[MNT] update pre commit hook versions and corresponding changes (skti…

…me#4680) Closes sktime#4676. What this PR does: 1. Update hook versions. 2. Apply code formatting changes identified by `black`. (affected ~140 files) 3. Apply docstring length/style changes identified by `flake8`+`pydocstyle`. (affected ~180 files) Notes for reviewers: * For the 3rd point above, used `docformatter` locally to automate few docstring changes, and these are part of d736b66. * In few places where it was unable to solve the issues (mostly `D205` and `D400`), used my own judgement to modify docstrings slightly to avoid lint failures. These possibly biased changes are part of ae526ad, and should be reviewed carefully.
CTFallon · Jun 21, 2023 · 0b181d9 · 0b181d9
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v4.4.0
     hooks:
       - id: check-added-large-files
         args: ["--maxkb=1000"]
@@ -22,27 +22,27 @@ repos:
         name: isort
 
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 23.3.0
     hooks:
       - id: black
         language_version: python3
         # args: [--line-length 79]
 
   - repo: https://github.com/pycqa/flake8
-    rev: 4.0.1
+    rev: 6.0.0
     hooks:
       - id: flake8
         exclude: docs/conf.py
         additional_dependencies: [flake8-bugbear, flake8-print]
 
   - repo: https://github.com/mgedmin/check-manifest
-    rev: "0.47"
+    rev: "0.49"
     hooks:
       - id: check-manifest
         stages: [manual]
 
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.2.2
+    rev: 1.7.0
     hooks:
       - id: nbqa-black
         args: [--nbqa-mutate, --nbqa-dont-skip-bad-cells]
@@ -55,15 +55,15 @@ repos:
         additional_dependencies: [flake8==3.8.3]
 
   - repo: https://github.com/pycqa/pydocstyle
-    rev: 6.1.1
+    rev: 6.3.0
     hooks:
       - id: pydocstyle
         args: ["--config=setup.cfg"]
 
   # We use the Python version instead of the original version which seems to require Docker
   # https://github.com/koalaman/shellcheck-precommit
   - repo: https://github.com/shellcheck-py/shellcheck-py
-    rev: v0.8.0.4
+    rev: v0.9.0.5
     hooks:
       - id: shellcheck
         name: shellcheck
diff --git a/build_tools/changelog.py b/build_tools/changelog.py
@@ -140,7 +140,6 @@ def render_changelog(prs, assigned):  # noqa
 
 
 if __name__ == "__main__":
-
     categories = [
         {"title": "Enhancements", "labels": ["feature", "enhancement"]},
         {"title": "Fixes", "labels": ["bug", "fix", "bugfix"]},

diff --git a/build_tools/make_release.py b/build_tools/make_release.py
@@ -1,8 +1,7 @@
 #!/usr/bin/env python3 -u
 # -*- coding: utf-8 -*-
 # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
-"""
-Do-nothing script for making a release.
+"""Do-nothing script for making a release.
 
 This idea comes from here:
 - https://blog.danslimmon.com/2019/07/15/do-nothing-scripting-the-key-to

diff --git a/docs/source/about/citation.md b/docs/source/about/citation.md
@@ -3,5 +3,5 @@
 If you use sktime in a scientific publication, we would appreciate
 citations to the following papers:
 
-* [Markus Löning, Anthony Bagnall, Sajaysurya Ganesh, Viktor Kazakov, Jason Lines, Franz Király (2019): “sktime: A Unified Interface for Machine Learning with Time Series”](http://learningsys.org/neurips19/assets/papers/sktime_ml_systems_neurips2019.pdf)
+* [Markus Löning, Anthony Bagnall, Sajaysurya Ganesh, Viktor Kazakov, Jason Lines, Franz Király (2019): "sktime: A Unified Interface for Machine Learning with Time Series"](http://learningsys.org/neurips19/assets/papers/sktime_ml_systems_neurips2019.pdf)
 * [Markus Löning, Tony Bagnall, Sajaysurya Ganesh, George Oastler, Jason Lines, ViktorKaz, …, Aadesh Deshmukh (2020). sktime/sktime. Zenodo. http://doi.org/10.5281/zenodo.3749000](http://doi.org/10.5281/zenodo.3749000)
diff --git a/docs/source/about/funding.rst b/docs/source/about/funding.rst
@@ -25,7 +25,7 @@ of the initial development under the UKRI Strategic Priorities Fund
 Systems <https://www.turing.ac.uk/events/tools-practices-and-systems-data-science-and-artificial-intelligence-scoping-workshop>`__
 theme within that grant.
 
-Markus Löning’s contributions between 2019 and 2021 were supported by:
+Markus Löning's contributions between 2019 and 2021 were supported by:
 
 * the `UK Economic and Social Research Council (ESRC) <https://esrc.ukri.org>`_,
 * the `Consumer Data Research Centre (CDRC) <https://www.cdrc.ac.uk>`_,

diff --git a/docs/source/about/showcase.rst b/docs/source/about/showcase.rst
@@ -14,7 +14,7 @@ Community Showcase
      -  Gives insights on importance of skime over scikit-learn, Proper Data Model for Time Series, and Highlights on unique features of sktime like sktime API, Code Examples of Time Series Models
      - :user:`Alexandra Amidon <lynnssi>`
    * - `Why start using sktime for forecasting? <https://medium.com/@jlenczuk/why-start-using-sktime-for-forecasting-8d6881c0a518>`_
-     - Overview of sktime’s features that distinguish it from other forecasting frameworks
+     - Overview of sktime's features that distinguish it from other forecasting frameworks
      - :user:`Joanna Lenczuk <joanlenczuk>`
    * - `Time Series Analysis with sktime on AWS SageMaker <https://datachef.co/blog/time-series-analysis-sktime-sagemaker/>`_
      - This guide explains the procedure of using sktime as a toolbox for time series analysis on the AWS SageMaker environment.

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -1,6 +1,5 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
-
 """Configuration file for the Sphinx documentation builder."""
 
 import os
@@ -305,8 +304,7 @@ def _make_estimator_overview(app):
     from sktime.registry import all_estimators
 
     def _process_author_info(author_info):
-        """
-        Process author information from source code files.
+        """Process author information from source code files.
 
         Parameters
         ----------

diff --git a/docs/source/contributing/enhancement_proposals.rst b/docs/source/contributing/enhancement_proposals.rst
@@ -11,7 +11,7 @@ Description
 An sktime enhancement proposal (STEP) is a software design document providing information to the sktime community.
 The proposal should provide a rationale and concise technical specification of proposed design.
 
-We collect and discuss proposals in sktime’s STEP `repository`_.
+We collect and discuss proposals in sktime's STEP `repository`_.
 
 .. _repository: https://github.com/sktime/enhancement-proposals
 

diff --git a/docs/source/contributing/reporting_bugs.rst b/docs/source/contributing/reporting_bugs.rst
@@ -25,5 +25,5 @@ rules before submitting:
 
 .. note::
 
-   To find out more about how to take part in sktime’s community, check out our `governance
+   To find out more about how to take part in sktime's community, check out our `governance
    guidelines <https://www.sktime.net/en/latest/governance.html>`__.
diff --git a/docs/source/developer_guide.rst b/docs/source/developer_guide.rst
@@ -24,9 +24,9 @@ New developers should:
 
 Further special topics are listed below.
 
-sktime follows `scikit-learn <https://scikit-learn.org/stable/>`_\ ’s API whenever possible.
-If you’re new to scikit-learn, take a look at their `getting-started guide <https://scikit-learn.org/stable/getting_started.html>`_.
-If you’re already familiar with scikit-learn, you may still learn something new from their `developers’ guide <https://scikit-learn.org/stable/developers/index.html>`_.
+sktime follows `scikit-learn <https://scikit-learn.org/stable/>`_\ 's API whenever possible.
+If you're new to scikit-learn, take a look at their `getting-started guide <https://scikit-learn.org/stable/getting_started.html>`_.
+If you're already familiar with scikit-learn, you may still learn something new from their `developers' guide <https://scikit-learn.org/stable/developers/index.html>`_.
 
 .. toctree::
    :maxdepth: 1

diff --git a/docs/source/developer_guide/coding_standards.rst b/docs/source/developer_guide/coding_standards.rst
@@ -48,7 +48,7 @@ Additional configurations can be found in
 -  Avoid multiple statements on one line. Prefer a line return after a
    control flow statement (``if``/``for``).
 -  Use absolute imports for references inside sktime.
--  Don’t use ``import *`` in the source code. It is considered
+-  Don't use ``import *`` in the source code. It is considered
    harmful by the official Python recommendations. It makes the code
    harder to read as the origin of symbols is no longer explicitly
    referenced, but most important, it prevents using a static analysis
@@ -110,8 +110,8 @@ API design
 ============
 
 The general design approach of sktime is described in the
-paper `“Designing Machine Learning Toolboxes: Concepts, Principles and
-Patterns” <https://arxiv.org/abs/2101.04938>`__.
+paper `"Designing Machine Learning Toolboxes: Concepts, Principles and
+Patterns" <https://arxiv.org/abs/2101.04938>`__.
 
 .. note::
 

diff --git a/docs/source/developer_guide/git_workflow.rst b/docs/source/developer_guide/git_workflow.rst
@@ -3,7 +3,7 @@
 Git and GitHub workflow
 =======================
 
-The preferred workflow for contributing to sktime’s repository is to
+The preferred workflow for contributing to sktime's repository is to
 fork the `main
 repository <https://github.com/sktime/sktime/>`__ on
 GitHub, clone, and develop on a new branch.

diff --git a/docs/source/get_involved/code_of_conduct.rst b/docs/source/get_involved/code_of_conduct.rst
@@ -121,11 +121,11 @@ hope you will consider to be appropriate community guidelines:
    unsure whether your behaviour towards another person is welcome, ask
    them. If someone tells you to stop, do so.
 -  **Respect the privacy and safety of others**. Do not take photographs
-   of others without their permission. Do not share other participant’s
+   of others without their permission. Do not share other participant's
    personal experiences without their express permission. Note that
    posting (or threatening to post) personally identifying information
    of others without their consent ("doxing") is a form of harassment.
--  **Be considerate of others’ participation**. Everyone should have an
+-  **Be considerate of others' participation**. Everyone should have an
    opportunity to be heard. In update sessions, please keep comments
    succinct so as to allow maximum engagement by all participants. Do
    not interrupt others on the basis of disagreement; hold such comments
@@ -135,7 +135,7 @@ hope you will consider to be appropriate community guidelines:
    crucial for fairness and diversity of our community, as well as its scientific quality.
    Free speech and constant scrutiny directed at those in power is also essential to ensure
    accountability and fair operations of our community, and to prevent groupthink or in-group dynamics.
--  **Don’t be a bystander**. If you see something inappropriate
+-  **Don't be a bystander**. If you see something inappropriate
    happening, speak up. If you don't feel comfortable intervening but
    feel someone should, please feel free to ask a member of the Code of
    Conduct response team for support.

diff --git a/docs/source/get_involved/contributing.rst b/docs/source/get_involved/contributing.rst
@@ -27,9 +27,9 @@ Recommended steps for first time contributors, or to get started with regular co
 1. Say hello (in the lobby on `Discord`_)!
 2. Get set up for development, see `instructions in the developer guide <https://www.sktime.net/en/stable/developer_guide.html>`_.
 3. Pick a good first issue to work on, see a collection `in this summary issue <https://github.com/sktime/sktime/issues/1147>`_ , or from `this list <https://github.com/sktime/sktime/issues?q=is%3Aopen+is%3Aissue+label%3A%22good+first+issue%22>`_
-   suggestion: pick something small with simple content to learn the “process”
+   suggestion: pick something small with simple content to learn the "process"
 4. Feel free to attend the regular community collab sessions or one of the topic specific stand-ups and tech sessions (see schedule on `Discord`_)
-5. Once your first PR is merged and you’ve seen how things work, you could consider contributing more regularly: optionally, continue attending the Friday community collaboration sessions and stand-ups; or, optionally, `apply for mentoring <https://www.sktime.net/en/stable/get_involved/mentoring.html#mentoring>`_
+5. Once your first PR is merged and you've seen how things work, you could consider contributing more regularly: optionally, continue attending the Friday community collaboration sessions and stand-ups; or, optionally, `apply for mentoring <https://www.sktime.net/en/stable/get_involved/mentoring.html#mentoring>`_
 
 .. _Discord: https://discord.com/invite/54ACzaFsn7
 

diff --git a/docs/source/get_involved/governance.rst b/docs/source/get_involved/governance.rst
@@ -205,7 +205,7 @@ Rights and responsibilities
    * - Right/responsibility
      - Description
    * - Direct access
-     - Being a core developer allows contributors to more easily carry on with their project related activities by giving them direct access to the project’s repository.
+     - Being a core developer allows contributors to more easily carry on with their project related activities by giving them direct access to the project's repository.
    * - Issue/PR management
      - Core developers are responsible for reviewing and managing issues and pull requests. This includes commenting on issues, reviewing code contributions, merging approved pull requests, and closing issues once resolved.
    * - Decision making
@@ -228,7 +228,7 @@ they have been nominated, there will be a vote by the current core
 developers.
 
 Voting on appointments is one of the few activities that takes
-place on the project’s private communication channels. The vote will be
+place on the project's private communication channels. The vote will be
 anonymous.
 
 While it is expected that most votes will be unanimous, a 2/3 majority of
@@ -438,11 +438,11 @@ used by the sktime project. We clarify:
 * how decisions are made, and
 * who participates in the decision making.
 
-sktime’s decision-making process is designed to take into account
+sktime's decision-making process is designed to take into account
 feedback from all community members and strives to find consensus, while
 avoiding deadlocks when no consensus can be found.
 
-All discussion and votes takes place on the project’s `issue
+All discussion and votes takes place on the project's `issue
 tracker <https://github.com/sktime/sktime/issues>`__,
 `pull requests <https://github.com/sktime/sktime/pulls>`__ or an :ref:`steps`. Some
 sensitive discussions and appointment votes occur on private chats.
@@ -475,7 +475,7 @@ corresponding decision making process is described in more detail below.
 Stage 1: lazy consensus with veto right
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-sktime uses a “consensus seeking” process for making decisions. The
+sktime uses a "consensus seeking" process for making decisions. The
 community tries to find a resolution that has no open objections among
 core developers.
 
@@ -573,7 +573,7 @@ comparison with alternative solutions, as outlined in our
 A complete STEP must always include at least a high-level design for the proposed change,
 not just a wishlist of features.
 
-Usually, we collect and discuss proposals in sktime’s `repository for
+Usually, we collect and discuss proposals in sktime's `repository for
 enhancement-proposals <https://github.com/sktime/enhancement-proposals>`__.
 
 For smaller changes, such as punctual changes to the API or governance documents,
@@ -632,7 +632,7 @@ If algorithms require major dependencies, we encourage to create a
 separate companion repository. For smaller
 dependencies which are limited to a few files, we encourage to use soft
 dependencies, which are only required for particular modules, but not
-for most of sktime’s functionality and not for installing sktime.
+for most of sktime's functionality and not for installing sktime.
 
 .. _acknowledging-contributions:
 
@@ -644,11 +644,11 @@ developers, users, educators, and other stakeholders. We value all kinds
 of contributions and are committed to recognising each of them fairly.
 
 We follow the `all-contributors <https://allcontributors.org>`__
-specification to recognise all contributors, including those that don’t
+specification to recognise all contributors, including those that don't
 contribute code. Please see `our list of all
 contributors <https://github.com/sktime/sktime/blob/main/CONTRIBUTORS.md>`__.
 
-If you think, we’ve missed anything, please let us know or open a PR
+If you think, we've missed anything, please let us know or open a PR
 with the appropriate changes to
 `sktime/.all-contributorsrc <https://github.com/sktime/sktime/blob/main/.all-contributorsrc>`__.
 
@@ -659,7 +659,7 @@ All contributors acknowledge that they have all the rights to the code
 they contribute to make it available under this license.
 
 The project belongs to the sktime community, and all parts of it are
-always considered “work in progress” so that they can evolve over time
+always considered "work in progress" so that they can evolve over time
 with newer contributions.
 
 .. _outlook:
@@ -668,7 +668,7 @@ Outlook
 -------
 
 We are open to improvement suggestions for our governance model. Once
-the community grows more and sktime’s code base becomes more
+the community grows more and sktime's code base becomes more
 consolidated, we will consider the following changes:
 
 -  Allow for more time to discuss changes, and more time to cast vote
@@ -681,17 +681,17 @@ In addition, we plan to add more roles for managing/coordinating
 specific project:
 
 * Community manager (mentorship, outreach, social media, etc),
-* Sub-councils for project-specific technical leadership (e.g.  for documentation, learning tasks, continuous integration)
+* Sub-councils for project-specific technical leadership (e.g.  for documentation, learning tasks, continuous integration)
 
 .. _references:
 
 References
 ----------
 
 Our governance model is inspired by various existing governance
-structures. In particular, we’d like to acknowledge:
+structures. In particular, we'd like to acknowledge:
 
-* scikit-learn’s `governance model <https://www.sktime.net/en/latest/governance.html>`__
+* scikit-learn's `governance model <https://www.sktime.net/en/latest/governance.html>`__
 * `The Turing Way <https://github.com/alan-turing-institute/the-turing-way>`__ project
 * `The Art of Community <https://www.jonobacon.com/books/artofcommunity/>`__ by Jono Bacon
 * The `astropy <https://www.astropy.org>`__ project

diff --git a/docs/source/glossary.rst b/docs/source/glossary.rst
@@ -105,7 +105,7 @@ sktime.
 
     Tabular
         Is a setting where each :term:`timepoint` of the :term:`univariate time series` being measured for each instance are treated as features and
-        stored as a primitive data type in the DataFrame’s cells. E.g., there are N :term:`instances <instance>` of time series and each has T
+        stored as a primitive data type in the DataFrame's cells. E.g., there are N :term:`instances <instance>` of time series and each has T
         :term:`timepoints <timepoint>`, this would yield a pandas DataFrame with shape (N, T): N rows, T columns.
 
     Framework

diff --git a/docs/source/user_guide.rst b/docs/source/user_guide.rst
@@ -15,7 +15,7 @@ To run the user guide notebooks interactively, you can
 `launch them on binder <https://mybinder.org/v2/gh/sktime/sktime/main?filepath=examples>`_
 without having to install anything.
 
-We assume basic familiarity with `scikit-learn`_. If you haven’t worked with scikit-learn before, check out their
+We assume basic familiarity with `scikit-learn`_. If you haven't worked with scikit-learn before, check out their
 `getting-started guide`_.
 
 The notebook files can be found `here <https://github.com/sktime/sktime/blob/main/examples>`_.

diff --git a/examples/feature_extraction_with_tsfresh.ipynb b/examples/feature_extraction_with_tsfresh.ipynb
@@ -224,7 +224,7 @@
     }
    ],
    "source": [
-    "#  binary classification task\n",
+    "#  binary classification task\n",
     "np.unique(y_train)"
    ]
   },
@@ -936,7 +936,7 @@
     }
    ],
    "source": [
-    "#  multivariate input data\n",
+    "#  multivariate input data\n",
     "X_train.head()"
    ]
   },

diff --git a/examples/minirocket.ipynb b/examples/minirocket.ipynb
@@ -471,7 +471,7 @@
     "\n",
     "\n",
     "### 4.1 Load japanese_vowels as unequal length dataset\n",
-    "Japanese vowels is a a UCI Archive dataset. 9 Japanese-male speakers were recorded saying the vowels ‘a’ and ‘e’. \n",
+    "Japanese vowels is a a UCI Archive dataset. 9 Japanese-male speakers were recorded saying the vowels 'a' and 'e'. \n",
     "The raw recordings are preprocessed to get a 12-dimensional (multivariate) classification probem. The series lengths are between 7 and 29. "
    ]
   },

diff --git a/examples/plateau_finder.ipynb b/examples/plateau_finder.ipynb
@@ -233,7 +233,7 @@
     }
    ],
    "source": [
-    "#  find plateaus\n",
+    "#  find plateaus\n",
     "t = PlateauFinder()\n",
     "Xt = t.fit_transform(X)\n",
     "Xt"

diff --git a/examples/segmentation_with_clasp.ipynb b/examples/segmentation_with_clasp.ipynb
@@ -355,7 +355,7 @@
    "source": [
     "# ClaSP - Window Size Selection\n",
     "\n",
-    "ClaSP takes the window size 𝑤 as a hyper-parameter. This parameter has data-dependent effects on ClaSP’s performance. When chosen too small, all windows tend to appear similar; when chosen too large, windows have a higher chance to overlap adjacent segments, blurring their discriminative power. \n",
+    "ClaSP takes the window size 𝑤 as a hyper-parameter. This parameter has data-dependent effects on ClaSP's performance. When chosen too small, all windows tend to appear similar; when chosen too large, windows have a higher chance to overlap adjacent segments, blurring their discriminative power. \n",
     "\n",
     "A simple, yet effective method for choosing the window size is the dominant frequency of the Fourier Transform."
    ]