Convert project to C++ with Python bindings

.editorconfig

@@ -7,6 +7,18 @@ trim_trailing_whitespace = true
 end_of_line = lf
 insert_final_newline = true
 indent_style = space
+max_line_length = 100
+
+[*.py]
+indent_style = space
+indent_size = 4
 
 [*.{c,cc,h,cpp,hpp}]
 indent_size = 2
+
+[*.md]
+indent_size = 4
+max_line_length = 120
+
+[*.{yaml,yml}]
+indent_size = 2

.github/workflows/CI.yml

@@ -1,40 +1,66 @@
-name: Clang CI
+name: CI
 
 on:
   push:
-    branches: [ "*" ]
+    branches:
+    - "main"
   pull_request:
-    branches: [ "main" ]
 
 env:
   # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
+  # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
   BUILD_TYPE: Release
 
 jobs:
-  build_test:
+  cpp_tests:
+    name: "C++ Unit Tests"
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-latest, macos-latest ]
-    # The CMake configure and build commands are platform-agnostic and should work equally well on Windows or Mac.
-    # You can convert this to a matrix build if you need cross-platform coverage.
-    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
+        os: [ ubuntu-latest ]
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - name: Configure CMake
-        # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
-        # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
+      - name: 'Install dependencies'
+        run: sudo apt-get install -y cmake pybind11-dev
+
+      - name: 'Configure CMake'
         run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}
 
-      - name: Build
-        # Build your program with the given configuration
+      - name: 'Build'
         run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}
 
-      - name: Test
+      - name: 'Test'
         working-directory: ${{github.workspace}}/build
-        # Execute tests defined by the CMake configuration.
         # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
         run: ctest -C ${{env.BUILD_TYPE}}
+
+  python_tests:
+    name: "Python Tests"
+    strategy:
+      matrix:
+        os: [ ubuntu-latest ]
+        python-version: [ '3.10', '3.11', '3.12', '3.13' ]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: 'Set up Python'
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: 'Install uv'
+        uses: astral-sh/setup-uv@v5
+        with:
+          cache-dependency-glob: "**/pyproject.toml"
+          enable-cache: true
+
+      - name: 'Install dependencies'
+        run: uv sync --locked --all-extras --dev
+
+      - name: 'Run unit tests'
+        run: uv run pytest -n auto

.gitignore

@@ -1,20 +1,33 @@
-# Compiled Object files
+# General
 **/.DS_Store
+**/*.bak*
+*.log
+
+## C/C++
+build/**/*
+include/*
+lib/*
+bin/*
+Testing
+tests/Temporary
+*.bin
 *.slo
 *.lo
 *.o
 *.obj
-
-# Compiled Dynamic libraries
 *.so
 *.dylib
 *.dll
-
-# Executables
 *.exe
 *.out
 *.app
 
+# Google Test
+googletest/
+_deps
+libseis_test[1]_include.cmake
+**/*.cmake
+
 # Cmake
 **/cmake-build-debug
 **/CMakeCache.txt
@@ -26,14 +39,30 @@
 **/*.cbp
 **/CMakeScripts
 **/compile_commands.json
+build.ninja
+.cmake/
 
-## Local
+# IDE
 .idea/
-build/**/*
-include/*
-lib/*
-bin/*
-test/test_runner
-Testing
-test/Temporary
-*.bin
+.vscode/
+
+# Python
+venv/
+.venv/
+*.egg-info/
+.ipynb_checkpoints/
+.mypy_cache/
+.ruff_cache/
+/data/
+/media/
+__pycache__/
+_build/
+build/
+dist/
+.coverage*
+coverage.*
+log.html
+output.xml
+.pytest_cache/
+report.html
+coverage_html/

.pre-commit-config.yaml

@@ -0,0 +1,65 @@
+# To use:
+#
+#     pre-commit run -a
+#
+# Or:
+#
+#     pre-commit install  # (runs every time you commit in git)
+#
+# To update this file:
+#
+#     pre-commit autoupdate
+#
+# See https://github.com/pre-commit/pre-commit
+
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+repos:
+# Standard hooks
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  - id: check-added-large-files
+  - id: check-case-conflict
+  - id: check-merge-conflict
+  - id: check-symlinks
+  - id: check-yaml
+    exclude: ^conda\.recipe/meta\.yaml$
+  - id: debug-statements
+  - id: end-of-file-fixer
+  - id: mixed-line-ending
+  - id: requirements-txt-fixer
+  - id: trailing-whitespace
+
+# Check linting and style issues
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: "v0.11.12"
+  hooks:
+    - id: ruff
+      args: ["--fix", "--show-fixes"]
+    - id: ruff-format
+      exclude: ^(docs)
+
+# Changes tabs to spaces
+- repo: https://github.com/Lucas-C/pre-commit-hooks
+  rev: v1.5.5
+  hooks:
+  - id: remove-tabs
+    exclude: ^(docs)
+
+# CMake formatting
+- repo: https://github.com/cheshirekow/cmake-format-precommit
+  rev: v0.6.13
+  hooks:
+  - id: cmake-format
+    additional_dependencies: [pyyaml]
+    types: [file]
+    files: (\.cmake|CMakeLists.txt)(.in)?$
+
+# .clang-format file
+- repo: https://github.com/pre-commit/mirrors-clang-format
+  rev: v13.0.0
+  hooks:
+    - id: clang-format