Merge pull request #7 from richardkoehler/dev

Add pre-commit, fix typing and linting, update version
richardkoehler · Feb 14, 2024 · eebec61 · eebec61
2 parents 590663a + 588af34
commit eebec61
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -2,22 +2,10 @@ name: Tests
 on:
   push:
     branches:
-      - main
-      - '*.x'
-    paths-ignore:
-      - 'docs/**'
-      - '*.md'
-      - '*.rst'
-      - '*.txt'
+      - "*"
   pull_request:
     branches:
-      - main
-      - '*.x'
-    paths-ignore:
-      - 'docs/**'
-      - '*.md'
-      - '*.rst'
-      - '*.txt'
+      - "*"
 jobs:
   tests:
     name: ${{ matrix.name }}
@@ -26,15 +14,25 @@ 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: Lint with pre-commit,
+              python: "3.12",
+              os: ubuntu-latest,
+              tox: lint,
+            }
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
       - name: update pip
@@ -44,9 +42,11 @@ jobs:
         id: pip-cache
         run: echo "::set-output name=dir::$(pip cache dir)"
       - name: cache pip
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         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 }}
diff --git a/.gitignore b/.gitignore
@@ -134,3 +134,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# Ruff litner
+.ruff_cache/
diff --git a/.pre-commit-config.yaml b/.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
diff --git a/LICENSE b/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.
diff --git a/README.md b/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
diff --git a/doc/CHANGELOG.md → docs/CHANGELOG.md b/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
diff --git a/env.yml b/env.yml
@@ -3,6 +3,6 @@ channels:
   - defaults
 dependencies:
   - pip
-  - python=3.10
+  - python>=3.10
   - pip:
-    - pte-stats
+      - pte-stats
diff --git a/env_dev.yml b/env_dev.yml
@@ -3,7 +3,6 @@ channels:
   - defaults
 dependencies:
   - pip
-  - python=3.10
+  - python>=3.10
   - pip:
-    - pte-stats[dev]
-
+      - -e .[dev]