Have evaluation of test coverage in new PRs

[Jannetty]

It would be great if we had a framework in place that presented the code coverage of all code in a PR. Currently Jacoco finds coverage of whole repo.

[afu5]

On the fu/jacoco-diff-test branch, I added Delta Coverage version 2.5.0 (later versions don't support Java 11) to build.gradle. I also edited the build.yml Action to run the delta coverage and publish a markdown summary when the action runs after each push. An example of the summary is at the bottom of this action (I branched from jain/prospero, which is branched off feature/add-flystemcells, which is where most of the delta comes from): https://github.com/bagherilab/ARCADE/actions/runs/24656371138.

The diff file is generated in comparison to main. If you want to compare one branch with another branch, you can change the diffSource in deltaCoverageReport in build.gradle. Change the .set() parameter in diffSource.git.diffBase.set("refs/remotes/origin/main") to the branch you want to compare to.

./gradlew clean test deltaCoverage runs the delta coverage locally and links a line-by-line coverage report highlighting only the new lines from the push.