build(cmake): only allow to build as python extension

[robertodr]

By opening this PR I confirm that I have read CONTRIBUTING.md and I agree to the terms of the Contributor License Agreement.

Summary

This project is purely a Python extension but the build system, and configuration around it, still offered the (vestigial) option of building as a C++-only project.

Re-hash of #106, where I made a hideous mistake with the git history.

Changes

• Remove CMake code that allowed to build as a standalone C++ project, as that is no longer meaningful. A warning is issued against compiling with direct invocation to CMake.

• C++ unit tests are gated behind a new CMake option monoprop_ENABLE_CXX_UNIT_TESTS, which is ON by default.

• CMakePresets.json changed accordingly, as it's effectively only needed for test autodiscovery.

• Edit justfile to account for loss of many presets for CMake.

• Overhaul CMake code for installation of artifacts. The package is installed under lib/python3.X/site-packages/monoprop all other artifacts are installed in subfolders of it:

  • libmonoprop.so is under lib (or lib64, depending on the machine)
  • all headers are under include with the proper hierarchical folder structure
  • CMake helper files are under cmake The header files are now explicitly listed (instead of globbed) and we use target_sources with FILE_SET pento handle them sanely (instead of appending to a global list)

  I have dropped the distinction between private and public for now.

• Simplified test.yml accordingly:

  • we no longer need separate jobs to run the C++ unit tests: they can be compiled within a wheel build and run, if need be.
  • Single coverage job running both Python and C++ tests.

Checklist

• Tests added or updated to cover the changes
• Documentation updated (docstrings, docs/, CONTRIBUTING.md) if needed
• CHANGELOG / release notes updated if applicable

AI/LLM disclosure

• I did not use LLM tooling, or used it only privately for ideation
• I used the following tool to help write this PR description:
• I used the following tool to generate or modify code: GitHub Copilot with auto-selection of model.

---

This is part 1 of 3 in a stack made with GitButler:

•  3  fix: 🧹 use hwloc instead of custom topology discovery #180
•  2  ci: create a quality assurance workflow #173
•  1  build(cmake): only allow to build as python extension #152 👈

[github-actions]

Docs preview: https://pr-152.monoprop-docs.pages.dev

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.31%. Comparing base (847b50f) to head (88dfbf7).
⚠️ Report is 4 commits behind head on main.
✅ All tests successful. No failed tests found.

Additional details and impacted files

@@             Coverage Diff             @@
##             main     #152       +/-   ##
===========================================
+ Coverage   84.66%   95.31%   +10.64%     
===========================================
  Files          59       14       -45     
  Lines        4239      704     -3535     
  Branches     1497       88     -1409     
===========================================
- Hits         3589      671     -2918     
+ Misses        254       20      -234     
+ Partials      396       13      -383     

Flag	Coverage Δ
cpp	95.31% <ø> (+12.76%)	⬆️
python	?

Flags with carried forward coverage won't be shown. Click here to find out more.

[robertodr]

The PR is still in progress, it's not marked as draft as I need all CI jobs to run on each commit to check I'm not losing functionality. Sorry for the confusion!

[robertodr]

this will also need to be merged by bypassing requirements, since the job names changed. Plus a change in required checks in the ruleset.

[robertodr]

This is now ready-ready to review

[Copilot]

Pull request overview

This PR refactors the build/CI tooling to treat monoprop as a scikit-build-core–driven Python extension only, removing the remaining “standalone CMake project” pathways, and reshaping install + test/coverage flows around the editable build trees that uv sync creates.

Changes:

• Make top-level CMake configuration scikit-build-core–centric (with direct-CMake invocation discouraged) and gate C++ unit tests behind a dedicated option.
• Rework CMake install and header handling to use target_sources(FILE_SET ...), installing artifacts under the Python package layout.
• Simplify developer/CI workflows (presets, VS Code tasks, just recipes, GitHub Actions) to build/test via the scikit-build-core editable trees and consolidate coverage.

Reviewed changes

Copilot reviewed 27 out of 28 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
uv.lock	Removes gcovr and its transitive lock entries from the locked environment.
pyproject.toml	Drops gcovr from dev deps; updates cibuildwheel env to explicitly disable C++ unit tests during wheel builds.
CMakeLists.txt	Moves to scikit-build-core–first configuration, adds monoprop_ENABLE_CXX_UNIT_TESTS, and gates tests/cpp accordingly.
src/CMakeLists.txt	Updates CMake package config install location and version-file generation for the new install layout.
src/monoprop/CMakeLists.txt	Switches to FILE_SET-based header installation, adjusts install destinations under the Python package, and reorganizes subdirectories.
src/monoprop/bindings/CMakeLists.txt	Removes local Python discovery, updates compile flag handling, and rewrites RPATH logic for the new package layout.
src/monoprop/algebra/CMakeLists.txt	Adds explicit header listing via FILE_SET.
src/monoprop/core/CMakeLists.txt	Adds explicit header listing via FILE_SET.
src/monoprop/detail/CMakeLists.txt	Adds explicit header listing via FILE_SET and enumerates detail subdirectories.
src/monoprop/detail/evolution/CMakeLists.txt	Adds explicit header listing via FILE_SET and includes layer_build.
src/monoprop/detail/evolution/layer_build/CMakeLists.txt	Adds explicit header listing via FILE_SET.
src/monoprop/detail/graph/CMakeLists.txt	Adds explicit header listing via FILE_SET.
src/monoprop/detail/graph_encoding/CMakeLists.txt	Adds explicit header listing via FILE_SET.
src/monoprop/detail/monomial_propagator/CMakeLists.txt	Adds explicit header listing via FILE_SET.
src/monoprop/detail/mpi/CMakeLists.txt	Adds explicit header listing via FILE_SET.
src/monoprop/detail/operator/CMakeLists.txt	Adds explicit header listing via FILE_SET.
src/monoprop/detail/pare/CMakeLists.txt	Adds explicit header listing and adds PareGraph.cpp as a private source.
src/monoprop/detail/partition/CMakeLists.txt	Adds explicit header listing via FILE_SET.
tests/cpp/CMakeLists.txt	Ensures CPM is included and configures msgpack-cxx via CPM for the C++ test suite.
tests/cpp/boostAddTests.cmake	Labels C++ tests with cxx for CTest filtering/reporting.
justfile	Consolidates test recipes and reworks the coverage flow to run via scikit-build-core editable trees.
CMakePresets.json	Replaces standalone configure/build/test presets with “adopt existing skbuild tree” presets.
.vscode/tasks.json	Switches VS Code tasks to uv sync-based install modes (Release/Debug/Coverage).
.vscode/settings.json	Disables CMake Tools auto-reconfigure and enables CTest Explorer integration for adopted build trees.
.github/workflows/test.yml	Overhauls CI into package-centric matrix runs, adds find_package(monoprop) smoke test, runs C++ unit tests via ctest, and consolidates coverage jobs.
.github/workflows/docpages.yml	Sets env to disable C++ unit tests for docs builds.
.github/workflows/copilot-setup-steps.yml	Sets CPM_USE_LOCAL_PACKAGES and updates uv sync invocation for setup.
.devcontainer/postStartCommand.sh	Makes prek install overwrite existing hooks in the devcontainer.

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud