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Prep for 0.7.0 (major update to dependencies, tests, documentation and build infra) (#225)
* Update changelog and version * Upgrade installation + tests (from Pingouin) * add pytest matrix * Update minimal dependency version * Update changelog.rst * Update doc * Apply ruff * Fix CI * Add conftest file * Fix pandas 3.0 hypno.to_numpy() str * Bump Scipy to 1.8.1 * Fix CI pandas 3.0 * remove maxfail * Update doc workflows * Fix warnings * Fix broken links * Update doc conf and contributing * Fix remaining CI and sphinx warnings * Ran and updated all notebooks * Add Hypnogram.from_integers * fix ruff * remove filterwarning pandas4 * Update changelog * Fix broken image slow_waves.png * Added evaluation module in changelog * disable --cov in addopts to enable single running pytest on single file * Add unit tests for evaluation module * Update readme, index and quickstart * Update docs * Update quickstart and add notebook + ruff * Fix CI for shapiro if N<3 * Set 0.7.0 release date to March 2026 * Remove paypal link * Remove contribution section in FAQ * Updated changelog 0.7.0 * Fix rst in evaluation * Update README * Update workflows * Add retry in fetch_sample and cache in GH workflows * Remove legacy hypno functions from README * Improve doc * Improve doc in evaluation.py * Improve doc of class Hypnogram * Fix doctest for yasa.hypno * Fix doctest in evaluation module * ruff format
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‎.github/workflows/deploy_doc.yml‎

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name: Deploy Documentation to GitHub Pages
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on:
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push:
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branches: [master]
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workflow_dispatch:
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# Cancel any in-progress job or run
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concurrency:
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group: "pages"
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cancel-in-progress: true
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jobs:
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deploy-docs:
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runs-on: ubuntu-latest
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permissions:
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pages: write
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id-token: write
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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env:
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FORCE_COLOR: true
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UV_SYSTEM_PYTHON: 1
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steps:
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- uses: actions/checkout@v6
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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python-version-file: "pyproject.toml"
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- name: Set up uv
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uses: astral-sh/setup-uv@v7
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- name: Install dependencies
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run: uv pip install --group=docs --editable .
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- name: Build documentation
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run: |
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make -C docs clean
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make -C docs html
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- name: Upload Pages artifact
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uses: actions/upload-pages-artifact@v3
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with:
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path: docs/build/html
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v4

‎.github/workflows/docs.yml‎

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# Workflow for building sphinx documentation remotely
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# and deploying the static HTML to a GitHub Pages site.
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# Note this approach does not require the static HTML
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# files to be stored/pushed/committed to an alternate
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# pages branch or anything like that. It uses GitHub Action artifacts.
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# https://github.com/sphinx-notes/pages
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name: Build and Deploy Sphinx Docs to GitHub Pages
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name: Build documentation and upload as artifact to GitHub Actions
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on:
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push:
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branches:
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- master
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release:
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types:
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- published
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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# Allow one concurrent deployment
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concurrency:
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group: "pages"
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cancel-in-progress: true
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branches: [master]
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pull_request:
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branches: [master]
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jobs:
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deploy:
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docs:
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runs-on: ubuntu-latest
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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permissions:
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pages: write
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id-token: write
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env:
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FORCE_COLOR: true
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UV_SYSTEM_PYTHON: 1
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steps:
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- name: Deploy to GitHub Pages
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id: deployment
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uses: sphinx-notes/pages@v3
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- uses: actions/checkout@v6
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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python-version-file: "pyproject.toml"
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- name: Set up uv
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uses: astral-sh/setup-uv@v7
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- name: Install dependencies
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run: uv pip install --group=docs --editable .
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- name: Build documentation
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run: |
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make -C docs clean
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make -C docs html
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- name: Upload documentation artifacts
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uses: actions/upload-artifact@v6
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with:
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name: docs-artifact
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path: docs/build/html

‎.github/workflows/python_tests.yml‎

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name: Python tests
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name: PyTest
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on:
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push:
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branches: [master]
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paths:
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- 'src/**'
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- 'tests/**'
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- 'pyproject.toml'
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pull_request:
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branches: [master]
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paths:
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- 'src/**'
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- 'tests/**'
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- 'pyproject.toml'
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env:
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FORCE_COLOR: 1
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UV_SYSTEM_PYTHON: 1
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YASA_DATA_DIR: ${{ github.workspace }}/.yasa_data
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jobs:
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build:
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test:
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strategy:
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fail-fast: false
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matrix:
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platform: [ubuntu-latest, macos-latest, windows-latest]
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python-version: ["3.9", "3.10", "3.11", "3.12"]
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python-version: ["3.10", "3.11", "3.12", "3.13"]
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runs-on: ${{ matrix.platform }}
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steps:
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- uses: actions/checkout@v6
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v6
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with:
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python-version: ${{ matrix.python-version }}
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- name: Set up uv
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uses: astral-sh/setup-uv@v7
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- name: Cache sample data
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uses: actions/cache@v4
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with:
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path: ${{ github.workspace }}/.yasa_data
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key: yasa-sample-data-14564285
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- name: Install libomp (macOS)
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if: ${{ matrix.platform == 'macos-latest' }}
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run: brew install libomp
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- name: Install dependencies
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run: uv pip install --group=test .
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- name: Test with pytest
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run: uv run pytest --verbose
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# Test against different dependency versions
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test-dependency-combinations:
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strategy:
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fail-fast: false
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matrix:
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platform: [ubuntu-latest, windows-latest]
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deps:
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# Minimum supported versions (as defined in pyproject.toml)
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- python-version: "3.10"
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numpy: "numpy==1.22.4"
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scipy: "scipy==1.8.1"
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pandas: "pandas==2.1.1"
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mne: "mne==1.3.0"
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numba: "numba==0.57.1"
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label: "minimum-versions"
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# Latest available versions (already tested above)
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# - python-version: "3.13"
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# numpy: "numpy"
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# scipy: "scipy"
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# pandas: "pandas"
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# mne: "mne"
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# numba: "numba"
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# label: "latest-versions"
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runs-on: ${{ matrix.platform }}
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steps:
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- uses: actions/checkout@v6
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- name: Set up Python ${{ matrix.deps.python-version }}
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uses: actions/setup-python@v6
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with:
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python-version: ${{ matrix.deps.python-version }}
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- name: Set up uv
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uses: astral-sh/setup-uv@v7
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- name: Cache sample data
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uses: actions/cache@v4
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with:
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path: ${{ github.workspace }}/.yasa_data
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key: yasa-sample-data-14564285
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- name: Install setuptools (required by mne==1.3.0)
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if: ${{ matrix.deps.label == 'minimum-versions' }}
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run: uv pip install setuptools
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- name: Install numpy (${{ matrix.deps.label }})
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run: uv pip install "${{ matrix.deps.numpy }}"
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- name: Install dependencies (${{ matrix.deps.label }})
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run: >-
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uv pip install --group=test .
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"${{ matrix.deps.scipy }}"
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"${{ matrix.deps.pandas }}"
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"${{ matrix.deps.mne }}"
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"${{ matrix.deps.numba }}"
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env:
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FORCE_COLOR: true
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- name: Display installed versions
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run: |
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python -c "import numpy; print(f'numpy: {numpy.__version__}')"
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python -c "import scipy; print(f'scipy: {scipy.__version__}')"
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python -c "import pandas; print(f'pandas: {pandas.__version__}')"
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python -c "import mne; print(f'mne: {mne.__version__}')"
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python -c "import numba; print(f'numba: {numba.__version__}')"
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- name: Test with pytest
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run: pytest --verbose
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coverage:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install libomp (macOS)
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if: ${{ matrix.platform == 'macos-latest' }}
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run: brew install libomp
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install ".[test]"
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- name: Test with pytest
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run: |
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pytest --cov --cov-report=xml --verbose
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- name: Upload coverage report
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if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == 3.9 }}
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uses: codecov/codecov-action@v4
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with:
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token: a58a0c62-fb11-4429-977b-65bec01ecb44
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file: ./coverage.xml
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- uses: actions/checkout@v6
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- name: Cache sample data
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uses: actions/cache@v4
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with:
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path: ${{ github.workspace }}/.yasa_data
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key: yasa-sample-data-14564285
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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python-version-file: "pyproject.toml"
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- name: Set up uv
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uses: astral-sh/setup-uv@v7
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- name: Install dependencies
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run: uv pip install --group=test .
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- name: Run tests with coverage
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run: pytest --cov --cov-report=xml --verbose
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v5
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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files: ./coverage.xml
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fail_ci_if_error: true

‎.github/workflows/ruff.yml‎

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name: Ruff
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on: [push, pull_request]
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on:
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push:
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paths-ignore:
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- '*.rst'
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- 'docs/**'
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pull_request:
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paths-ignore:
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- '*.rst'
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- 'docs/**'
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jobs:
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ruff:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v6
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- uses: astral-sh/setup-uv@v7
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- name: "Linting"
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uses: astral-sh/ruff-action@v3
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run: uvx ruff check
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- name: "Formatting"
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uses: astral-sh/ruff-action@v3
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with:
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args: "format --check"
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run: uvx ruff format --check

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