsistent double quotes * A fix to inconsistent double quotes * A fix to inconsistent double quotes * Revert "A fix to inconsistent double quotes" This reverts commit ff98c81a6c29b61d053e66c80f9f167b718172f5. * A fix to inconsistent double quotes * A fix to inconsistent double quotes * fix inconsistent double ticks * Automatic `pre-commit` fixes * Update _elastic_ensemble.py * Update _proximity_forest.py --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * 📝 Add Ahmed-Zahran02 as a contributor for doc (#2892) * 📝 Update CONTRIBUTORS.md [skip ci] * 📝 Update .all-contributorsrc [skip ci] --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> * [BUG] Forecasting regressor fix and notebook (#2885) * stop returning an array * notebook * Create window.png * fix test and typo * remove unfinished sentence * 📝 Add AnaghDeshpande as a contributor for doc (#2896) * 📝 Update CONTRIBUTORS.md [skip ci] * 📝 Update .all-contributorsrc [skip ci] --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> * [GOV] Use the NumFOCUS code of conduct and rename `aeon` workgroup (#2852) * code of conduct update and readmes * typo --------- Co-authored-by: Sebastian Schmidl <10573700+SebastianSchmidl@users.noreply.github.com> * [DOC] resolved the inconsistency of double ticks for the anomaly detection module #809 (#2546) * resolved the inconsistency of double quotes * resolved the inconsistency of double ticks * resolved the pre-commit errors occuring due to flake8 * Update _cblof.py made changes in line number 19 and 145. * Automatic `pre-commit` fixes * Update _copod.py made changes in line number 76 * Automatic `pre-commit` fixes * Update _iforest.py made changes in line number 19 * Automatic `pre-commit` fixes * Update _kmeans.py made changes in line number 178 * Automatic `pre-commit` fixes * Update _merlin.py made changes in line number 215 * Automatic `pre-commit` fixes * Update _one_class_svm.py made changes in line number 19 * Automatic `pre-commit` fixes * Update _pyodadapter.py made changes in line number 165 * Update _stomp.py made changes in line number 125 * Automatic `pre-commit` fixes * converted directives to single ticks * added double ticks to code ref * fixed link in cblof.py and some other minor changes * Update base.py --------- Co-authored-by: Patrick Schäfer <patrick.schaefer@hu-berlin.de> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [ENH] Forecasting testing (#2891) * call forecasting checks * basic cleanup * fix * add assert error messages * remove fit_is_empty check (see #2893) * remove extra argument to fit * remove extra argument to predict * correct forecast argument * Update _yield_forecasting_checks.py * add test for predict --------- Co-authored-by: Tony Bagnall <ajb@uea.ac.uk> * [MNT] Fixing CI issues and separate doctests from regular CI runners (#2902) * trying to fix CI stuff * use numba in codecov * try cov * no cov * doctest-plus * doctest-plus * addopts * dedicated doctest test * periodic * [BUG] Fixes a bug with SFAFast throwing an error when calling transform after fit (#2897) * Bugfix for SFA_Fast with transform called after fit * [MNT] Bump stefanzweifel/git-auto-commit-action from 5 to 6 in the github-actions group (#2906) * [MNT] Bump stefanzweifel/git-auto-commit-action Bumps the github-actions group with 1 update: [stefanzweifel/git-auto-commit-action](https://github.com/stefanzweifel/git-auto-commit-action). Updates `stefanzweifel/git-auto-commit-action` from 5 to 6 - [Release notes](https://github.com/stefanzweifel/git-auto-commit-action/releases) - [Changelog](https://github.com/stefanzweifel/git-auto-commit-action/blob/master/CHANGELOG.md) - [Commits](https://github.com/stefanzweifel/git-auto-commit-action/compare/v5...v6) --- updated-dependencies: - dependency-name: stefanzweifel/git-auto-commit-action dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> * Update issue_comment_edited.yml * Update pr_precommit.yml --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [ENH] Added RNN in networks (#2875) * RNN net architecture added * Fixed activation function for both str and list * RNN test mesage corrected * reverted workflow * reverted workflow * requested changes applied * convo resolved * Update README.md (#2908) * [ENH] Add recursive and direct methods to forecasting base class (#2899) * base class methods * direct * recursive * base * direct_forecasting * recursive_forecasting * recursive_forecasting * recursive_forecasting * direct notebook * direct notebook * direct notebook * switch to iterative * switch to iterative * iterative * iterative notebook * append change * append change * fix regression bug * comment * [ENH] remove horizon from ETS constructor, parametrize ETS tests (#2898) * remove horizon from ETS argument, parametrize tests * remove horizon from example * docstring * [ENH] Refactor example dataset for unequal length univariate (#2859) * deprecate PLAID * add pickup * deprecated * [ENH, REF]Refactored time-point based ROCKAD implementation (#2804) * mockup * init * decorator * correct import and tag * base docs * wrappers * tests * docs and imports * test params * register * big refactor * smoothing refactor * Revert "smoothing refactor" This reverts commit c245ccbd0c1481b188a9094ccd7ff493613a89cd. * fixes * final bits and docs for refactor * move predict_proba logic into inner_predict for code consistency * Added reference and example code, updated description * Adapted tests to be semi-supervised * Added semi-supervised labeling to description * moved Attributes above References and Examples, updated path of collection based rockad implementation * merge 2 * CI errors * maintainer * doctest --------- Co-authored-by: MatthewMiddlehurst <m.middlehurst@uea.ac.uk> Co-authored-by: MatthewMiddlehurst <pfm15hbu@gmail.com> * [ENH] enhance naive forecaster with new strategies (#2869) * naive forecaster with new strategies * few modifications according to reviews * made modifications and add documentation * modifications according to reviews * try to pass the test * delete one comment * modify 1)more test cases for seasonal_last 2)raise exception for y input in _predict, and related documentation * fix typo * take y * Update _naive.py --------- Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> Co-authored-by: MatthewMiddlehurst <pfm15hbu@gmail.com> * [ENH,REF] Unequal length collection transforms (#2903) * move and update unequal transforms * unequal transforms * comment * better sorting * extra transform test * changes for review * Release v1.2.0 (#2912) * release prep * changelog * Automated `pre-commit` hook update (#2914) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * [MNT] Comments on numba caching and release CI fix (#2916) * release CI jank * comment * swap * [ENH] Improves `create_multi_comparison_matrix` parameters and saving (#2657) * Empty-Commit * condensed parameters and showing output * test cases updated * changes * updated examples * point 2 working * [DOC] Clarify comments regarding issue assignment limits and user notifications * condensed parameters and showing output * test cases updated * changes * dir -> save_path * Reverted _mcm.py and its test to match main * requested changes done, pdf not showing yet * changes * changes * updated docstring * changes * requested changes * example file changes * changed formats default to None --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [MNT] Prevents assignment on Restricted Labels (#2706) * restricted labels * set * resolve conflicts * merge assign PRs and small change --------- Co-authored-by: MatthewMiddlehurst <pfm15hbu@gmail.com> * [MNT] Update scikit-learn requirement from <1.7.0,>=1.0.0 to >=1.0.0,<1.8.0 in the python-packages group (#2907) * [MNT] Update scikit-learn requirement in the python-packages group Updates the requirements on [scikit-learn](https://github.com/scikit-learn/scikit-learn) to permit the latest version. Updates `scikit-learn` to 1.7.0 - [Release notes](https://github.com/scikit-learn/scikit-learn/releases) - [Commits](https://github.com/scikit-learn/scikit-learn/compare/1.0...1.7.0) --- updated-dependencies: - dependency-name: scikit-learn dependency-version: 1.7.0 dependency-type: direct:production dependency-group: python-packages ... Signed-off-by: dependabot[bot] <support@github.com> * new validation * Update test_rockad.py * Update _rockad.py --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: MatthewMiddlehurst <pfm15hbu@gmail.com> * [MNT] issue-assign-bot - only users with write access should be able to assign others (#2739) * only admins can assign others * improve comment message * Automatic `pre-commit` fixes * fixes according to latest code * Automatic `pre-commit` fixes * changes according to latest code * resolve merge conflicts * Automatic `pre-commit` fixes * adjust according to latest code * merge --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * [MNT] Created workflow for closing "AI Spam" pull requests (#2750) * added ai_spam * Automatic `pre-commit` fixes * fixed comment text * fixed comment text * updated to python 3.11 --------- Co-authored-by: Ramana-Raja <ramanarajakesavaraja@gamil.com> * [ENH] Use `np.argpartition` for efficient top-k selection instead of `np.argsort` (#2805) * use argpartition for efficient selection instead of argsort * made the required changes * [EHN] Allow exogenous variables in regression forecasters (#2915) * add exogenous variable feature to base and regression forecasters * delete self._check_X for exog --------- Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> * Automated `pre-commit` hook update (#2922) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * [MNT] Bump actions/create-github-app-token in the github-actions group (#2923) Bumps the github-actions group with 1 update: [actions/create-github-app-token](https://github.com/actions/create-github-app-token). Updates `actions/create-github-app-token` from 1 to 2 - [Release notes](https://github.com/actions/create-github-app-token/releases) - [Commits](https://github.com/actions/create-github-app-token/compare/v1...v2) --- updated-dependencies: - dependency-name: actions/create-github-app-token dependency-version: '2' dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [ENH] Added RecurrentRegressor for time series regression (#2894) * RNN net architecture added * Fixed activation function for both str and list * RNN test mesage corrected * RNN regressor added * init updated w rnn * reverted workflow * reverted workflow * requested changes applied * updated with latest recurrent network * merged with main * [MNT] Add testing workflow for multithreading and make threaded estimators use `check_n_jobs` (#2913) * multithreading test * njons and workflow fix * tde and base test * _n_jobs in testing * _n_jobs in testing * more test fixes * fixes * more n_jobs * more n_jobs * more n_jobs * more n_jobs * more n_jobs * test fix * test fix * test fix * test fix * hopefully last * hopefully last again * dont enumerate * periodic test * [DOC,MNT] Documentation configuration clean-up (#2911) * start * remove old parameter * numpydoc config * conf tidy * headers * exclude unused methods and update gsoc in about * changelog * binder button * myst config * remove extra bullet point * changelog * Automatic `pre-commit` fixes --------- Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * [DOC] fix incorrect references of classes in getting started page (#2762) * fix: incorrect references of classes in getting started page * fix: typo in BaseSimilaritySearch --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * Automated `pre-commit` hook update (#2932) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * [DOC] Add RecurrentRegressor and RecurrentNetowork to api_reference (#2935) * Recurrent Regressor added to API doc * Recurrent network added to API doc * [ENH] Refactor to set forecast_ in fit and to require y in predict (#2927) * require y in predict * forecast_ * remove calls to predict * doc examples * regression forecaster rework * other tests * docstrings * refactor forecasting checks * test * test * regression notebook * test_ets * Revert "test_ets" This reverts commit 827a12a0a2fa3fec2d55d481a97aed62bd290059. * Revert "regression notebook" This reverts commit 27978022921c8c436d1ae458511ce5885d425c09. * ets * notebook * naive testing * [ENH] Clone estimator in direct forecast (#2936) * clone estimator * clone estimator * tests * test update * [ENH] Implement Time-Varying Parameter (TVP) regression forecaster using Kalman filter (#2920) * TVP * bug * refactor * test * test * add notebook * docstring * add an intercept * includes * squeeze predict * format * remove incomplete example * add test params * dummy test * dummy test * clone estimator * clone estimator * remove y is none * notebook * tests * tests * test update * remove pointless test * docstring update * [MNT] Add codespell support (config, workflow to detect/not fix) and make it fix a "few" typos (#2653) * Add github action to codespell main on push and PRs * Add rudimentary codespell config * Add pre-commit definition for codespell * Some skips for codespell -- lots of work todo * [DATALAD RUNCMD] run codespell throughout fixing typos automagically (but ignoring overall fail due to ambigous ones) === Do not change lines below === { "chain": [], "cmd": "codespell -w || :", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ * codespeed notebook and testing * incorrect typos and notebooks * more typos * config and fixes * Update similarity_search.ipynb fix notebook typos * update skip * temp typo and annotation workflow * annotations * fix typos --------- Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> Co-authored-by: Antoine Guillaume <antoine.guillaume45@gmail.com> * typo (#2944) * correct checkout (#2945) * DOC: fix typos in MatrixProfileSeriesTransformer (#2940) (#2941) Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> * 📝 Add CodeFor2001 as a contributor for doc (#2946) * 📝 Update CONTRIBUTORS.md [skip ci] * 📝 Update .all-contributorsrc [skip ci] --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> * [ENH] Rework ETS Forecaster (#2939) * iterative * iterative ETS * notebook * Fix bug in seasonality calculation * Add example for ETS iterative forecasting * ets tests * holding notebook * example * Run Itertive notebook --------- Co-authored-by: Alex Banwell <arb1g19@soton.ac.uk> * [MNT] add n_jobs parameter for sax invertion (#2953) * add n_jobs * add tag * Automated `pre-commit` hook update (#2949) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * [DEP] Deprecate PLAID dataset (#2928) * remove PLAID * remove PLAID * [DOC] Classification notebook links (#2942) * fix links * fix links --------- Co-authored-by: Antoine Guillaume <antoine.guillaume45@gmail.com> * [ENH] Added TemporalConvolutionalNetwork in aeon/networks (#2933) * tcn network added * tcn_net pytest added * tcn_network updated with default params * tcn reshaped * tcn changed * tcn updated * doctest corrected * tcn rshaped * workflow corrected * [BUG] Improve signature docs (#2929) * signature docs * tests * typo * notebook * correct image * fix test * decalre in init * switch classifier to store SignatureTransformer * revert classifier * revert transformer * embed image rather than link * equation * equation * remove tests * maths * maths * add eq * add eq * remove example * line break --------- Co-authored-by: Antoine Guillaume <antoine.guillaume45@gmail.com> * [MNT] Workflow maintenance (#2919) * keep running doctests on fail * renames * remove 3.13.5 * [ENH] Add Basic ARIMA model (#2860) * arima first * move utils * make functions private * Modularise SARIMA model * Add ARIMA forecaster to forecasting package * Add example to ARIMA forecaster, this also tests the forecaster is producing the expected results * Basic ARIMA model * Convert ARIMA to numba version * Adjust parameters to allow modification in fit * Update example and return native python type * Fix examples for tests * Fix Nelder-Mead Optimisation Algorithm Example * Fix Nelder-Mead Optimisation Algorithm Example #2 * Remove Nelder-Mead Example due to issues with numba caching functions * Fix return type issue * Address PR Feedback * Ignore small tolerances in floating point value in output of example * Fix kpss_test example * Fix kpss_test example #2 * Update documentation for ARIMAForecaster, change constant_term to be bool, and fix bug with it not operating on differemced data * Modify ARIMA to allow predicting multiple values by updating the state without refitting the model * Fix bug using self.d rather than self.d_ * refactor ARIMA * docstring * find forecast_ in fit * remove optional y * add iterative * typo * typo * calculate forecast_ * use differenced * example * iterative * arima tests * revert to float * switch nelder_mead version * isolate loss function * isolate loss function * remove the utils version of nelder mead * set self.c_ correctly * numba optimise * numba optimise * numba optimise * Add missing _extract_paras file * initial residuals bug and proper differencing d>1 * loss function ignores zeroed start points * fix test * revert FLOAT_CMP * refactor into forecasting * remove example --------- Co-authored-by: Tony Bagnall <ajb@uea.ac.uk> Co-authored-by: Alex Banwell <arb1g19@soton.ac.uk> Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> Co-authored-by: Matthew Middlehurst <pfm15hbu@gmail.com> * Automated `pre-commit` hook update (#2959) Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> * clean space for swap CI to stop sporadic failue (#2965) * [MNT] Bump crs-k/stale-branches in the github-actions group (#2950) --- updated-dependencies: - dependency-name: crs-k/stale-branches dependency-version: 8.2.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [ENH] New experimental module: imbalance in collection transformers (#2498) * first draft * [ENH] wrapper for smote and adasyn of the imbalance module in collection transformers (#2501) * smote & adasyn in aeon.transformation.imbalance * smote & adasyn in aeon.transformation.imbalance * smote & adasyn in aeon.transformation.imbalance * smote & adasyn in aeon.transformation.imbalance * make experimental * inherit from SMOTE * test equivalence to imblearn * move tests * format * import * add test parameters * Ported OHIT (#2573) * Automatic `pre-commit` fixes * docstrings * remove import * remove incorrect test parameters * docstrings * examples * examples * refactor variable name * format comments and reference * typos --------- Co-authored-by: Chuanhang Qiu <80885865+LinGinQiu@users.noreply.github.com> Co-authored-by: MatthewMiddlehurst <25731235+MatthewMiddlehurst@users.noreply.github.com> * stop overwriting y (#2969) * [BUG] Fix redcomets bug when using only one sample (#2952) * Fix * fix exemples * Empty commit for CI * Rework examples and add test * Try fixing example indentation error * Fix examples --------- Co-authored-by: baraline <10759117+baraline@users.noreply.github.com> Co-authored-by: Patrick Schäfer <patrick.schaefer@hu-berlin.de> * [DEP] Remove deprecated transforms (#2961) * remove depcated transforms * fixes * updated dtw gi * debug * debug * debug * debug * fix * refactored regressor * removed file * added test for knn regressor kneighbors * fixed sklearn compatiability tests * cleaned up and commented kneighbors function * fixed when list passed * added public and private methods for kneigbors and additionally expanded testing with comments * removed threaded decorator and swapped to private method --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Antoine 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Ayush Singh <rawatsinghayush9720@gmail.com> Co-authored-by: ayushsingh9720 <199482418+ayushsingh9720@users.noreply.github.com> Co-authored-by: HaroonAzamFiza <haroonazamfiza@gmail.com> Co-authored-by: adityagh006 <142653450+adityagh006@users.noreply.github.com> Co-authored-by: Tony Bagnall <a.j.bagnall@soton.ac.uk> Co-authored-by: V_26@ <valencia.saldanha26@gmail.com> Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Ramana Raja <83065061+Ramana-Raja@users.noreply.github.com> Co-authored-by: Ramana-Raja <ramanarajakesavaraja@gamil.com> Co-authored-by: Ahmed Zahran <136983104+Ahmed-Zahran02@users.noreply.github.com> Co-authored-by: Adarsh Dubey <dubeyadarshmain@gmail.com> Co-authored-by: Ali El Hadi ISMAIL FAWAZ <54309336+hadifawaz1999@users.noreply.github.com> Co-authored-by: Somto Onyekwelu <117727947+SomtoOnyekwelu@users.noreply.github.com> Co-authored-by: Saad Al-Tohamy <92796871+saadaltohamy@users.noreply.github.com> Co-authored-by: Patrick Schäfer <patrick.schaefer@hu-berlin.de> Co-authored-by: baraline <10759117+baraline@users.noreply.github.com> Co-authored-by: Aadya Chinubhai <77720426+aadya940@users.noreply.github.com> Co-authored-by: Balgopal Moharana <99070111+lucifer4073@users.noreply.github.com> Co-authored-by: Massimiliano <117172198+nMaax@users.noreply.github.com> Co-authored-by: steenrotsman <78110080+steenrotsman@users.noreply.github.com> Co-authored-by: stijn <s.j.rotman@tilburguniversity.edu> Co-authored-by: Kevin Shah <161136814+kevinzb56@users.noreply.github.com> Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com> Co-authored-by: alexbanwell1 <31886108+alexbanwell1@users.noreply.github.com> Co-authored-by: Anagh.B.Deshpande <125550290+AnaghDeshpande@users.noreply.github.com> Co-authored-by: Tony Bagnall <ajb@uea.ac.uk> Co-authored-by: Patrick <55019140+pattplatt@users.noreply.github.com> Co-authored-by: MatthewMiddlehurst <m.middlehurst@uea.ac.uk> Co-authored-by: Yaroslav Halchenko <debian@onerussian.com> Co-authored-by: Saniya S Inamdar <39870781+CodeFor2001@users.noreply.github.com> Co-authored-by: Alex Banwell <arb1g19@soton.ac.uk> Co-authored-by: Chuanhang Qiu <80885865+LinGinQiu@users.noreply.github.com>

Automated pre-commit hook update

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aeon-actions-bot bot added full pre-commit Run pre-commit for all files on a PR maintenance Continuous integration, unit testing & package distribution no changelog PR should not be added to the changelog labels May 19, 2025

MatthewMiddlehurst approved these changes May 19, 2025

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MatthewMiddlehurst merged commit 3271d4b into main May 19, 2025
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MatthewMiddlehurst deleted the pre-commit-hooks-update branch May 19, 2025 10:12

TinaJin0228 pushed a commit to TinaJin0228/aeon that referenced this pull request May 23, 2025

Automated pre-commit hook update (aeon-toolkit#2820)

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chrisholder pushed a commit that referenced this pull request Jul 30, 2025

Automated pre-commit hook update (#2820)

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Co-authored-by: TonyBagnall <9594042+TonyBagnall@users.noreply.github.com>

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[MNT] Automated `pre-commit` hook update#2820

[MNT] Automated `pre-commit` hook update#2820
MatthewMiddlehurst merged 1 commit intomainfrom
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