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Prepare1.2 (#490)
* Bump Version and update README * Update changelog * Rename trapz to trapezoid * Update github actions * revent gauss norm * Add par0 to dockstring * Updated github actions * Closes #507 * Start of doc page for DeerLab 1.2 * Pathways example bug fixed: * Updated Github actions * Dipolar Spectrum example * `fitresult.modelUncert` exports properly for bootstrapped fits * Updated changelog * Example bug fix * Updated README.md and setup.py * Updated reference.rst
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‎.github/workflows/ci_PR.yml‎

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name: DeerLab PR tests
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on:
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pull_request:
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branches:
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- "**"
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jobs:
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tests:
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name: python test
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-latest, windows-latest]
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python-version: ['3.11','3.12']
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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cache: 'pip'
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cache-dependency-path: setup.py
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- run: |
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python -m pip install --upgrade pip
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pip install wheel
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pip install .
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- name: Test with pytest
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run: |
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pytest
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name: DeerLab PR tests
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on:
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pull_request:
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branches:
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- "**"
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permissions:
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contents: read
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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tests:
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name: python test
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-latest, windows-latest]
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python-version: ['3.12', '3.13', '3.14']
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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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cache: 'pip'
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cache-dependency-path: setup.py
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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 .
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- name: Test with pytest
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run: pytest

‎.github/workflows/ci_scheduled.yml‎

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name: Scheduled DeerLab tests
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on:
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workflow_dispatch:
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schedule:
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# Run once a week on Monday at 6:30 AM
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- cron: '30 6 * * 1'
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jobs:
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matrix_test:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-latest, windows-latest]
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python-version: [3.9, "3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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cache: 'pip'
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cache-dependency-path: setup.py
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- run: |
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python -m pip install --upgrade pip
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pip install wheel
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pip install .
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# - uses: actions/cache@v2
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# if: startsWith(runner.os, 'Windows')
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# with:
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# path: |
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# ~\AppData\Local\pip\Cache
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# key: ${{ runner.os }}-${{ hashFiles('**/setup.py') }}
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# restore-keys: |
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# {{ runner.os }}-pip-
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# - uses: actions/cache@v2
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# if: startsWith(runner.os, 'macOS')
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# with:
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# path: |
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# ~/Library/Caches/pip
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# key: ${{ runner.os }}-${{ hashFiles('**/setup.py') }}
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# restore-keys: |
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# {{ runner.os }}-pip-
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# - uses: actions/cache@v2
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# if: startsWith(runner.os, 'Linux')
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# with:
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# path: |
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# ~/.cache/pip
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# key: ${{ runner.os }}-${{ hashFiles('**/setup.py') }}
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# restore-keys: |
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# {{ runner.os }}-pip-
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# - name: Install dependencies
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# if: steps.cache.outputs.cache-hit != 'false'
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# run: |
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# python -m pip install --upgrade pip
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# pip install wheel
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# pip install .
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# - name: Windows MKL linking
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# if: matrix.os == 'windows-latest'
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# run: |
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# python upgrade_mkl.py
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- name: Test with pytest
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run: pytest
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name: Scheduled DeerLab tests
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on:
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workflow_dispatch:
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schedule:
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# Run once a week on Monday at 6:30 AM UTC
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- cron: '30 6 * * 1'
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permissions:
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contents: read
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jobs:
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matrix_test:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-latest, windows-latest]
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python-version: ["3.10", "3.11", "3.12", "3.13"]
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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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cache: 'pip'
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cache-dependency-path: setup.py
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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 .
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- name: Test with pytest
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run: pytest

‎.github/workflows/deploy_ghpages.yml‎

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name: Docs Build & Deployment
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on:
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on:
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workflow_dispatch:
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release:
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types: [published]
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permissions:
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contents: read
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pages: write
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id-token: write
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jobs:
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build:
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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 3.13
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uses: actions/setup-python@v5
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with:
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python-version: '3.13'
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cache: 'pip'
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cache-dependency-path: setup.py
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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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python -m pip install furo numpydoc sphinx-gallery sphinxcontrib-httpdomain sphinxcontrib-ghcontributors sphinx-issues sphinx-copybutton sphinx sphinx-design .
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sudo apt-get update -y
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sudo apt-get install -y latexmk texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended
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- name: Configure Pages
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uses: actions/configure-pages@v5
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- name: Build with Sphinx
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run: sphinx-build -E -b html ./docsrc/source ./docs
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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
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deploy:
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needs: build
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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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steps:
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- uses: actions/checkout@v3
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- name: Set up Python 3.10
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uses: actions/setup-python@v4
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with:
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python-version: '3.10'
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cache: 'pip'
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cache-dependency-path: setup.py
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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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python -m pip install furo
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python -m pip install numpydoc
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python -m pip install sphinx-gallery
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python -m pip install sphinxcontrib-httpdomain
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python -m pip install sphinxcontrib-ghcontributors
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python -m pip install sphinx-issues
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python -m pip install sphinx-copybutton
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python -m pip install sphinx
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python -m pip install sphinx-design
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python -m pip install .
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sudo apt-get update -y
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sudo apt-get install -y latexmk texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended
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- name: Build with Sphinx
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run: |
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sphinx-build -E -b html ./docsrc/source ./docs
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- name: Deploy to GH-Pages
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if: always()
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uses: peaceiris/actions-gh-pages@v3
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./docs
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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_PR.yml‎

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name: Test documentation build PR
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on:
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pull_request:
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branches:
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- "**"
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paths:
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- 'docsrc/**'
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- '.github/workflows/deploy_ghpages.yml'
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- '.github/workflows/docs_PR.yml'
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- '.github/workflows/examples_PR.yml'
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jobs:
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docsbuild:
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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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- name: Set up Python 3.10
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uses: actions/setup-python@v4
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with:
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python-version: '3.10'
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cache: 'pip'
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cache-dependency-path: setup.py
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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 furo
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pip install numpydoc
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pip install sphinx-gallery
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pip install sphinxcontrib-httpdomain
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pip install sphinxcontrib-ghcontributors
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pip install sphinx-issues
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pip install sphinx-copybutton
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pip install sphinx
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pip install sphinx-design
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python -m pip install .
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sudo apt-get update -y
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sudo apt-get install -y latexmk texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended
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- name: Build with Sphinx
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run: |
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sphinx-build -E -b html ./docsrc/source ./docs -D plot_gallery=0
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name: Test documentation build PR
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on:
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pull_request:
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branches:
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- "**"
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paths:
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- 'docsrc/**'
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- '.github/workflows/deploy_ghpages.yml'
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- '.github/workflows/docs_PR.yml'
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- '.github/workflows/examples_PR.yml'
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permissions:
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contents: read
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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docsbuild:
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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 3.13
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uses: actions/setup-python@v5
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with:
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python-version: '3.13'
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cache: 'pip'
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cache-dependency-path: setup.py
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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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python -m pip install furo numpydoc sphinx-gallery sphinxcontrib-httpdomain sphinxcontrib-ghcontributors sphinx-issues sphinx-copybutton sphinx sphinx-design .
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sudo apt-get update -y
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sudo apt-get install -y latexmk texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended
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- name: Build with Sphinx
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run: sphinx-build -E -b html ./docsrc/source ./docs -D plot_gallery=0

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