Improve Testing, Documentation, and CI/CD for GLIMPSE2 DevelopmentSome

[Truongphi20]

I’m submitting this PR to contribute some improvements that I thought could be helpful for GLIMPSE2. The changes focus on testing, documentation, and development workflow, aiming to make the project easier to use and maintain.

Updates

• Test concordance Truongphi20/GLIMPSE2#1
• Implement testing Truongphi20/GLIMPSE2#3
• Make test Truongphi20/GLIMPSE2#4
• Make docs Truongphi20/GLIMPSE2#5
• Polishing Truongphi20/GLIMPSE2#6
• Fix actions Truongphi20/GLIMPSE2#7
• Format documentation Truongphi20/GLIMPSE2#8

Summarize

This PR introduces improvements across the development workflow, testing, and documentation:

• Development environment

  • Added a devcontainer to ensure consistent preproduction setup during development.

• Testing

  • Implemented unit tests for major modules (chunk, split_ref, phase, ligate, concordance) using CMake.
  • Created dedicated CMake targets for running test suites.

• Documentation

  • Integrated Doxygen to generate developer documentation (preview here).
  • Polished and reformatted docstrings and comments.

• CI/CD (GitHub Actions)

  • Configured workflows to build and test automatically.
  • Added steps to build and push Docker images to GHCR.
  • Deployment of Doxygen docs to GitHub Pages.

• Codebase improvements

  • Refactored and combined modules into a unified entry point (main.cpp, demo: https://github.com/Truongphi20/GLIMPSE2/releases/tag/trial-deploy).
  • Applied formatting and style consistency across the codebase.

[srubinacci]

Hi, this is great, but it might be require careful cheching for us to accept those. Can you send me an email, so we can perhaps coordinate on this?

(Please use my helsinki.fi email address).

Thanks!