Merge branch 'baseobject-refactor' into baseobject-refactor-part2

.all-contributorsrc

@@ -1218,7 +1218,7 @@
       "login": "moradabaz",
       "name": "Morad :)",
       "avatar_url": "https://avatars.githubusercontent.com/u/29915156?v=4",
-      "profile": "https://moradisten.github.io/",
+      "profile": "https://moradabaz.github.io/",
       "contributions": [
         "code",
         "test",
@@ -2117,6 +2117,45 @@
       "contributions": [
         "code"
       ]
+    },
+    {
+      "login": "ShivamPathak99",
+      "name": "Shivam Pathak",
+      "avatar_url": "https://avatars.githubusercontent.com/u/98941325?s=400&v=4",
+      "profile": "https://github.com/ShivamPathak99",
+      "contributions": [
+        "doc"
+      ]
+    },
+    {
+      "login": "SamiAlavi",
+      "name": "Sami Alavi",
+      "avatar_url": "https://avatars.githubusercontent.com/u/32700289?v=4",
+      "profile": "https://github.com/SamiAlavi",
+      "contributions": [
+        "code",
+        "maintenance"
+      ]
+    },
+    {
+      "login": "yarnabrina",
+      "name": "Anirban Ray",
+      "avatar_url": "https://avatars.githubusercontent.com/u/39331844?v=4",
+      "profile": "https://github.com/yarnabrina/",
+      "contributions": [
+        "bug",
+        "code",
+        "test"
+      ]
+    },
+    {
+      "login": "dashapetr",
+      "name": "Darya Petrashka",
+      "avatar_url": "https://avatars.githubusercontent.com/u/54349415?v=4",
+      "profile": "https://github.com/dashapetr",
+      "contributions": [
+        "doc"
+      ]
     }
   ]
 }

.dockerignore

@@ -0,0 +1,15 @@
+.binder
+.eggs
+.git
+.github
+.ipynb_checkpoints
+.pytest_cache
+.vscode
+build
+dist
+docs/_build
+htmlcov
+sktime.egg-info
+testdir
+**/*.pyc
+**/__pycache__

.github/ISSUE_TEMPLATE/bug_report.md

@@ -38,7 +38,7 @@ Add any other context about the problem here.
 
 <!--
 Please run the following code snippet and paste the output here:
- 
+
 from sktime import show_versions; show_versions()
 -->
 

.github/ISSUE_TEMPLATE/config.yml

@@ -1,6 +1,6 @@
 contact_links:
   - name: "\U0001F4AC All other questions and general chat"
-    url: https://discord.com/invite/gqSab2K
+    url: https://discord.com/invite/54ACzaFsn7
     about: Chat with the sktime community on Discord
   - name: "\u2709\uFE0F Code of Conduct incident reporting"
     url: https://www.sktime.net/en/latest/get_involved/code_of_conduct.html#incident-reporting-guidelines

.github/workflows/test.yml

@@ -110,10 +110,39 @@ jobs:
       - name: Run tests
         run: make PYTESTOPTIONS="--cov --cov-report=xml --timeout=600" test_mlflow
 
+  test-cython-estimators:
+    needs: test-nosoftdeps
+    runs-on: macOS-11
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+
+      - name: Install OS packages
+        run: brew install libomp
+
+      - name: Install sktime and dependencies
+        run: |
+          python -m pip install .[dev,cython_extras] --no-cache-dir
+
+      - name: Show dependencies
+        run: python -m pip list
+
+      - name: Run tests
+        run: make PYTESTOPTIONS="--cov --cov-report=xml --only_cython_estimators=True --matrixdesign=False --timeout=600" test_check_suite
+
+      - name: Publish code coverage
+        uses: codecov/codecov-action@v3
+
   test-windows:
     needs: test-nosoftdeps
     runs-on: windows-2019
     strategy:
+      fail-fast: false  # to not fail all combinations if just one fail
       matrix:
         python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
 
@@ -155,6 +184,7 @@ jobs:
   test-unix:
     needs: test-nosoftdeps
     strategy:
+      fail-fast: false  # to not fail all combinations if just one fail
       matrix:
         python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
         os: [ubuntu-20.04, macOS-11]

.github/workflows/update_contributors.yml

@@ -2,8 +2,6 @@ name: Update Contributors
 
 on:
   push:
-    branches:
-      - main
     paths:
       - '.all-contributorsrc'
 

Makefile

@@ -30,6 +30,13 @@ test: ## Run unit tests
 	cp setup.cfg ${TEST_DIR}
 	python -m pytest
 
+test_check_suite: ## run only estimator contract tests in TestAll classes
+	-rm -rf ${TEST_DIR}
+	mkdir -p ${TEST_DIR}
+	cp .coveragerc ${TEST_DIR}
+	cp setup.cfg ${TEST_DIR}
+	python -m pytest -k 'TestAll' $(PYTESTOPTIONS)
+
 test_softdeps: ## Run unit tests to check soft dependency handling in estimators
 	-rm -rf ${TEST_DIR}
 	mkdir -p ${TEST_DIR}
@@ -84,3 +91,7 @@ nb: clean
 	rm -rf .venv || true
 	python3 -m venv .venv
 	. .venv/bin/activate && python -m pip install .[all_extras,binder] && ./build_tools/run_examples.sh
+
+dockertest:
+	docker build -t sktime -f build_tools/docker/$(PYTHON_VERSION).dockerfile .
+	docker run -it --name sktime sktime bash -c "make test"

README.md

@@ -4,7 +4,7 @@
 
 > A unified interface for machine learning with time series
 
-:rocket: **Version 0.16.1 out now!** [Check out the release notes here](https://www.sktime.net/en/latest/changelog.html).
+:rocket: **Version 0.17.2 out now!** [Check out the release notes here](https://www.sktime.net/en/latest/changelog.html).
 
 sktime is a library for time series analysis in Python. It provides a unified interface for multiple time series learning tasks. Currently, this includes time series classification, regression, clustering, annotation and forecasting. It comes with [time series algorithms](https://www.sktime.net/en/stable/estimator_overview.html) and [scikit-learn] compatible tools to build, tune and validate time series models.
 
@@ -15,7 +15,7 @@ sktime is a library for time series analysis in Python. It provides a unified in
 | **CI/CD** | [![github-actions](https://img.shields.io/github/actions/workflow/status/sktime/sktime/wheels.yml?logo=github)](https://github.com/sktime/sktime/actions/workflows/wheels.yml) [![!codecov](https://img.shields.io/codecov/c/github/sktime/sktime?label=codecov&logo=codecov)](https://codecov.io/gh/sktime/sktime) [![readthedocs](https://img.shields.io/readthedocs/sktime?logo=readthedocs)](https://www.sktime.net/en/latest/?badge=latest) [![platform](https://img.shields.io/conda/pn/conda-forge/sktime)](https://github.com/sktime/sktime) |
 | **Code** |  [![!pypi](https://img.shields.io/pypi/v/sktime?color=orange)](https://pypi.org/project/sktime/) [![!conda](https://img.shields.io/conda/vn/conda-forge/sktime)](https://anaconda.org/conda-forge/sktime) [![!python-versions](https://img.shields.io/pypi/pyversions/sktime)](https://www.python.org/) [![!black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/sktime/sktime/main?filepath=examples) |
 | **Downloads**| [![Downloads](https://static.pepy.tech/personalized-badge/sktime?period=week&units=international_system&left_color=grey&right_color=blue&left_text=weekly%20(pypi))](https://pepy.tech/project/sktime) [![Downloads](https://static.pepy.tech/personalized-badge/sktime?period=month&units=international_system&left_color=grey&right_color=blue&left_text=monthly%20(pypi))](https://pepy.tech/project/sktime) [![Downloads](https://static.pepy.tech/personalized-badge/sktime?period=total&units=international_system&left_color=grey&right_color=blue&left_text=cumulative%20(pypi))](https://pepy.tech/project/sktime) |
-| **Community** | [![!discord](https://img.shields.io/static/v1?logo=discord&label=discord&message=chat&color=lightgreen)](https://discord.com/invite/gqSab2K) [![!slack](https://img.shields.io/static/v1?logo=linkedin&label=LinkedIn&message=news&color=lightblue)](https://www.linkedin.com/company/sktime/) [![!twitter](https://img.shields.io/static/v1?logo=twitter&label=Twitter&message=news&color=lightblue)](https://twitter.com/sktime_toolbox) [![!youtube](https://img.shields.io/static/v1?logo=youtube&label=YouTube&message=tutorials&color=red)](https://www.youtube.com/playlist?list=PLKs3UgGjlWHqNzu0LEOeLKvnjvvest2d0) |
+| **Community** | [![!discord](https://img.shields.io/static/v1?logo=discord&label=discord&message=chat&color=lightgreen)](https://discord.com/invite/54ACzaFsn7) [![!slack](https://img.shields.io/static/v1?logo=linkedin&label=LinkedIn&message=news&color=lightblue)](https://www.linkedin.com/company/scikit-time/) [![!youtube](https://img.shields.io/static/v1?logo=youtube&label=YouTube&message=tutorials&color=red)](https://www.youtube.com/playlist?list=PLKs3UgGjlWHqNzu0LEOeLKvnjvvest2d0) |
 | **Citation** | [![!zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.3749000.svg)](https://doi.org/10.5281/zenodo.3749000) |
 
 ## :books: Documentation
@@ -51,13 +51,13 @@ Questions and feedback are extremely welcome! Please understand that we won't be
 | :sparkles: **Feature Requests & Ideas** | [GitHub Issue Tracker]                       |
 | :woman_technologist: **Usage Questions**          | [GitHub Discussions] · [Stack Overflow] |
 | :speech_balloon: **General Discussion**        | [GitHub Discussions] |
-| :factory: **Contribution & Development** | [Slack], contributors channel · [Discord] |
-| :globe_with_meridians: **Community collaboration session** | [Discord] - Fridays 4pm UTC, dev/meet-ups channel |
+| :factory: **Contribution & Development** | contributors channel · [Discord] |
+| :globe_with_meridians: **Community collaboration session** | [Discord] - Fridays 3pm UTC, dev/meet-ups channel |
 
 [github issue tracker]: https://github.com/sktime/sktime/issues
 [github discussions]: https://github.com/sktime/sktime/discussions
 [stack overflow]: https://stackoverflow.com/questions/tagged/sktime
-[discord]: https://discord.com/invite/gqSab2K
+[discord]: https://discord.com/invite/54ACzaFsn7
 
 ## :dizzy: Features
 Our aim is to make the time series analysis ecosystem more interoperable and usable as a whole. sktime provides a __unified interface for distinct but related time series learning tasks__. It features [__dedicated time series algorithms__](https://www.sktime.net/en/stable/estimator_overview.html) and __tools for composite model building__ including pipelining, ensembling, tuning and reduction that enables users to apply an algorithm for one task to another.
@@ -73,13 +73,15 @@ For **deep learning**, see our companion package: [sktime-dl](https://github.com
 
 | Module | Status | Links |
 |---|---|---|
-| **[Forecasting]** | stable | [Tutorial](https://www.sktime.net/en/latest/examples/01_forecasting.html) · [API Reference](https://www.sktime.net/en/latest/api_reference.html#sktime-forecasting-time-series-forecasting) · [Extension Template](https://github.com/sktime/sktime/blob/main/extension_templates/forecasting.py)  |
-| **[Time Series Classification]** | stable | [Tutorial](https://github.com/sktime/sktime/blob/main/examples/02_classification.ipynb) · [API Reference](https://www.sktime.net/en/latest/api_reference.html#sktime-classification-time-series-classification) · [Extension Template](https://github.com/sktime/sktime/blob/main/extension_templates/classification.py) |
-| **[Time Series Regression]** | stable | [API Reference](https://www.sktime.net/en/latest/api_reference.html#sktime-classification-time-series-regression) |
-| **[Transformations]** | stable | [API Reference](https://www.sktime.net/en/latest/api_reference.html#sktime-transformations-time-series-transformers) · [Extension Template](https://github.com/sktime/sktime/blob/main/extension_templates/transformer.py)  |
-| **[Time Series Clustering]** | maturing | [Extension Template](https://github.com/sktime/sktime/blob/main/extension_templates/clustering.py) |
-| **[Time Series Distances/Kernels]** | experimental | [Extension Template](https://github.com/sktime/sktime/blob/main/extension_templates/dist_kern_panel.py) |
+| **[Forecasting]** | stable | [Tutorial](https://www.sktime.net/en/latest/examples/01_forecasting.html) · [API Reference](https://www.sktime.net/en/latest/api_reference/forecasting.html) · [Extension Template](https://github.com/sktime/sktime/blob/main/extension_templates/forecasting.py)  |
+| **[Time Series Classification]** | stable | [Tutorial](https://github.com/sktime/sktime/blob/main/examples/02_classification.ipynb) · [API Reference](https://www.sktime.net/en/latest/api_reference/classification.html) · [Extension Template](https://github.com/sktime/sktime/blob/main/extension_templates/classification.py) |
+| **[Time Series Regression]** | stable | [API Reference](https://www.sktime.net/en/latest/api_reference/regression.html) |
+| **[Transformations]** | stable | [Tutorial](https://github.com/sktime/sktime/blob/main/examples/03_transformers.ipynb) · [API Reference](https://www.sktime.net/en/latest/api_reference/transformations.html) · [Extension Template](https://github.com/sktime/sktime/blob/main/extension_templates/transformer.py)  |
+| **[Parameter fitting]** | maturing | [API Reference](https://www.sktime.net/en/latest/api_reference/param_est.html) · [Extension Template](https://github.com/sktime/sktime/blob/main/extension_templates/transformer.py)  |
+| **[Time Series Clustering]** | maturing | [API Reference](https://www.sktime.net/en/latest/api_reference/clustering.html) ·  [Extension Template](https://github.com/sktime/sktime/blob/main/extension_templates/clustering.py) |
+| **[Time Series Distances/Kernels]** | maturing | [Tutorial](https://github.com/sktime/sktime/blob/main/examples/03_transformers.ipynb) · [API Reference](https://www.sktime.net/en/latest/api_reference/dists_kernels.html) · [Extension Template](https://github.com/sktime/sktime/blob/main/extension_templates/dist_kern_panel.py) |
 | **[Annotation]** | experimental | [Extension Template](https://github.com/sktime/sktime/blob/main/extension_templates/annotation.py) |
+| **[Distributions and simulation]** | experimental |  |
 
 [forecasting]: https://github.com/sktime/sktime/tree/main/sktime/forecasting
 [time series classification]: https://github.com/sktime/sktime/tree/main/sktime/classification
@@ -88,6 +90,8 @@ For **deep learning**, see our companion package: [sktime-dl](https://github.com
 [annotation]: https://github.com/sktime/sktime/tree/main/sktime/annotation
 [time series distances/kernels]: https://github.com/sktime/sktime/tree/main/sktime/dists_kernels
 [transformations]: https://github.com/sktime/sktime/tree/main/sktime/transformations
+[distributions and simulation]: https://github.com/sktime/sktime/tree/main/sktime/proba
+[parameter fitting]: https://github.com/sktime/sktime/tree/main/sktime/param_est
 
 
 ## :hourglass_flowing_sand: Install sktime

build_tools/docker/py310.dockerfile

@@ -0,0 +1,8 @@
+FROM python:3.10.10-bullseye
+
+WORKDIR /usr/src/sktime
+
+COPY . .
+
+RUN python -m pip install -U pip
+RUN python -m pip install .[all_extras,dev,binder]

build_tools/docker/py311.dockerfile

@@ -0,0 +1,8 @@
+FROM python:3.11.2-bullseye
+
+WORKDIR /usr/src/sktime
+
+COPY . .
+
+RUN python -m pip install -U pip
+RUN python -m pip install .[all_extras,dev,binder]

build_tools/docker/py37.dockerfile

@@ -0,0 +1,8 @@
+FROM python:3.7.16-bullseye
+
+WORKDIR /usr/src/sktime
+
+COPY . .
+
+RUN python -m pip install -U pip
+RUN python -m pip install .[all_extras,dev,binder]

build_tools/docker/py38.dockerfile

@@ -0,0 +1,8 @@
+FROM python:3.8.16-bullseye
+
+WORKDIR /usr/src/sktime
+
+COPY . .
+
+RUN python -m pip install -U pip
+RUN python -m pip install .[all_extras,dev,binder]

build_tools/docker/py39.dockerfile

@@ -0,0 +1,8 @@
+FROM python:3.9.16-bullseye
+
+WORKDIR /usr/src/sktime
+
+COPY . .
+
+RUN python -m pip install -U pip
+RUN python -m pip install .[all_extras,dev,binder]

conftest.py

@@ -13,8 +13,6 @@
 
 __author__ = ["fkiraly"]
 
-from sktime.tests import test_all_estimators
-
 
 def pytest_addoption(parser):
     """Pytest command line parser options adder."""
@@ -23,9 +21,18 @@ def pytest_addoption(parser):
         default=False,
         help="sub-sample estimators in tests by os/version matrix partition design",
     )
+    parser.addoption(
+        "--only_cython_estimators",
+        default=False,
+        help="test only cython estimators, with tag requires_cython=True",
+    )
 
 
 def pytest_configure(config):
     """Pytest configuration preamble."""
+    from sktime.tests import test_all_estimators
+
     if config.getoption("--matrixdesign") in [True, "True"]:
         test_all_estimators.MATRIXDESIGN = True
+    if config.getoption("--only_cython_estimators") in [True, "True"]:
+        test_all_estimators.CYTHON_ESTIMATORS = True

docs/source/about/team.rst

@@ -9,13 +9,26 @@ A list of all contributors can be found `here <contributors.md>`_.
 
 Community Council
 -----------------
+
+transitional working group (in delegation),
+subject to `widening of governance model <https://github.com/sktime/community-org/issues/46>`_.
+
 .. list-table::
    :header-rows: 1
 
    * - Name
      - GitHub ID
+   * - Jonathan Bechtel
+     - :user:`jonathanbechtel`
    * - Franz Király
      - :user:`fkiraly`
+   * - Sagar Mishra
+     - :user:`achieveordie`
+   * - Kiril Ralinovski
+     - :user:`kirilral`
+   * - Marc Rovira
+     - :user:`marrov`
+
 
 Community Council Observers
 ---------------------------
@@ -25,6 +38,8 @@ Community Council Observers
 
    * - Name
      - GitHub ID
+   * - Jana Schmidberger
+     - :user:`janasberger`
    * - Lovkush Agarwal
      - :user:`lovkush-a`
    * - Mirae Parker
@@ -40,6 +55,8 @@ Code of Conduct Committee
      - GitHub ID
    * - Franz Király
      - :user:`fkiraly`
+   * - Marc Rovira
+     - :user:`marrov`
 
 Core Developers
 ---------------
@@ -49,18 +66,24 @@ Core Developers
 
    * - Name
      - GitHub ID
+   * - Anirban Ray
+     - :user:`yarnabrina`
    * - Daniel Bartling
      - :user:`danbartl`
+   * - Jonathan Bechtel
+     - :user:`jonathanbechtel`
    * - Franz Király
      - :user:`fkiraly`
    * - Freddy A Boulton
      - :user:`freddyaboulton`
+   * - Kiril Ralinovski
+     - :user:`kirilral`
    * - Lovkush Agarwal
      - :user:`lovkush-a`
+   * - Marc Rovira
+     - :user:`marrov`
    * - Mirae Parker
      - :user:`miraep8`
-   * - Ryan Kuhns
-     - :user:`rnkuhns`
    * - Sagar Mishra
      - :user:`achieveordie`
    * - Stanislav Khrapov
@@ -92,6 +115,8 @@ Former Core Developers
      - :user:`james-large`
    * - Jason Lines
      - :user:`jasonlines`
+   * - Ryan Kuhns
+     - :user:`rnkuhns`
    * - Leonidas Tsaprounis
      - :user:`ltsaprounis`
    * - Łukasz Mentel