Add pre-commit, fix typing and linting errors

.github/workflows/tests.yml

@@ -1,23 +1,5 @@
 name: Tests
-on:
-  push:
-    branches:
-      - main
-      - '*.x'
-    paths-ignore:
-      - 'docs/**'
-      - '*.md'
-      - '*.rst'
-      - '*.txt'
-  pull_request:
-    branches:
-      - main
-      - '*.x'
-    paths-ignore:
-      - 'docs/**'
-      - '*.md'
-      - '*.rst'
-      - '*.txt'
+on: [push, pull_request]
 jobs:
   tests:
     name: ${{ matrix.name }}
@@ -26,12 +8,22 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - {name: 3.10 Linux, python: '3.10', os: ubuntu-latest, tox: py310}
-          - {name: 3.10 Windows, python: '3.10', os: windows-latest, tox: py310}
-          - {name: 3.10 Mac, python: '3.10', os: macos-latest, tox: py310}
-          - {name: Lint, python: '3.10', os: ubuntu-latest, tox: lint}
-          - {name: Typing, python: '3.10', os: ubuntu-latest, tox: typing}
-          - {name: Style, python: '3.10', os: ubuntu-latest, tox: style}
+          # - { name: 3.12 Linux, python: "3.12", os: ubuntu-latest, tox: py312 }
+          # - { name: 3.11 Linux, python: "3.11", os: ubuntu-latest, tox: py311 }
+          # - { name: 3.10 Linux, python: "3.10", os: ubuntu-latest, tox: py310 }
+          # - {
+          #     name: 3.12 Windows,
+          #     python: "3.12",
+          #     os: windows-latest,
+          #     tox: py312,
+          #   }
+          # - { name: 3.12 Mac, python: "3.12", os: macos-latest, tox: py312 }
+          - {
+              name: Pre-commit,
+              python: "3.12",
+              os: ubuntu-latest,
+              tox: pre-commit,
+            }
     steps:
       - uses: actions/checkout@v2
       - uses: actions/setup-python@v2
@@ -47,6 +39,8 @@ jobs:
         uses: actions/cache@v2
         with:
           path: ${{ steps.pip-cache.outputs.dir }}
-          key: pip|${{ runner.os }}|${{ matrix.python }}|${{ hashFiles('setup.py') }}|${{ hashFiles('requirements/*.txt') }}
+          key:
+            pip|${{ runner.os }}|${{ matrix.python }}|${{
+            hashFiles('setup.py')}}
       - run: pip install tox
       - run: tox -e ${{ matrix.tox }}

.pre-commit-config.yaml

@@ -0,0 +1,91 @@
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+repos:
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: "23.10.1"
+    hooks:
+      - id: black-jupyter
+
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.16.0"
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==23.*]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.5.0"
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      # - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: "v1.10.0"
+    hooks:
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+
+  # - repo: https://github.com/pre-commit/mirrors-prettier
+  #   rev: "v3.0.3"
+  #   hooks:
+  #     - id: prettier
+  #       types_or: [yaml, markdown, html, css, scss, javascript, json]
+  #       args: [--prose-wrap=always]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.1.3"
+    hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.6.1"
+    hooks:
+      - id: mypy
+        files: src|tests
+        args: []
+        additional_dependencies:
+          - pytest
+          - pandas-stubs
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.2.6"
+    hooks:
+      - id: codespell
+
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: "v0.9.0.6"
+    hooks:
+      - id: shellcheck
+
+  - repo: local
+    hooks:
+      - id: disallow-caps
+        name: Disallow improper capitalization
+        language: pygrep
+        entry: PyBind|Numpy|Cmake|CCache|Github|PyTest
+        exclude: .pre-commit-config.yaml
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.15
+    hooks:
+      - id: validate-pyproject
+
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.27.0
+    hooks:
+      - id: check-dependabot
+      - id: check-github-workflows
+      - id: check-readthedocs

LICENSE

@@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+SOFTWARE.

README.md

@@ -1,18 +1,16 @@
-[![Python Versions][python-shield]][python-url]
-[![PyPi][pypi-shield]][pypi-url]
-[![Tests][tests-shield]][tests-url]
-[![License][license-shield]][license-url]
+[![Python Versions][python-shield]][python-url] [![PyPi][pypi-shield]][pypi-url]
+[![Tests][tests-shield]][tests-url] [![License][license-shield]][license-url]
 [![Contributors][contributors-shield]][contributors-url]
 [![Code Style][codestyle-shield]][codestyle-url]
 [![Homepage][homepage-shield]][homepage-url]
 
-
 # PTE Stats - Python tools for electrophysiology
 
 PTE Stats is an open-source software package for statistics with time series.
 
-It builds upon [PTE](https://github.com/richardkoehler/pte) and provides statistical tools for time-series.
-PTE Stats is particularly useful with intracranial EEG (iEEG) data such as local field potentials (LFP) and electrocorticography (ECoG).
+It builds upon [PTE](https://github.com/richardkoehler/pte) and provides
+statistical tools for time-series. PTE Stats is particularly useful with
+intracranial EEG data such as local field potentials and electrocorticography.
 
 ## Installing pte-stats
 
@@ -26,7 +24,7 @@ $ pip install pte-stats
 
 ### Development version
 
-To install the latest delevopment version, first clone this repository:
+To install the latest development version, first clone this repository:
 
 ```bash
 $ git clone https://github.com/richardkoehler/pte-stats
@@ -45,25 +43,27 @@ If you want to install pte-stats into an existing environment, type:
 $ pip install -e .
 ```
 
-
 ## Usage
 
 ```python
 import pte_stats
-
-# Examples coming soon
 ```
 
 ## Contributing
 
-Please feel free to contribute yourselves or to open an **issue** when you encounter a bug or to request a new feature.
+Please feel free to contribute yourselves or to open an **issue** when you
+encounter a bug or to request a new feature.
 
-For any minor additions or bugfixes, you may simply create a **pull request**. 
+For any minor additions or bugfixes, you may simply create a **pull request**.
 
-For any major changes, make sure to open an **issue** first. When you then create a pull request, be sure to **link the pull request** to the open issue in order to close the issue automatically after merging.
+For any major changes, make sure to open an **issue** first. When you then
+create a pull request, be sure to **link the pull request** to the open issue in
+order to close the issue automatically after merging.
 
 ### How to contribute
-To contribute yourselves, you should fork this repository, and then create a development branch from your fork.
+
+To contribute yourselves, you should fork this repository, and then create a
+development branch from your fork.
 
 Then, inside your development branch run the commands:
 
@@ -78,24 +78,36 @@ $ conda activate pte-stats-dev
 $ pip install -e .[dev]
 ```
 
-This will additionally install packages for development, such as black, pylint, mypy and isort.
+This will additionally install packages for development, such as black, pylint,
+mypy and isort.
 
 ## License
+
 PTE Stats is licensed under the [MIT license](license-url).
 
 <!-- MARKDOWN LINKS & IMAGES -->
 <!-- https://www.markdownguide.org/basic-syntax/#reference-style-links -->
-[python-shield]: https://img.shields.io/static/v1?label=Python&message=3.10&logoColor=black&labelColor=grey&color=blue
+
+[python-shield]:
+  https://img.shields.io/static/v1?label=Python&message=3.10&logoColor=black&labelColor=grey&color=blue
 [python-url]: https://pypi.org/project/pte-stats/
-[pypi-shield]: https://img.shields.io/static/v1?label=PyPi&message=v0.2.0&logoColor=black&labelColor=grey&color=blue
+[pypi-shield]:
+  https://img.shields.io/static/v1?label=PyPi&message=v0.2.0&logoColor=black&labelColor=grey&color=blue
 [pypi-url]: https://pypi.org/project/pte-stats/
-[tests-shield]: https://github.com/richardkoehler/pte-stats/actions/workflows/tests.yml/badge.svg
-[tests-url]: https://github.com/richardkoehler/pte-stats/actions/workflows/tests.yml
-[homepage-shield]: https://img.shields.io/static/v1?label=Homepage&message=ICN&logoColor=black&labelColor=grey&color=9cf
+[tests-shield]:
+  https://github.com/richardkoehler/pte-stats/actions/workflows/tests.yml/badge.svg
+[tests-url]:
+  https://github.com/richardkoehler/pte-stats/actions/workflows/tests.yml
+[homepage-shield]:
+  https://img.shields.io/static/v1?label=Homepage&message=ICN&logoColor=black&labelColor=grey&color=9cf
 [homepage-url]: https://www.icneuromodulation.org/
-[contributors-shield]: https://img.shields.io/github/contributors/richardkoehler/pte-stats.svg
-[contributors-url]: https://github.com/richardkoehler/pte-stats/graphs/contributors
-[license-shield]: https://img.shields.io/static/v1?label=License&message=MIT&logoColor=black&labelColor=grey&color=yellow
+[contributors-shield]:
+  https://img.shields.io/github/contributors/richardkoehler/pte-stats.svg
+[contributors-url]:
+  https://github.com/richardkoehler/pte-stats/graphs/contributors
+[license-shield]:
+  https://img.shields.io/static/v1?label=License&message=MIT&logoColor=black&labelColor=grey&color=yellow
 [license-url]: https://github.com/richardkoehler/pte-stats/blob/main/LICENSE/
-[codestyle-shield]: https://img.shields.io/static/v1?label=CodeStyle&message=black&logoColor=black&labelColor=grey&color=black
+[codestyle-shield]:
+  https://img.shields.io/static/v1?label=CodeStyle&message=black&logoColor=black&labelColor=grey&color=black
 [codestyle-url]: https://github.com/psf/black

doc/CHANGELOG.md → docs/CHANGELOG.md

@@ -1,19 +1,27 @@
 # Changelog
+
 All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
-and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+and this project adheres to
+[Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+
 ### Added
+
 ### Fixed
+
 ### Changed
+
 ### Deprecated
-### Removed
 
+### Removed
 
 ## [0.1.0] - 2022-02-01
+
 ### Added
+
 - Initial release
 
-[Unreleased]: https://github.com/richardkoehler/pte-stats
+[Unreleased]: https://github.com/richardkoehler/pte-stats

env.yml

@@ -3,6 +3,6 @@ channels:
   - defaults
 dependencies:
   - pip
-  - python=3.10
+  - python>=3.10
   - pip:
-    - pte-stats
+      - pte-stats

env_dev.yml

@@ -3,7 +3,6 @@ channels:
   - defaults
 dependencies:
   - pip
-  - python=3.10
+  - python>=3.10
   - pip:
-    - pte-stats[dev]
-
+      - -e .[dev]

pylintrc

@@ -45,7 +45,7 @@ confidence=
 # can either give multiple identifiers separated by comma (,) or put this
 # option multiple times (only on the command line, not in the configuration
 # file where it should appear only once).You can also use "--disable=all" to
-# disable everything first and then reenable specific checks. For example, if
+# disable everything first and then re-enable specific checks. For example, if
 # you want to run only the similarities checker, you can use "--disable=all
 # --enable=similarities". If you want to run only the classes checker, but have
 # no Warning level messages displayed, use"--disable=all --enable=classes

pyproject.toml

@@ -24,6 +24,7 @@ readme = {file = "README.md", content-type = "text/markdown"}
 requires-python = ">=3.10"
 
 dependencies = [
+  "joblib",
   "numba",
   "numpy",
   "scikit-image",
@@ -35,10 +36,13 @@ dev = [
   "black",
   "isort",
   "mypy",
+  "pandas-stubs",
   "pip-tools",
+  "pre-commit",
   "pylint",
   "pytest",
   "pytest-cov",
+  "ruff",
   "tox",
 ]
 
@@ -67,7 +71,11 @@ line-length = 79
 [[tool.mypy.overrides]]
 ignore_missing_imports = true
 module = [
+  "joblib",
   "numba",
+  "numpy",
+  "scipy",
+  "scipy.stats",
   "skimage",
   "statsmodels.stats.multitest",
 ]

requirements/requirements.in

@@ -1,4 +1,4 @@
   numba
   numpy
   scikit-image
-  statsmodels
+  statsmodels

requirements/requirements_deploy.in

@@ -1,3 +1,3 @@
 -c requirements.txt
 -c requirements_dev.txt
-flit
+flit

requirements/requirements_dev.in

@@ -6,4 +6,4 @@ pip-tools
 pylint
 pytest
 pytest-cov
-tox
+tox