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Add SymPy integration and Devito wave solver infrastructure
Phase 0 and 0.5 of the Devito book refactoring: - src/symbols.py: Common SymPy symbols for variables, parameters - src/operators.py: Finite difference operators with Taylor series analysis - src/display.py: LaTeX rendering utilities for Quarto documents - src/verification.py: Tools for verifying mathematical derivations - src/plotting.py: Reproducible plotting with fixed seed (42) - src/wave/wave1D_devito.py: 1D wave equation solver using Devito DSL Testing infrastructure: - tests/test_operators.py: 37 tests for FD operators - tests/test_derivations.py: 22 tests for heat, wave, advection equations - tests/test_wave_devito.py: 13 tests for Devito wave solver - tests/conftest.py: Shared pytest fixtures CI/CD: - .github/workflows/ci.yml: GitHub Actions workflow - codecov.yml: Coverage reporting configuration - pytest.ini: Pytest configuration Dependencies: - Add optional devito and devito-petsc dependencies from GitHub
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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
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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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ruff check src/ tests/ --select=E,W,F --ignore=F403,F405,E501
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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()

‎.gitignore‎

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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/

‎.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)'

‎codecov.yml‎

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# Codecov configuration
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# https://docs.codecov.com/docs/codecov-yaml
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coverage:
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precision: 2
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round: down
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range: "60...100"
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status:
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project:
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default:
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target: auto
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threshold: 5%
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informational: true
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patch:
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default:
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target: auto
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threshold: 5%
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informational: true
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parsers:
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gcov:
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branch_detection:
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conditional: yes
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loop: yes
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method: no
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macro: no
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comment:
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layout: "reach,diff,flags,files"
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behavior: default
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require_changes: false
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flags:
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derivations:
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paths:
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- src/symbols.py
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- src/operators.py
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- src/verification.py
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- src/display.py
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carryforward: true
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devito:
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paths:
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- src/wave/
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- src/diffu/
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- src/advec/
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- src/vib/
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carryforward: true
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ignore:
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- "tests/**/*"
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- "**/__init__.py"
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- "src/legacy/**/*"

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