Modernize repository

[nbassler]

Project to bring the codebase up to modern standards.

No physics logic changes — tooling and infrastructure only.

Branch

• Rename master → main on GitHub and update CI references

Formatting & Style

• Add .clang-format config (based on LLVM or Google style, C11 mode)
• Run clang-format across all source files and commit

Testing Infrastructure

• Rename test executable to dedx_test (conflicts with CTest reserved name)
• Move enable_testing() to root CMakeLists.txt
• Add ctest --output-on-failure step to GitHub Actions workflow
• Add clang-format workflow (separate clang-format.yml)
• Rewrite test.c as individually registered CTest cases (deleted — superseded by test_*.c)
• Remove loadTest.c and its 9 legacy add_test entries (superseded by test_*.c)
• Move existing install/consumer smoke test to CTest
• Expand test coverage

CI/CD

• Add ctest --test-dir build step to GitHub Actions workflow
• Add clang-format check workflow
• Remove continue-on-error: true and valgrind step from ci.yml (once CI is green)
• Add clang-tidy or cppcheck static analysis step
• Consider adding a code coverage step (gcov + codecov.io)

Code Quality

• [-] Resolve 5 outstanding TODO/FIXME comments in source (wont fix, moved to Resolve outstanding TODO/FIXME comments in source #74)
  • Possible memory leak in dedx.c (dedx_allocate_workspace)
  • Broken path check in dedx_file_access.c
  • ion_a vs ion_A naming ambiguity in dedx_tools.c
• Audit dedx_file_access.c static 256-byte buffer for safety (fixed: folder[512])
• [-] Refactor global mutable folder into workspace/config struct (wont fix here, move to Refactor global mutable \folder #70)

CMake

• Bump cmake_minimum_required to 3.21
• Use target_include_directories consistently instead of legacy include_directories
• Enable testing unconditionally via enable_testing() in root CMakeLists.txt
• Version derived from git tag via git describe, no more manual version bumping
• dedx_config.h generated to build dir, removed from git tracking
• CMAKE_EXPORT_COMPILE_COMMANDS ON (needed for clangd)
• Fixed binary_table build ordering with add_dependencies + $<TARGET_FILE:dedx_build_bin>
• Make binary table generation (dedx_build_bin) an opt-in option

VS Code Integration

• Add .vscode/tasks.json (cmake configure, build, test tasks)
• Add .vscode/settings.json (clangd path, format-on-save)
• Add .vscode/extensions.json (recommend clangd, CMake Tools)
• Add .vscode/launch.json with working debug configuration
• Add CMakePresets.json for build presets

Python Bindings

• Migrate from deprecated distutils to pyproject.toml + setuptools
• Test bindings on Python 3.12+
• Add Python binding tests to CI

Documentation

• Add Doxygen config and annotate public API headers (dedx.h, dedx_wrappers.h)
• Expand README.md (currently 3 lines)
• Remove dead Sourceforge URLs from docs

Cleanup

• /gui/ wxWidgets frontend — remove since it is unmaintained
• Update Sphinx doc theme (pydata-sphinx-theme 0.8.1 → current)