Initial Implementation of Continous Integration

[debeshmandal]

I have implemented a simple set of GitHub Actions to automatically build and run some scripts each time there are updates to the code.

Hopefully, the 2 different jobs should run as part of this PR (if they don't then they should in a future PR)

I am very open to any suggestions or changes in the testing structure.

Summary

• .github/workflows directory - all .yml files will be parsed and run by GitHub
• .github/workflows/build-linux.yml - builds oxDNA without CUDA (runs on all commits)
• .github/workflows/test-linux.yml - builds oxDNA without CUDA and runs all of the quick_input files in the testing folder (this is populated manually at the moment) (only runs on PRs because it takes more time)
• ci directory - a directory that contains CI scripts made for the GitHub Actions runners
• ci/oxDNA-verify_build.sh - runs a quick simulation to check that oxDNA builds properly
• ci/oxDNA-quick_input.sh - runs all of the quick_input input files in the test directory (currently populated manually)

Outlook

I hope that this demonstrates some of the basics of doing CI (it is quite simple and has a lot of customisability). Here are my plans for the next steps:

• Add Build - Passing badge to README.md - e.g.
• Automate the testing a bit more (e.g. use find to find all of the quick_input input files)
• Compare to benchmarks as part of the testing
• Add pytest jobs to verify the building and testing of oxpy
• After pytest has been implemented, look at testing for code coverage
• Investigate C++ testing strategies - I'm not very experienced with this so any advice would be appreciated, in the end I might not be able to do this
• Investigate using GPU images to test the CUDA code
• Investigate building on macos-latest and windows-latest images

[debeshmandal]

Here is an example of what the GitHub Actions look like:

https://github.com/debeshmandal/oxDNA/actions

[lorenzo-rovigatti]

Thanks a lot for the PR Debesh. I don't know much about actions but I'll try to understand them better asap. Quick question: can't we use make test_quick (which is a target that runs all the quick_input files) instead of the custom bash script you wrote?

[debeshmandal]

Sorry, I did not realise this - I have changed it to use make_test now - and will shortly remove the shell script