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Merge pull request #98 from devitocodes/devito
Devito Edition
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‎.github/workflows/ci.yml‎

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name: CI
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on:
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push:
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branches: [main, devito]
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pull_request:
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branches: [main]
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jobs:
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# Run tests for mathematical derivations and operators with coverage
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test-derivations:
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name: Test Mathematical Derivations
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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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 pytest pytest-cov numpy sympy matplotlib ipython
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- name: Run tests with coverage
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run: |
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pytest tests/test_operators.py tests/test_derivations.py -v --cov=src --cov-report=xml --cov-report=term-missing
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v4
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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files: ./coverage.xml
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flags: derivations
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name: derivations-coverage
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fail_ci_if_error: false
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# Run explicit Devito solver tests with coverage
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test-devito-explicit:
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name: Test Devito Explicit Solvers
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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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 pytest pytest-cov numpy sympy matplotlib
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pip install devito
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- name: Run Devito tests with coverage
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run: |
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pytest tests/ -v -m "devito" --cov=src --cov-report=xml --cov-report=term-missing --tb=short
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continue-on-error: true # Allow to continue even if Devito tests fail initially
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v4
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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files: ./coverage.xml
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flags: devito
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name: devito-coverage
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fail_ci_if_error: false
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# Lint and style checks
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lint:
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name: Lint and Style
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Install linting tools
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run: |
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python -m pip install --upgrade pip
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pip install ruff isort
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- name: Run ruff check
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run: |
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# Check only new Devito code (skip legacy code with many pre-existing issues)
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ruff check src/wave/*_devito.py src/diffu/*_devito.py src/advec/*_devito.py src/nonlin/ src/symbols.py src/operators.py src/display.py src/verification.py src/plotting.py tests/ --select=E,W,F --ignore=F403,F405,E501,E741,E743,E731,E402,F841,E722
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- name: Check import ordering
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run: |
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isort --check-only src/ tests/ --skip __init__.py
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continue-on-error: true
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# Build Quarto book
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build-book:
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name: Build Quarto Book
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Install Python dependencies
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run: |
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python -m pip install --upgrade pip
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pip install numpy sympy matplotlib jupyter
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- name: Set up Quarto
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uses: quarto-dev/quarto-actions/setup@v2
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with:
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version: '1.4.554'
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- name: Install TinyTeX
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run: |
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quarto install tinytex
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- name: Render book
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run: |
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quarto render --to pdf
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continue-on-error: true # Book may not build initially
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- name: Upload book artifact
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uses: actions/upload-artifact@v4
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with:
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name: book-pdf
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path: _book/*.pdf
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if: success()

‎.github/workflows/publish.yml‎

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name: Publish Book
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on:
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push:
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branches: [main]
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workflow_dispatch: # Allow manual triggers
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# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
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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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# Allow only one concurrent deployment
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concurrency:
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group: "pages"
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cancel-in-progress: false
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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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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.12'
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cache: 'pip'
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- name: Set up Quarto
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uses: quarto-dev/quarto-actions/setup@v2
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with:
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version: '1.6.40'
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- name: Install TeX Live
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run: |
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sudo apt-get update
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sudo apt-get install -y --no-install-recommends \
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texlive-latex-base \
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texlive-latex-recommended \
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texlive-latex-extra \
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texlive-fonts-recommended \
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texlive-fonts-extra \
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texlive-science \
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texlive-pictures \
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texlive-bibtex-extra \
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texlive-plain-generic \
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lmodern \
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biber \
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latexmk \
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cm-super \
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dvipng \
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ghostscript
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- name: Install Python dependencies
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run: |
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python -m pip install --upgrade pip
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pip install numpy scipy matplotlib sympy jupyter
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- name: Build HTML
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run: quarto render --to html
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- name: Build PDF
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run: quarto render --to pdf
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- name: Copy PDF to HTML output
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run: |
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cp _book/Finite-Difference-Computing-with-PDEs.pdf _book/book.pdf
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- name: Upload artifact
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uses: actions/upload-pages-artifact@v3
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with:
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path: _book
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deploy:
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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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runs-on: ubuntu-latest
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needs: build
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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: actions/deploy-pages@v4

‎.gitignore‎

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.idea
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__pycache__
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_minted-*
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# doconce:
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.*_html_file_collection
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.*.exerinfo
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.*.copyright
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sphinx-rootdir
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Trash
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# Generated/published content (regenerated by build scripts):
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doc/pub/
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# Generated LaTeX files (in doc/.src/book/):
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book.tex
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book.pdf
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book.dlog
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latex_figs/
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svmonodo.cls
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t4do.sty
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newcommands_keep.tex
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tmp_mako__*.do.txt
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tmp_preprocess__*.do.txt
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# Test files:
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title_test.*
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/.quarto/
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/_book/
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**/*.quarto_ipynb
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# Coverage
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.coverage
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coverage.xml
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htmlcov/
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.pytest_cache/
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devito_repo/

‎.markdownlint-cli2.yaml‎

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globs:
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- "**/*.md"
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- "**/*.qmd"
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# Exclude external and generated directories
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ignores:
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- "devito_repo/**"
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- "venv/**"
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- ".venv/**"
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- "node_modules/**"
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- "_book/**"
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- "doc/pub/**"
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- "devito-plan.md"

‎.markdownlint.yaml‎

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# MD012 - Multiple consecutive blank lines (false positives in Python code blocks with PEP8 style)
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MD012: false
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# MD004 - Unordered list style (allow both dash and plus - converted from DocOnce)
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# MD018 - No space after hash (false positive from #!/bin/bash shebangs in code blocks)
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MD018: false
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# MD036 - Emphasis as heading (false positive from a) b) c) exercise labels)
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MD036: false
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# MD004 - Unordered list style (allow both dash and plus)
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MD004: false
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# MD031 - Blanks around fences (false positives in nested documentation examples)

‎.markdownlintignore‎

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# Virtual environments
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venv/
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.venv/
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# External repositories
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devito_repo/
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# Planning documents (not code)
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devito-plan.md

‎.pre-commit-config.yaml‎

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- id: markdownlint-cli2
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name: "Check markdown files"
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stages: [pre-commit]
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exclude: '^(devito_repo/|venv/|devito-plan\.md)'
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#
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# These stages modify the files applying fixes where possible
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# Since this may be undesirable they will not run automatically
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name: "Fix markdown files"
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args: [--fix]
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stages: [manual]
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exclude: '^(devito_repo/|venv/|devito-plan\.md)'

‎.typos.toml‎

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Thi = "Thi"
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# Equation label suffix (exact solution "u_e")
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ue = "ue"
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# Strang splitting (named after mathematician Gilbert Strang)
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strang = "strang"
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Strang = "Strang"

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