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domnadomna
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Merge branch 'master' into joss-paper
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‎.github/dependabot.yml‎

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# To get started with Dependabot version updates, you'll need to specify which
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# package ecosystems to update and where the package manifests are located.
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# Please see the documentation for all configuration options:
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# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
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version: 2
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updates:
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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# Check for updates to GitHub Actions every week
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interval: "weekly"

‎.github/workflows/benchmark.yml‎

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name: Benchmark
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on:
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push:
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branches:
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- master
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branches: [master]
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pull_request:
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branches: [master]
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permissions:
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contents: write
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name: Run pytest-benchmark benchmark example
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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with:
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submodules: recursive
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- uses: actions/setup-python@v4
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- uses: actions/setup-python@v5
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with:
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python-version: "3.10"
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python-version: "3.13"
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- name: Install deps
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run: |
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pip install -r requirements/fitting-requirements.txt
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pip install pytest pytest-benchmark pytest-coverage
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curl -LsSf https://astral.sh/uv/install.sh | sh
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uv pip install --system -r requirements/dev-requirements.txt
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uv pip install --system torch --index-url https://download.pytorch.org/whl/cpu
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- name: Install module
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run: |
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pip install .
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uv pip install --system .
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- name: Run benchmark
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run: |
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pytest tests/benchmark*.py --benchmark-json output.json
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- name: Store benchmark result
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if: github.ref == 'refs/heads/master'
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uses: benchmark-action/github-action-benchmark@v1
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with:
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name: Python Benchmark with pytest-benchmark
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auto-push: true
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# Show alert with commit comment on detecting possible performance regression
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alert-threshold: "200%"
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comment-on-alert: false
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fail-on-alert: false
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- name: Check benchmark threshold
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if: github.ref != 'refs/heads/master'
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uses: benchmark-action/github-action-benchmark@v1
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with:
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name: Python Benchmark with pytest-benchmark
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tool: "pytest"
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output-file-path: output.json
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github-token: ${{ secrets.GITHUB_TOKEN }}
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auto-push: false
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# Show alert with commit comment on detecting possible performance regression
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alert-threshold: "200%"
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comment-on-alert: true
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fail-on-alert: true
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fail-on-alert: false

‎.github/workflows/build-docker.yml‎

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runs-on: ubuntu-latest
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steps:
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- name: Check out the repo
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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with:
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submodules: recursive
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- name: Log in to Docker Hub

‎.github/workflows/linting.yml‎

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branches: [master]
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jobs:
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black-lint:
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linting:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: psf/black@stable
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sphinx-lint:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-python@v4
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: "3.10"
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python-version: "3.13"
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- name: Install deps
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run: |
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pip install sphinx-lint
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pip install sphinx-lint ruff==0.8.5
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- name: ruff
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run: |
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ruff check src/elli tests
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- name: ruff formatting
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run: |
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ruff format --check src/elli tests
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- name: Run Sphinx Linting
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run: |
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sphinx-lint .

‎.github/workflows/pytest.yml‎

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test_python:
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strategy:
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fail-fast: false
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matrix:
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python_version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
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python_version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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with:
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submodules: recursive
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- name: Set up Python ${{ matrix.python_version }}
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uses: actions/setup-python@v4
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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 dependencies
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run: |
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python -m pip install --upgrade pip
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- name: Install module
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run: |
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pip install .[fitting,testing]
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curl -LsSf https://astral.sh/uv/install.sh | sh
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uv pip install --system ".[fitting,dev]"
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uv pip install --system torch --index-url https://download.pytorch.org/whl/cpu
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- name: Test with pytest
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pytest --nbmake

‎.github/workflows/python-publish.yml‎

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# This workflow will upload a Python Package using Twine when a release is created
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# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
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name: Publish 📦
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# This workflow uses actions that are not certified by GitHub.
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# They are provided by a third-party and are governed by
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# separate terms of service, privacy policy, and support
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# documentation.
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name: Upload Python Package
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on:
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release:
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types: [published]
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on: push
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jobs:
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deploy:
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build:
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name: Build distribution 📦
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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with:
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submodules: recursive
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- name: Set up Python
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: "3.x"
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- name: Install pypa/build
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run: >-
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python3 -m
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pip install
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build
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--user
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- name: Build a binary wheel and a source tarball
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run: python3 -m build
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- name: Store the distribution packages
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uses: actions/upload-artifact@v4
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with:
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name: python-package-distributions
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path: dist/
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publish-to-pypi:
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name: >-
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Publish to PyPi
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if: startsWith(github.ref, 'refs/tags/')
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needs:
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- build
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runs-on: ubuntu-latest
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environment:
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name: pypi
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url: https://pypi.org/p/pyElli/
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permissions:
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id-token: write
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steps:
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- name: Download all the dists
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uses: actions/download-artifact@v4
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with:
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name: python-package-distributions
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path: dist/
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- name: Publish distribution 📦 to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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github-release:
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name: >-
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GitHub Release
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needs:
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- publish-to-pypi
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runs-on: ubuntu-latest
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permissions:
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contents: write
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id-token: write
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steps:
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- name: Download all the dists
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uses: actions/download-artifact@v4
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with:
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python-version: '3.x'
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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 build
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- name: Build package
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run: python -m build
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- name: Publish package
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uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
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name: python-package-distributions
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path: dist/
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- name: Sign the dists with Sigstore
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uses: sigstore/[email protected]
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with:
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user: __token__
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password: ${{ secrets.PYPI_API_TOKEN }}
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inputs: >-
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./dist/*.tar.gz
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./dist/*.whl
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- name: Create GitHub Release
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env:
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GITHUB_TOKEN: ${{ github.token }}
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run: >-
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gh release create
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'${{ github.ref_name }}'
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--repo '${{ github.repository }}'
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--notes ""
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- name: Upload artifact signatures to GitHub Release
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env:
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GITHUB_TOKEN: ${{ github.token }}
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run: >-
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gh release upload
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'${{ github.ref_name }}' dist/**
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--repo '${{ github.repository }}'

‎.github/workflows/requirements.yml‎

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name: Check requirements
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name: Dev requirements for target python
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test_python:
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: recursive
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- name: Set up Python 3.10
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uses: actions/setup-python@v4
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- name: Set up Python 3.13
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uses: actions/setup-python@v5
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with:
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python-version: "3.10"
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- name: Install dev requirements
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python-version: "3.13"
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- name: Install package (no deps)
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run: |
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python -m pip install --upgrade pip
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python -m pip install -r requirements/dev-requirements.txt
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- name: Install module
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curl -LsSf https://astral.sh/uv/install.sh | sh
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uv pip install --system --no-deps .[fitting,dev]
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uv pip install --system torch --index-url https://download.pytorch.org/whl/cpu
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- name: Install dev requirements
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run: |
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pip install .[fitting,testing]
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uv pip install --system -r requirements/dev-requirements.txt
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pytest --nbmake

‎.gitignore‎

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.pydevproject
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.settings
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.idea
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.vscode
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tags
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# Package files

‎.pre-commit-config.yaml‎

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- repo: https://github.com/astral-sh/ruff-pre-commit
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# Ruff version.
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rev: v0.8.5
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hooks:
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- id: black
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language_version: python3.10
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# - repo: local
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# hooks:
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# - id: pylint
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# name: pylint
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# entry: pylint
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# language: system
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# types: [python]
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# args: ["-rn", "--rcfile", ".pylintrc"]
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# Run the linter.
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- id: ruff
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# Run the formatter.
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- id: ruff-format
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- repo: local
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hooks:
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- id: sphinx-lint

‎.readthedocs.yml‎

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# Required
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version: 2
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build:
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os: ubuntu-22.04
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tools:
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python: "3.11"
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# Build documentation in the docs/ directory with Sphinx
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sphinx:
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configuration: docs/conf.py
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- pdf
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python:
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version: 3.8
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install:
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- requirements: docs/requirements.txt
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- { path: ., method: pip }

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