Release v0.6.0 (#965)

* release 0.6.0

* changelog

* new label and link fix

.github/PULL_REQUEST_TEMPLATE.md

@@ -48,7 +48,7 @@ Please go through the checklist below. Please feel free to remove points if they
 
 ##### For all contributions
 - [ ] I've added myself to the [list of contributors](https://github.com/aeon-toolkit/aeon/blob/main/.all-contributorsrc). Alternatively, you can use the [@all-contributors](https://allcontributors.org/docs/en/bot/usage) bot to do this for you.
-- [ ] The PR title starts with either [ENH], [MNT], [DOC], [BUG], [REF] or [GOV] indicating whether the PR topic is related to enhancement, maintenance, documentation, bugs, refactoring or governance.
+- [ ] The PR title starts with either [ENH], [MNT], [DOC], [BUG], [REF], [DEP] or [GOV] indicating whether the PR topic is related to enhancement, maintenance, documentation, bugs, refactoring, deprecation or governance.
 
 ##### For new estimators and functions
 - [ ] I've added the estimator to the online [API documentation](https://www.aeon-toolkit.org/en/latest/api_reference.html).

README.md

@@ -13,7 +13,7 @@ We strive to provide a broad library of time series algorithms including the
 latest advances, offer efficient implementations using numba, and interfaces with other
 time series packages to provide a single framework for algorithm comparison.
 
-The latest `aeon` release is `v0.5.0`. You can view the full changelog
+The latest `aeon` release is `v0.6.0`. You can view the full changelog
 [here](https://www.aeon-toolkit.org/en/latest/changelog.html).
 
 Our webpage and documentation is available at https://aeon-toolkit.org.

aeon/__init__.py

@@ -1,6 +1,6 @@
 """aeon."""
 
-__version__ = "0.5.0"
+__version__ = "0.6.0"
 
 __all__ = ["show_versions"]
 

build_tools/changelog_generator.py

@@ -18,6 +18,8 @@
     "github-actions[bot]",
     "allcontributors[bot]",
     "sweep-ai[bot]",
+    "aeon-actions-bot[bot]",
+    "dependabot[bot]",
 ]
 
 
@@ -205,7 +207,7 @@ def render_changelog(prs: List[Dict], assigned: Dict):
 
     # if you edit these, consider editing the PR template as well
     packages = [
-        ["Annotation", ["annotation"]],
+        ["Anomaly Detection", ["anomaly detection"]],
         ["Benchmarking", ["benchmarking"]],
         ["Classification", ["classification"]],
         ["Clustering", ["clustering"]],
@@ -214,6 +216,8 @@ def render_changelog(prs: List[Dict], assigned: Dict):
         ["Forecasting", ["forecasting"]],
         ["Networks", ["networks"]],
         ["Regression", ["regression"]],
+        ["Segmentation", ["segmentation"]],
+        ["Similarity Search", ["similarity search"]],
         ["Transformations", ["transformations"]],
     ]
     categories = [
@@ -222,6 +226,7 @@ def render_changelog(prs: List[Dict], assigned: Dict):
         ["Enhancements", ["enhancement"]],
         ["Maintenance", ["maintenance"]],
         ["Refactored", ["refactor"]],
+        ["Deprecation", ["deprecation"]],
     ]
 
     pulls = fetch_pull_requests_since_last_release()

build_tools/pr_open_commenter.py

@@ -53,8 +53,8 @@
 if len(title_labels) == 0:
     title_labels_str = (
         "I did not find any labels to add based on the title. Please "
-        "add the ENH, MNT, BUG, DOC and/or GOV tag to your pull "
-        "requests titles. For now you can add the labels manually."
+        "add the [ENH], [MNT], [BUG], [DOC], [REF], [DEP] and/or [GOV] tags to your "
+        "pull requests titles. For now you can add the labels manually."
     )
 elif len(title_labels_new) != 0:
     arr_str = str(title_labels_new).strip("[]").replace("'", "")

docs/changelog.md

@@ -13,6 +13,7 @@ For upcoming changes and next releases, see our
 [milestones](https://github.com/aeon-toolkit/aeon/milestones). For our long-term plan,
 see our [roadmap](roadmap).
 
+- [Version 0.6.0](changelogs/v0.6.md)
 - [Version 0.5.0](changelogs/v0.5.md)
 - [Version 0.4.0](changelogs/v0.4.md)
 - [Version 0.3.0](changelogs/v0.3.md)

docs/changelogs/v0.6.md

@@ -0,0 +1,272 @@
+# v0.6.0
+
+December 2023
+
+## Highlights
+
+- A [deprecation policy](../developer_guide/deprecation.md) is now in place for `aeon` and its subpackages.
+- New `classification` algorithms are available in `RED CoMETS` and `LITETime`.
+- A `clustering` subpackage for deep learning clustering has been added.
+- A new experimental `similarity search` subpackage has been added, and the `annotation` module has been split into `segmentation` and `anomaly detection`.
+- Minkowski distance has been added to `distances`.
+- Lots of small improvements and bug fixes!
+
+## Anomaly Detection
+
+### Other
+
+- [ENH] refactor annotation into segmentation and anomaly detection ({pr}`782`) {user}`TonyBagnall`
+
+## Benchmarking
+
+### Bug Fixes
+
+- [ENH,BUG] CD plot function has been simplified, fixing some errors.  ({pr}`902`) {user}`dguijo`
+- [BUG, ENH] Fixes several issues and enhances plotting module ({pr}`950`) {user}`dguijo`
+
+### Enhancements
+
+- [ENH,BUG] CD plot function has been simplified, fixing some errors.  ({pr}`902`) {user}`dguijo`
+- [ENH] remove two calls to convert_to ({pr}`947`) {user}`TonyBagnall`
+- [BUG, ENH] Fixes several issues and enhances plotting module ({pr}`950`) {user}`dguijo`
+
+## Classification
+
+### Bug Fixes
+
+- [BUG] Correct pipeline test fails ({pr}`855`) {user}`TonyBagnall`
+- [BUG] Callables for KNN ({pr}`967`) {user}`TonyBagnall`
+
+### Documentation
+
+- [DOC] Enhance distance function related docs ({pr}`969`) {user}`TonyBagnall`
+
+### Enhancements
+
+- [ENH] Adds RED CoMETS classifier  ({pr}`779`) {user}`zy18811`
+- [ENH] Shapelet transform changes ({pr}`857`) {user}`TonyBagnall`
+- [ENH] change collection conversions from convert_to to convert_collection ({pr}`838`) {user}`TonyBagnall`
+- [ENH] Support unequal length for rdst ({pr}`891`) {user}`baraline`
+- [ENH] Remove case sensitivity from Rocket transform argument ({pr}`911`) {user}`TonyBagnall`
+- [ENH] Adding LITETime for Deep Learning classifiers ({pr}`923`) {user}`hadifawaz1999`
+- [ENH] DL Refactor ({pr}`937`) {user}`TonyBagnall`
+- [ENH] Swap transformer used in `SummaryClassifier` ({pr}`978`) {user}`MatthewMiddlehurst`
+
+### Other
+
+- [ENH] Adapt ShapeletTransform to work with unequal length ({pr}`820`) {user}`TonyBagnall`
+
+## Clustering
+
+### Bug Fixes
+
+- [ENH] Allow callables in TimeSeriesKMedoids ({pr}`925`) {user}`TonyBagnall`
+
+### Documentation
+
+- [DOC] Kmeans updated default for averaging method ({pr}`880`) {user}`chrisholder`
+- [DOC] Enhance distance function related docs ({pr}`969`) {user}`TonyBagnall`
+
+### Enhancements
+
+- [ENH] Deep Clustering module basis with an auto encoder FCN based example ({pr}`697`) {user}`hadifawaz1999`
+- [ENH] Allow callables in TimeSeriesKMedoids ({pr}`925`) {user}`TonyBagnall`
+- [ENH] Make clustering files private ({pr}`943`) {user}`TonyBagnall`
+
+### Maintenance
+
+- [MNT] Reduce test params for `AEFCNClusterer` ({pr}`868`) {user}`hadifawaz1999`
+- [MNT] Replacing BA by Mean in AEFCNClusterer test params ({pr}`879`) {user}`hadifawaz1999`
+
+## Datasets
+
+### Bug Fixes
+
+- [BUG] Ignore extra whitespace in loader ({pr}`884`) {user}`TonyBagnall`
+- [ENH] Add timestamped data loading for collections ({pr}`887`) {user}`TonyBagnall`
+- [BUG] Check if multiindex store unequal length series ({pr}`928`) {user}`TonyBagnall`
+- [BUG] test forecasting loader return meta data ({pr}`972`) {user}`TonyBagnall`
+
+### Enhancements
+
+- [ENH] Error message for incorrect unequal length multivariate input ({pr}`867`) {user}`TonyBagnall`
+- [ENH] Improve coverage for datasets module ({pr}`888`) {user}`TonyBagnall`
+- [ENH] Add timestamped data loading for collections ({pr}`887`) {user}`TonyBagnall`
+- [ENH] Add download_dataset function to _data_loaders.py ({pr}`906`) {user}`PaulRabich`
+- [ENH] Results loaders for published results ({pr}`890`) {user}`TonyBagnall`
+- [ENH] default loaders to not return meta data ({pr}`953`) {user}`TonyBagnall`
+- [ENH] Tidy up and restructure load to nested univariate ({pr}`987`) {user}`TonyBagnall`
+
+## Distances
+
+### Bug Fixes
+
+- [ENH] Allow callables in TimeSeriesKMedoids ({pr}`925`) {user}`TonyBagnall`
+- [BUG] Callables for KNN ({pr}`967`) {user}`TonyBagnall`
+
+### Documentation
+
+- [DOC] Enhance distance function related docs ({pr}`969`) {user}`TonyBagnall`
+
+### Enhancements
+
+- [ENH] Allow callables in TimeSeriesKMedoids ({pr}`925`) {user}`TonyBagnall`
+- [ENH] Minkowski distance ({pr}`904`) {user}`akshatvishu`
+
+## Networks
+
+### Enhancements
+
+- [ENH] Adding LITETime for Deep Learning classifiers ({pr}`923`) {user}`hadifawaz1999`
+- [ENH] DL Refactor ({pr}`937`) {user}`TonyBagnall`
+
+### Maintenance
+
+- [MNT] Default InceptionTime to use original model and not H version ({pr}`921`) {user}`hadifawaz1999`
+- [MNT] Update custom filters in H-InceptionTime and LITETime ot work with new tf versions ({pr}`949`) {user}`hadifawaz1999`
+
+## Regression
+
+### Bug Fixes
+
+- [BUG] Correct pipeline test fails ({pr}`855`) {user}`TonyBagnall`
+
+### Enhancements
+
+- [ENH] Shapelet transform changes ({pr}`857`) {user}`TonyBagnall`
+- [ENH] Speed up regression pipeline example ({pr}`860`) {user}`TonyBagnall`
+- [ENH] change collection conversions from convert_to to convert_collection ({pr}`838`) {user}`TonyBagnall`
+- [ENH] DL Refactor ({pr}`937`) {user}`TonyBagnall`
+
+## Segmentation
+
+### Other
+
+- [ENH] refactor annotation into segmentation and anomaly detection ({pr}`782`) {user}`TonyBagnall`
+
+## Similarity Search
+
+### Enhancements
+
+- [ENH] New similarity search module ({pr}`724`) {user}`TonyBagnall`
+
+## Transformations
+
+### Bug Fixes
+
+- [BUG] shapelet transform square root ({pr}`915`) {user}`TonyBagnall`
+
+### Documentation
+
+- [ENH] Introduce the "Tabular" output type tag and convert remaining Transformers to CollectionTransformers ({pr}`825`) {user}`TonyBagnall`
+
+### Enhancements
+
+- [ENH] BaseCollectionTransformer inherits from BaseCollectionEstimator and BaseTransformer ({pr}`709`) {user}`TonyBagnall`
+- [ENH] Shapelet transform changes ({pr}`857`) {user}`TonyBagnall`
+- [ENH] Support unequal length for rdst ({pr}`891`) {user}`baraline`
+- [ENH] remove nested_univ from Tabularizer ({pr}`897`) {user}`TonyBagnall`
+- [ENH]   Add algorithm type tag to convolutional transformers ({pr}`930`) {user}`TonyBagnall`
+- [ENH] Add algorithm type tag to dictionary transformers ({pr}`931`) {user}`TonyBagnall`
+- [ENH] Add algorithm type tag to shapelet transformers ({pr}`932`) {user}`TonyBagnall`
+- [ENH] remove nested_univ from TSFresh test ({pr}`945`) {user}`TonyBagnall`
+- [ENH] Remove the TimeBinner transformer ({pr}`933`) {user}`TonyBagnall`
+- [ENH] Refactor polymorphic transformers out of series directory into root ({pr}`959`) {user}`TonyBagnall`
+
+### Refactored
+
+- [ENH] Refactor interval based transformers into their own subpackage ({pr}`916`) {user}`TonyBagnall`
+- [ENH] Refactor feature based transformers into their own subpackage ({pr}`929`) {user}`TonyBagnall`
+
+### Other
+
+- [ENH] Make MiniRocketMultivariateVariable conform to API ({pr}`839`) {user}`TonyBagnall`
+- [ENH] Adapt ShapeletTransform to work with unequal length ({pr}`820`) {user}`TonyBagnall`
+
+## Other
+
+### Bug Fixes
+
+- [BUG] Improve sweep.yaml comment trigger ({pr}`843`) {user}`wwzeng1`
+- [BUG] Update sweep.yaml spacing ({pr}`901`) {user}`wwzeng1`
+
+### Documentation
+
+- [DOC] network docstrings ({pr}`799`) {user}`TonyBagnall`
+- [DOC] Add a notebook to describe inheritance structure of base classes ({pr}`789`) {user}`TonyBagnall`
+- [ENH] scitype variable name and doc string purge ({pr}`798`) {user}`TonyBagnall`
+- [DOC] Update documentation files to allow easier local builds and raise `sphinx` bound ({pr}`796`) {user}`MatthewMiddlehurst`
+- [MNT] Proposed aeon deprecation policy ({pr}`723`) {user}`TonyBagnall`
+- [GOV] Code of Conduct revision ({pr}`806`) {user}`MatthewMiddlehurst`
+- [DOC] Update documentation to add workgroups ({pr}`842`) {user}`MatthewMiddlehurst`
+- [DOC] Updates remaining first level website pages ({pr}`847`) {user}`MatthewMiddlehurst`
+- [Sweep Rules] Remove commented code and improve instructive comments ({pr}`850`) {user}`sweep-ai[bot]`
+- [DOC] change n_dimensions to n_channels in all files ({pr}`918`) {user}`xiaopu222`
+- [DOC] Add warning to installation guide for some shells ({pr}`963`) {user}`MatthewMiddlehurst`
+- [DOC] Remove "Time series" from API titles ({pr}`980`) {user}`TonyBagnall`
+
+### Enhancements
+
+- [ENH] Fix pre-commit fails ({pr}`851`) {user}`TonyBagnall`
+- [ENH] Refactor X_inner_mtype ({pr}`859`) {user}`TonyBagnall`
+- [ENH] Set Draft to true in sweep.yaml ({pr}`900`) {user}`wwzeng1`
+- [ENH] Remove upper bounds for `tslearn` and `pmdarima` ({pr}`939`) {user}`MatthewMiddlehurst`
+- [ENH] Update `numpy` version ({pr}`935`) {user}`MatthewMiddlehurst`
+- [ENH] Update `scikit-learn` version ({pr}`940`) {user}`MatthewMiddlehurst`
+- [ENH] Update `tensorflow`  ({pr}`912`) {user}`MatthewMiddlehurst`
+- [ENH] Refactor numpyflat to be numpy2D ({pr}`941`) {user}`TonyBagnall`
+- [ENH] Remove the alignment ADT from datatypes ({pr}`979`) {user}`TonyBagnall`
+
+### Maintenance
+
+- [MNT] Consolidate config files and add new pre-commit functionality ({pr}`340`) {user}`MatthewMiddlehurst`
+- [MNT] Comment out `mypy` pre-commit hook and run pre-commit on all files. Remove individual copyright notices ({pr}`801`) {user}`MatthewMiddlehurst`
+- [MNT] Update sweep.yaml ({pr}`821`) {user}`kevinlu1248`
+- [MNT] Add PR testing to `test-nosoftdeps-full` ({pr}`823`) {user}`MatthewMiddlehurst`
+- [MNT] Update Pull Request template ({pr}`829`) {user}`MatthewMiddlehurst`
+- [MNT] Add new `sweep` rules and make current rules more specific ({pr}`828`) {user}`MatthewMiddlehurst`
+- [MNT] Add auto label and welcoming comment workflow for PRs  ({pr}`832`) {user}`MatthewMiddlehurst`
+- [MNT] Add new periodic tests and tidy workflows ({pr}`830`) {user}`MatthewMiddlehurst`
+- [MNT] Add workflow to update `pre-commit` hooks and make a PR ({pr}`831`) {user}`MatthewMiddlehurst`
+- [MNT] Improve coverage for utils/validation ({pr}`793`) {user}`TonyBagnall`
+- [MNT] Stop pre-commit bot on draft PR ({pr}`854`) {user}`MatthewMiddlehurst`
+- [MNT] Always create a pull request on `pre-commit` update even if full run fails ({pr}`863`) {user}`MatthewMiddlehurst`
+- [MNT] Allow manual run of certain workflows ({pr}`865`) {user}`MatthewMiddlehurst`
+- [MNT] Remove `sweep` rules and sandbox options ({pr}`874`) {user}`MatthewMiddlehurst`
+- [MNT] Always generate token for `pre-commit` version update workflow ({pr}`876`) {user}`MatthewMiddlehurst`
+- [MNT] Give more time for codecov workflow tests ({pr}`877`) {user}`MatthewMiddlehurst`
+- [MNT] Try to fix `pre-commit` auto update ({pr}`881`) {user}`MatthewMiddlehurst`
+- [MNT] Use app token for other GitHub workflows ({pr}`886`) {user}`MatthewMiddlehurst`
+- [MNT] Retry aeon install on failure for GitHub workflows ({pr}`885`) {user}`MatthewMiddlehurst`
+- [MNT] Setup file for Dependabot (automatic dependency updates) ({pr}`892`) {user}`MatthewMiddlehurst`
+- [MNT] Dependabot validation workflow ({pr}`903`) {user}`MatthewMiddlehurst`
+
+### Refactored
+
+- [MNT] Proposed aeon deprecation policy ({pr}`723`) {user}`TonyBagnall`
+
+### Other
+
+- [ENH] Bug and coverage for BaseCollectionTransformer ({pr}`808`) {user}`TonyBagnall`
+- [ENH] Refactor tags to remove scitype ({pr}`800`) {user}`TonyBagnall`
+- Improve docstrings formatting in deep learning classifiers ({pr}`814`) {user}`sweep-ai[bot]`
+- [ENH] Refactor scitype:y to y_input_type and y_inner_mtype to y_inner_type ({pr}`810`) {user}`TonyBagnall`
+- [GOV] New `aeon` governance document. ({pr}`195`) {user}`MatthewMiddlehurst`
+- Update sweep.yaml to disable rules and fix sandbox ({pr}`878`) {user}`kevinlu1248`
+
+## Contributors
+
+The following have contributed to this release through a collective 100 GitHub Pull Requests:
+
+{user}`akshatvishu`,
+{user}`baraline`,
+{user}`chrisholder`,
+{user}`dguijo`,
+{user}`hadifawaz1999`,
+{user}`kevinlu1248`,
+{user}`MatthewMiddlehurst`,
+{user}`PaulRabich`,
+{user}`TonyBagnall`,
+{user}`wwzeng1`,
+{user}`xiaopu222`,
+{user}`zy18811`

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "aeon"
-version = "0.5.0"
+version = "0.6.0"
 description = "A toolkit for conducting machine learning tasks with time series data"
 authors = [
     {name = "aeon developers", email = "[email protected]"},